This is a list of selected publications by EVBC members. For all virus related publications published by members of the EVBC (from the time of being member) see our Google Scholar account. For a full list of publications from EVBC members, see PubMed.

Authors: Type:

2019

  • [DOI] K. C. Wolthers, P. Susi, D. Jochmans, J. Koskinen, O. Landt, N. Sanchez, K. Palm, J. Neyts, and S. J. Butcher, “Progress in human picornavirus research: new findings from the AIROPico consortium,” Antiviral Res, vol. 161, p. 100–107, 2019.
    [Bibtex]
    @Article{Wolthers:19,
    author = {Katja C. Wolthers and Petri Susi and Dirk Jochmans and Janne Koskinen and Olfert Landt and Neus Sanchez and Kaia Palm and Johan Neyts and Sarah J. Butcher},
    title = {Progress in human picornavirus research: New findings from the {AIROPico} consortium},
    journal = {{Antiviral Res}},
    year = {2019},
    volume = {161},
    pages = {100--107},
    doi = {10.1016/j.antiviral.2018.11.010},
    publisher = {Elsevier {BV}},
    }
  • [DOI] P. A. de Jonge, F. L. Nobrega, S. J. J. Brouns, and B. E. Dutilh, “Molecular and evolutionary determinants of bacteriophage host range,” Trends Microbiol, vol. 27, iss. 1, p. 51–63, 2019.
    [Bibtex]
    @Article{Jonge:19,
    author = {Patrick A. de Jonge and Franklin L. Nobrega and Stan J.J. Brouns and Bas E. Dutilh},
    title = {Molecular and Evolutionary Determinants of Bacteriophage Host Range},
    journal = {{Trends Microbiol}},
    year = {2019},
    volume = {27},
    number = {1},
    pages = {51--63},
    doi = {10.1016/j.tim.2018.08.006},
    publisher = {Elsevier {BV}},
    }
  • D. Desirò, M. Hölzer, B. Ibrahim, and M. Marz, “Silentmutations (sim): a tool for analyzing long-range rna–rna interactions in viral genomes and structured rnas,” Virus Res, vol. 260, p. 135–141, 2019.
    [Bibtex]
    @Article{Desiro:19,
    author = {Desir{\`o}, Daniel and H{\"o}lzer, Martin and Ibrahim, Bashar and Marz, Manja},
    title = {SilentMutations (SIM): A tool for analyzing long-range RNA--RNA interactions in viral genomes and structured RNAs},
    journal = {{Virus Res}},
    year = {2019},
    volume = {260},
    pages = {135--141},
    publisher = {Elsevier},
    }
  • [DOI] J. D. Wuerth and F. Weber, “Ferreting out viral pathogenesis,” Nat Microbiol, vol. 4, iss. 3, p. 384–385, 2019.
    [Bibtex]
    @Article{Wuerth:19,
    author = {Jennifer Deborah Wuerth and Friedemann Weber},
    title = {Ferreting out viral pathogenesis},
    journal = {{Nat Microbiol}},
    year = {2019},
    volume = {4},
    number = {3},
    pages = {384--385},
    doi = {10.1038/s41564-019-0390-0},
    publisher = {Springer Nature},
    }
  • [DOI] A. Sulovari and D. Li, “VIpower: simulation-based tool for estimating power of viral integration detection via high-throughput sequencing,” Genomics, 2019.
    [Bibtex]
    @Article{Sulovari:19,
    author = {Arvis Sulovari and Dawei Li},
    title = {{VIpower}: Simulation-based tool for estimating power of viral integration detection via high-throughput sequencing},
    journal = {Genomics},
    year = {2019},
    doi = {10.1016/j.ygeno.2019.01.015},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Fritz, P. Hofmann, S. Majda, E. Dahms, J. Dröge, J. Fiedler, T. R. Lesker, P. Belmann, M. Z. DeMaere, A. E. Darling, A. Sczyrba, A. Bremges, and A. C. McHardy, “CAMISIM: simulating metagenomes and microbial communities,” Microbiome, vol. 7, iss. 1, 2019.
    [Bibtex]
    @Article{Fritz:19,
    author = {Adrian Fritz and Peter Hofmann and Stephan Majda and Eik Dahms and Johannes Dröge and Jessika Fiedler and Till R. Lesker and Peter Belmann and Matthew Z. DeMaere and Aaron E. Darling and Alexander Sczyrba and Andreas Bremges and Alice C. McHardy},
    title = {{CAMISIM}: simulating metagenomes and microbial communities},
    journal = {Microbiome},
    year = {2019},
    volume = {7},
    number = {1},
    doi = {10.1186/s40168-019-0633-6},
    publisher = {Springer Nature},
    }
  • [DOI] T. Kustin, G. Ling, S. Sharabi, D. Ram, N. Friedman, N. Zuckerman, E. D. Bucris, A. Glatman-Freedman, A. Stern, and M. Mandelboim, “A method to identify respiratory virus infections in clinical samples using next-generation sequencing,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Kustin:19,
    author = {Talia Kustin and Guy Ling and Sivan Sharabi and Daniela Ram and Nehemya Friedman and Neta Zuckerman and Efrat Dahan Bucris and Aharona Glatman-Freedman and Adi Stern and Michal Mandelboim},
    title = {A method to identify respiratory virus infections in clinical samples using next-generation sequencing},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-37483-w},
    publisher = {Springer Nature},
    }
  • [DOI] S. Kouchaki, A. Tapinos, and D. L. Robertson, “A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Kouchaki:19,
    author = {Samaneh Kouchaki and Avraam Tapinos and David L. Robertson},
    title = {A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-38197-9},
    publisher = {Springer Nature},
    }
  • [DOI] V. Ravindran, J. C. Nacher, T. Akutsu, M. Ishitsuka, A. Osadcenco, V. Sunitha, G. Bagler, J. Schwartz, and D. L. Robertson, “Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Ravindran:19,
    author = {Vandana Ravindran and Jose C. Nacher and Tatsuya Akutsu and Masayuki Ishitsuka and Adrian Osadcenco and V. Sunitha and Ganesh Bagler and Jean-Marc Schwartz and David L. Robertson},
    title = {Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-38224-9},
    publisher = {Springer Nature},
    }
  • [DOI] M. Ahmad, V. Helms, O. V. Kalinina, and T. Lengauer, “Relative principal components analysis: application to analyzing biomolecular conformational changes,” J Chem Theory Comput, 2019.
    [Bibtex]
    @Article{Ahmad:19,
    author = {Mazen Ahmad and Volkhard Helms and Olga V. Kalinina and Thomas Lengauer},
    title = {Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes},
    journal = {{J Chem Theory Comput}},
    year = {2019},
    doi = {10.1021/acs.jctc.8b01074},
    publisher = {American Chemical Society ({ACS})},
    }
  • [DOI] R. I. Amann, S. Baichoo, B. J. Blencowe, P. Bork, M. Borodovsky, C. Brooksbank, P. S. G. Chain, R. R. Colwell, D. G. Daffonchio, A. Danchin, V. de Lorenzo, P. C. Dorrestein, R. D. Finn, C. M. Fraser, J. A. Gilbert, S. J. Hallam, P. Hugenholtz, J. P. A. Ioannidis, J. K. Jansson, J. F. Kim, H. Klenk, M. G. Klotz, R. Knight, K. T. Konstantinidis, N. C. Kyrpides, C. E. Mason, A. C. McHardy, F. Meyer, C. A. Ouzounis, A. A. N. Patrinos, M. Podar, K. S. Pollard, J. Ravel, A. R. Muñoz, R. J. Roberts, R. Rosselló-Móra, S. Sansone, P. D. Schloss, L. M. Schriml, J. C. Setubal, R. Sorek, R. L. Stevens, J. M. Tiedje, A. Turjanski, G. W. Tyson, D. W. Ussery, G. M. Weinstock, O. White, W. B. Whitman, and I. Xenarios, “Toward unrestricted use of public genomic data,” Science, vol. 363, iss. 6425, p. 350–352, 2019.
    [Bibtex]
    @Article{Amann:19,
    author = {Rudolf I. Amann and Shakuntala Baichoo and Benjamin J. Blencowe and Peer Bork and Mark Borodovsky and Cath Brooksbank and Patrick S. G. Chain and Rita R. Colwell and Daniele G. Daffonchio and Antoine Danchin and Victor de Lorenzo and Pieter C. Dorrestein and Robert D. Finn and Claire M. Fraser and Jack A. Gilbert and Steven J. Hallam and Philip Hugenholtz and John P. A. Ioannidis and Janet K. Jansson and Jihyun F. Kim and Hans-Peter Klenk and Martin G. Klotz and Rob Knight and Konstantinos T. Konstantinidis and Nikos C. Kyrpides and Christopher E. Mason and Alice C. McHardy and Folker Meyer and Christos A. Ouzounis and Aristides A. N. Patrinos and Mircea Podar and Katherine S. Pollard and Jacques Ravel and Alejandro Reyes Mu{\~{n}}oz and Richard J. Roberts and Ramon Rossell{\'{o}}-M{\'{o}}ra and Susanna-Assunta Sansone and Patrick D. Schloss and Lynn M. Schriml and Jo{\~{a}}o C. Setubal and Rotem Sorek and Rick L. Stevens and James M. Tiedje and Adrian Turjanski and Gene W. Tyson and David W. Ussery and George M. Weinstock and Owen White and William B. Whitman and Ioannis Xenarios},
    title = {Toward unrestricted use of public genomic data},
    journal = {Science},
    year = {2019},
    volume = {363},
    number = {6425},
    pages = {350--352},
    doi = {10.1126/science.aaw1280},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] M. Golumbeanu, S. Desfarges, C. Hernandez, M. Quadroni, S. Rato, P. Mohammadi, A. Telenti, N. Beerenwinkel, and A. Ciuffi, “Proteo-transcriptomic dynamics of cellular response to HIV-1 infection,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Golumbeanu:19,
    author = {Monica Golumbeanu and S{\'{e}}bastien Desfarges and C{\'{e}}line Hernandez and Manfredo Quadroni and Sylvie Rato and Pejman Mohammadi and Amalio Telenti and Niko Beerenwinkel and Angela Ciuffi},
    title = {Proteo-Transcriptomic Dynamics of Cellular Response to {HIV}-1 Infection},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-36135-3},
    publisher = {Springer Nature},
    }
  • [DOI] C. M. Zmasek, D. M. Knipe, P. E. Pellett, and R. H. Scheuermann, “Classification of human Herpesviridae proteins using domain-architecture aware inference of orthologs (DAIO),” Virology, vol. 529, p. 29–42, 2019.
    [Bibtex]
    @Article{Zmasek:19,
    author = {Christian M. Zmasek and David M. Knipe and Philip E. Pellett and Richard H. Scheuermann},
    title = {Classification of human {H}erpesviridae proteins using Domain-architecture Aware Inference of Orthologs ({DAIO})},
    journal = {Virology},
    year = {2019},
    volume = {529},
    pages = {29--42},
    doi = {10.1016/j.virol.2019.01.005},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. F. Cotmore, M. Agbandje-McKenna, M. Canuti, J. A. Chiorini, A. Eis-Hubinger, J. Hughes, M. Mietzsch, S. Modha, M. Ogliastro, J. J. Pénzes, D. J. Pintel, J. Qiu, M. Soderlund-Venermo, P. Tattersall, and P. T. and, “ICTV virus taxonomy profile: Parvoviridae,” J Gen Virol, vol. 100, iss. 3, p. 367–368, 2019.
    [Bibtex]
    @Article{Cotmore:19,
    author = {Susan F. Cotmore and Mavis Agbandje-McKenna and Marta Canuti and John A. Chiorini and Anna-Maria Eis-Hubinger and Joseph Hughes and Mario Mietzsch and Sejal Modha and Myl{\`{e}}ne Ogliastro and Judit J. P{\'{e}}nzes and David J. Pintel and Jianming Qiu and Maria Soderlund-Venermo and Peter Tattersall and Peter Tijssen and},
    title = {{ICTV} Virus Taxonomy Profile: {P}arvoviridae},
    journal = {{J Gen Virol}},
    year = {2019},
    volume = {100},
    number = {3},
    pages = {367--368},
    doi = {10.1099/jgv.0.001212},
    publisher = {Microbiology Society},
    }
  • [DOI] S. G. Siddell, P. J. Walker, E. J. Lefkowitz, A. R. Mushegian, M. J. Adams, B. E. Dutilh, A. E. Gorbalenya, B. Harrach, R. L. Harrison, S. Junglen, N. J. Knowles, A. M. Kropinski, M. Krupovic, J. H. Kuhn, M. Nibert, L. Rubino, S. Sabanadzovic, H. Sanfaçon, P. Simmonds, A. Varsani, F. M. Zerbini, and A. J. Davison, “Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018),” Arch Virol, vol. 164, iss. 3, p. 943–946, 2019.
    [Bibtex]
    @Article{Siddell:19,
    author = {Stuart G. Siddell and Peter J. Walker and Elliot J. Lefkowitz and Arcady R. Mushegian and Michael J. Adams and Bas E. Dutilh and Alexander E. Gorbalenya and Bal{\'{a}}zs Harrach and Robert L. Harrison and Sandra Junglen and Nick J. Knowles and Andrew M. Kropinski and Mart Krupovic and Jens H. Kuhn and Max Nibert and Luisa Rubino and Sead Sabanadzovic and H{\'{e}}l{\`{e}}ne Sanfa{\c{c}}on and Peter Simmonds and Arvind Varsani and Francisco Murilo Zerbini and Andrew J. Davison},
    title = {Additional changes to taxonomy ratified in a special vote by the {International Committee on Taxonomy of Viruses} ({O}ctober 2018)},
    journal = {{Arch Virol}},
    year = {2019},
    volume = {164},
    number = {3},
    pages = {943--946},
    doi = {10.1007/s00705-018-04136-2},
    publisher = {Springer Nature},
    }
  • [DOI] U. Ashraf, C. Benoit-Pilven, V. Lacroix, V. Navratil, and N. Naffakh, “Advances in analyzing virus-induced alterations of host cell splicing,” Trends Microbiol, vol. 27, iss. 3, p. 268–281, 2019.
    [Bibtex]
    @Article{Ashraf:19,
    author = {Usama Ashraf and Clara Benoit-Pilven and Vincent Lacroix and Vincent Navratil and Nadia Naffakh},
    title = {Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing},
    journal = {{Trends Microbiol}},
    year = {2019},
    volume = {27},
    number = {3},
    pages = {268--281},
    doi = {10.1016/j.tim.2018.11.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] C. M. Kinsella, M. Deijs, and L. van der Hoek, “Enhanced bioinformatic profiling of VIDISCA libraries for virus detection and discovery,” Virus Res, vol. 263, p. 21–26, 2019.
    [Bibtex]
    @Article{Kinsella:19,
    author = {Cormac M. Kinsella and Martin Deijs and Lia van der Hoek},
    title = {Enhanced bioinformatic profiling of {VIDISCA} libraries for virus detection and discovery},
    journal = {{Virus Res}},
    year = {2019},
    volume = {263},
    pages = {21--26},
    doi = {10.1016/j.virusres.2018.12.010},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. Wernike and M. Beer, “Misinterpretation of Schmallenberg virus sequence variations: the sample material makes the difference,” Virus genes, 2019.
    [Bibtex]
    @Article{Wernike:19,
    author = {Kerstin Wernike and Martin Beer},
    title = {Misinterpretation of {S}chmallenberg virus sequence variations: the sample material makes the difference},
    journal = {Virus Genes},
    year = {2019},
    doi = {10.1007/s11262-018-1628-2},
    publisher = {Springer Nature},
    }
  • [DOI] P. Hubel, C. Urban, V. Bergant, W. M. Schneider, B. Knauer, A. Stukalov, P. Scaturro, A. Mann, L. Brunotte, H. H. Hoffmann, J. W. Schoggins, M. Schwemmle, M. Mann, C. M. Rice, and A. Pichlmair, “A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape,” Nat Immunol, 2019.
    [Bibtex]
    @Article{Hubel:19,
    author = {Philipp Hubel and Christian Urban and Valter Bergant and William M. Schneider and Barbara Knauer and Alexey Stukalov and Pietro Scaturro and Angelika Mann and Linda Brunotte and Heinrich H. Hoffmann and John W. Schoggins and Martin Schwemmle and Matthias Mann and Charles M. Rice and Andreas Pichlmair},
    title = {A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape},
    journal = {{Nat Immunol}},
    year = {2019},
    doi = {10.1038/s41590-019-0323-3},
    publisher = {Springer Nature},
    }
  • [DOI] K. Brown, I. Olendraite, S. M. Valles, A. E. Firth, Y. Chen, D. M. A. Guérin, Y. Hashimoto, S. Herrero, J. R. de Miranda, E. Ryabov, and ICTV Report Consortium, “ICTV virus taxonomy profile: Solinviviridae,” J Gen Virol, 2019.
    [Bibtex]
    @Article{Brown:19,
    author = {Katherine Brown and Ingrida Olendraite and Steven M. Valles and Andrew E. Firth and Yanping Chen and Diego M. A. Gu{\'{e}}rin and Yoshifumi Hashimoto and Salvador Herrero and Joachim R. de Miranda and Eugene Ryabov and {ICTV Report Consortium}},
    title = {{ICTV} Virus Taxonomy Profile: {S}olinviviridae},
    journal = {{J Gen Virol}},
    year = {2019},
    doi = {10.1099/jgv.0.001242},
    publisher = {Microbiology Society},
    }
  • [DOI] I. Olendraite, K. Brown, S. M. Valles, A. E. Firth, Y. Chen, D. M. A. Guérin, Y. Hashimoto, S. Herrero, J. R. de Miranda, E. Ryabov, and ICTV Report Consortium, “ICTV virus taxonomy profile: Polycipiviridae,” J Gen Virol, 2019.
    [Bibtex]
    @Article{Olendraite:19,
    author = {Ingrida Olendraite and Katherine Brown and Steven M. Valles and Andrew E. Firth and Yanping Chen and Diego M. A. Gu{\'{e}}rin and Yoshifumi Hashimoto and Salvador Herrero and Joachim R. de Miranda and Eugene Ryabov and {ICTV Report Consortium}},
    title = {{ICTV} Virus Taxonomy Profile: {P}olycipiviridae},
    journal = {{J Gen Virol}},
    year = {2019},
    doi = {10.1099/jgv.0.001241},
    publisher = {Microbiology Society},
    }
  • [DOI] S. Hansen, S. Hotop, O. Faye, O. Ndiaye, S. Böhlken-Fascher, R. Pessôa, F. Hufert, C. Stahl-Hennig, R. Frank, C. Czerny, J. Schmidt-Chanasit, S. S. Sanabani, A. A. Sall, M. Niedrig, M. Brönstrup, H. Fritz, and A. A. E. Wahed, “Diagnosing zika virus infection against a background of other flaviviruses: studies in high resolution serological analysis,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Hansen:19,
    author = {Sören Hansen and Sven-Kevin Hotop and Oumar Faye and Oumar Ndiaye and Susanne B\"{o}hlken-Fascher and Rodrigo Pess{\^{o}}a and Frank Hufert and Christiane Stahl-Hennig and Ronald Frank and Claus-Peter Czerny and Jonas Schmidt-Chanasit and Sabri S. Sanabani and Amadou A. Sall and Matthias Niedrig and Mark Br\"{o}nstrup and Hans-Joachim Fritz and Ahmed Abd El Wahed},
    title = {Diagnosing Zika virus infection against a background of other flaviviruses: Studies in high resolution serological analysis},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-019-40224-2},
    publisher = {Springer Nature},
    }
  • [DOI] M. Thijssen, P. Lemey, S. Amini-Bavil-Olyaee, S. Dellicour, S. M. Alavian, F. Tacke, C. Verslype, F. Nevens, and M. R. Pourkarim, “Mass migration to Europe: an opportunity for elimination of hepatitis B virus?,” Lancet Gastroenterol Hepatol, vol. 4, p. 315–323, 2019.
