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Virus-X: Viral Metagenomics for Innovation Value

Deliverables

WP1 - Scientific publications, patents or congress contribution and outreach

Scientific publications, patents or congress contribution and outreach

WP6 - Scientific publications, patents or congress contribution and outreach

Scientific publications, patents or congress contribution and outreach involving work performed in WP6 Cloning & Expression Optimization

WP4 - Scientific publications, patents or congress contribution and outreach

Scientific publications, patents or congress contribution and outreach involving work in WP4

Scientific publications, patents or congress contribution and outreach

Scientific publications, patents or congress contribution and outreach involving work carried out in WP8 Activity Screening & Characterization

WP3 - Scientific publications, patents or congress contribution and outreach

Scientific publications, patents or congress contribution and outreach

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Publications

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Author(s): Martin Steinegger, Johannes Söding
Published in: Nature Biotechnology, Issue 35, 2017, Page(s) 1026–1028, ISSN 1087-0156
DOI: 10.1038/nbt.3988

Structure and function of the Ts2631 endolysin of Thermus scotoductus phage vB_Tsc2631 with unique N-terminal extension used for peptidoglycan binding

Author(s): Magdalena Plotka, Enea Sancho-Vaello, Sebastian Dorawa, Anna-Karina Kaczorowska, Lukasz P. Kozlowski, Tadeusz Kaczorowski, Kornelius Zeth
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
DOI: 10.1038/s41598-018-37417-6

WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs

Author(s): Clovis Galiez, Matthias Siebert, François Enault, Jonathan Vincent, Johannes Söding
Published in: Bioinformatics, Issue 33/19, 2017, Page(s) 3113-3114, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btx383

Rolling-circle replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial transposases of the IS91 family insertion sequences

Author(s): Yuchen Wang, Beibei Chen, Mengzhuo Cao, Linshan Sima, David Prangishvili, Xiangdong Chen, Mart Krupovic
Published in: Journal of General Virology, Issue 99/3, 2018, Page(s) 416-421, ISSN 0022-1317
DOI: 10.1099/jgv.0.001009

Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging

Author(s): Denis Ptchelkine, Ashley Gillum, Tomohiro Mochizuki, Soizick Lucas-Staat, Ying Liu, Mart Krupovic, Simon E. V. Phillips, David Prangishvili, Juha T. Huiskonen
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
DOI: 10.1038/s41467-017-01668-0

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author(s): Roux , Simon; Adriaenssens , Evelien; Dutilh , Bas ,; Koonin , Eugene; Kropinski , Andrew; Krupovic , Mart; Kuhn , Jens; Lavigne , Rob; Brister , J Rodney; Varsani , Arvind; Amid , Clara; Aziz , Ramy; Bordenstein , Seth; Bork , Peer; Breitbart , Mya; Cochrane , Guy; Daly , Rebecca; Desnues , Christelle; Duhaime , Melissa; Emerson , Joanne; Enault , François; Fuhrman , Jed; Hingamp , Pascal; Hugen
Published in: https://hal.archives-ouvertes.fr/hal-01982207, Issue 10, 2019, ISSN 1087-0156
DOI: 10.3929/ethz-b-000315358

Viruses of archaea: Structural, functional, environmental and evolutionary genomics

Author(s): Mart Krupovic, Virginija Cvirkaite-Krupovic, Jaime Iranzo, David Prangishvili, Eugene V. Koonin
Published in: Virus Research, Issue 244, 2018, Page(s) 181-193, ISSN 0168-1702
DOI: 10.1016/j.virusres.2017.11.025

Is the Virus Important? And Some Other Questions

Author(s): Ruth-Anne Sandaa, Gunnar Bratbak
Published in: Viruses, Issue 10/8, 2018, Page(s) 442, ISSN 1999-4915
DOI: 10.3390/v10080442

Uniclust databases of clustered and deeply annotated protein sequences and alignments

Author(s): Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria J. Martin, Johannes Söding, Martin Steinegger
Published in: Nucleic Acids Research, Issue 45/D1, 2017, Page(s) D170-D176, ISSN 0305-1048
DOI: 10.1093/nar/gkw1081

Structure of a filamentous virus uncovers familial ties within the archaeal virosphere

Author(s): Fengbin Wang, Diana P Baquero, Zhangli Su, Tomasz Osinski, David Prangishvili, Edward H Egelman, Mart Krupovic
Published in: Virus Evolution, Issue 6/1, 2020, ISSN 2057-1577
DOI: 10.1093/ve/veaa023

Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile

Author(s): Ying Liu, Tomasz Osinski, Fengbin Wang, Mart Krupovic, Stefan Schouten, Peter Kasson, David Prangishvili, Edward H. Egelman
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
DOI: 10.1038/s41467-018-05684-6

The enigmatic archaeal virosphere

Author(s): David Prangishvili, Dennis H. Bamford, Patrick Forterre, Jaime Iranzo, Eugene V. Koonin, Mart Krupovic
Published in: Nature Reviews Microbiology, Issue 15/12, 2017, Page(s) 724-739, ISSN 1740-1526
DOI: 10.1038/nrmicro.2017.125

