Virus-X: Viral Metagenomics for Innovation Value

Resultado final

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

Project website built and online

Publicaciones

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

Autores: Martin Steinegger, Johannes Söding
Publicado en: Nature Biotechnology, Edición 35, 2017, Página(s) 1026–1028, ISSN 1087-0156
Editor: Nature Publishing Group
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

Autores: Magdalena Plotka, Enea Sancho-Vaello, Sebastian Dorawa, Anna-Karina Kaczorowska, Lukasz P. Kozlowski, Tadeusz Kaczorowski, Kornelius Zeth
Publicado en: Scientific Reports, Edición 9/1, 2019, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-018-37417-6

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

Autores: Clovis Galiez, Matthias Siebert, François Enault, Jonathan Vincent, Johannes Söding
Publicado en: Bioinformatics, Edición 33/19, 2017, Página(s) 3113-3114, ISSN 1367-4803
Editor: Oxford University Press
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

Autores: Yuchen Wang, Beibei Chen, Mengzhuo Cao, Linshan Sima, David Prangishvili, Xiangdong Chen, Mart Krupovic
Publicado en: Journal of General Virology, Edición 99/3, 2018, Página(s) 416-421, ISSN 0022-1317
Editor: Society for General Microbiology
DOI: 10.1099/jgv.0.001009

Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging

Autores: Denis Ptchelkine, Ashley Gillum, Tomohiro Mochizuki, Soizick Lucas-Staat, Ying Liu, Mart Krupovic, Simon E. V. Phillips, David Prangishvili, Juha T. Huiskonen
Publicado en: Nature Communications, Edición 8/1, 2017, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-017-01668-0

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Autores: 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
Publicado en: https://hal.archives-ouvertes.fr/hal-01982207, Edición 10, 2019, ISSN 1087-0156
Editor: Nature Publishing Group
DOI: 10.3929/ethz-b-000315358

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

Autores: Mart Krupovic, Virginija Cvirkaite-Krupovic, Jaime Iranzo, David Prangishvili, Eugene V. Koonin
Publicado en: Virus Research, Edición 244, 2018, Página(s) 181-193, ISSN 0168-1702
Editor: Elsevier BV
DOI: 10.1016/j.virusres.2017.11.025

Is the Virus Important? And Some Other Questions

Autores: Ruth-Anne Sandaa, Gunnar Bratbak
Publicado en: Viruses, Edición 10/8, 2018, Página(s) 442, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v10080442

Uniclust databases of clustered and deeply annotated protein sequences and alignments

Autores: Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria J. Martin, Johannes Söding, Martin Steinegger
Publicado en: Nucleic Acids Research, Edición 45/D1, 2017, Página(s) D170-D176, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkw1081

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

Autores: Fengbin Wang, Diana P Baquero, Zhangli Su, Tomasz Osinski, David Prangishvili, Edward H Egelman, Mart Krupovic
Publicado en: Virus Evolution, Edición 6/1, 2020, ISSN 2057-1577
Editor: oxford university press
DOI: 10.1093/ve/veaa023

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

Autores: Ying Liu, Tomasz Osinski, Fengbin Wang, Mart Krupovic, Stefan Schouten, Peter Kasson, David Prangishvili, Edward H. Egelman
Publicado en: Nature Communications, Edición 9/1, 2018, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-018-05684-6

The enigmatic archaeal virosphere

Autores: David Prangishvili, Dennis H. Bamford, Patrick Forterre, Jaime Iranzo, Eugene V. Koonin, Mart Krupovic
Publicado en: Nature Reviews Microbiology, Edición 15/12, 2017, Página(s) 724-739, ISSN 1740-1526
Editor: Nature Publishing Group
DOI: 10.1038/nrmicro.2017.125

Integrated mobile genetic elements in Thaumarchaeota

Autores: Mart Krupovic, Kira S. Makarova, Yuri I. Wolf, Sofia Medvedeva, David Prangishvili, Patrick Forterre, Eugene V. Koonin
Publicado en: Environmental Microbiology, Edición 21/6, 2019, Página(s) 2056-2078, ISSN 1462-2912
Editor: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14564

Numerous cultivated and uncultivated viruses encode ribosomal proteins

Autores: Carolina M. Mizuno, Charlotte Guyomar, Simon Roux, Régis Lavigne, Francisco Rodriguez-Valera, Matthew B. Sullivan, Reynald Gillet, Patrick Forterre, Mart Krupovic
Publicado en: Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-08672-6

A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea

Autores: Ying Liu, Sonoko Ishino, Yoshizumi Ishino, Gérard Pehau-Arnaudet, Mart Krupovic, David Prangishvili
Publicado en: Journal of Virology, Edición 91/13, 2017, ISSN 0022-538X
Editor: American Society for Microbiology
DOI: 10.1128/JVI.00589-17

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

Autores: Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding
Publicado en: BMC Bioinformatics, Edición 20/1, 2019, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-019-3019-7

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

Autores: 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
Publicado en: Viruses, Edición 10/5, 2018, Página(s) 256, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v10050256