    [Bibtex]
    @Article{Thijssen:19,
    author = {Thijssen, Marijn and Lemey, Philippe and Amini-Bavil-Olyaee, Samad and Dellicour, Simon and Alavian, Seyed Moayed and Tacke, Frank and Verslype, Chris and Nevens, Frederik and Pourkarim, Mahmoud Reza},
    title = {Mass migration to {E}urope: an opportunity for elimination of hepatitis {B} virus?},
    journal = {{Lancet Gastroenterol Hepatol}},
    year = {2019},
    volume = {4},
    pages = {315--323},
    abstract = {People from low-to-middle income countries have been migrating to western Europe on a large scale in recent years. Data indicate that the number of first-time asylum applications by non-EU members increased from 290 000 in 2011 to more than 1·3 million in 2015. During the peak period of migration, The Global Health Sector Strategy on Viral Hepatitis was adopted by WHO. Viral hepatitis, and particularly hepatitis B virus (HBV), is an important disease because of its high prevalence and associated mortality. In some cases, HBV can be carried by refugees arriving from regions of high and intermediate prevalence. Refugees with HBV might not show clinical symptoms and not be diagnosed in destination countries with a low prevalence, where screening is not regularly done. Although transmission to the host population is low, dedicated surveillance and tailored public health policies are required. It is important to note that some of the countries that receive many migrants do not have a universal HBV vaccination programme. In this Viewpoint, we argue that the current large-scale movement from regions with high or intermediate HBV prevalence should be taken as an opportunity to achieve viral hepatitis elimination targets, by establishing a well prepared infrastructure for HBV screening, vaccination, and treatment.},
    doi = {10.1016/S2468-1253(19)30014-7},
    issue = {4},
    pmid = {30860067},
    }
  • [DOI] A. Jariani, C. Warth, K. Deforche, P. Libin, A. J. Drummond, A. Rambaut, F. A. Matsen IV, and K. Theys, “SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination,” Virus Evol, vol. 5, iss. 1, 2019.
    [Bibtex]
    @Article{Jariani:19,
    author = {Abbas Jariani and Christopher Warth and Koen Deforche and Pieter Libin and Alexei J Drummond and Andrew Rambaut and Frederick A {Matsen IV} and Kristof Theys},
    title = {{SANTA}-{SIM}: simulating viral sequence evolution dynamics under selection and recombination},
    journal = {{Virus Evol}},
    year = {2019},
    volume = {5},
    number = {1},
    doi = {10.1093/ve/vez003},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] X. Chen and D. Li, “ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data,” Bioinformatics, 2019.
    [Bibtex]
    @Article{Chen:19,
    author = {Xun Chen and Dawei Li},
    title = {{ERVcaller}: Identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data},
    journal = {Bioinformatics},
    year = {2019},
    doi = {10.1093/bioinformatics/btz205},
    editor = {Inanc Birol},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] N. Altan-Bonnet, C. Perales, and E. Domingo, “Extracellular vesicles: vehicles of en bloc viral transmission.,” Virus Res, 2019.
    [Bibtex]
    @Article{Altan-Bonnet:19,
    author = {Altan-Bonnet, Nihal and Perales, Celia and Domingo, Esteban},
    title = {Extracellular vesicles: vehicles of en bloc viral transmission.},
    journal = {{Virus Res}},
    year = {2019},
    abstract = {En Bloc transmission of viruses allow multiple genomes to collectivelly penetrate and initiate infection in the same cell, often resulting in enhanced infectivity. Given the quasispecies (mutant cloud) nature of RNA viruses and many DNA viruses, the multiple genomes provide different starting points in sequence space to initiate adaptive walks. Moreover, en bloc transmission has implications for modulation of viral fitness and for the response of viral populations to lethal mutagenesis. Mechanisms that can enable multiple viral genomes to be transported en bloc among hosts has only recently been gaining attention. A growing body of research suggests that extracellular vesicles (EV) are highly prevalent and robust vehicles for en bloc delivery of viral particles and naked infectious genomes among organisms. Both RNA and DNA viruses exploit these vesicles to increase multiplicity of infection and enhance virulence.},
    doi = {10.1016/j.virusres.2019.03.023},
    pmid = {30928427},
    }
  • [DOI] O. Ratmann, K. M. and Grabowski, M. Hall, T. Golubchik, C. Wymant, L. Abeler-Dörner, D. Bonsall, A. Hoppe, A. L. Brown, T. de Oliveira, A. Gall, P. Kellam, D. Pillay, J. Kagaayi, G. Kigozi, T. C. Quinn, M. J. Wawer, O. Laeyendecker, D. Serwadda, R. H. Gray, and C. Fraser, “Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis,” Nat Commun, vol. 10, iss. 1, 2019.
    [Bibtex]
    @Article{Ratmann:19,
    author = {Oliver Ratmann and and M. Kate Grabowski and Matthew Hall and Tanya Golubchik and Chris Wymant and Lucie Abeler-Dörner and David Bonsall and Anne Hoppe and Andrew Leigh Brown and Tulio de Oliveira and Astrid Gall and Paul Kellam and Deenan Pillay and Joseph Kagaayi and Godfrey Kigozi and Thomas C. Quinn and Maria J. Wawer and Oliver Laeyendecker and David Serwadda and Ronald H. Gray and Christophe Fraser},
    title = {Inferring {HIV}-1 transmission networks and sources of epidemic spread in {A}frica with deep-sequence phylogenetic analysis},
    journal = {{Nat Commun}},
    year = {2019},
    volume = {10},
    number = {1},
    doi = {10.1038/s41467-019-09139-4},
    publisher = {Springer Nature},
    }
  • [DOI] F. Mock, A. Viehweger, E. Barth, and M. Marz, “Viral host prediction with deep learning,” bioRxiv, p. 575571, 2019.
    [Bibtex]
    @Article{Mock:19,
    author = {Florian Mock and Adrian Viehweger and Emanuel Barth and Manja Marz},
    title = {Viral host prediction with Deep Learning},
    journal = {{bioRxiv}},
    year = {2019},
    pages = {575571},
    doi = {10.1101/575571},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] H. F. Löchel, D. Eger, T. Sperlea, and D. Heider, “Deep learning on chaos game representation for proteins,” bioRxiv, p. 575324, 2019.
    [Bibtex]
    @Article{Löchel:19,
    author = {Hannah F. Löchel and Dominic Eger and Theodor Sperlea and Dominik Heider},
    title = {Deep Learning on Chaos Game Representation for Proteins},
    journal = {{bioRxiv}},
    year = {2019},
    pages = {575324},
    doi = {10.1101/575324},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] L. de Borba, S. M. Villordo, F. L. Marsico, J. M. Carballeda, C. V. Filomatori, L. G. Gebhard, H. M. Pallarés, S. Lequime, L. Lambrechts, I. S. Vargas, C. D. Blair, and A. V. Gamarnik, “RNA structure duplication in the dengue virus 3$\prime$ UTR: redundancy or host specificity?,” mBio, vol. 10, iss. 1, 2019.
    [Bibtex]
    @Article{Borba:19,
    author = {Luana de Borba and Sergio M. Villordo and Franco L. Marsico and Juan M. Carballeda and Claudia V. Filomatori and Leopoldo G. Gebhard and Horacio M. Pallar{\'{e}}s and Sebastian Lequime and Louis Lambrechts and Irma S{\'{a}}nchez Vargas and Carol D. Blair and Andrea V. Gamarnik},
    title = {{RNA} Structure Duplication in the Dengue Virus 3$\prime$ {UTR}: Redundancy or Host Specificity?},
    journal = {{mBio}},
    year = {2019},
    volume = {10},
    number = {1},
    doi = {10.1128/mbio.02506-18},
    editor = {Carolyn B. Coyne},
    publisher = {American Society for Microbiology},
    }
  • [DOI] R. Bouckaert, T. G. Vaughan, J. Barido-Sottani, S. Duchêne, M. Fourment, A. Gavryushkina, J. Heled, G. Jones, D. Kühnert, N. D. Maio, M. Matschiner, F. K. Mendes, N. F. Müller, H. A. Ogilvie, L. du Plessis, A. Popinga, A. Rambaut, D. Rasmussen, I. Siveroni, M. A. Suchard, C. Wu, D. Xie, C. Zhang, T. Stadler, and A. J. Drummond, “BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis,” PLOS Comput Biol, vol. 15, iss. 4, p. e1006650, 2019.
    [Bibtex]
    @Article{Bouckaert:19,
    author = {Remco Bouckaert and Timothy G. Vaughan and Joëlle Barido-Sottani and Sebasti{\'{a}}n Duch{\^{e}}ne and Mathieu Fourment and Alexandra Gavryushkina and Joseph Heled and Graham Jones and Denise Kühnert and Nicola De Maio and Michael Matschiner and F{\'{a}}bio K. Mendes and Nicola F. Müller and Huw A. Ogilvie and Louis du Plessis and Alex Popinga and Andrew Rambaut and David Rasmussen and Igor Siveroni and Marc A. Suchard and Chieh-Hsi Wu and Dong Xie and Chi Zhang and Tanja Stadler and Alexei J. Drummond},
    title = {{BEAST} 2.5: An advanced software platform for {B}ayesian evolutionary analysis},
    journal = {{PLOS Comput Biol}},
    year = {2019},
    volume = {15},
    number = {4},
    pages = {e1006650},
    doi = {10.1371/journal.pcbi.1006650},
    editor = {Mihaela Pertea},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] E. Domingo, A. I. de Ávila, I. Gallego, J. Sheldon, and C. Perales, “Viral fitness: history and relevance for viral pathogenesis and antiviral interventions,” Pathog Dis, 2019.
    [Bibtex]
    @Article{Domingo:19,
    author = {Esteban Domingo and Ana I de {\'{A}}vila and Isabel Gallego and Julie Sheldon and Celia Perales},
    title = {Viral fitness: history and relevance for viral pathogenesis and antiviral interventions},
    journal = {{Pathog Dis}},
    year = {2019},
    doi = {10.1093/femspd/ftz021},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] J. V. Membrebe, M. A. Suchard, A. Rambaut, G. Baele, and P. Lemey, “Bayesian inference of evolutionary histories under time-dependent substitution rates,” Mol Biol Evol, 2019.
    [Bibtex]
    @Article{Membrebe:19,
    author = {Jade Vincent Membrebe and Marc A Suchard and Andrew Rambaut and Guy Baele and Philippe Lemey},
    title = {Bayesian inference of evolutionary histories under time-dependent substitution rates},
    journal = {{Mol Biol Evol}},
    year = {2019},
    doi = {10.1093/molbev/msz094},
    editor = {Jeffrey Thorne},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] J. Singer, E. Thomson, J. Hughes, E. Aranday-Cortes, J. McLauchlan, A. S. da Filipe, L. Tong, C. Manso, R. Gifford, D. Robertson, E. Barnes, M. Ansari, J. Mbisa, D. Bibby, D. Bradshaw, and D. Smith, “Interpreting viral deep sequencing data with GLUE,” Viruses, vol. 11, iss. 4, p. 323, 2019.
    [Bibtex]
    @Article{Singer:19,
    author = {Joshua Singer and Emma Thomson and Joseph Hughes and Elihu Aranday-Cortes and John McLauchlan and Ana da Silva Filipe and Lily Tong and Carmen Manso and Robert Gifford and David Robertson and Eleanor Barnes and M. Ansari and Jean Mbisa and David Bibby and Daniel Bradshaw and David Smith},
    title = {Interpreting Viral Deep Sequencing Data with {GLUE}},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {4},
    pages = {323},
    doi = {10.3390/v11040323},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] A. W. Whisnant, C. S. Jürges, T. Hennig, E. Wyler, B. Prusty, A. J. Rutkowski, A. L’hernault, M. Göbel, K. Döring, J. Menegatti, R. Antrobus, N. J. Matheson, F. W. H. Künzig, G. Mastrobuoni, C. Bielow, S. Kempa, L. Chunguang, T. Dandekar, R. Zimmer, M. Landthaler, F. Grässer, P. J. Lehner, C. C. Friedel, F. Erhard, and L. Dölken, “Integrative functional genomics decodes herpes simplex virus 1,” bioRxiv, p. 603654, 2019.
    [Bibtex]
    @Article{Whisnant:19,
    author = {Adam W. Whisnant and Christopher S. Jürges and Thomas Hennig and Emanuel Wyler and Bhupesh Prusty and Andrzej J Rutkowski and Anne L'hernault and Margarete Göbel and Kristina Döring and Jennifer Menegatti and Robin Antrobus and Nicholas J. Matheson and Florian W.H. Künzig and Guido Mastrobuoni and Chris Bielow and Stefan Kempa and Liang Chunguang and Thomas Dandekar and Ralf Zimmer and Markus Landthaler and Friedrich Grässer and Paul J. Lehner and Caroline C. Friedel and Florian Erhard and Lars Dölken},
    title = {Integrative functional genomics decodes herpes simplex virus 1},
    journal = {{bioRxiv}},
    year = {2019},
    pages = {603654},
    doi = {10.1101/603654},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Nachtweide and M. Stanke, “Multi-genome annotation with AUGUSTUS,” in Methods Mol Biol, Springer New York, 2019, p. 139–160.
    [Bibtex]
    @InCollection{Nachtweide:19,
    author = {Stefanie Nachtweide and Mario Stanke},
    title = {Multi-Genome Annotation with {AUGUSTUS}},
    booktitle = {{Methods Mol Biol}},
    publisher = {Springer New York},
    year = {2019},
    pages = {139--160},
    doi = {10.1007/978-1-4939-9173-0_8},
    }
  • [DOI] A. B. de Schneider and M. T. Wolfinger, “Musashi binding elements in zika and related flavivirus 3’UTRs: a comparative study in silico,” Sci rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{BernardiSchneider:19,
    author = {Adriano de Bernardi Schneider and Michael T. Wolfinger},
    title = {Musashi binding elements in Zika and related Flavivirus 3'{UTRs}: A comparative study in silico},
    journal = {Sci Rep},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-019-43390-5},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] F. Hufsky, B. Ibrahim, S. Modha, M. R. J. Clokie, S. Deinhardt-Emmer, B. E. Dutilh, S. Lycett, P. Simmonds, V. Thiel, A. Abroi, E. M. Adriaenssens, M. Escalera-Zamudio, J. N. Kelly, K. Lamkiewicz, L. Lu, J. Susat, T. Sicheritz, D. L. Robertson, and M. Marz, “The third annual meeting of the European Virus Bioinformatics Center,” Viruses, vol. 11, iss. 5, p. 420, 2019.
    [Bibtex]
    @Article{Hufsky:19,
    author = {Franziska Hufsky and Bashar Ibrahim and Sejal Modha and Martha R. J. Clokie and Stefanie Deinhardt-Emmer and Bas E. Dutilh and Samantha Lycett and Peter Simmonds and Volker Thiel and Aare Abroi and Evelien M. Adriaenssens and Marina Escalera-Zamudio and Jenna Nicole Kelly and Kevin Lamkiewicz and Lu Lu and Julian Susat and Thomas Sicheritz and David L. Robertson and Manja Marz},
    title = {The Third Annual Meeting of the {E}uropean {V}irus {B}ioinformatics {C}enter},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {420},
    doi = {10.3390/v11050420},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] S. Peter, M. Hölzer, K. Lamkiewicz, P. S. di Fenizio, H. A. Hwaeer, M. Marz, S. Schuster, P. Dittrich, and B. Ibrahim, “Structure and hierarchy of influenza virus models revealed by reaction network analysis,” Viruses, vol. 11, iss. 5, p. 449, 2019.
    [Bibtex]
    @Article{Peter:19,
    author = {Stephan Peter and Martin Hölzer and Kevin Lamkiewicz and Pietro Speroni di Fenizio and Hassan Al Hwaeer and Manja Marz and Stefan Schuster and Peter Dittrich and Bashar Ibrahim},
    title = {Structure and Hierarchy of Influenza Virus Models Revealed by Reaction Network Analysis},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {449},
    doi = {10.3390/v11050449},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Kiening, R. Ochsenreiter, H. Hellinger, T. Rattei, I. Hofacker, and D. Frishman, “Conserved secondary structures in viral mRNAs,” Viruses, vol. 11, iss. 5, p. 401, 2019.
    [Bibtex]
    @Article{Kiening:19,
    author = {Michael Kiening and Roman Ochsenreiter and Hans-Jörg Hellinger and Thomas Rattei and Ivo Hofacker and Dmitrij Frishman},
    title = {Conserved Secondary Structures in Viral {mRNAs}},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {401},
    doi = {10.3390/v11050401},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] A. C. Gregory, A. A. Zayed, N. Conceição-Neto, B. Temperton, B. Bolduc, A. Alberti, M. Ardyna, K. Arkhipova, M. Carmichael, C. Cruaud, C. Dimier, G. Domínguez-Huerta, J. Ferland, S. Kandels, Y. Liu, C. Marec, S. Pesant, M. Picheral, S. Pisarev, J. Poulain, J. Tremblay, D. Vik, M. Babin, C. Bowler, A. I. Culley, C. de Vargas, B. E. Dutilh, D. Iudicone, L. Karp-Boss, S. Roux, S. Sunagawa, P. Wincker, M. B. Sullivan, S. G. Acinas, M. Babin, P. Bork, E. Boss, C. Bowler, G. Cochrane, C. de Vargas, M. Follows, G. Gorsky, N. Grimsley, L. Guidi, P. Hingamp, D. Iudicone, O. Jaillon, S. Kandels-Lewis, L. Karp-Boss, E. Karsenti, F. Not, H. Ogata, S. Pesant, N. Poulton, J. Raes, C. Sardet, S. Speich, L. Stemmann, M. B. Sullivan, S. Sunagawa, and P. Wincker, “Marine DNA viral macro- and microdiversity from pole to pole,” Cell, vol. 177, iss. 5, p. 1109–1123.e14, 2019.
    [Bibtex]
    @Article{Gregory:19,
    author = {Ann C. Gregory and Ahmed A. Zayed and N{\'{a}}dia Concei{\c{c}}{\~{a}}o-Neto and Ben Temperton and Ben Bolduc and Adriana Alberti and Mathieu Ardyna and Ksenia Arkhipova and Margaux Carmichael and Corinne Cruaud and C{\'{e}}line Dimier and Guillermo Dom{\'{\i}}nguez-Huerta and Joannie Ferland and Stefanie Kandels and Yunxiao Liu and Claudie Marec and St{\'{e}}phane Pesant and Marc Picheral and Sergey Pisarev and Julie Poulain and Jean-{\'{E}}ric Tremblay and Dean Vik and Marcel Babin and Chris Bowler and Alexander I. Culley and Colomban de Vargas and Bas E. Dutilh and Daniele Iudicone and Lee Karp-Boss and Simon Roux and Shinichi Sunagawa and Patrick Wincker and Matthew B. Sullivan and Silvia G. Acinas and Marcel Babin and Peer Bork and Emmanuel Boss and Chris Bowler and Guy Cochrane and Colomban de Vargas and Michael Follows and Gabriel Gorsky and Nigel Grimsley and Lionel Guidi and Pascal Hingamp and Daniele Iudicone and Olivier Jaillon and Stefanie Kandels-Lewis and Lee Karp-Boss and Eric Karsenti and Fabrice Not and Hiroyuki Ogata and St{\'{e}}phane Pesant and Nicole Poulton and Jeroen Raes and Christian Sardet and Sabrina Speich and Lars Stemmann and Matthew B. Sullivan and Shinichi Sunagawa and Patrick Wincker},
    title = {Marine {DNA} Viral Macro- and Microdiversity from Pole to Pole},
    journal = {Cell},
    year = {2019},
    volume = {177},
    number = {5},
    pages = {1109--1123.e14},
    doi = {10.1016/j.cell.2019.03.040},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Tapinos, B. Constantinides, M. V. T. Phan, S. Kouchaki, M. Cotten, and D. L. Robertson, “The utility of data transformation for alignment, de novo assembly and classification of short read virus sequences,” Viruses, vol. 11, iss. 5, p. 394, 2019.