Integrated mobile genetic elements in Thaumarchaeota

Author(s): Mart Krupovic, Kira S. Makarova, Yuri I. Wolf, Sofia Medvedeva, David Prangishvili, Patrick Forterre, Eugene V. Koonin
Published in: Environmental Microbiology, Issue 21/6, 2019, Page(s) 2056-2078, ISSN 1462-2912
DOI: 10.1111/1462-2920.14564

Numerous cultivated and uncultivated viruses encode ribosomal proteins

Author(s): Carolina M. Mizuno, Charlotte Guyomar, Simon Roux, Régis Lavigne, Francisco Rodriguez-Valera, Matthew B. Sullivan, Reynald Gillet, Patrick Forterre, Mart Krupovic
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-08672-6

A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea

Author(s): Ying Liu, Sonoko Ishino, Yoshizumi Ishino, Gérard Pehau-Arnaudet, Mart Krupovic, David Prangishvili
Published in: Journal of Virology, Issue 91/13, 2017, ISSN 0022-538X
DOI: 10.1128/JVI.00589-17

HH-suite3 for fast remote homology detection and deep protein annotation

Author(s): Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding
Published in: BMC Bioinformatics, Issue 20/1, 2019, ISSN 1471-2105
DOI: 10.1186/s12859-019-3019-7

Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting

Author(s): Bashar Ibrahim, Ksenia Arkhipova, Arno Andeweg, Susana Posada-Céspedes, François Enault, Arthur Gruber, Eugene Koonin, Anne Kupczok, Philippe Lemey, Alice McHardy, Dino McMahon, Brett Pickett, David Robertson, Richard Scheuermann, Alexandra Zhernakova, Mark Zwart, Alexander Schönhuth, Bas Dutilh, Manja Marz
Published in: Viruses, Issue 10/5, 2018, Page(s) 256, ISSN 1999-4915
DOI: 10.3390/v10050256

Virus-borne mini-CRISPR arrays are involved in interviral conflicts

Author(s): Sofia Medvedeva, Ying Liu, Eugene V. Koonin, Konstantin Severinov, David Prangishvili, Mart Krupovic
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-13205-2

New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures

Author(s): Ying Liu, David Brandt, Sonoko Ishino, Yoshizumi Ishino, Eugene V. Koonin, Jörn Kalinowski, Mart Krupovic, David Prangishvili
Published in: Environmental Microbiology, Issue 21/6, 2019, Page(s) 2002-2014, ISSN 1462-2912
DOI: 10.1111/1462-2920.14479

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Author(s): Jakub Barylski, François Enault, Bas E Dutilh, Margo BP Schuller, Robert A Edwards, Annika Gillis, Jochen Klumpp, Petar Knezevic, Mart Krupovic, Jens H Kuhn, Rob Lavigne, Hanna M Oksanen, Matthew B Sullivan, Ho Bin Jang, Peter Simmonds, Pakorn Aiewsakun, Johannes Wittmann, Igor Tolstoy, J Rodney Brister, Andrew M Kropinski, Evelien M Adriaenssens
Published in: Systematic Biology, Issue 69/1, 2019, Page(s) 110-123, ISSN 1063-5157
DOI: 10.1093/sysbio/syz036

A Mitochondrial Autonomously Replicating Sequence from Pichia pastoris for Uniform High Level Recombinant Protein Production

Author(s): Jan-Philipp Schwarzhans, Tobias Luttermann, Daniel Wibberg, Anika Winkler, Wolfgang Hübner, Thomas Huser, Jörn Kalinowski, Karl Friehs
Published in: Frontiers in Microbiology, Issue 8, 2017, ISSN 1664-302X
DOI: 10.3389/fmicb.2017.00780

Discovery of High Abundances of Aster-Like Nanoparticles in Pelagic Environments: Characterization and Dynamics

Author(s): Jonathan Colombet, Hermine Billard, Bernard Viguès, Stéphanie Balor, Christelle Boulé, Lucie Geay, Karim Benzerara, Nicolas Menguy, Guy Ilango, Maxime Fuster, François Enault, Corinne Bardot, Véronique Gautier, Angia Sriram Pradeep Ram, Télesphore Sime-Ngando
Published in: Frontiers in Microbiology, Issue 10, 2019, ISSN 1664-302X
DOI: 10.3389/fmicb.2019.02376

Clustering huge protein sequence sets in linear time

Author(s): Martin Steinegger, Johannes Söding
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
DOI: 10.1038/s41467-018-04964-5

MMseqs2 desktop and local web server app for fast, interactive sequence searches

Author(s): Milot Mirdita, Martin Steinegger, Johannes Söding
Published in: Bioinformatics, Issue 35/16, 2019, Page(s) 2856-2858, ISSN 1367-4803
DOI: 10.1093/bioinformatics/bty1057

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics

Author(s): Eli Levy Karin, Milot Mirdita, Johannes Söding
Published in: Microbiome, Issue 8/1, 2020, ISSN 2049-2618
DOI: 10.1186/s40168-020-00808-x

Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS

Author(s): Stefanie Freitag-Pohl, Andrius Jasilionis, Maria Håkansson, L. Anders Svensson, Rebeka Kovačič, Martin Welin, Hildegard Watzlawick, Lei Wang, Josef Altenbuchner, Magdalena Płotka, Anna Karina Kaczorowska, Tadeusz Kaczorowski, Eva Nordberg Karlsson, Salam Al-Karadaghi, Björn Walse, Arnthór Aevarsson, Ehmke Pohl
Published in: Acta Crystallographica Section D Structural Biology, Issue 75/11, 2019, Page(s) 1028-1039, ISSN 2059-7983
DOI: 10.1107/s2059798319013330

How to Stabilize Protein: Stability Screens for Thermal Shift Assays and Nano Differential Scanning Fluorimetry in the Virus-X Project

Author(s): Daniel Bruce, Emily Cardew, Stefanie Freitag-Pohl, Ehmke Pohl
Published in: Journal of Visualized Experiments, Issue 144, 2019, ISSN 1940-087X
DOI: 10.3791/58666

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author(s): Simon Roux, Evelien M Adriaenssens, Bas E Dutilh, Eugene V Koonin, Andrew M Kropinski, Mart Krupovic, Jens H Kuhn, Rob Lavigne, J Rodney Brister, Arvind Varsani, Clara Amid, Ramy K Aziz, Seth R Bordenstein, Peer Bork, Mya Breitbart, Guy R Cochrane, Rebecca A Daly, Christelle Desnues, Melissa B Duhaime, Joanne B Emerson, François Enault, Jed A Fuhrman, Pascal Hingamp, Philip Hugenholtz, Bonnie L H
Published in: Nature Biotechnology, Issue 37/1, 2019, Page(s) 29-37, ISSN 1087-0156
DOI: 10.1038/nbt.4306

Ts2631 Endolysin from the Extremophilic Thermus scotoductus Bacteriophage vB_Tsc2631 as an Antimicrobial Agent against Gram-Negative Multidrug-Resistant Bacteria

Author(s): Magdalena Plotka, Malgorzata Kapusta, Sebastian Dorawa, Anna-Karina Kaczorowska, Tadeusz Kaczorowski
Published in: Viruses, Issue 11/7, 2019, Page(s) 657, ISSN 1999-4915
DOI: 10.3390/v11070657

Seasonality Drives Microbial Community Structure, Shaping both Eukaryotic and Prokaryotic Host–Viral Relationships in an Arctic Marine Ecosystem

Author(s): Ruth-Anne Sandaa, Julia E. Storesund, Emily Olesin, Maria Lund Paulsen, Aud Larsen, Gunnar Bratbak, Jessica Ray
Published in: Viruses, Issue 10/12, 2018, Page(s) 715, ISSN 1999-4915
DOI: 10.3390/v10120715

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

Author(s): Martin Steinegger, Milot Mirdita, Johannes Söding
Published in: Nature Methods, Issue 16/7, 2019, Page(s) 603-606, ISSN 1548-7091
DOI: 10.1038/s41592-019-0437-4

New CRISPR-Cas9 vectors for genetic modifications of Bacillus species

Author(s): Anna A Toymentseva, Josef Altenbuchner
Published in: FEMS Microbiology Letters, Issue 366/1, 2018, ISSN 1574-6968
DOI: 10.1093/femsle/fny284

New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities

Author(s): Diana P. Baquero, Patrizia Contursi, Monica Piochi, Simonetta Bartolucci, Ying Liu, Virginija Cvirkaite-Krupovic, David Prangishvili, Mart Krupovic
Published in: The ISME Journal, 2020, ISSN 1751-7362
DOI: 10.1038/s41396-020-0653-z

A packing for A-form DNA in an icosahedral virus

Author(s): Fengbin Wang, Ying Liu, Zhangli Su, Tomasz Osinski, Guilherme A. P. de Oliveira, James F. Conway, Stefan Schouten, Mart Krupovic, David Prangishvili, Edward H. Egelman
Published in: Proceedings of the National Academy of Sciences, Issue 116/45, 2019, Page(s) 22591-22597, ISSN 0027-8424
DOI: 10.1073/pnas.1908242116

Clustering huge protein sequence sets in linear time.

Author(s): Martin Steinegger and Johannes Soeding
Published in: Nature Communications, Issue 9(1), 2018, Page(s) 2542
DOI: 10.1101/104034

Les virus à la source

Author(s): Arnthor Ævarsson
Published in: La Recherche, 2018, ISSN 0029-5671

Posters

Author(s): Jasilionis A, Akutsu M, Håkansson M, Wang L, Welin M, Kovačič R, Liu Y, Watzlawick H, Ævarsson A, Prangishvili D, Altenbuchner J, Al-Karadaghi S, Nordberg Karlsson E.
Published in: FEBS Open Bio, Issue 9/S1, 2019, Page(s) 65-431, ISSN 2211-5463
DOI: 10.1002/2211-5463.12675