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

Autores: Sofia Medvedeva, Ying Liu, Eugene V. Koonin, Konstantin Severinov, David Prangishvili, Mart Krupovic
Publicado en: Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-13205-2

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

Autores: Ying Liu, David Brandt, Sonoko Ishino, Yoshizumi Ishino, Eugene V. Koonin, Jörn Kalinowski, Mart Krupovic, David Prangishvili
Publicado en: Environmental Microbiology, Edición 21/6, 2019, Página(s) 2002-2014, ISSN 1462-2912
Editor: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14479

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

Autores: 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
Publicado en: Systematic Biology, Edición 69/1, 2019, Página(s) 110-123, ISSN 1063-5157
Editor: Taylor & Francis
DOI: 10.1093/sysbio/syz036

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

Autores: Jan-Philipp Schwarzhans, Tobias Luttermann, Daniel Wibberg, Anika Winkler, Wolfgang Hübner, Thomas Huser, Jörn Kalinowski, Karl Friehs
Publicado en: Frontiers in Microbiology, Edición 8, 2017, ISSN 1664-302X
Editor: Frontiers Media
DOI: 10.3389/fmicb.2017.00780

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

Autores: 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
Publicado en: Frontiers in Microbiology, Edición 10, 2019, ISSN 1664-302X
Editor: Frontiers Media
DOI: 10.3389/fmicb.2019.02376

Clustering huge protein sequence sets in linear time

Autores: Martin Steinegger, Johannes Söding
Publicado en: Nature Communications, Edición 9/1, 2018, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-018-04964-5

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

Autores: Milot Mirdita, Martin Steinegger, Johannes Söding
Publicado en: Bioinformatics, Edición 35/16, 2019, Página(s) 2856-2858, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/bty1057

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

Autores: Eli Levy Karin, Milot Mirdita, Johannes Söding
Publicado en: Microbiome, Edición 8/1, 2020, ISSN 2049-2618
Editor: Springer Nature
DOI: 10.1186/s40168-020-00808-x

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

Autores: 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
Publicado en: Acta Crystallographica Section D Structural Biology, Edición 75/11, 2019, Página(s) 1028-1039, ISSN 2059-7983
Editor: International Union of Crystallography
DOI: 10.1107/s2059798319013330

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

Autores: Daniel Bruce, Emily Cardew, Stefanie Freitag-Pohl, Ehmke Pohl
Publicado en: Journal of Visualized Experiments, Edición 144, 2019, ISSN 1940-087X
Editor: MYJoVE Corporation
DOI: 10.3791/58666

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Autores: 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
Publicado en: Nature Biotechnology, Edición 37/1, 2019, Página(s) 29-37, ISSN 1087-0156
Editor: Nature Publishing Group
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

Autores: Magdalena Plotka, Malgorzata Kapusta, Sebastian Dorawa, Anna-Karina Kaczorowska, Tadeusz Kaczorowski
Publicado en: Viruses, Edición 11/7, 2019, Página(s) 657, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v11070657

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

Autores: Ruth-Anne Sandaa, Julia E. Storesund, Emily Olesin, Maria Lund Paulsen, Aud Larsen, Gunnar Bratbak, Jessica Ray
Publicado en: Viruses, Edición 10/12, 2018, Página(s) 715, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v10120715

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

Autores: Martin Steinegger, Milot Mirdita, Johannes Söding
Publicado en: Nature Methods, Edición 16/7, 2019, Página(s) 603-606, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/s41592-019-0437-4

New CRISPR-Cas9 vectors for genetic modifications of Bacillus species

Autores: Anna A Toymentseva, Josef Altenbuchner
Publicado en: FEMS Microbiology Letters, Edición 366/1, 2018, ISSN 1574-6968
Editor: Oxford University Press
DOI: 10.1093/femsle/fny284

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

Autores: Diana P. Baquero, Patrizia Contursi, Monica Piochi, Simonetta Bartolucci, Ying Liu, Virginija Cvirkaite-Krupovic, David Prangishvili, Mart Krupovic
Publicado en: The ISME Journal, 2020, ISSN 1751-7362
Editor: Nature Publishing Group
DOI: 10.1038/s41396-020-0653-z

A packing for A-form DNA in an icosahedral virus

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, Edición 116/45, 2019, Página(s) 22591-22597, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.1908242116

Clustering huge protein sequence sets in linear time.

Autores: Martin Steinegger and Johannes Soeding
Publicado en: Nature Communications, Edición 9(1), 2018, Página(s) 2542
Editor: Nature press
DOI: 10.1101/104034

Les virus à la source

Autores: Arnthor Ævarsson
Publicado en: La Recherche, 2018, ISSN 0029-5671
Editor: Societe d'Editions Scientifiques

Posters

Autores: 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.
Publicado en: FEBS Open Bio, Edición 9/S1, 2019, Página(s) 65-431, ISSN 2211-5463
Editor: Elsevier BV
DOI: 10.1002/2211-5463.12675

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