    [Bibtex]
    @Article{Tapinos:19a,
    author = {Avraam Tapinos and Bede Constantinides and My V. T. Phan and Samaneh Kouchaki and Matthew Cotten and David L. Robertson},
    title = {The Utility of Data Transformation for Alignment, de novo Assembly and Classification of Short Read Virus Sequences},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {394},
    doi = {10.3390/v11050394},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] B. Zhao, C. Dewald, M. Hennig, J. Bossert, M. Bauer, M. W. Pletz, and K. D. Jandt, “Microorganisms at materials surfaces in aircraft: potential risks for public health? – a systematic review,” Travel Med Infect Dis, vol. 28, p. 6–14, 2019.
    [Bibtex]
    @Article{Zhao:19,
    author = {Bin Zhao and Carolin Dewald and Max Hennig and Jörg Bossert and Michael Bauer and Mathias W. Pletz and Klaus D. Jandt},
    title = {Microorganisms at materials surfaces in aircraft: Potential risks for public health? - A systematic review},
    journal = {{Travel Med Infect Dis}},
    year = {2019},
    volume = {28},
    pages = {6--14},
    doi = {10.1016/j.tmaid.2018.07.011},
    publisher = {Elsevier {BV}},
    }
  • [DOI] V. Fonseca, P. J. K. Libin, K. Theys, N. R. Faria, M. R. T. Nunes, M. I. Restovic, M. Freire, M. Giovanetti, L. Cuypers, A. Nowé, A. Abecasis, K. Deforche, G. A. Santiago, I. C. de Siqueira, E. J. San, K. C. B. Machado, V. Azevedo, A. M. B. Filippis, R. V. da Cunha, O. G. Pybus, A. Vandamme, L. C. J. Alcantara, and T. de Oliveira, “A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes,” PLoS Negl Trop Dis, vol. 13, iss. 5, p. e0007231, 2019.
    [Bibtex]
    @Article{Fonseca:19,
    author = {Vagner Fonseca and Pieter J. K. Libin and Kristof Theys and Nuno R. Faria and Marcio R. T. Nunes and Maria I. Restovic and Murilo Freire and Marta Giovanetti and Lize Cuypers and Ann Now{\'{e}} and Ana Abecasis and Koen Deforche and Gilberto A. Santiago and Isadora C. de Siqueira and Emmanuel J. San and Kaliane C. B. Machado and Vasco Azevedo and Ana Maria Bispo-de Filippis and Rivaldo Ven{\^{a}}ncio da Cunha and Oliver G. Pybus and Anne-Mieke Vandamme and Luiz C. J. Alcantara and Tulio de Oliveira},
    title = {A computational method for the identification of {D}engue, {Z}ika and {C}hikungunya virus species and genotypes},
    journal = {{PLoS Negl Trop Dis}},
    year = {2019},
    volume = {13},
    number = {5},
    pages = {e0007231},
    doi = {10.1371/journal.pntd.0007231},
    editor = {Isabel Rodriguez-Barraquer},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] M. Hölzer and M. Marz, “de novo transcriptome assembly: a comprehensive cross-species comparison of short-read RNA-seq assemblers,” GigaScience, vol. 8, iss. 5, 2019.
    [Bibtex]
    @Article{Hölzer:19,
    author = {Martin Hölzer and Manja Marz},
    title = {De novo transcriptome assembly: A comprehensive cross-species comparison of short-read {RNA}-Seq assemblers},
    journal = {{GigaScience}},
    year = {2019},
    volume = {8},
    number = {5},
    doi = {10.1093/gigascience/giz039},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Schuster, P. Miesen, and R. P. van Rij, “Antiviral RNAi in insects and mammals: parallels and differences,” Viruses, vol. 11, iss. 5, p. 448, 2019.
    [Bibtex]
    @Article{Schuster:19,
    author = {Susan Schuster and Pascal Miesen and Ronald P. van Rij},
    title = {Antiviral {RNAi} in Insects and Mammals: Parallels and Differences},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {448},
    doi = {10.3390/v11050448},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] F. Pfaff, S. Hägglund, M. Zoli, S. Blaise-Boisseau, E. Laloy, S. Koethe, D. Zühlke, K. Riedel, S. Zientara, L. Bakkali-Kassimi, J. Valarcher, D. Höper, M. Beer, and M. Eschbaumer, “Proteogenomics uncovers critical elements of host response in bovine soft palate epithelial cells following in vitro infection with foot-and-mouth disease virus,” Viruses, vol. 11, iss. 1, p. 53, 2019.
    [Bibtex]
    @Article{Pfaff:19,
    author = {Florian Pfaff and Sara Hägglund and Martina Zoli and Sandra Blaise-Boisseau and Eve Laloy and Susanne Koethe and Daniela Zühlke and Katharina Riedel and Stephan Zientara and Labib Bakkali-Kassimi and Jean-Fran{\c{c}}ois Valarcher and Dirk Höper and Martin Beer and Michael Eschbaumer},
    title = {Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {1},
    pages = {53},
    doi = {10.3390/v11010053},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] B. Röder, N. Kersten, M. Herr, N. K. Speicher, and N. Pfeifer, “Web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning,” Nucleic Acids Res, 2019.
    [Bibtex]
    @Article{Röder:19,
    author = {Benedict Röder and Nicolas Kersten and Marius Herr and Nora K Speicher and Nico Pfeifer},
    title = {web-{rMKL}: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning},
    journal = {{Nucleic Acids Res}},
    year = {2019},
    doi = {10.1093/nar/gkz422},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] K. Theys, P. J. K. Libin, K. V. Laethem, and A. B. Abecasis, “An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to HIV-1 subtypes and integrase inhibitors.,” Antimicrob Agents Chemother, 2019.
    [Bibtex]
    @Article{Theys:19,
    author = {Kristof Theys and Pieter J. K. Libin and Kristel Van Laethem and Ana B Abecasis},
    title = {An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to {HIV}-1 subtypes and integrase inhibitors.},
    journal = {{Antimicrob Agents Chemother}},
    year = {2019},
    doi = {10.1128/aac.00539-19},
    publisher = {American Society for Microbiology},
    }
  • [DOI] R. Kallies, M. Hölzer, R. Brizola Toscan, U. Nunes da Rocha, J. Anders, M. Marz, and A. Chatzinotas, “Evaluation of sequencing library preparation protocols for viral metagenomic analysis from pristine aquifer groundwaters.,” Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Kallies:19,
    author = {Kallies, René and Hölzer, Martin and Brizola Toscan, Rodolfo and Nunes da Rocha, Ulisses and Anders, John and Marz, Manja and Chatzinotas, Antonis},
    title = {Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Viral ecology of terrestrial habitats is yet-to be extensively explored, in particular the terrestrial subsurface. One problem in obtaining viral sequences from groundwater aquifer samples is the relatively low amount of virus particles. As a result, the amount of extracted DNA may not be sufficient for direct sequencing of such samples. Here we compared three DNA amplification methods to enrich viral DNA from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory to evaluate potential bias created by the different amplification methods as determined by viral metagenomics. Linker amplification shotgun libraries resulted in lowest redundancy among the sequencing reads and showed the highest diversity, while multiple displacement amplification produced the highest number of contigs with the longest average contig size, suggesting a combination of these two methods is suitable for the successful enrichment of viral DNA from pristine groundwater samples. In total, we identified 27,173, 5,886 and 32,613 viral contigs from the three samples from which 11.92 to 18.65% could be assigned to taxonomy using blast. Among these, members of the order were the most abundant group (52.20 to 69.12%) dominated by and . Those, and the high number of unknown viral sequences, substantially expand the known virosphere.},
    doi = {10.3390/v11060484},
    issue = {6},
    keywords = {AquaDiva; aquifer; groundwater; sequencing library preparation; viral metagenome},
    pmid = {31141902},
    }
  • [DOI] A. Dukhovny, K. Lamkiewicz, Q. Chen, M. Fricke, N. Jabrane-Ferrat, M. Marz, J. U. Jung, and E. H. Sklan, “A CRISPR activation screen identifies genes protecting from Zika virus infection,” J Virol, 2019.
    [Bibtex]
    @Article{Dukhovny:19,
    author = {Dukhovny, Anna and Lamkiewicz, Kevin and Chen, Qian and Fricke, Markus and Jabrane-Ferrat, Nabila and Marz, Manja and Jung, Jae U. and Sklan, Ella H.},
    title = {A {CRISPR} activation screen identifies genes protecting from {Z}ika virus infection},
    journal = {{J Virol}},
    year = {2019},
    abstract = {Zika virus (ZIKV) is an arthropod borne emerging pathogen causing febrile illness. ZIKV is associated Guillain-Barr{\'e} syndrome and other neurological complications. Infection during pregnancy is associated with pregnancy complications and developmental and neurological abnormalities collectively defined as congenital Zika syndrome. There is still no vaccine or specific treatment for ZIKV infection. To identify host factors that can rescue cells from ZIKV infection we used a genome scale CRISPR activation screen. Our highly ranking hits included a short list of interferon stimulated genes (ISGs) previously reported to have antiviral activity. Validation of the screen results highlighted IFNL2 and IFI6 as genes providing high levels of protection from ZIKV. Activation of these genes had an effect on an early stage in viral infection. In addition, infected cells expressing sgRNAs for both of these genes displayed lower levels of cell death compared to controls. Furthermore, the identified genes were significantly induced in ZIKV infected placenta explants. Thus, these results highlight a set of ISGs directly relevant for rescuing cells from ZIKV infection or its associated cell death and substantiates CRISPR activation screens as a tool to identify host factors impeding pathogen infection.IMPORTANCE Zika virus (ZIKV) is an emerging vector-borne pathogen causing a febrile disease. ZIKV infection might also trigger Guillain-Barr{\'e} syndrome, neuropathy and myelitis. Vertical transmission of ZIKV can cause fetus demise, still birth or severe congenital abnormalities and neurological complications. There is no vaccine or specific antiviral treatment against ZIKV. We used a genome wide CRISPR activation screen, where genes are activated from their native promoters to identify host cell factors that protect cells from ZIKV infection or associated cell death. The results provide better understanding of key host factors that protect cells from ZIKV infection and might assist in identifying novel antiviral targets.},
    doi = {10.1128/JVI.00211-19},
    elocation-id = {JVI.00211-19},
    eprint = {https://jvi.asm.org/content/early/2019/05/23/JVI.00211-19.full.pdf},
    publisher = {American Society for Microbiology Journals},
    url = {https://jvi.asm.org/content/early/2019/05/23/JVI.00211-19},
    }
  • [DOI] S. Jansen, A. Heitmann, R. Lühken, M. Leggewie, M. Helms, M. Badusche, G. Rossini, J. Schmidt-Chanasit, and E. Tannich, “Culex torrentium: a potent vector for the transmission of West Nile Virus in central europe,” Viruses, vol. 11, iss. 6, p. 492, 2019.
    [Bibtex]
    @Article{Jansen:19,
    author = {Stephanie Jansen and Anna Heitmann and Renke Lühken and Mayke Leggewie and Michelle Helms and Marlis Badusche and Giada Rossini and Jonas Schmidt-Chanasit and Egbert Tannich},
    title = {{C}ulex torrentium: A Potent Vector for the Transmission of {W}est {N}ile {V}irus in Central Europe},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {6},
    pages = {492},
    doi = {10.3390/v11060492},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] L. A. Carlisle, T. Turk, K. Kusejko, K. J. Metzner, C. Leemann, C. Schenkel, N. Bachmann, S. Posada, N. Beerenwinkel, J. Böni, S. Yerly, T. Klimkait, M. Perreau, D. L. Braun, A. Rauch, A. Calmy, M. Cavassini, M. Battegay, P. Vernazza, E. Bernasconi, H. F. Günthard, R. D. Kouyos, and Swiss HIV Cohort Study, “Viral diversity from next-generation sequencing of HIV-1 samples provides precise estimates of infection recency and time since infection.,” J Infect Dis, 2019.
    [Bibtex]
    @Article{Carlisle:19,
    author = {Carlisle, Louisa A and Turk, Teja and Kusejko, Katharina and Metzner, Karin J and Leemann, Christine and Schenkel, Corinne and Bachmann, Nadine and Posada, Susana and Beerenwinkel, Niko and Böni, Jürg and Yerly, Sabine and Klimkait, Thomas and Perreau, Matthieu and Braun, Dominique L and Rauch, Andri and Calmy, Alexandra and Cavassini, Matthias and Battegay, Manuel and Vernazza, Pietro and Bernasconi, Enos and Günthard, Huldrych F and Kouyos, Roger D and {Swiss HIV Cohort Study}},
    title = {Viral diversity from next-generation sequencing of {HIV}-1 samples provides precise estimates of infection recency and time since infection.},
    journal = {{J Infect Dis}},
    year = {2019},
    abstract = {HIV-1 genetic diversity increases over the course of infection, and can be used to infer time since infection (TSI) and consequently also infection recency, crucial quantities for HIV-1 surveillance and the understanding of viral pathogenesis. We considered 313 HIV-infected individuals for whom reliable estimates of infection dates and next-generation sequencing (NGS)-derived nucleotide frequency data were available. Fraction of ambiguous nucleotides (FAN) obtained by population sequencing were available for 207 samples. We assessed whether average pairwise diversity (APD) calculated using NGS sequences provided a more exact prediction of TSI and classification of infection recency (<1 year post-infection) compared to FAN. NGS-derived APD classifies an infection as recent with a sensitivity of 88% and specificity of 85%. When considering only the 207 samples for which FAN were available, NGS-derived APD exhibited a higher sensitivity (90% vs 78%) and specificity (95% vs 67%) than FAN. Additionally, APD can estimate TSI with a mean absolute error of 0.84 years, compared to 1.03 years for FAN.},
    doi = {10.1093/infdis/jiz094},
    keywords = {HIV-1; diversity; infection recency; next-generation sequencing; time since infection},
    pmid = {30835266},
    }
  • [DOI] V. Kinast, T. L. Burkard, D. Todt, and E. Steinmann, "Hepatitis E virus drug development.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Kinast:19,
    author = {Kinast, Volker and Burkard, Thomas L and Todt, Daniel and Steinmann, Eike},
    title = {Hepatitis {E} Virus Drug Development.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Hepatitis E virus (HEV) is an underestimated disease, leading to estimated 20 million infections and up to 70,000 deaths annually. Infections are mostly asymptomatic but can reach mortality rates up to 25% in pregnant women or become chronic in immunocompromised patients. The current therapy options are limited to the unspecific antivirals Ribavirin (RBV) and pegylated Interferon-α (pegIFN-α). RBV leads to viral clearance in only 80% of patients treated, and is, similar to pegIFN-α, contraindicated in the major risk group of pregnant women, emphasizing the importance of new therapy options. In this review, we focus on the urgent need and current efforts in HEV drug development. We provide an overview of the current status of HEV antiviral research. Furthermore, we discuss strategies for drug development and the limitations of the approaches with respect to HEV.},
    doi = {10.3390/v11060485},
    issue = {6},
    keywords = {antivirals; drug development; hepatitis E virus; ribavirin; sofosbuvir; therapy; vaccine},
    pmid = {31141919},
    }
  • [DOI] A. Brinkmann, A. Andrusch, A. Belka, C. Wylezich, D. Höper, A. Pohlmann, T. N. Petersen, P. Lucas, Y. Blanchard, A. Papa, A. Melidou, B. B. Oude Munnink, J. Matthijnssens, W. Deboutte, R. J. Ellis, F. Hansmann, W. Baumgärtner, E. van der Vries, A. Osterhaus, C. Camma, I. Mangone, A. Lorusso, M. Maracci, A. Nunes, M. Pinto, V. Borges, A. Kroneman, D. Schmitz, V. M. Corman, C. Drosten, T. C. Jones, R. S. Hendriksen, F. M. Aarestrup, M. Koopmans, M. Beer, and A. Nitsche, "Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets.," J Clin Microbiol, 2019.
    [Bibtex]
    @Article{Brinkmann:19,
    author = {Brinkmann, Annika and Andrusch, Andreas and Belka, Ariane and Wylezich, Claudia and Höper, Dirk and Pohlmann, Anne and Petersen, Thomas Nordahl and Lucas, Pierrick and Blanchard, Yannick and Papa, Anna and Melidou, Angeliki and Oude Munnink, Bas B and Matthijnssens, Jelle and Deboutte, Ward and Ellis, Richard J and Hansmann, Florian and Baumgärtner, Wolfgang and van der Vries, Erhard and Osterhaus, Albert and Camma, Cesare and Mangone, Iolanda and Lorusso, Alessio and Maracci, Maurilia and Nunes, Alexandra and Pinto, Miguel and Borges, Vítor and Kroneman, Annelies and Schmitz, Dennis and Corman, Victor Max and Drosten, Christian and Jones, Terry C and Hendriksen, Rene S and Aarestrup, Frank M and Koopmans, Marion and Beer, Martin and Nitsche, Andreas},
    title = {Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets.},
    journal = {{J Clin Microbiol}},
    year = {2019},
    abstract = {Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. Sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing, using publicly available and custom tools and databases, and differ widely between individuals and institutions.Here, we present the results of the COMPARE (COllaborative Management Platform for detection and Analyses of [Re-] emerging and foodborne outbreaks in Europe) virus proficiency test. An artificial, simulated dataset of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis towards the identification of viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple dataset. The identification of slightly mutated and highly divergent virus genomes has been identified as being most challenging: Furthermore, the interpretation of the results together with a fictitious case report by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings.External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve harmonization, comparability, and reproducibility of results. Similar to what is established for conventional laboratory tests like PCR, there is a need for the establishment of international proficiency testing for bioinformatics pipelines and interpretation of such results.},
    doi = {10.1128/JCM.00466-19},
    pmid = {31167846},
    }
  • [DOI] P. J. Walker, S. G. Siddell, E. J. Lefkowitz, A. R. Mushegian, D. M. Dempsey, B. E. Dutilh, B. Harrach, R. L. Harrison, C. R. Hendrickson, S. Junglen, N. J. Knowles, A. M. Kropinski, M. Krupovic, J. H. Kuhn, M. Nibert, L. Rubino, S. Sabanadzovic, P. Simmonds, A. Varsani, F. M. Zerbini, and A. J. Davison, "Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)," Arch Virol, 2019.
