Metagenomic Course and Virus Discovery

Arthur Gruber - Recommended bibliography

Allen EE, Banfield JF. (2005). Community genomics in microbial ecology and evolution. Nat Rev Microbiol. 3(6):489-98.
Alves, J.M.P., Oliveira, A.L., Sandberg, T.O.M. Gallego, J.L.M., Toledo, M.A., Moura, E.M., Mehnert, D.U., Oliveira, L.S., Durham, A.M., Zanotto, P.M.A., Reyes, A. and Gruber A. (2016). GenSeed-HMM: A tool for progressive assembly using profile HMMs as seeds and its application in Alpavirinae viral discovery from metagenomic data. Front Microbiol. 7, 269.
Bexfield, N., and Kellam, P. (2011). Metagenomics and the molecular identification of novel viruses. Vet J 190, 191-198.
Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM. (2013). CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol. 10(5):817-827.

Bibby, K., and Peccia, J. (2013). Identification of viral pathogen diversity in sewage sludge by metagenome analysis. Environ Sci Technol 47, 1945-1951.
Brown CT, Olm MR, Thomas BC, Banfield JF. (2016). Measurement of bacterial replication rates in microbial communities. Nat Biotechnol. 34(12):1256-1263.
Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA. (2014). A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 5:4498.

Dutilh, B.E., Schmieder, R., Nulton, J., Felts, B., Salamon, P., Edwards, R.A., and Mokili, J.L. (2012). Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics 28, 3225-3231.

Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. (2016). Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol Rev. 40, 258-272.
Fancello, L., Raoult, D., and Desnues, C. (2012). Computational tools for viral metagenomics and their application in clinical research. Virology 434, 162-174.
Grazziotin AL, Koonin EV, Kristensen DM. (2017). Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res 45(D1):D491-D498.

Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. (1998). Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 5(10):R245-9.
Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M.C., Rattei, T., Mende, D.R., Sunagawa, S., Kuhn, M., Jensen, L.J., Von Mering, C., and Bork, P. (2015). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44, D286-D293.
Ibrahim, B. et al. (2018). Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting. Viruses,10(5). pii: E256.
Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, Matot E, Jona G, Harmelin A, Cohen N, Sirota-Madi A, Thaiss CA, Pevsner-Fischer M, Sorek R, Xavier RJ, Elinav E, Segal E. (2015). Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science. 349(6252):1101-1106.
Kristensen, D.M., Waller, A.S., Yamada, T., Bork, P., Mushegian, A.R., and Koonin, E.V. (2013). Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. J Bacteriol 195, 941-950.
Krupovic M, Koonin EV. (2017). Multiple origins of viral capsid proteins from cellular ancestors. Proc Natl Acad Sci U S A. 114(12):E2401-E2410.

Mokili, J.L., Rohwer, F., and Dutilh, B.E. (2012). Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2, 63-77.
Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DP, Keshavarzian A, Mutlu EA, Sauk J, Gevers D, Xavier RJ, Wang D, Parkes M, Virgin HW. (2015). Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160(3): 447-460.

Reyes, A., Alves, J.M.P., Durham, A.M. and Gruber A. (2017). Use of profile hidden Markov models in viral discovery: current insights. Advances in Genomics and Genetics 7: 29–45.
Reyes, A., Haynes, M., Hanson, N., Angly, F.E., Heath, A.C., Rohwer, F., and Gordon, J.I. (2010). Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334-338.
Roux, S., Enault, F., Hurwitz, B.L., and Sullivan, M.B. (2015). VirSorter: mining viral signal from microbial genomic data. PeerJ 3, e985.
Roux S, Krupovic M, Poulet A, Debroas D, Enault F. (2012). Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads. PLoS One. 7(7):e40418.

Sharma, D., Priyadarshini, P., and Vrati, S. (2015). Unraveling the web of viroinformatics: computational tools and databases in virus research. J Virol 89, 1489-1501.
Skewes-Cox, P., Sharpton, T.J., Pollard, K.S., and Derisi, J.L. (2014). Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One 9, e105067.
Smits, S.L., Bodewes, R., Ruiz-Gonzalez, A., Baumgartner, W., Koopmans, M.P., Osterhaus, A.D., and Schurch, A.C. (2015). Recovering full-length viral genomes from metagenomes. Front Microbiol 6, 1069.
Yutin, N., Wolf, Y.I., Raoult, D., and Koonin, E.V. (2009). Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol J 6, 223.

Manja Marz - Recommended bibliography

Beth L. Nicholson and K. Andrew White (2014). Functional long-range RNA-RNA interactions in positive-strand RNA viruses. Nature Reviews
Microbiology 12: 493–504.
Chicco, D. (2017). Ten quick tips for machine learning in computational biology. BioData Min. 10: 35.
Eraslan, G., Avsec, Z., Gagneur, J. and Theis, F.J. (2019). Deep learning: new computational modelling techniques for genomics. Nature Reviews Genetics 20: 389–340.
Fricke, M. and Marz, M. (2016). Prediction of conserved long-range RNA-RNA interactions in full viral genomes. Bioinformatics 32: 2928–2935.
Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.. (2011). ViennaRNA Package 2.0. Algorithms for Molecular Biology 6: article 26.
Nawrocki, E.P. and Eddy, S.R. (2013). Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29: 2933-2935.
Larrañaga P, Calvo B, Santana R, Bielza C, Galdiano J, Inza I, Lozano JA, Armañanzas R, Santafé G, Pérez A and Robles V. (2006). Machine learning in bioinformatics. Briefing in Bioinformatics 7(1): 86-112.
Marz, M., Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler and Armin Töpfer. (2014). Challenges in RNA virus bioinformatics. Bioinformatics 30: 1793–1799.
Nooij, S., Dennis Schmitz, Harry Vennema, Annelies Kroneman and Marion P. G. Koopmans (2018). Overview of Virus Metagenomic Classification Methods and Their Biological Applications. Front. Microbiol. 9: article 749.
Raden, M., Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen. (2018). Freiburg RNA tools: a central online resource for RNA-focused research and teaching. Nucleic Acids Research 46(W1): W25-W29.
Will, S., Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. (2007). Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLoS Computational Biology 3(4): e65.