    [Bibtex]
    @Article{Walker:19,
    author = {Peter J. Walker and Stuart G. Siddell and Elliot J. Lefkowitz and Arcady R. Mushegian and Donald M. Dempsey and Bas E. Dutilh and Bal{\'{a}}zs Harrach and Robert L. Harrison and R. Curtis Hendrickson and Sandra Junglen and Nick J. Knowles and Andrew M. Kropinski and Mart Krupovic and Jens H. Kuhn and Max Nibert and Luisa Rubino and Sead Sabanadzovic and Peter Simmonds and Arvind Varsani and Francisco Murilo Zerbini and Andrew J. Davison},
    title = {Changes to virus taxonomy and the {I}nternational {C}ode of {V}irus {C}lassification and {N}omenclature ratified by the {I}nternational {C}ommittee on {T}axonomy of {V}iruses (2019)},
    journal = {{Arch Virol}},
    year = {2019},
    doi = {10.1007/s00705-019-04306-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] J. Lechner, F. Hartkopf, P. Hiort, A. Nitsche, M. Grossegesse, J. Doellinger, B. Y. Renard, and T. Muth, "Purple: a computational workflow for strategic selection of peptides for viral diagnostics using MS-based targeted proteomics.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Lechner:19,
    author = {Lechner, Johanna and Hartkopf, Felix and Hiort, Pauline and Nitsche, Andreas and Grossegesse, Marica and Doellinger, Joerg and Renard, Bernhard Y and Muth, Thilo},
    title = {Purple: A Computational Workflow for Strategic Selection of Peptides for Viral Diagnostics Using {MS}-Based Targeted Proteomics.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Emerging virus diseases present a global threat to public health. To detect viral pathogens in time-critical scenarios, accurate and fast diagnostic assays are required. Such assays can now be established using mass spectrometry-based targeted proteomics, by which viral proteins can be rapidly detected from complex samples down to the strain-level with high sensitivity and reproducibility. Developing such targeted assays involves tedious steps of peptide candidate selection, peptide synthesis, and assay optimization. Peptide selection requires extensive preprocessing by comparing candidate peptides against a large search space of background proteins. Here we present Purple (Picking unique relevant peptides for viral experiments), a software tool for selecting target-specific peptide candidates directly from given proteome sequence data. It comes with an intuitive graphical user interface, various parameter options and a threshold-based filtering strategy for homologous sequences. Purple enables peptide candidate selection across various taxonomic levels and filtering against backgrounds of varying complexity. Its functionality is demonstrated using data from different virus species and strains. Our software enables to build taxon-specific targeted assays and paves the way to time-efficient and robust viral diagnostics using targeted proteomics.},
    doi = {10.3390/v11060536},
    issue = {6},
    keywords = {data analysis; mass spectrometry; parallel reaction monitoring; peptide selection; targeted proteomics; virus diagnostics; virus proteomics},
    pmid = {31181768},
    }
  • [DOI] E. Karatzas, G. Kolios, and G. M. Spyrou, "An application of computational drug repurposing based on transcriptomic signatures.," Methods Mol Biol, vol. 1903, p. 149–177, 2019.
    [Bibtex]
    @Article{Karatzas:19,
    author = {Karatzas, Evangelos and Kolios, George and Spyrou, George M},
    title = {An Application of Computational Drug Repurposing Based on Transcriptomic Signatures.},
    journal = {{Methods Mol Biol}},
    year = {2019},
    volume = {1903},
    pages = {149--177},
    abstract = {Drug repurposing is a methodology where already existing drugs are tested against diseases outside their initial usage, in order to reduce the high cost and long periods of new drug development. In silico drug repurposing further speeds up the process, by testing a large number of drugs against the biological signatures of known diseases. In this chapter, we present a step-by-step methodology of a transcriptomics-based computational drug repurposing pipeline providing a comprehensive guide to the whole procedure, from proper dataset selection to short list derivation of repurposed drugs which might act as inhibitors against the studied disease. The presented pipeline contains the selection and curation of proper transcriptomics datasets, statistical analysis of the datasets in order to extract the top over- and under-expressed gene identifiers, appropriate identifier conversion, drug repurposing analysis, repurposed drugs filtering, cross-tool screening, drug-list re-ranking, and results' validation.},
    doi = {10.1007/978-1-4939-8955-3_9},
    keywords = {Algorithms; Computational Biology, methods; Databases, Pharmaceutical; Drug Repositioning, methods; Gene Expression Profiling; Gene Expression Regulation, drug effects; Humans; Reproducibility of Results; Software; Transcriptome; User-Computer Interface; Web Browser; Workflow; Computational pipeline; Drug repositioning; Drug repurposing; Gene expression; Microarrays; RNA-Seq; Transcriptomics},
    pmid = {30547441},
    }
  • [DOI] L. Beller and J. Matthijnssens, "What is (not) known about the dynamics of the human gut virome in health and disease.," Curr opin virol, vol. 37, p. 52–57, 2019.
    [Bibtex]
    @Article{Beller:19,
    author = {Beller, Leen and Matthijnssens, Jelle},
    title = {What is (not) known about the dynamics of the human gut virome in health and disease.},
    journal = {Curr Opin Virol},
    year = {2019},
    volume = {37},
    pages = {52--57},
    abstract = {The human gut virome has an important role in human health but its dynamics remain poorly understood. Few longitudinal studies in healthy adults showed a stable temporal gut virome, with high inter-individual diversity. In contrast, the infant virome shows a high temporal intra-individual diversity. Unfortunately, these virome studies ignore an enormous amount of unknown 'dark matter' sequences, leading to incomplete analyses and possibly incorrect conclusions. Also, the interactions between prokaryotes and bacteriophages in the gut seem to be too complex for currently available models. Therefore, there is a huge need of larger longitudinal cohort studies focusing on both the bacterial and viral component of the microbiome to be able to describe and understand this complex ecosystem.},
    doi = {10.1016/j.coviro.2019.05.013},
    pmid = {31255903},
    }
  • [DOI] S. Tu and C. Upton, "Bioinformatics for analysis of poxvirus genomes.," Methods Mol Biol, vol. 2023, p. 29–62, 2019.
    [Bibtex]
    @Article{Tu:19,
    author = {Tu, Shin-Lin and Upton, Chris},
    title = {Bioinformatics for Analysis of Poxvirus Genomes.},
    journal = {{Methods Mol Biol}},
    year = {2019},
    volume = {2023},
    pages = {29--62},
    abstract = {In recent years, there have been numerous technological advances in the field of molecular biology; these include next- and third-generation sequencing of DNA genomes and mRNA transcripts and mass spectrometry of proteins. Perhaps, however, it is genome sequencing that impacts a virologist the most. In 2017, more than 480 complete genome sequences of poxviruses have been generated, and are constantly used in many different ways by almost all molecular virologists. Matching this growth in data acquisition is an explosion of the relatively new field of bioinformatics, providing databases to store and organize this valuable/expensive data and algorithms to analyze it. For the bench virologist, access to intuitive, easy-to-use, software is often critical for performing bioinformatics-based experiments. Three common hurdles for the researcher are (1) selection, retrieval, and reformatting genomics data from large databases; (2) use of tools to compare/analyze the genomics data; and (3) display and interpretation of complex sets of results. This chapter is directed at the bench virologist and describes the software that helps overcome these obstacles, with a focus on the comparison and analysis of poxvirus genomes. Although poxvirus genomes are stored in public databases such as GenBank, this resource can be cumbersome and tedious to use if large amounts of data must to be collected. Therefore, we also highlight our Viral Orthologous Clusters database system and integrated tools that we developed specifically for the management and analysis of complete viral genomes.},
    doi = {10.1007/978-1-4939-9593-6_2},
    keywords = {BBB; BLAST; Bioinformatics; Dotplot; Genomics; JDotter; MSA; Multiple sequence alignment; Poxvirus; Smallpox; VGO; VOCs; Vaccinia virus},
    pmid = {31240669},
    }
  • [DOI] A. Ariza-Mateos, C. Briones, C. Perales, E. Domingo, and J. Gómez, "The archaeology of coding RNA.," Ann NY Acad Sci, 2019.
    [Bibtex]
    @Article{Ariza-Mateos:19,
    author = {Ariza-Mateos, Ascensión and Briones, Carlos and Perales, Celia and Domingo, Esteban and Gómez, Jordi},
    title = {The archaeology of coding {RNA}.},
    journal = {{Ann NY Acad Sci}},
    year = {2019},
    abstract = {Different theories concerning the origin of RNA (and, in particular, mRNA) point to the concatenation and expansion of proto-tRNA-like structures. Different biochemical and biophysical tools have been used to search for ancient-like RNA elements with a specific structure in genomic viral RNAs, including that of the hepatitis C virus, as well as in cellular mRNA populations, in particular those of human hepatocytes. We define this method as "archaeological," and it has been designed to discover evolutionary patterns through a nonphylogenetic and nonrepresentational strategy. tRNA-like elements were found in structurally or functionally relevant positions both in viral RNA and in one of the liver mRNAs examined, the antagonist interferon-alpha subtype 5 (IFNA5) mRNA. Additionally, tRNA-like elements are highly represented within the hepatic mRNA population, which suggests that they could have participated in the formation of coding RNAs in the distant past. Expanding on this finding, we have observed a recurring dsRNA-like motif next to the tRNA-like elements in both viral RNAs and IFNA5 mRNA. This suggested that the concatenation of these RNA motifs was an activity present in the RNA pools that might have been relevant in the RNA world. The extensive alteration of sequences that likely triggered the transition from the predecessors of coding RNAs to the first fully functional mRNAs (which was not the case in the stepwise construction of noncoding rRNAs) hinders the phylogeny-based identification of RNA elements (both sequences and structures) that might have been active before the advent of protein synthesis. Therefore, our RNA archaeological method is presented as a way to better understand the structural/functional versatility of a variety of RNA elements, which might represent "the losers" in the process of RNA evolution as they had to adapt to the selective pressures favoring the coding capacity of the progressively longer mRNAs.},
    doi = {10.1111/nyas.14173},
    keywords = {RNA world; RNase III; RNase P; biocommunication; biosemiotics; quasispecies},
    pmid = {31237363},
    }
  • [DOI] R. A. Edwards, A. A. Vega, H. M. Norman, M. Ohaeri, K. Levi, E. A. Dinsdale, O. Cinek, R. K. Aziz, K. McNair, J. J. Barr, K. Bibby, S. J. J. Brouns, A. Cazares, P. A. de Jonge, C. Desnues, S. D. L. Muñoz, P. C. Fineran, A. Kurilshikov, R. Lavigne, K. Mazankova, D. T. McCarthy, F. L. Nobrega, A. R. Muñoz, G. Tapia, N. Trefault, A. V. Tyakht, P. Vinuesa, J. Wagemans, A. Zhernakova, F. M. Aarestrup, G. Ahmadov, A. Alassaf, J. Anton, A. Asangba, E. K. Billings, V. A. Cantu, J. M. Carlton, D. Cazares, G. Cho, T. Condeff, P. Cortés, M. Cranfield, D. A. Cuevas, R. D. la Iglesia, P. Decewicz, M. P. Doane, N. J. Dominy, L. Dziewit, B. M. Elwasila, M. A. Eren, C. Franz, J. Fu, C. Garcia-Aljaro, E. Ghedin, K. M. Gulino, J. M. Haggerty, S. R. Head, R. S. Hendriksen, C. Hill, H. Hyöty, E. N. Ilina, M. T. Irwin, T. C. Jeffries, J. Jofre, R. E. Junge, S. T. Kelley, M. K. Mirzaei, M. Kowalewski, D. Kumaresan, S. R. Leigh, D. Lipson, E. S. Lisitsyna, M. Llagostera, J. M. Maritz, L. C. Marr, A. McCann, S. Molshanski-Mor, S. Monteiro, B. Moreira-Grez, M. Morris, L. Mugisha, M. Muniesa, H. Neve, N. Nguyen, O. D. Nigro, A. S. Nilsson, T. O'Connell, R. Odeh, A. Oliver, M. Piuri, A. P. J. II, U. Qimron, Z. Quan, P. Rainetova, A. Ramírez-Rojas, R. Raya, K. Reasor, G. A. O. Rice, A. Rossi, R. Santos, J. Shimashita, E. N. Stachler, L. C. Stene, R. Strain, R. Stumpf, P. J. Torres, A. Twaddle, M. U. Ibekwe, N. Villagra, S. Wandro, B. White, A. Whiteley, K. L. Whiteson, C. Wijmenga, M. M. Zambrano, H. Zschach, and B. E. Dutilh, "Global phylogeography and ancient evolution of the widespread human gut virus crAssphage," Nat Microbiol, 2019.
    [Bibtex]
    @Article{Edwards:19,
    author = {Robert A. Edwards and Alejandro A. Vega and Holly M. Norman and Maria Ohaeri and Kyle Levi and Elizabeth A. Dinsdale and Ondrej Cinek and Ramy K. Aziz and Katelyn McNair and Jeremy J. Barr and Kyle Bibby and Stan J. J. Brouns and Adrian Cazares and Patrick A. de Jonge and Christelle Desnues and Samuel L. D{\'{\i}}az Mu{\~{n}}oz and Peter C. Fineran and Alexander Kurilshikov and Rob Lavigne and Karla Mazankova and David T. McCarthy and Franklin L. Nobrega and Alejandro Reyes Mu{\~{n}}oz and German Tapia and Nicole Trefault and Alexander V. Tyakht and Pablo Vinuesa and Jeroen Wagemans and Alexandra Zhernakova and Frank M. Aarestrup and Gunduz Ahmadov and Abeer Alassaf and Josefa Anton and Abigail Asangba and Emma K. Billings and Vito Adrian Cantu and Jane M. Carlton and Daniel Cazares and Gyu-Sung Cho and Tess Condeff and Pilar Cort{\'{e}}s and Mike Cranfield and Daniel A. Cuevas and Rodrigo De la Iglesia and Przemyslaw Decewicz and Michael P. Doane and Nathaniel J. Dominy and Lukasz Dziewit and Bashir Mukhtar Elwasila and A. Murat Eren and Charles Franz and Jingyuan Fu and Cristina Garcia-Aljaro and Elodie Ghedin and Kristen M. Gulino and John M. Haggerty and Steven R. Head and Rene S. Hendriksen and Colin Hill and Heikki Hyöty and Elena N. Ilina and Mitchell T. Irwin and Thomas C. Jeffries and Juan Jofre and Randall E. Junge and Scott T. Kelley and Mohammadali Khan Mirzaei and Martin Kowalewski and Deepak Kumaresan and Steven R. Leigh and David Lipson and Eugenia S. Lisitsyna and Montserrat Llagostera and Julia M. Maritz and Linsey C. Marr and Angela McCann and Shahar Molshanski-Mor and Silvia Monteiro and Benjamin Moreira-Grez and Megan Morris and Lawrence Mugisha and Maite Muniesa and Horst Neve and Nam-phuong Nguyen and Olivia D. Nigro and Anders S. Nilsson and Taylor O'Connell and Rasha Odeh and Andrew Oliver and Mariana Piuri and Aaron J. Prussin II and Udi Qimron and Zhe-Xue Quan and Petra Rainetova and Ad{\'{a}}n Ram{\'{\i}}rez-Rojas and Raul Raya and Kim Reasor and Gillian A. O. Rice and Alessandro Rossi and Ricardo Santos and John Shimashita and Elyse N. Stachler and Lars C. Stene and Ronan Strain and Rebecca Stumpf and Pedro J. Torres and Alan Twaddle and MaryAnn Ugochi Ibekwe and Nicol{\'{a}}s Villagra and Stephen Wandro and Bryan White and Andy Whiteley and Katrine L. Whiteson and Cisca Wijmenga and Maria M. Zambrano and Henrike Zschach and Bas E. Dutilh},
    title = {Global phylogeography and ancient evolution of the widespread human gut virus {crAssphage}},
    journal = {{Nat Microbiol}},
    year = {2019},
    doi = {10.1038/s41564-019-0494-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] H. B. Jang, B. Bolduc, O. Zablocki, J. H. Kuhn, S. Roux, E. M. Adriaenssens, R. J. Brister, A. M. Kropinski, M. Krupovic, R. Lavigne, D. Turner, and M. B. Sullivan, "Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks," Nat Biotechnol, vol. 37, iss. 6, p. 632–639, 2019.
    [Bibtex]
    @Article{Jang:19,
    author = {Ho Bin Jang and Benjamin Bolduc and Olivier Zablocki and Jens H. Kuhn and Simon Roux and Evelien M. Adriaenssens and J. Rodney Brister and Andrew M Kropinski and Mart Krupovic and Rob Lavigne and Dann Turner and Matthew B. Sullivan},
    title = {Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks},
    journal = {{Nat Biotechnol}},
    year = {2019},
    volume = {37},
    number = {6},
    pages = {632--639},
    doi = {10.1038/s41587-019-0100-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] F. Erhard, M. A. P. Baptista, T. Krammer, T. Hennig, M. Lange, P. Arampatzi, C. S. Jürges, F. J. Theis, A. Saliba, and L. Dölken, "scSLAM-seq reveals core features of transcription dynamics in single cells.," Nature, 2019.
    [Bibtex]
    @Article{Erhard:19,
    author = {Erhard, Florian and Baptista, Marisa A P and Krammer, Tobias and Hennig, Thomas and Lange, Marius and Arampatzi, Panagiota and Jürges, Christopher S and Theis, Fabian J and Saliba, Antoine-Emmanuel and Dölken, Lars},
    title = {{scSLAM-seq} reveals core features of transcription dynamics in single cells.},
    journal = {Nature},
    year = {2019},
    abstract = {Single-cell RNA sequencing (scRNA-seq) has highlighted the important role of intercellular heterogeneity in phenotype variability in both health and disease . However, current scRNA-seq approaches provide only a snapshot of gene expression and convey little information on the true temporal dynamics and stochastic nature of transcription. A further key limitation of scRNA-seq analysis is that the RNA profile of each individual cell can be analysed only once. Here we introduce single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing (scSLAM-seq), which integrates metabolic RNA labelling , biochemical nucleoside conversion and scRNA-seq to record transcriptional activity directly by differentiating between new and old RNA for thousands of genes per single cell. We use scSLAM-seq to study the onset of infection with lytic cytomegalovirus in single mouse fibroblasts. The cell-cycle state and dose of infection deduced from old RNA enable dose-response analysis based on new RNA. scSLAM-seq thereby both visualizes and explains differences in transcriptional activity at the single-cell level. Furthermore, it depicts 'on-off' switches and transcriptional burst kinetics in host gene expression with extensive gene-specific differences that correlate with promoter-intrinsic features (TBP-TATA-box interactions and DNA methylation). Thus, gene-specific, and not cell-specific, features explain the heterogeneity in transcriptomes between individual cells and the transcriptional response to perturbations.},
    doi = {10.1038/s41586-019-1369-y},
    pmid = {31292545},
    }
  • [DOI] C. N. Agoti, M. V. T. Phan, P. K. Munywoki, G. Githinji, G. F. Medley, P. A. Cane, P. Kellam, M. Cotten, and J. D. Nokes, "Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.," Sci Rep, vol. 9, p. 10076, 2019.
    [Bibtex]
    @Article{Agoti:19,
    author = {Agoti, Charles N and Phan, My V T and Munywoki, Patrick K and Githinji, George and Medley, Graham F and Cane, Patricia A and Kellam, Paul and Cotten, Matthew and Nokes, D James},
    title = {Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    pages = {10076},
    abstract = {Infants (under 1-year-old) are at most risk of life threatening respiratory syncytial virus (RSV) disease. RSV epidemiological data alone has been insufficient in defining who acquires infection from whom (WAIFW) within households. We investigated RSV genomic variation within and between infected individuals and assessed its potential utility in tracking transmission in households. Over an entire single RSV season in coastal Kenya, nasal swabs were collected from members of 20 households every 3-4 days regardless of symptom status and screened for RSV nucleic acid. Next generation sequencing was used to generate >90% RSV full-length genomes for 51.1% of positive samples (191/374). Single nucleotide polymorphisms (SNPs) observed during household infection outbreaks ranged from 0-21 (median: 3) while SNPs observed during single-host infection episodes ranged from 0-17 (median: 1). Using the viral genomic data alone there was insufficient resolution to fully reconstruct within-household transmission chains. For households with clear index cases, the most likely source of infant infection was via a toddler (aged 1 to <3 years-old) or school-aged (aged 6 to <12 years-old) co-occupant. However, for best resolution of WAIFW within households, we suggest an integrated analysis of RSV genomic and epidemiological data.},
    doi = {10.1038/s41598-019-46509-w},
    issue = {1},
    pmid = {31296922},
    }
  • [DOI] J. M. Bartoszewicz, A. Seidel, R. Rentzsch, and B. Y. Renard, "DeePaC: predicting pathogenic potential of novel dna with reverse-complement neural networks.," Bioinformatics, 2019.
    [Bibtex]
    @Article{Bartoszewicz:19,
    author = {Bartoszewicz, Jakub M and Seidel, Anja and Rentzsch, Robert and Renard, Bernhard Y},
    title = {{DeePaC}: Predicting pathogenic potential of novel DNA with reverse-complement neural networks.},
    journal = {Bioinformatics},
    year = {2019},
    abstract = {We expect novel pathogens to arise due to their fast-paced evolution, and new species to be discovered thanks to advances in DNA sequencing and metagenomics. Moreover, recent developments in synthetic biology raise concerns that some strains of bacteria could be modified for malicious purposes. Traditional approaches to open-view pathogen detection depend on databases of known organisms, which limits their performance on unknown, unrecognized, and unmapped sequences. In contrast, machine learning methods can infer pathogenic phenotypes from single NGS reads, even though the biological context is unavailable. We present DeePaC, a Deep Learning Approach to Pathogenicity Classification. It includes a flexible framework allowing easy evaluation of neural architectures with reverse-complement parameter sharing. We show that convolutional neural networks and LSTMs outperform the state-of-the-art based on both sequence homology and machine learning. Combining a deep learning approach with integrating the predictions for both mates in a read pair results in cutting the error rate almost in half in comparison to the previous state-of-the-art. The code and the models are available at: https://gitlab.com/rki_bioinformatics/DeePaC. Supplementary data are available at Bioinformatics online.},
    doi = {10.1093/bioinformatics/btz541},
    pmid = {31298694},
    }
  • [DOI] N. Bachmann, C. von Siebenthal, V. Vongrad, T. Turk, K. Neumann, N. Beerenwinkel, J. Bogojeska, J. Fellay, V. Roth, Y. L. Kok, C. W. Thorball, A. Borghesi, S. Parbhoo, M. Wieser, J. Böni, M. Perreau, T. Klimkait, S. Yerly, M. Battegay, A. Rauch, M. Hoffmann, E. Bernasconi, M. Cavassini, R. D. Kouyos, H. F. Günthard, K. J. Metzner, and S. H. C. Study, "Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART.," Nat Commun, vol. 10, p. 3193, 2019.
    [Bibtex]
    @Article{Bachmann:19,
    author = {Bachmann, Nadine and von Siebenthal, Chantal and Vongrad, Valentina and Turk, Teja and Neumann, Kathrin and Beerenwinkel, Niko and Bogojeska, Jasmina and Fellay, Jaques and Roth, Volker and Kok, Yik Lim and Thorball, Christian W and Borghesi, Alessandro and Parbhoo, Sonali and Wieser, Mario and Böni, Jürg and Perreau, Matthieu and Klimkait, Thomas and Yerly, Sabine and Battegay, Manuel and Rauch, Andri and Hoffmann, Matthias and Bernasconi, Enos and Cavassini, Matthias and Kouyos, Roger D and Günthard, Huldrych F and Metzner, Karin J and Swiss HIV Cohort Study},
    title = {Determinants of {HIV}-1 reservoir size and long-term dynamics during suppressive {ART}.},
    journal = {{Nat Commun}},
    year = {2019},
    volume = {10},
    pages = {3193},
    abstract = {The HIV-1 reservoir is the major hurdle to a cure. We here evaluate viral and host characteristics associated with reservoir size and long-term dynamics in 1,057 individuals on suppressive antiretroviral therapy for a median of 5.4 years. At the population level, the reservoir decreases with diminishing differences over time, but increases in 26.6% of individuals. Viral blips and low-level viremia are significantly associated with slower reservoir decay. Initiation of ART within the first year of infection, pretreatment viral load, and ethnicity affect reservoir size, but less so long-term dynamics. Viral blips and low-level viremia are thus relevant for reservoir and cure studies.},
    doi = {10.1038/s41467-019-10884-9},
    investigator = {Anagnostopoulos, Alexia and Battegay, Manuel and Bernasconi, Enos and Böni, Jürg and Braun, Dominique L and Bucher, Heiner C and Calmy, Alexandra and Cavassini, Matthias and Ciuffi, Angela and Dollenmaier, Günter and Egger, Matthias and Elzi, Luigia and Fehr, Jan and Fellay, Jacques and Furrer, Hansjakob and Fux, Christoph A and Günthard, Huldrych F and Haerry, David and Hasse, Barbara and Hirsch, Hans H and Hoffmann, Matthias and Hösli, Irene and Huber, Michael and Kahlert, Christian and Kaiser, Laurent and Keiser, Olivia and Klimkait, Thomas and Kouyos, Roger D and Kovari, Helen and Ledergerber, Bruno and Martinetti, Gladys and Tejada, Begona Martinez de and Marzolini, Catia and Metzner, Karin J and Müller, Nicolas and Nicca, Dunja and Paioni, Paolo and Pantaleo, Guiseppe and Perreau, Matthieu and Rauch, Andri and Rudin, Christoph and Scherrer, Alexandra U and Schmid, Patrick and Speck, Roberto and Stöckle, Marcel and Tarr, Philip and Trkola, Alexandra and Vernazza, Pietro and Wandeler, Gilles and Weber, Rainer and Yerly, Sabine},
    issue = {1},
    pmid = {31324762},
    }
  • [DOI] A. Michelitsch, K. Wernike, C. Klaus, G. Dobler, and M. Beer, "Exploring the reservoir hosts of tick-borne encephalitis virus," Viruses, vol. 11, iss. 7, p. 669, 2019.
    [Bibtex]
    @Article{Michelitsch:19,
    author = {Anna Michelitsch and Kerstin Wernike and Christine Klaus and Gerhard Dobler and Martin Beer},
    title = {Exploring the Reservoir Hosts of Tick-Borne Encephalitis Virus},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {7},
    pages = {669},
    doi = {10.3390/v11070669},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Döring, C. Kreer, N. Lehnen, F. Klein, and N. Pfeifer, "Modeling the amplification of immunoglobulins through machine learning on sequence-specific features," Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Döring:19,
    author = {Matthias Döring and Christoph Kreer and Nathalie Lehnen and Florian Klein and Nico Pfeifer},
    title = {Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-019-47173-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Wylezich, A. Belka, D. Hanke, M. Beer, S. Blome, and D. Höper, "Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples.," International journal for parasitology, 2019.
    [Bibtex]
    @Article{Wylezich:19,
    author = {Wylezich, Claudia and Belka, Ariane and Hanke, Dennis and Beer, Martin and Blome, Sandra and Höper, Dirk},
    title = {Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples.},
    journal = {International journal for parasitology},
    year = {2019},
    abstract = {Efficient and reliable identification of emerging pathogens is crucial for the design and implementation of timely and proportionate control strategies. This is difficult if the pathogen is so far unknown or only distantly related with known pathogens. Diagnostic metagenomics - an undirected, broad and sensitive method for the efficient identification of pathogens - was frequently used for virus and bacteria detection, but seldom applied to parasite identification. Here, metagenomics datasets prepared from swine faeces using an unbiased sample processing approach with RNA serving as starting material were re-analysed with respect to parasite detection. The taxonomic identification tool RIEMS, used for initial detection, provided basic hints on potential pathogens contained in the datasets. The suspected parasites/intestinal protists (Blastocystis, Entamoeba, Iodamoeba, Neobalantidium, Tetratrichomonas) were verified using subsequently applied reference mapping analyses on the base of rRNA sequences. Nearly full-length gene sequences could be extracted from the RNA-derived datasets. In the case of Blastocystis, subtyping was possible with subtype (ST)15 discovered for the first known time in swine faeces. Using RIEMS, some of the suspected candidates turned out to be false-positives caused by the poor status of sequences in publicly available databases. Altogether, 11 different species/STs of parasites/intestinal protists were detected in 34 out of 41 datasets extracted from metagenomics data. The approach operates without any primer bias that typically hampers the analysis of amplicon-based approaches, and allows the detection and taxonomic classification including subtyping of protist and metazoan endobionts (parasites, commensals or mutualists) based on an abundant biomarker, the 18S rRNA. The generic nature of the approach also allows evaluation of interdependencies that induce mutualistic or pathogenic effects that are often not clear for many intestinal protists and perhaps other parasites. Thus, metagenomics has the potential for generic pathogen identification beyond the characterization of viruses and bacteria when starting from RNA instead of DNA.},
    doi = {10.1016/j.ijpara.2019.04.007},
    keywords = {False-positives; Intestinal protists; Parasite detection; Pig faeces; RIEMS; Shotgun metagenomics; Subtyping; Taxonomic assignment},
    pmid = {31361998},
    }
  • [DOI] I. H. E. Korf, J. P. Meier-Kolthoff, E. M. Adriaenssens, A. M. Kropinski, M. Nimtz, M. Rohde, M. J. van Raaij, and J. Wittmann, "Still something to discover: novel insights into Escherichia coli phage diversity and taxonomy.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Korf:19,
    author = {Korf, Imke H E and Meier-Kolthoff, Jan P and Adriaenssens, Evelien M and Kropinski, Andrew M and Nimtz, Manfred and Rohde, Manfred and van Raaij, Mark J and Wittmann, Johannes},
    title = {Still Something to Discover: Novel Insights into {Escherichia coli} Phage Diversity and Taxonomy.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {The aim of this study was to gain further insight into the diversity of Escherichia coli phagesfollowed by enhanced work on taxonomic issues in that field. Therefore, we present the genomiccharacterization and taxonomic classification of 50 bacteriophages against isolated fromvarious sources, such as manure or sewage. All phages were examined for their host range on a setof different strains, originating, e.g., from human diagnostic laboratories or poultry farms.Transmission electron microscopy revealed a diversity of morphotypes (70% Myo-, 22% Sipho-, and8% Podoviruses), and genome sequencing resulted in genomes sizes from ~44 to ~370 kb.Annotation and comparison with databases showed similarities in particular to T4- and T5-likephages, but also to less-known groups. Though various phages against are already describedin literature and databases, we still isolated phages that showed no or only few similarities to otherphages, namely phages Goslar, PTXU04, and KWBSE43-6. Genome-based phylogeny andclassification of the newly isolated phages using VICTOR resulted in the proposal of new generaand led to an enhanced taxonomic classification of phages.},
    doi = {10.3390/v11050454},
    issue = {5},
    keywords = {Escherichia coli; bacteriophage; diversity; genomics; taxonomy},
    pmid = {31109012},
    }
  • [DOI] M. Džunková, S. J. Low, J. N. Daly, L. Deng, C. Rinke, and P. Hugenholtz, "Defining the human gut host-phage network through single-cell viral tagging.," Nat Microbiol, 2019.
    [Bibtex]
    @Article{Dzunkova:19,
    author = {Džunková, Mária and Low, Soo Jen and Daly, Joshua N and Deng, Li and Rinke, Christian and Hugenholtz, Philip},
    title = {Defining the human gut host-phage network through single-cell viral tagging.},
    journal = {{Nat Microbiol}},
    year = {2019},
    abstract = {Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host-phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then individually sorted as host-phage pairs, followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host-phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple individual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host-phage network, suggesting that phages are not major vectors of inter-species horizontal gene transfer in the human gut. A high level of cross-reactivity between phages and bacteria from different subjects was noted despite subject-specific viral profiles, which has implications for faecal microbiota transplant therapy.},
    doi = {10.1038/s41564-019-0526-2},
    pmid = {31384000},
    }
  • [DOI] M. Hölzer, A. Schoen, J. Wulle, M. A. Müller, C. Drosten, M. Marz, and F. Weber, "Virus- and interferon alpha-induced transcriptomes of cells from the microbat Myotis daubentonii," iScience, 2019.
    [Bibtex]
    @Article{Hölzer:19a,
    author = {Martin Hölzer and Andreas Schoen and Julia Wulle and Marcel A. Müller and Christian Drosten and Manja Marz and Friedemann Weber},
    title = {Virus- and interferon alpha-induced transcriptomes of cells from the microbat {Myotis daubentonii}},
    journal = {{iScience}},
    year = {2019},
    doi = {10.1016/j.isci.2019.08.016},
    publisher = {Elsevier {BV}},
    }

2018

  • [DOI] T. R. Klingen, S. Reimering, C. A. Guzmán, and A. C. McHardy, "In silico vaccine strain prediction for human influenza viruses," Trends Microbiol, vol. 26, p. 119–131, 2018.
    [Bibtex]
    @Article{Klingen:18,
    author = {Klingen, Thorsten R and Reimering, Susanne and Guzmán, Carlos A and McHardy, Alice C},
    title = {In Silico Vaccine Strain Prediction for Human Influenza Viruses},
    journal = {{Trends Microbiol}},
    year = {2018},
    volume = {26},
    pages = {119--131},
    abstract = {Vaccines preventing seasonal influenza infections save many lives every year; however, due to rapid viral evolution, they have to be updated frequently to remain effective. To identify appropriate vaccine strains, the World Health Organization (WHO) operates a global program that continually generates and interprets surveillance data. Over the past decade, sophisticated computational techniques, drawing from multiple theoretical disciplines, have been developed that predict viral lineages rising to predominance, assess their suitability as vaccine strains, link genetic to antigenic alterations, as well as integrate and visualize genetic, epidemiological, structural, and antigenic data. These could form the basis of an objective and reproducible vaccine strain-selection procedure utilizing the complex, large-scale data types from surveillance. To this end, computational techniques should already be incorporated into the vaccine-selection process in an independent, parallel track, and their performance continuously evaluated.},
    doi = {10.1016/j.tim.2017.09.001},
    issue = {2},
    keywords = {Antibodies, Viral, immunology; Antigens, Viral, immunology; Biological Evolution; Computational Biology; Forecasting; Global Health; Humans; Influenza A Virus, H3N2 Subtype, immunology; Influenza Vaccines, immunology; Influenza, Human, epidemiology, prevention & control, virology; Orthomyxoviridae, immunology; Seasons; Vaccination, methods; World Health Organization; GISRS; computational predictions; influenza viruses; vaccine; viral evolution},
    pmid = {29032900},
    }
  • [DOI] V. Lulla, A. M. Dinan, M. Hosmillo, Y. Chaudhry, L. Sherry, N. Irigoyen, K. M. Nayak, N. J. Stonehouse, M. Zilbauer, I. Goodfellow, and A. E. Firth, "An upstream protein-coding region in enteroviruses modulates virus infection in gut epithelial cells," Nat Microbiol, vol. 4, iss. 2, p. 280–292, 2018.
    [Bibtex]
    @Article{Lulla:18,
    author = {Valeria Lulla and Adam M. Dinan and Myra Hosmillo and Yasmin Chaudhry and Lee Sherry and Nerea Irigoyen and Komal M. Nayak and Nicola J. Stonehouse and Matthias Zilbauer and Ian Goodfellow and Andrew E. Firth},
    title = {An upstream protein-coding region in enteroviruses modulates virus infection in gut epithelial cells},
    journal = {{Nat Microbiol}},
    year = {2018},
    volume = {4},
    number = {2},
    pages = {280--292},
    doi = {10.1038/s41564-018-0297-1},
    publisher = {Springer Nature},
    }
  • [DOI] F. L. Nobrega, M. Vlot, P. A. de Jonge, L. L. Dreesens, H. J. E. Beaumont, R. Lavigne, B. E. Dutilh, and S. J. J. Brouns, "Targeting mechanisms of tailed bacteriophages," Nat Rev Microbiol, vol. 16, iss. 12, p. 760–773, 2018.
    [Bibtex]
    @Article{Nobrega:18,
    author = {Franklin L. Nobrega and Marnix Vlot and Patrick A. de Jonge and Lisa L. Dreesens and Hubertus J. E. Beaumont and Rob Lavigne and Bas E. Dutilh and Stan J. J. Brouns},
    title = {Targeting mechanisms of tailed bacteriophages},
    journal = {{Nat Rev Microbiol}},
    year = {2018},
    volume = {16},
    number = {12},
    pages = {760--773},
    doi = {10.1038/s41579-018-0070-8},
    publisher = {Springer Nature},
    }
  • [DOI] J. Huerta-Cepas, D. Szklarczyk, D. Heller, A. Hernández-Plaza, S. K. Forslund, H. Cook, D. R. Mende, I. Letunic, T. Rattei, L. J. Jensen, C. von~Mering, and P. Bork, "eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses," Nucleic Acids Res, vol. 47, iss. D1, p. D309–D314, 2018.
    [Bibtex]
    @Article{Huerta-Cepas:18,
    author = {Jaime Huerta-Cepas and Damian Szklarczyk and Davide Heller and Ana Hern{\'{a}}ndez-Plaza and Sofia K Forslund and Helen Cook and Daniel R Mende and Ivica Letunic and Thomas Rattei and Lars Juhl Jensen and Christian von~Mering and Peer Bork},
    title = {{eggNOG} 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses},
    journal = {{Nucleic Acids Res}},
    year = {2018},
    volume = {47},
    number = {D1},
    pages = {D309--D314},
    doi = {10.1093/nar/gky1085},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Reimering, S. Muñoz, and A. C. McHardy, "A Fréchet tree distance measure to compare phylogeographic spread paths across trees," Sci Rep, vol. 8, iss. 1, 2018.
    [Bibtex]
    @Article{Reimering:18,
    author = {Susanne Reimering and Sebastian Mu{\~{n}}oz and Alice C. McHardy},
    title = {A {F}r{\'{e}}chet tree distance measure to compare phylogeographic spread paths across trees},
    journal = {{Sci Rep}},
    year = {2018},
    volume = {8},
    number = {1},
    doi = {10.1038/s41598-018-35421-4},
    publisher = {Springer Nature},
    }
  • [DOI] S. Tu, J. Staheli, C. McClay, K. McLeod, T. Rose, and C. Upton, "Base-By-Base version 3: new comparative tools for large virus genomes," Viruses, vol. 10, iss. 11, p. 637, 2018.
    [Bibtex]
    @Article{Tu:18,
    author = {Shin-Lin Tu and Jeannette Staheli and Colum McClay and Kathleen McLeod and Timothy Rose and Chris Upton},
    title = {{Base-By-Base} Version 3: New Comparative Tools for Large Virus Genomes},
    journal = {Viruses},
    year = {2018},
    volume = {10},
    number = {11},
    pages = {637},
    doi = {10.3390/v10110637},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] Wasimuddin, S. D. Brändel, M. Tschapka, R. Page, A. Rasche, V. M. Corman, C. Drosten, and S. Sommer, "Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats," The ISME Journal, vol. 12, iss. 12, p. 2883–2893, 2018.
    [Bibtex]
    @Article{Wasimuddin:18,
    author = {Wasimuddin and Stefan Dominik Brändel and Marco Tschapka and Rachel Page and Andrea Rasche and Victor M. Corman and Christian Drosten and Simone Sommer},
    title = {Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats},
    journal = {{The ISME Journal}},
    year = {2018},
    volume = {12},
    number = {12},
    pages = {2883--2893},
    doi = {10.1038/s41396-018-0239-1},
    publisher = {Springer Nature},
    }
  • [DOI] E. Mittler, G. Schudt, S. Halwe, C. Rohde, and S. Becker, "A fluorescently labeled marburg virus glycoprotein as a new tool to study viral transport and assembly," J Infect Dis, vol. 218, iss. suppl{_}5, p. S318–S326, 2018.
    [Bibtex]
    @Article{Mittler:18,
    author = {Eva Mittler and Gordian Schudt and Sandro Halwe and Cornelius Rohde and Stephan Becker},
    title = {A Fluorescently Labeled Marburg Virus Glycoprotein as a New Tool to Study Viral Transport and Assembly},
    journal = {{J Infect Dis}},
    year = {2018},
    volume = {218},
    number = {suppl{\_}5},
    pages = {S318--S326},
    doi = {10.1093/infdis/jiy424},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. E. Gorbalenya, "Increasing the number of available ranks in virus taxonomy from five to ten and adopting the Baltimore classes as taxa at the basal rank," Arch virol, vol. 163, iss. 10, p. 2933–2936, 2018.
    [Bibtex]
    @Article{Gorbalenya:18,
    author = {Alexander E. Gorbalenya},
    title = {Increasing the number of available ranks in virus taxonomy from five to ten and adopting the {B}altimore classes as taxa at the basal rank},
    journal = {Arch Virol},
    year = {2018},
    volume = {163},
    number = {10},
    pages = {2933--2936},
    doi = {10.1007/s00705-018-3915-6},
    publisher = {Springer Nature},
    }
  • [DOI] R. Schmidt, L. C. Beltzig, B. Sawatsky, O. Dolnik, E. Dietzel, V. Krähling, A. Volz, G. Sutter, S. Becker, and V. von Messling, "Generation of therapeutic antisera for emerging viral infections," Npj vaccines, vol. 3, iss. 1, 2018.
    [Bibtex]
    @Article{Schmidt:18,
    author = {Rebecca Schmidt and Lea C. Beltzig and Bevan Sawatsky and Olga Dolnik and Erik Dietzel and Verena Krähling and Asisa Volz and Gerd Sutter and Stephan Becker and Veronika von Messling},
    title = {Generation of therapeutic antisera for emerging viral infections},
    journal = {npj Vaccines},
    year = {2018},
    volume = {3},
    number = {1},
    doi = {10.1038/s41541-018-0082-4},
    publisher = {Springer Nature},
    }
  • [DOI] S. H. Tausch, B. Strauch, A. Andrusch, T. P. Loka, M. S. Lindner, A. Nitsche, and B. Y. Renard, "LiveKraken––real-time metagenomic classification of illumina data," Bioinformatics, vol. 34, iss. 21, p. 3750–3752, 2018.
    [Bibtex]
    @Article{Tausch:18,
    author = {Simon H Tausch and Benjamin Strauch and Andreas Andrusch and Tobias P Loka and Martin S Lindner and Andreas Nitsche and Bernhard Y Renard},
    title = {{LiveKraken}{\textendash}{\textendash}real-time metagenomic classification of illumina data},
    journal = {Bioinformatics},
    year = {2018},
    volume = {34},
    number = {21},
    pages = {3750--3752},
    doi = {10.1093/bioinformatics/bty433},
    editor = {Bonnie Berger},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] J. Kruppa, W. K. Jo, E. van der Vries, M. Ludlow, A. Osterhaus, W. Baumgaertner, and K. Jung, "Virus detection in high-throughput sequencing data without a reference genome of the host," Infect Genet Evol, vol. 66, p. 180–187, 2018.
    [Bibtex]
    @Article{Kruppa:18,
    author = {Jochen Kruppa and Wendy K. Jo and Erhard van der Vries and Martin Ludlow and Albert Osterhaus and Wolfgang Baumgaertner and Klaus Jung},
    title = {Virus detection in high-throughput sequencing data without a reference genome of the host},
    journal = {{Infect Genet Evol}},
    year = {2018},
    volume = {66},
    pages = {180--187},
    doi = {10.1016/j.meegid.2018.09.026},
    publisher = {Elsevier {BV}},
    }
  • [DOI] H. Cook, N. T. Doncheva, D. Szklarczyk, C. von Mering, and L. J. Jensen, "Viruses.STRING: a virus-host protein-protein interaction database," Viruses, vol. 10, iss. 10, p. 519, 2018.
    [Bibtex]
    @Article{Cook:18,
    author = {Helen Cook and Nadezhda Tsankova Doncheva and Damian Szklarczyk and Christian {von Mering} and Lars Juhl Jensen},
    title = {Viruses.{STRING}: A Virus-Host Protein-Protein Interaction Database},
    journal = {Viruses},
    year = {2018},
    volume = {10},
    number = {10},
    pages = {519},
    doi = {10.3390/v10100519},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] A. Saberi, A. A. Gulyaeva, J. L. Brubacher, P. A. Newmark, and A. E. Gorbalenya, "A planarian nidovirus expands the limits of RNA genome size," PLoS Pathog, vol. 14, iss. 11, p. e1007314, 2018.
    [Bibtex]
    @Article{Saberi:18,
    author = {Amir Saberi and Anastasia A. Gulyaeva and John L. Brubacher and Phillip A. Newmark and Alexander E. Gorbalenya},
    title = {A planarian nidovirus expands the limits of {RNA} genome size},
    journal = {{PLoS Pathog}},
    year = {2018},
    volume = {14},
    number = {11},
    pages = {e1007314},
    doi = {10.1371/journal.ppat.1007314},
    editor = {Stanley Perlman},
    publisher = {Public Library of Science ({PLoS})},
    }
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    @Article{Libin:18,
    author = {Pieter J K Libin and Koen Deforche and Ana B Abecasis and Kristof Theys},
    title = {{VIRULIGN}: fast codon-correct alignment and annotation of viral genomes},
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    @InCollection{McNair:18,
    author = {McNair, Katelyn and Aziz, Ramy Karam and Pusch, Gordon D and Overbeek, Ross and Dutilh, Bas E and Edwards, Robert},
    title = {Phage genome annotation using the {RAST} pipeline},
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    title = {Sweep Dynamics ({SD}) plots: Computational identification of selective sweeps to monitor the adaptation of influenza {A} viruses},
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    @Article{Arkhipova:18,
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    title = {Temporal dynamics of uncultured viruses: a new dimension in viral diversity},
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    title = {Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza},
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    title = {Tunneling nanotubes as a novel route of cell-to-cell spread of Herpesviruses},
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    title = {New lineage of {L}assa virus, {T}ogo, 2016},
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    @Article{Maticzka:18,
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    title = {{uvCLAP} is a fast and non-radioactive method to identify in vivo targets of {RNA}-binding proteins},
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    @Article{Rivers-Auty:18,
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    title = {Redefining the ancestral origins of the interleukin-1 superfamily},
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    title = {Improved {R}ibo-seq enables identification of cryptic translation events},
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    @Article{Eggenhofer:18,
    author = {Eggenhofer, Florian and Hofacker, Ivo L and Backofen, Rolf and H{\"o}ner zu Siederdissen, Christian},
    title = {{CMV}: visualization for {RNA} and protein family models and their comparisons},
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    @Article{Kupczok:18,
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    title = {Rates of mutation and recombination in {S}iphoviridae phage genome evolution over three decades},
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    @Article{Milewska:18,
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    title = {{APOBEC3}-mediated restriction of {RNA} virus replication},
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    @Article{Blanco-Melo:18,
    author = {Blanco-Melo, Daniel and Gifford, Robert J and Bieniasz, Paul D},
    title = {Reconstruction of a replication-competent ancestral murine endogenous retrovirus-{L}},
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    @Article{Ibrahim:18,
    author = {Ibrahim, Bashar and McMahon, Dino P and Hufsky, Franziska and Beer, Martin and Deng, Li and Le Mercier, Philippe and Palmarini, Massimo and Thiel, Volker and Marz, Manja},
    title = {A new era of virus bioinformatics},
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    @Article{Krupovic:18,
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    title = {Ortervirales: new virus order unifying five families of reverse-transcribing viruses},
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    @Article{Bastys:18,
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    title = {Consistent prediction of mutation effect on drug binding in {HIV}-1 protease using alchemical calculations},
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    title = {Bayesian phylogenetic and phylodynamic data integration using {BEAST} 1.10},
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    @Article{Theuns:18,
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    title = {Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus},
    journal = {{Sci Rep}},
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    author = {Zitzmann, Carolin and Kaderali, Lars},
    title = {Mathematical Analysis of Viral Replication Dynamics and Antiviral Treatment Strategies: From Basic Models to Age-Based Multi-Scale Modeling},
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    @Article{Cowton:18,
    author = {Cowton, Vanessa M and Singer, Joshua B and Gifford, Robert James and Patel, Arvind H},
    title = {Predicting the effectiveness of hepatitis {C} virus neutralizing antibodies by Bioinformatic analysis of conserved epitope residues Using Public sequence Data},
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    @Article{Vilsker:18,
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    title = {{Genome Detective}: an automated system for virus identification from high-throughput sequencing data},
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    @Article{Chen:18,
    author = {Xun Chen and Jason Kost and Dawei Li},
    title = {Comprehensive comparative analysis of methods and software for identifying viral integrations},
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    @Article{Kostaki:18,
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    title = {Unravelling the history of hepatitis {B} virus genotypes {A} and {D} infection using a full-genome phylogenetic and phylogeographic approach},
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    author = {Robert J. Gifford and Jonas Blomberg and John M. Coffin and Hung Fan and Thierry Heidmann and Jens Mayer and Jonathan Stoye and Michael Tristem and Welkin E. Johnson},
    title = {Nomenclature for endogenous retrovirus ({ERV}) loci},
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    @Article{Mendoza:18,
    author = {Pilar Mendoza and Henning Gruell and Lilian Nogueira and Joy A. Pai and Allison L. Butler and Katrina Millard and Clara Lehmann and Isabelle Su{\'{a}}rez and Thiago Y. Oliveira and Julio C. C. Lorenzi and Yehuda Z. Cohen and Christoph Wyen and Tim Kümmerle and Theodora Karagounis and Ching-Lan Lu and Lisa Handl and Cecilia Unson-O'Brien and Roshni Patel and Carola Ruping and Maike Schlotz and Maggi Witmer-Pack and Irina Shimeliovich and Gisela Kremer and Eleonore Thomas and Kelly E. Seaton and Jill Horowitz and Anthony P. West and Pamela J. Bjorkman and Georgia D. Tomaras and Roy M. Gulick and Nico Pfeifer and Gerd Fätkenheuer and Michael S. Seaman and Florian Klein and Marina Caskey and Michel C. Nussenzweig},
    title = {Combination therapy with anti-{HIV}-1 antibodies maintains viral suppression},
    journal = {Nature},
    year = {2018},
    volume = {561},
    number = {7724},
    pages = {479--484},
    doi = {10.1038/s41586-018-0531-2},
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    @Article{Bar-On:18,
    author = {Yotam Bar-On and Henning Gruell and Till Schoofs and Joy A. Pai and Lilian Nogueira and Allison L. Butler and Katrina Millard and Clara Lehmann and Isabelle Su{\'{a}}rez and Thiago Y. Oliveira and Theodora Karagounis and Yehuda Z. Cohen and Christoph Wyen and Stefan Scholten and Lisa Handl and Shiraz Belblidia and Juan P. Dizon and Jörg J. Vehreschild and Maggi Witmer-Pack and Irina Shimeliovich and Kanika Jain and Kerstin Fiddike and Kelly E. Seaton and Nicole L. Yates and Jill Horowitz and Roy M. Gulick and Nico Pfeifer and Georgia D. Tomaras and Michael S. Seaman and Gerd Fätkenheuer and Marina Caskey and Florian Klein and Michel C. Nussenzweig},
    title = {Safety and antiviral activity of combination {HIV}-1 broadly neutralizing antibodies in viremic individuals},
    journal = {{Nat Med}},
    year = {2018},
    volume = {24},
    number = {11},
    pages = {1701--1707},
    doi = {10.1038/s41591-018-0186-4},
    publisher = {Springer Nature},
    }
  • [DOI] S. Stanelle-Bertram, K. Walendy-Gnirß, T. Speiseder, S. Thiele, I. A. Asante, C. Dreier, N. M. Kouassi, A. Preuß, G. Pilnitz-Stolze, U. Müller, S. Thanisch, M. Richter, R. Scharrenberg, V. Kraus, R. Dörk, L. Schau, V. Herder, I. Gerhauser, V. M. Pfankuche, C. Käufer, I. Waltl, T. Moraes, J. Sellau, S. Hoenow, J. Schmidt-Chanasit, S. Jansen, B. Schattling, H. Ittrich, U. Bartsch, T. Renné, R. Bartenschlager, P. Arck, D. Cadar, M. A. Friese, O. Vapalahti, H. Lotter, S. Benites, L. Rolling, M. Gabriel, W. Baumgärtner, F. Morellini, S. M. Hölter, O. Amarie, H. Fuchs, M. H. de Angelis, W. Löscher, F. C. de Anda, and G. Gabriel, "Male offspring born to mildly ZIKV-infected mice are at risk of developing neurocognitive disorders in adulthood," Nat Microbiol, vol. 3, iss. 10, p. 1161–1174, 2018.
    [Bibtex]
    @Article{Stanelle-Bertram:18,
    author = {Stephanie Stanelle-Bertram and Kerstin Walendy-Gnir{\ss} and Thomas Speiseder and Swantje Thiele and Ivy Asantewaa Asante and Carola Dreier and Nancy Mounogou Kouassi and Annette Preu{\ss} and Gundula Pilnitz-Stolze and Ursula Müller and Stefanie Thanisch and Melanie Richter and Robin Scharrenberg and Vanessa Kraus and Ronja Dörk and Lynn Schau and Vanessa Herder and Ingo Gerhauser and Vanessa Maria Pfankuche and Christopher Käufer and Inken Waltl and Thais Moraes and Julie Sellau and Stefan Hoenow and Jonas Schmidt-Chanasit and Stephanie Jansen and Benjamin Schattling and Harald Ittrich and Udo Bartsch and Thomas Renn{\'{e}} and Ralf Bartenschlager and Petra Arck and Daniel Cadar and Manuel A. Friese and Olli Vapalahti and Hanna Lotter and Sany Benites and Lane Rolling and Martin Gabriel and Wolfgang Baumgärtner and Fabio Morellini and Sabine M. Hölter and Oana Amarie and Helmut Fuchs and Martin Hrabe de Angelis and Wolfgang Löscher and Froylan Calderon de Anda and Gülsah Gabriel},
    title = {Male offspring born to mildly {ZIKV}-infected mice are at risk of developing neurocognitive disorders in adulthood},
    journal = {{Nat Microbiol}},
    year = {2018},
    volume = {3},
    number = {10},
    pages = {1161--1174},
    doi = {10.1038/s41564-018-0236-1},
    publisher = {Springer Nature},
    }
  • [DOI] H. Fröhlich, R. Balling, N. Beerenwinkel, O. Kohlbacher, S. Kumar, T. Lengauer, M. H. Maathuis, Y. Moreau, S. A. Murphy, T. M. Przytycka, M. Rebhan, H. Röst, A. Schuppert, M. Schwab, R. Spang, D. Stekhoven, J. Sun, A. Weber, D. Ziemek, and B. Zupan, "From hype to reality: data science enabling personalized medicine," BMC Medicine, vol. 16, iss. 1, 2018.
    [Bibtex]
    @Article{Fröhlich:18,
    author = {Holger Fr\"{o}hlich and Rudi Balling and Niko Beerenwinkel and Oliver Kohlbacher and Santosh Kumar and Thomas Lengauer and Marloes H. Maathuis and Yves Moreau and Susan A. Murphy and Teresa M. Przytycka and Michael Rebhan and Hannes R\"{o}st and Andreas Schuppert and Matthias Schwab and Rainer Spang and Daniel Stekhoven and Jimeng Sun and Andreas Weber and Daniel Ziemek and Blaz Zupan},
    title = {From hype to reality: data science enabling personalized medicine},
    journal = {{BMC Medicine}},
    year = {2018},
    volume = {16},
    number = {1},
    doi = {10.1186/s12916-018-1122-7},
    publisher = {Springer Nature},
    }
  • [DOI] P. Barbera, A. M. Kozlov, L. Czech, B. Morel, D. Darriba, T. Flouri, and A. Stamatakis, "EPA-ng: massively parallel evolutionary placement of genetic sequences," Syst Biol, vol. 68, iss. 2, p. 365–369, 2018.
    [Bibtex]
    @Article{Barbera:18,
    author = {Pierre Barbera and Alexey M Kozlov and Lucas Czech and Benoit Morel and Diego Darriba and Tom{\'{a}}{\v{s}} Flouri and Alexandros Stamatakis},
    title = {{EPA}-ng: Massively Parallel Evolutionary Placement of Genetic Sequences},
    journal = {{Syst Biol}},
    year = {2018},
    volume = {68},
    number = {2},
    pages = {365--369},
    doi = {10.1093/sysbio/syy054},
    editor = {David Posada},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] G. Baele, S. Dellicour, M. A. Suchard, P. Lemey, and B. Vrancken, "Recent advances in computational phylodynamics," Curr Opin Virol, vol. 31, p. 24–32, 2018.
    [Bibtex]
    @Article{Baele:18,
    author = {Guy Baele and Simon Dellicour and Marc A Suchard and Philippe Lemey and Bram Vrancken},
    title = {Recent advances in computational phylodynamics},
    journal = {{Curr Opin Virol}},
    year = {2018},
    volume = {31},
    pages = {24--32},
    doi = {10.1016/j.coviro.2018.08.009},
    publisher = {Elsevier {BV}},
    }
  • [DOI] C. Wylezich, A. Papa, M. Beer, and D. Höper, "A versatile sample processing workflow for metagenomic pathogen detection," Sci Rep, vol. 8, iss. 1, 2018.
    [Bibtex]
    @Article{Wylezich:18,
    author = {Claudia Wylezich and Anna Papa and Martin Beer and Dirk H\"{o}per},
    title = {A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection},
    journal = {{Sci Rep}},
    year = {2018},
    volume = {8},
    number = {1},
    doi = {10.1038/s41598-018-31496-1},
    publisher = {Springer Nature},
    }
  • [DOI] A. Mostafa, E. Abdelwhab, T. C. Mettenleiter, and S. Pleschka, "Zoonotic potential of influenza a viruses: a comprehensive overview," Viruses, vol. 10, iss. 9, p. 497, 2018.
    [Bibtex]
    @Article{Mostafa:18,
    author = {Ahmed Mostafa and Elsayed Abdelwhab and Thomas C Mettenleiter and Stephan Pleschka},
    title = {Zoonotic Potential of Influenza A Viruses: A Comprehensive Overview},
    journal = {Viruses},
    year = {2018},
    volume = {10},
    number = {9},
    pages = {497},
    doi = {10.3390/v10090497},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] S. Dellicour, B. Vrancken, N. S. Trovão, D. Fargette, and P. Lemey, "On the importance of negative controls in viral landscape phylogeography," Virus Evol, vol. 4, iss. 2, 2018.
    [Bibtex]
    @Article{Dellicour:18,
    author = {Simon Dellicour and Bram Vrancken and N{\'{\i}}dia S Trov{\~{a}}o and Denis Fargette and Philippe Lemey},
    title = {On the importance of negative controls in viral landscape phylogeography},
    journal = {{Virus Evol}},
    year = {2018},
    volume = {4},
    number = {2},
    doi = {10.1093/ve/vey023},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] K. Lamkiewicz, E. Barth, M. Marz, and B. Ibrahim, "Identification of potential microRNAs associated with Herpesvirus family based on bioinformatic analysis," bioRxiv, 2018.
    [Bibtex]
    @Article{Lamkiewicz:18,
    author = {Kevin Lamkiewicz and Emanuel Barth and Manja Marz and Bashar Ibrahim},
    title = {Identification of potential {microRNAs} associated with {H}erpesvirus family based on bioinformatic analysis},
    journal = {{bioRxiv}},
    year = {2018},
    doi = {10.1101/417782},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Roux, E. M. Adriaenssens, B. E. Dutilh, E. V. Koonin, A. M. Kropinski, M. Krupovic, J. H. Kuhn, R. Lavigne, R. J. Brister, A. Varsani, C. Amid, R. K. Aziz, S. R. Bordenstein, P. Bork, M. Breitbart, G. R. Cochrane, R. A. Daly, C. Desnues, M. B. Duhaime, J. B. Emerson, F. Enault, J. A. Fuhrman, P. Hingamp, P. Hugenholtz, B. L. Hurwitz, N. N. Ivanova, J. M. Labonté, K. Lee, R. R. Malmstrom, M. Martinez-Garcia, I. K. Mizrachi, H. Ogata, D. Páez-Espino, M. A. Petit, C. Putonti, T. Rattei, A. Reyes, F. Rodriguez-Valera, K. Rosario, L. Schriml, F. Schulz, G. F. Steward, M. B. Sullivan, S. Sunagawa, C. A. Suttle, B. Temperton, S. G. Tringe, R. V. Thurber, N. S. Webster, K. L. Whiteson, S. W. Wilhelm, E. K. Wommack, T. Woyke, K. C. Wrighton, P. Yilmaz, T. Yoshida, M. J. Young, N. Yutin, L. Z. Allen, N. C. Kyrpides, and E. A. Eloe-Fadrosh, "Minimum information about an uncultivated virus genome (MIUViG)," Nat Biotechnol, vol. 37, iss. 1, p. 29–37, 2018.
    [Bibtex]
    @Article{Roux:18,
    author = {Simon Roux and Evelien M Adriaenssens and Bas E Dutilh and Eugene V Koonin and Andrew M Kropinski and Mart Krupovic and Jens H Kuhn and Rob Lavigne and J Rodney Brister and Arvind Varsani and Clara Amid and Ramy K Aziz and Seth R Bordenstein and Peer Bork and Mya Breitbart and Guy R Cochrane and Rebecca A Daly and Christelle Desnues and Melissa B Duhaime and Joanne B Emerson and Fran{\c{c}}ois Enault and Jed A Fuhrman and Pascal Hingamp and Philip Hugenholtz and Bonnie L Hurwitz and Natalia N Ivanova and Jessica M Labont{\'{e}} and Kyung-Bum Lee and Rex R Malmstrom and Manuel Martinez-Garcia and Ilene Karsch Mizrachi and Hiroyuki Ogata and David P{\'{a}}ez-Espino and Marie A Petit and Catherine Putonti and Thomas Rattei and Alejandro Reyes and Francisco Rodriguez-Valera and Karyna Rosario and Lynn Schriml and Frederik Schulz and Grieg F Steward and Matthew B Sullivan and Shinichi Sunagawa and Curtis A Suttle and Ben Temperton and Susannah G Tringe and Rebecca Vega Thurber and Nicole S Webster and Katrine L Whiteson and Steven W Wilhelm and K Eric Wommack and Tanja Woyke and Kelly C Wrighton and Pelin Yilmaz and Takashi Yoshida and Mark J Young and Natalya Yutin and Lisa Zeigler Allen and Nikos C Kyrpides and Emiley A Eloe-Fadrosh},
    title = {Minimum Information about an Uncultivated Virus Genome ({MIUViG})},
    journal = {{Nat Biotechnol}},
    year = {2018},
    volume = {37},
    number = {1},
    pages = {29--37},
    doi = {10.1038/nbt.4306},
    publisher = {Springer Nature},
    }
  • [DOI] J. Cui, F. Li, and Z. Shi, "Origin and evolution of pathogenic coronaviruses," Nat Rev Microbiol, vol. 17, iss. 3, p. 181–192, 2018.
    [Bibtex]
    @Article{Cui:18,
    author = {Jie Cui and Fang Li and Zheng-Li Shi},
    title = {Origin and evolution of pathogenic coronaviruses},
    journal = {{Nat Rev Microbiol}},
    year = {2018},
    volume = {17},
    number = {3},
    pages = {181--192},
    doi = {10.1038/s41579-018-0118-9},
    publisher = {Springer Nature},
    }
  • [DOI] N. D. Grubaugh, J. T. Ladner, P. Lemey, O. G. Pybus, A. Rambaut, E. C. Holmes, and K. G. Andersen, "Tracking virus outbreaks in the twenty-first century," Nat Microbiol, vol. 4, iss. 1, p. 10–19, 2018.
    [Bibtex]
    @Article{Grubaugh:18,
    author = {Nathan D. Grubaugh and Jason T. Ladner and Philippe Lemey and Oliver G. Pybus and Andrew Rambaut and Edward C. Holmes and Kristian G. Andersen},
    title = {Tracking virus outbreaks in the twenty-first century},
    journal = {{Nat Microbiol}},
    year = {2018},
    volume = {4},
    number = {1},
    pages = {10--19},
    doi = {10.1038/s41564-018-0296-2},
    publisher = {Springer Nature},
    }
  • [DOI] D. M. Brown, A. M. Hixon, L. M. Oldfield, Y. Zhang, M. Novotny, W. Wang, S. R. Das, R. S. Shabman, K. L. Tyler, and R. H. Scheuermann, "Contemporary circulating enterovirus d68 strains have acquired the capacity for viral entry and replication in human neuronal cells," mBio, vol. 9, iss. 5, 2018.
    [Bibtex]
    @Article{Brown:18,
    author = {David M. Brown and Alison M. Hixon and Lauren M. Oldfield and Yun Zhang and Mark Novotny and Wei Wang and Suman R. Das and Reed S. Shabman and Kenneth L. Tyler and Richard H. Scheuermann},
    title = {Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells},
    journal = {{mBio}},
    year = {2018},
    volume = {9},
    number = {5},
    doi = {10.1128/mbio.01954-18},
    editor = {Diane E. Griffin},
    publisher = {American Society for Microbiology},
    }
  • [DOI] C. Gruber, E. Giombini, M. Selleri, S. Tausch, A. Andrusch, A. Tyshaieva, G. Cardeti, R. Lorenzetti, L. D. Marco, F. Carletti, A. Nitsche, M. Capobianchi, G. Ippolito, G. Autorino, and C. Castilletti, "Whole genome characterization of orthopoxvirus (OPV) abatino, a zoonotic virus representing a putative novel clade of old world orthopoxviruses," Viruses, vol. 10, iss. 10, p. 546, 2018.
    [Bibtex]
    @Article{Gruber:18,
    author = {Cesare Gruber and Emanuela Giombini and Marina Selleri and Simon Tausch and Andreas Andrusch and Alona Tyshaieva and Giusy Cardeti and Raniero Lorenzetti and Lorenzo De Marco and Fabrizio Carletti and Andreas Nitsche and Maria Capobianchi and Giuseppe Ippolito and Gian Autorino and Concetta Castilletti},
    title = {Whole Genome Characterization of Orthopoxvirus ({OPV}) Abatino, a Zoonotic Virus Representing a Putative Novel Clade of Old World Orthopoxviruses},
    journal = {Viruses},
    year = {2018},
    volume = {10},
    number = {10},
    pages = {546},
    doi = {10.3390/v10100546},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] J. B. Singer, E. C. Thomson, J. McLauchlan, J. Hughes, and R. J. Gifford, "GLUE: a flexible software system for virus sequence data," BMC Bioinformatics, vol. 19, iss. 1, 2018.
    [Bibtex]
    @Article{Singer:18,
    author = {Joshua B. Singer and Emma C. Thomson and John McLauchlan and Joseph Hughes and Robert J. Gifford},
    title = {{GLUE}: a flexible software system for virus sequence data},
    journal = {{BMC Bioinformatics}},
    year = {2018},
    volume = {19},
    number = {1},
    doi = {10.1186/s12859-018-2459-9},
    publisher = {Springer Nature},
    }
  • [DOI] Y. Zhang, C. Zmasek, G. Sun, C. N. Larsen, and R. H. Scheuermann, "Hepatitis C virus database and bioinformatics analysis tools in the virus pathogen resource (ViPR)," in Methods in molecular biology, Springer New York, 2018, p. 47–69.
    [Bibtex]
    @InCollection{Zhang:18,
    author = {Yun Zhang and Christian Zmasek and Guangyu Sun and Christopher N. Larsen and Richard H. Scheuermann},
    title = {Hepatitis {C} Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource ({ViPR})},
    booktitle = {Methods in Molecular Biology},
    publisher = {Springer New York},
    year = {2018},
    pages = {47--69},
    doi = {10.1007/978-1-4939-8976-8_3},
    }
  • [DOI] A. Viehweger, S. Krautwurst, K. Lamkiewicz, R. Madhugiri, J. Ziebuhr, M. Hölzer, and M. Marz, "Nanopore direct RNA sequencing reveals modification in full-length coronavirus genomes," bioRxiv, 2018.
    [Bibtex]
    @Article{Viehweger:18,
    author = {Adrian Viehweger and Sebastian Krautwurst and Kevin Lamkiewicz and Ramakanth Madhugiri and John Ziebuhr and Martin Hölzer and Manja Marz},
    title = {Nanopore direct {RNA} sequencing reveals modification in full-length coronavirus genomes},
    journal = {{bioRxiv}},
    year = {2018},
    doi = {10.1101/483693},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] H. Zhu, T. Dennis, J. Hughes, and R. J. Gifford, "Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database.," bioRxiv, 2018.
    [Bibtex]
    @Article{Zhu:18,
    author = {Henan Zhu and Tristan Dennis and Joseph Hughes and Robert J Gifford},
    title = {Database-integrated genome screening ({DIGS}): exploring genomes heuristically using sequence similarity search tools and a relational database.},
    journal = {{bioRxiv}},
    year = {2018},
    doi = {10.1101/246835},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] H. F. Löchel, M. Riemenschneider, D. Frishman, and D. Heider, "SCOTCH: subtype a coreceptor tropism classification in HIV-1," Bioinformatics, vol. 34, iss. 15, p. 2575–2580, 2018.
    [Bibtex]
    @Article{Löchel:18,
    author = {Hannah F Löchel and Mona Riemenschneider and Dmitrij Frishman and Dominik Heider},
    title = {{SCOTCH}: subtype A coreceptor tropism classification in {HIV}-1},
    journal = {Bioinformatics},
    year = {2018},
    volume = {34},
    number = {15},
    pages = {2575--2580},
    doi = {10.1093/bioinformatics/bty170},
    editor = {John Hancock},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] M. Riemenschneider, J. Wienbeck, A. Scherag, and D. Heider, "Data science for molecular diagnostics applications: from academia to clinic to industry," Systems medicine, vol. 1, iss. 1, p. 13–17, 2018.
    [Bibtex]
    @Article{Riemenschneider:18,
    author = {Mona Riemenschneider and Joachim Wienbeck and Andr{\'{e}} Scherag and Dominik Heider},
    title = {Data Science for Molecular Diagnostics Applications: From Academia to Clinic to Industry},
    journal = {Systems Medicine},
    year = {2018},
    volume = {1},
    number = {1},
    pages = {13--17},
    doi = {10.1089/sysm.2018.0002},
    publisher = {Mary Ann Liebert Inc},
    }
  • [DOI] J. Schwarz and D. Heider, "GUESS: projecting machine learning scores to well-calibrated probability estimates for clinical decision-making," Bioinformatics, 2018.
    [Bibtex]
    @Article{Schwarz:18,
    author = {Johanna Schwarz and Dominik Heider},
    title = {{GUESS}: projecting machine learning scores to well-calibrated probability estimates for clinical decision-making},
    journal = {Bioinformatics},
    year = {2018},
    doi = {10.1093/bioinformatics/bty984},
    editor = {Jonathan Wren},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] M. Döring, J. Büch, G. Friedrich, A. Pironti, P. Kalaghatgi, E. Knops, E. Heger, M. Obermeier, M. Däumer, A. Thielen, R. Kaiser, T. Lengauer, and N. Pfeifer, "Geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data.," Nucleic Acids Res, vol. 46, p. W271–W277, 2018.
    [Bibtex]
    @Article{Doering:18,
    author = {Döring, Matthias and Büch, Joachim and Friedrich, Georg and Pironti, Alejandro and Kalaghatgi, Prabhav and Knops, Elena and Heger, Eva and Obermeier, Martin and Däumer, Martin and Thielen, Alexander and Kaiser, Rolf and Lengauer, Thomas and Pfeifer, Nico},
    title = {geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data.},
    journal = {{Nucleic Acids Res}},
    year = {2018},
    volume = {46},
    pages = {W271--W277},
    abstract = {Identifying resistance to antiretroviral drugs is crucial for ensuring the successful treatment of patients infected with viruses such as human immunodeficiency virus (HIV) or hepatitis C virus (HCV). In contrast to Sanger sequencing, next-generation sequencing (NGS) can detect resistance mutations in minority populations. Thus, genotypic resistance testing based on NGS data can offer novel, treatment-relevant insights. Since existing web services for analyzing resistance in NGS samples are subject to long processing times and follow strictly rules-based approaches, we developed geno2pheno[ngs-freq], a web service for rapidly identifying drug resistance in HIV-1 and HCV samples. By relying on frequency files that provide the read counts of nucleotides or codons along a viral genome, the time-intensive step of processing raw NGS data is eliminated. Once a frequency file has been uploaded, consensus sequences are generated for a set of user-defined prevalence cutoffs, such that the constructed sequences contain only those nucleotides whose codon prevalence exceeds a given cutoff. After locally aligning the sequences to a set of references, resistance is predicted using the well-established approaches of geno2pheno[resistance] and geno2pheno[hcv]. geno2pheno[ngs-freq] can assist clinical decision making by enabling users to explore resistance in viral populations with different abundances and is freely available at http://ngs.geno2pheno.org.},
    doi = {10.1093/nar/gky349},
    issue = {W1},
    pmid = {29718426},
    }

2017

  • [DOI] J. Fuchs, M. Hölzer, M. Schilling, C. Patzina, A. Schoen, T. Hoenen, G. Zimmer, M. Marz, F. Weber, M. A. Müller, and G. Kochs, "Evolution and antiviral specificities of interferon-induced mx proteins of bats against Ebola, Influenza, and other RNA viruses," J Virol, vol. 91, iss. 15, 2017.
    [Bibtex]
    @Article{Fuchs:17,
    author = {Jonas Fuchs and Martin H\"{o}lzer and Mirjam Schilling and Corinna Patzina and Andreas Schoen and Thomas Hoenen and Gert Zimmer and Manja Marz and Friedemann Weber and Marcel A. M\"{u}ller and Georg Kochs},
    title = {Evolution and Antiviral Specificities of Interferon-Induced Mx Proteins of Bats against {E}bola, {I}nfluenza, and Other {RNA} Viruses},
    journal = {{J Virol}},
    year = {2017},
    volume = {91},
    number = {15},
    doi = {10.1128/jvi.00361-17},
    editor = {Bryan R. G. Williams},
    publisher = {American Society for Microbiology},
    }
  • [DOI] A. Brinkmann, K. Ergünay, A. Radonić, Z. Kocak Tufan, C. Domingo, and A. Nitsche, "Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics," PLoS Negl Trop Dis, vol. 11, p. e0006075, 2017.
    [Bibtex]
    @Article{Brinkmann:17,
    author = {Brinkmann, Annika and Erg\"{u}nay, Koray and Radoni\'{c}, Aleksandar and Kocak Tufan, Zeliha and Domingo, Cristina and Nitsche, Andreas},
    title = {Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics},
    journal = {{PLoS Negl Trop Dis}},
    year = {2017},
    volume = {11},
    pages = {e0006075},
    abstract = {We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours. Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.},
    doi = {10.1371/journal.pntd.0006075},
    issue = {11},
    keywords = {Adult; Chikungunya virus, genetics, isolation & purification; DNA, Viral, genetics; Ebolavirus, genetics, isolation & purification; Hemorrhagic Fever Virus, Crimean-Congo, genetics, isolation & purification; Hemorrhagic Fevers, Viral, diagnosis, virology; High-Throughput Nucleotide Sequencing, methods; Humans; Junin virus, genetics, isolation & purification; Nucleic Acid Amplification Techniques, methods; Rift Valley fever virus, genetics, isolation & purification; Sensitivity and Specificity; Sequence Analysis, DNA; Yellow fever virus, genetics, isolation & purification},
    pmid = {29155823},
    }
  • [DOI] J. Trimpert, N. Groenke, M. Jenckel, S. He, D. Kunec, M. L. Szpara, S. J. Spatz, N. Osterrieder, and D. P. McMahon, "A phylogenomic analysis of Marek's disease virus reveals independent paths to virulence in Eurasia and North America," Evol Appl, vol. 10, p. 1091–1101, 2017.
    [Bibtex]
    @Article{Trimpert:17,
    author = {Trimpert, Jakob and Groenke, Nicole and Jenckel, Maria and He, Shulin and Kunec, Dusan and Szpara, Moriah L and Spatz, Stephen J and Osterrieder, Nikolaus and McMahon, Dino P},
    title = {A phylogenomic analysis of {M}arek's disease virus reveals independent paths to virulence in {E}urasia and {N}orth {A}merica},
    journal = {{Evol Appl}},
    year = {2017},
    volume = {10},
    pages = {1091--1101},
    abstract = {Virulence determines the impact a pathogen has on the fitness of its host, yet current understanding of the evolutionary origins and causes of virulence of many pathogens is surprisingly incomplete. Here, we explore the evolution of Marek's disease virus (MDV), a herpesvirus commonly afflicting chickens and rarely other avian species. The history of MDV in the 20th century represents an important case study in the evolution of virulence. The severity of MDV infection in chickens has been rising steadily since the adoption of intensive farming techniques and vaccination programs in the 1950s and 1970s, respectively. It has remained uncertain, however, which of these factors is causally more responsible for the observed increase in virulence of circulating viruses. We conducted a phylogenomic study to understand the evolution of MDV in the context of dramatic changes to poultry farming and disease control. Our analysis reveals evidence of geographical structuring of MDV strains, with reconstructions supporting the emergence of virulent viruses independently in North America and Eurasia. Of note, the emergence of virulent viruses appears to coincide approximately with the introduction of comprehensive vaccination on both continents. The time-dated phylogeny also indicated that MDV has a mean evolutionary rate of ~1.6 × 10 substitutions per site per year. An examination of gene-linked mutations did not identify a strong association between mutational variation and virulence phenotypes, indicating that MDV may evolve readily and rapidly under strong selective pressures and that multiple genotypic pathways may underlie virulence adaptation in MDV.},
    doi = {10.1111/eva.12515},
    issue = {10},
    keywords = {disease; emergence; evolution; resistance; virulence},
    pmid = {29151863},
    }
  • [DOI] W. Wan, L. Kolesnikova, M. Clarke, A. Koehler, T. Noda, S. Becker, and J. A. G. Briggs, "Structure and assembly of the Ebola virus nucleocapsid," Nature, vol. 551, p. 394–397, 2017.
    [Bibtex]
    @Article{Wan:17,
    author = {Wan, William and Kolesnikova, Larissa and Clarke, Mairi and Koehler, Alexander and Noda, Takeshi and Becker, Stephan and Briggs, John A G},
    title = {Structure and assembly of the {E}bola virus nucleocapsid},
    journal = {Nature},
    year = {2017},
    volume = {551},
    pages = {394--397},
    abstract = {Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein and other viral proteins to form a helical nucleocapsid. The nucleocapsid acts as a scaffold for virus assembly and as a template for genome transcription and replication. Insights into nucleoprotein-nucleoprotein interactions have been derived from structural studies of oligomerized, RNA-encapsidating nucleoprotein, and cryo-electron microscopy of nucleocapsid or nucleocapsid-like structures. There have been no high-resolution reconstructions of complete mononegavirus nucleocapsids. Here we apply cryo-electron tomography and subtomogram averaging to determine the structure of Ebola virus nucleocapsid within intact viruses and recombinant nucleocapsid-like assemblies. These structures reveal the identity and arrangement of the nucleocapsid components, and suggest that the formation of an extended α-helix from the disordered carboxy-terminal region of nucleoprotein-core links nucleoprotein oligomerization, nucleocapsid condensation, RNA encapsidation, and accessory protein recruitment.},
    doi = {10.1038/nature24490},
    issue = {7680},
    keywords = {Animals; Cercopithecus aethiops; Cryoelectron Microscopy; Ebolavirus, chemistry, ultrastructure; Electron Microscope Tomography; HEK293 Cells; Humans; Marburgvirus, chemistry; Models, Molecular; Molecular Conformation; Nucleocapsid, chemistry, ultrastructure; Nucleocapsid Proteins, chemistry, ultrastructure; RNA, Viral, chemistry, ultrastructure; Vero Cells},
    pmid = {29144446},
    }
  • [DOI] M. Grossegesse, J. Doellinger, A. Tyshaieva, L. Schaade, and A. Nitsche, "Combined proteomics/genomics approach reveals proteomic changes of mature virions as a novel poxvirus adaptation mechanism," Viruses, vol. 9, 2017.
    [Bibtex]
    @Article{Grossegesse:17,
    author = {Grossegesse, Marica and Doellinger, Joerg and Tyshaieva, Alona and Schaade, Lars and Nitsche, Andreas},
    title = {Combined Proteomics/Genomics Approach Reveals Proteomic Changes of Mature Virions as a Novel Poxvirus Adaptation Mechanism},
    journal = {Viruses},
    year = {2017},
    volume = {9},
    abstract = {DNA viruses, like poxviruses, possess a highly stable genome, suggesting that adaptation of virus particles to specific cell types is not restricted to genomic changes. Cowpox viruses are zoonotic poxviruses with an extraordinarily broad host range, demonstrating their adaptive potential in vivo. To elucidate adaptation mechanisms of poxviruses, we isolated cowpox virus particles from a rat and passaged them five times in a human and a rat cell line. Subsequently, we analyzed the proteome and genome of the non-passaged virions and each passage. While the overall viral genome sequence was stable during passaging, proteomics revealed multiple changes in the virion composition. Interestingly, an increased viral fitness in human cells was observed in the presence of increased immunomodulatory protein amounts. As the only minor variant with increasing frequency during passaging was located in a viral RNA polymerase subunit and, moreover, most minor variants were found in transcription-associated genes, protein amounts were presumably regulated at transcription level. This study is the first comparative proteome analysis of virus particles before and after cell culture propagation, revealing proteomic changes as a novel poxvirus adaptation mechanism.},
    doi = {10.3390/v9110337},
    issue = {11},
    keywords = {Adaptation, Physiological, genetics; Amino Acid Sequence; Animals; Cell Line; Cowpox virus, chemistry, genetics; DNA-Directed RNA Polymerases; Gene Expression Regulation; Genetic Fitness; Genome, Viral, genetics; High-Throughput Nucleotide Sequencing; Host Specificity; Immunomodulation; Proteome, genetics; Rats; Rats, Wistar; Sequence Analysis, DNA; Viral Proteins, analysis, genetics; Virion, chemistry; Virus Cultivation; Virus Replication; adaptation; cell culture; cowpox virus; genomics; passaging; poxvirus; proteomics},
    pmid = {29125539},
    }
  • [DOI] S. Giese, K. Ciminski, H. Bolte, É. A. Moreira, S. Lakdawala, Z. Hu, Q. David, L. Kolesnikova, V. Götz, Y. Zhao, J. Dengjel, E. Y. Chin, K. Xu, and M. Schwemmle, "Role of influenza A virus NP acetylation on viral growth and replication," Nat Commun, vol. 8, p. 1259, 2017.
    [Bibtex]
    @Article{Giese:17,
    author = {Giese, Sebastian and Ciminski, Kevin and Bolte, Hardin and Moreira, \'{E}tori Aguiar and Lakdawala, Seema and Hu, Zehan and David, Quinnlan and Kolesnikova, Larissa and G\"{o}tz, Veronika and Zhao, Yongxu and Dengjel, J\"{o}rn and Chin, Y Eugene and Xu, Ke and Schwemmle, Martin},
    title = {Role of influenza {A} virus {NP} acetylation on viral growth and replication},
    journal = {{Nat Commun}},
    year = {2017},
    volume = {8},
    pages = {1259},
    abstract = {Lysine acetylation is a post-translational modification known to regulate protein functions. Here we identify several acetylation sites of the influenza A virus nucleoprotein (NP), including the lysine residues K77, K113 and K229. Viral growth of mutant virus encoding K229R, mimicking a non-acetylated NP lysine residue, is severely impaired compared to wildtype or the mutant viruses encoding K77R or K113R. This attenuation is not the result of decreased polymerase activity, altered protein expression or disordered vRNP co-segregation but rather caused by impaired particle release. Interestingly, release deficiency is also observed mimicking constant acetylation at this site (K229Q), whereas virus encoding NP-K113Q could not be generated. However, mimicking NP hyper-acetylation at K77 and K229 severely diminishes viral polymerase activity, while mimicking NP hypo-acetylation at these sites has no effect on viral replication. These results suggest that NP acetylation at K77, K113 and K229 impacts multiple steps in viral replication of influenza A viruses.},
    doi = {10.1038/s41467-017-01112-3},
    issue = {1},
    keywords = {Acetylation; Animals; Dogs; HEK293 Cells; Humans; Influenza A virus, genetics, growth & development, metabolism; Lysine, metabolism; Madin Darby Canine Kidney Cells; Mutation; RNA-Binding Proteins, genetics, metabolism; Viral Core Proteins, genetics, metabolism; Virus Replication, genetics},
    pmid = {29097654},
    }
  • [DOI] E. Wyler, J. Menegatti, V. Franke, C. Kocks, A. Boltengagen, T. Hennig, K. Theil, A. Rutkowski, C. Ferrai, L. Baer, L. Kermas, C. Friedel, N. Rajewsky, A. Akalin, L. Dölken, F. Grässer, and M. Landthaler, "Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection," Genome Biol, vol. 18, p. 209, 2017.
    [Bibtex]
    @Article{Wyler:17,
    author = {Wyler, Emanuel and Menegatti, Jennifer and Franke, Vedran and Kocks, Christine and Boltengagen, Anastasiya and Hennig, Thomas and Theil, Kathrin and Rutkowski, Andrzej and Ferrai, Carmelo and Baer, Laura and Kermas, Lisa and Friedel, Caroline and Rajewsky, Nikolaus and Akalin, Altuna and Dölken, Lars and Grässer, Friedrich and Landthaler, Markus},
    title = {Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection},
    journal = {{Genome Biol}},
    year = {2017},
    volume = {18},
    pages = {209},
    abstract = {Herpesviruses can infect a wide range of animal species. Herpes simplex virus 1 (HSV-1) is one of the eight herpesviruses that can infect humans and is prevalent worldwide. Herpesviruses have evolved multiple ways to adapt the infected cells to their needs, but knowledge about these transcriptional and post-transcriptional modifications is sparse. Here, we show that HSV-1 induces the expression of about 1000 antisense transcripts from the human host cell genome. A subset of these is also activated by the closely related varicella zoster virus. Antisense transcripts originate either at gene promoters or within the gene body, and they show different susceptibility to the inhibition of early and immediate early viral gene expression. Overexpression of the major viral transcription factor ICP4 is sufficient to turn on a subset of antisense transcripts. Histone marks around transcription start sites of HSV-1-induced and constitutively transcribed antisense transcripts are highly similar, indicating that the genetic loci are already poised to transcribe these novel RNAs. Furthermore, an antisense transcript overlapping with the BBC3 gene (also known as PUMA) transcriptionally silences this potent inducer of apoptosis in cis. We show for the first time that a virus induces widespread antisense transcription of the host cell genome. We provide evidence that HSV-1 uses this to downregulate a strong inducer of apoptosis. Our findings open new perspectives on global and specific alterations of host cell transcription by viruses.},
    doi = {10.1186/s13059-017-1329-5},
    issue = {1},
    keywords = {Apoptosis Regulatory Proteins, genetics, metabolism; Gene Expression Regulation, Viral, drug effects; Genome, Human; HeLa Cells; Herpes Simplex, virology; Herpesvirus 1, Human, physiology; Histone Code; Host-Pathogen Interactions, drug effects, genetics; Humans; Lipopolysaccharides, pharmacology; Monocytes, drug effects, metabolism; NF-kappa B, metabolism; Promoter Regions, Genetic, genetics; Proto-Oncogene Proteins, genetics, metabolism; RNA, Antisense, genetics, metabolism; RNA, Messenger, genetics, metabolism; Reproducibility of Results; Sequence Analysis, RNA; Transcription, Genetic, drug effects; Viral Proteins, metabolism; Antisense; BBC3; Herpes; ICP4; NFKB; Transcription; Virus; lncRNA},
    pmid = {29089033},
    }
  • [DOI] A. Hake and N. Pfeifer, "Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time," PLoS Comput Biol, vol. 13, p. e1005789, 2017.
    [Bibtex]
    @Article{Hake:17,
    author = {Hake, Anna and Pfeifer, Nico},
    title = {Prediction of {HIV}-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time},
    journal = {{PLoS Comput Biol}},
    year = {2017},
    volume = {13},
    pages = {e1005789},
    abstract = {Treatment with broadly neutralizing antibodies (bNAbs) has proven effective against HIV-1 infections in humanized mice, non-human primates, and humans. Due to the high mutation rate of HIV-1, resistance testing of the patient's viral strains to the bNAbs is still inevitable. So far, bNAb resistance can only be tested in expensive and time-consuming neutralization experiments. Here, we introduce well-performing computational models that predict the neutralization response of HIV-1 to bNAbs given only the envelope sequence of the virus. Using non-linear support vector machines based on a string kernel, the models learnt even the important binding sites of bNAbs with more complex epitopes, i.e., the CD4 binding site targeting bNAbs, proving thereby the biological relevance of the models. To increase the interpretability of the models, we additionally provide a new kind of motif logo for each query sequence, visualizing those residues of the test sequence that influenced the prediction outcome the most. Moreover, we predicted the neutralization sensitivity of around 34,000 HIV-1 samples from different time points to a broad range of bNAbs, enabling the first analysis of HIV resistance to bNAbs on a global scale. The analysis showed for many of the bNAbs a trend towards antibody resistance over time, which had previously only been discovered for a small non-representative subset of the global HIV-1 population.},
    doi = {10.1371/journal.pcbi.1005789},
    issue = {10},
    keywords = {Antibodies, Neutralizing, chemistry, immunology; Binding Sites; CD4 Antigens; Drug Resistance, Viral, immunology; Epitope Mapping, methods; HIV Antibodies, chemistry, immunology; HIV-1, chemistry, immunology; Humans; Protein Binding; Protein Interaction Mapping, methods; Sequence Analysis, Protein, methods; Time Factors},
    pmid = {29065122},
    }
  • [DOI] B. Vrancken, M. A. Suchard, and P. Lemey, "Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling," Virus Evol, vol. 3, p. vex028, 2017.
    [Bibtex]
    @Article{Vrancken:17,
    author = {Vrancken, Bram and Suchard, Marc A and Lemey, Philippe},
    title = {Accurate quantification of within- and between-host {HBV} evolutionary rates requires explicit transmission chain modelling},
    journal = {{Virus Evol}},
    year = {2017},
    volume = {3},
    pages = {vex028},
    abstract = {Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, , 89/7: 3512-22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the 'colonization-adaptation-transmission' model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates. Here, we revisit this dataset using a full probabilistic Bayesian phylogenetic framework that adequately accounts for the non-independence of sequence data when estimating evolutionary parameters. Examination of the transmission chain data under a flexible coalescent prior reveals a general inconsistency between the estimated timings and clustering patterns and the known transmission history, highlighting the need to incorporate host transmission information in the analysis. Using an explicit genealogical transmission chain model, we find strong support for a transmission-associated decrease of the overall evolutionary rate. However, in contrast to the initially reported larger transmission effect on non-synonymous substitution rate, we find a similar decrease in both non-synonymous and synonymous substitution rates that cannot be adequately explained by the colonization-adaptation-transmission model. An alternative explanation may involve a transmission/establishment advantage of hepatitis B virus variants that have accumulated fewer within-host substitutions, perhaps by spending more time in the covalently closed circular DNA state between each round of viral replication. More generally, this study illustrates that ignoring phylogenetic relationships can lead to misleading evolutionary estimates.},
    doi = {10.1093/ve/vex028},
    issue = {2},
    keywords = {BEAST; hepatitis B virus; statistical phylogenetics; substitution rate; transmission chain},
    pmid = {29026650},
    }
  • [DOI] A. Sczyrba, P. Hofmann, P. Belmann, D. Koslicki, S. Janssen, J. Dröge, I. Gregor, S. Majda, J. Fiedler, E. Dahms, A. Bremges, A. Fritz, R. Garrido-Oter, T. S. Jørgensen, N. Shapiro, P. D. Blood, A. Gurevich, Y. Bai, D. Turaev, M. Z. DeMaere, R. Chikhi, N. Nagarajan, C. Quince, F. Meyer, M. Balvočiūtė, L. H. Hansen, S. J. Sørensen, B. K. H. Chia, B. Denis, J. L. Froula, Z. Wang, R. Egan, D. Don Kang, J. J. Cook, C. Deltel, M. Beckstette, C. Lemaitre, P. Peterlongo, G. Rizk, D. Lavenier, Y. Wu, S. W. Singer, C. Jain, M. Strous, H. Klingenberg, P. Meinicke, M. D. Barton, T. Lingner, H. Lin, Y. Liao, G. G. Z. Silva, D. A. Cuevas, R. A. Edwards, S. Saha, V. C. Piro, B. Y. Renard, M. Pop, H. Klenk, M. Göker, N. C. Kyrpides, T. Woyke, J. A. Vorholt, P. Schulze-Lefert, E. M. Rubin, A. E. Darling, T. Rattei, and A. C. McHardy, "Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software," Nat Methods, vol. 14, p. 1063–1071, 2017.
    [Bibtex]
    @Article{Sczyrba:17,
    author = {Sczyrba, Alexander and Hofmann, Peter and Belmann, Peter and Koslicki, David and Janssen, Stefan and Dröge, Johannes and Gregor, Ivan and Majda, Stephan and Fiedler, Jessika and Dahms, Eik and Bremges, Andreas and Fritz, Adrian and Garrido-Oter, Ruben and Jørgensen, Tue Sparholt and Shapiro, Nicole and Blood, Philip D and Gurevich, Alexey and Bai, Yang and Turaev, Dmitrij and DeMaere, Matthew Z and Chikhi, Rayan and Nagarajan, Niranjan and Quince, Christopher and Meyer, Fernando and Balvočiūtė, Monika and Hansen, Lars Hestbjerg and Sørensen, Søren J and Chia, Burton K H and Denis, Bertrand and Froula, Jeff L and Wang, Zhong and Egan, Robert and Don Kang, Dongwan and Cook, Jeffrey J and Deltel, Charles and Beckstette, Michael and Lemaitre, Claire and Peterlongo, Pierre and Rizk, Guillaume and Lavenier, Dominique and Wu, Yu-Wei and Singer, Steven W and Jain, Chirag and Strous, Marc and Klingenberg, Heiner and Meinicke, Peter and Barton, Michael D and Lingner, Thomas and Lin, Hsin-Hung and Liao, Yu-Chieh and Silva, Genivaldo Gueiros Z and Cuevas, Daniel A and Edwards, Robert A and Saha, Surya and Piro, Vitor C and Renard, Bernhard Y and Pop, Mihai and Klenk, Hans-Peter and Göker, Markus and Kyrpides, Nikos C and Woyke, Tanja and Vorholt, Julia A and Schulze-Lefert, Paul and Rubin, Edward M and Darling, Aaron E and Rattei, Thomas and McHardy, Alice C},
    title = {{C}ritical {A}ssessment of {M}etagenome {I}nterpretation-a benchmark of metagenomics software},
    journal = {{Nat Methods}},
    year = {2017},
    volume = {14},
    pages = {1063--1071},
    abstract = {Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.},
    doi = {10.1038/nmeth.4458},
    issue = {11},
    keywords = {Algorithms; Benchmarking; Metagenomics; Sequence Analysis, DNA; Software},
    pmid = {28967888},
    }
  • [DOI] M. Kiening, F. Weber, and D. Frishman, "Conserved RNA structures in the intergenic regions of ambisense viruses," Sci Rep, vol. 7, p. 16625, 2017.
    [Bibtex]
    @Article{Kiening:17,
    author = {Kiening, Michael and Weber, Friedemann and Frishman, Dmitrij},
    title = {Conserved {RNA} structures in the intergenic regions of ambisense viruses},
    journal = {{Sci Rep}},
    year = {2017},
    volume = {7},
    pages = {16625},
    abstract = {Ambisense viruses are negative-sense single-stranded RNA viruses that use a unique expression strategy. Their genome contains at least one ambisense RNA segment that carries two oppositely oriented reading frames separated by an intergenic region. It is believed that a structural RNA element within the intergenic region is involved in transcription termination. However, a general overview over the structural repertoire of ambisense intergenic regions is currently lacking. In this study we investigated the structural potential of the intergenic regions of all known ambisense viruses and compared their structural repertoire by structure-guided clustering. Intergenic regions of most ambisense viruses possess a high potential to build stable secondary structures and many viruses share common structural motifs in the intergenic regions of their ambisense segments. We demonstrate that (i) within the phylogenetic virus groups sets of conserved functional structures are present, but that (ii) between the groups conservation is low to non-existent. These results reflect a high degree of freedom to regulate ambisense transcription termination and also imply that the genetic strategy of having an ambisense RNA genome has evolved several times independently.},
    doi = {10.1038/s41598-017-16875-4},
    issue = {1},
    pmid = {29192224},
    }
  • K. Meixenberger, K. P. Yousef, M. R. Smith, S. Somogyi, S. Fiedler, B. Bartmeyer, O. Hamouda, N. Bannert, M. von Kleist, and C. Kücherer, "Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors," Virol J, vol. 14, iss. 1, p. 223, 2017.
    [Bibtex]
    @Article{Meixenberger:17,
    author = {Meixenberger, Karolin and Yousef, Kaveh Pouran and Smith, Maureen Rebecca and Somogyi, Sybille and Fiedler, Stefan and Bartmeyer, Barbara and Hamouda, Osamah and Bannert, Norbert and von Kleist, Max and K{\"u}cherer, Claudia},
    title = {Molecular evolution of {HIV}-1 integrase during the 20 years prior to the first approval of integrase inhibitors},
    journal = {{Virol J}},
    year = {2017},
    volume = {14},
    number = {1},
    pages = {223},
    publisher = {BioMed Central},
    }
  • A. E. Shaw, J. Hughes, Q. Gu, A. Behdenna, J. B. Singer, T. Dennis, R. J. Orton, M. Varela, R. J. Gifford, S. J. Wilson, and others, "Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type i interferon responses," PLoS Biol, vol. 15, iss. 12, p. e2004086, 2017.
    [Bibtex]
    @Article{Shaw:17,
    author = {Shaw, Andrew E and Hughes, Joseph and Gu, Quan and Behdenna, Abdelkader and Singer, Joshua B and Dennis, Tristan and Orton, Richard J and Varela, Mariana and Gifford, Robert J and Wilson, Sam J and others},
    title = {Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses},
    journal = {{PLoS Biol}},
    year = {2017},
    volume = {15},
    number = {12},
    pages = {e2004086},
    publisher = {Public Library of Science},
    }