Virus-X: Viral Metagenomics for Innovation Value

Risultati finali

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

Pubblicazioni

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

Autori: Martin Steinegger, Johannes Söding
Pubblicato in: Nature Biotechnology, Numero 35, 2017, Pagina/e 1026–1028, ISSN 1087-0156
Editore: 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

Autori: Magdalena Plotka, Enea Sancho-Vaello, Sebastian Dorawa, Anna-Karina Kaczorowska, Lukasz P. Kozlowski, Tadeusz Kaczorowski, Kornelius Zeth
Pubblicato in: Scientific Reports, Numero 9/1, 2019, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-018-37417-6

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

Autori: Clovis Galiez, Matthias Siebert, François Enault, Jonathan Vincent, Johannes Söding
Pubblicato in: Bioinformatics, Numero 33/19, 2017, Pagina/e 3113-3114, ISSN 1367-4803
Editore: 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

Autori: Yuchen Wang, Beibei Chen, Mengzhuo Cao, Linshan Sima, David Prangishvili, Xiangdong Chen, Mart Krupovic
Pubblicato in: Journal of General Virology, Numero 99/3, 2018, Pagina/e 416-421, ISSN 0022-1317
Editore: Society for General Microbiology
DOI: 10.1099/jgv.0.001009

Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging

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

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Autori: 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
Pubblicato in: https://hal.archives-ouvertes.fr/hal-01982207, Numero 10, 2019, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.3929/ethz-b-000315358

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

Autori: Mart Krupovic, Virginija Cvirkaite-Krupovic, Jaime Iranzo, David Prangishvili, Eugene V. Koonin
Pubblicato in: Virus Research, Numero 244, 2018, Pagina/e 181-193, ISSN 0168-1702
Editore: Elsevier BV
DOI: 10.1016/j.virusres.2017.11.025

Is the Virus Important? And Some Other Questions

Autori: Ruth-Anne Sandaa, Gunnar Bratbak
Pubblicato in: Viruses, Numero 10/8, 2018, Pagina/e 442, ISSN 1999-4915
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v10080442

Uniclust databases of clustered and deeply annotated protein sequences and alignments

Autori: Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria J. Martin, Johannes Söding, Martin Steinegger
Pubblicato in: Nucleic Acids Research, Numero 45/D1, 2017, Pagina/e D170-D176, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkw1081

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

Autori: Fengbin Wang, Diana P Baquero, Zhangli Su, Tomasz Osinski, David Prangishvili, Edward H Egelman, Mart Krupovic
Pubblicato in: Virus Evolution, Numero 6/1, 2020, ISSN 2057-1577
Editore: oxford university press
DOI: 10.1093/ve/veaa023

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

Autori: Ying Liu, Tomasz Osinski, Fengbin Wang, Mart Krupovic, Stefan Schouten, Peter Kasson, David Prangishvili, Edward H. Egelman
Pubblicato in: Nature Communications, Numero 9/1, 2018, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-018-05684-6

The enigmatic archaeal virosphere

Autori: David Prangishvili, Dennis H. Bamford, Patrick Forterre, Jaime Iranzo, Eugene V. Koonin, Mart Krupovic
Pubblicato in: Nature Reviews Microbiology, Numero 15/12, 2017, Pagina/e 724-739, ISSN 1740-1526
Editore: Nature Publishing Group
DOI: 10.1038/nrmicro.2017.125

Integrated mobile genetic elements in Thaumarchaeota

Autori: Mart Krupovic, Kira S. Makarova, Yuri I. Wolf, Sofia Medvedeva, David Prangishvili, Patrick Forterre, Eugene V. Koonin
Pubblicato in: Environmental Microbiology, Numero 21/6, 2019, Pagina/e 2056-2078, ISSN 1462-2912
Editore: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14564

Numerous cultivated and uncultivated viruses encode ribosomal proteins

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

A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea

Autori: Ying Liu, Sonoko Ishino, Yoshizumi Ishino, Gérard Pehau-Arnaudet, Mart Krupovic, David Prangishvili
Pubblicato in: Journal of Virology, Numero 91/13, 2017, ISSN 0022-538X
Editore: American Society for Microbiology
DOI: 10.1128/JVI.00589-17

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

Autori: Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding
Pubblicato in: BMC Bioinformatics, Numero 20/1, 2019, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-019-3019-7

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

Autori: 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
Pubblicato in: Viruses, Numero 10/5, 2018, Pagina/e 256, ISSN 1999-4915
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v10050256

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

Autori: Sofia Medvedeva, Ying Liu, Eugene V. Koonin, Konstantin Severinov, David Prangishvili, Mart Krupovic
Pubblicato in: Nature Communications, Numero 10/1, 2019, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-019-13205-2

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

Autori: Ying Liu, David Brandt, Sonoko Ishino, Yoshizumi Ishino, Eugene V. Koonin, Jörn Kalinowski, Mart Krupovic, David Prangishvili
Pubblicato in: Environmental Microbiology, Numero 21/6, 2019, Pagina/e 2002-2014, ISSN 1462-2912
Editore: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14479

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

Autori: 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
Pubblicato in: Systematic Biology, Numero 69/1, 2019, Pagina/e 110-123, ISSN 1063-5157
Editore: Taylor & Francis
DOI: 10.1093/sysbio/syz036

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

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

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

Autori: 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
Pubblicato in: Frontiers in Microbiology, Numero 10, 2019, ISSN 1664-302X
Editore: Frontiers Media
DOI: 10.3389/fmicb.2019.02376

Clustering huge protein sequence sets in linear time

Autori: Martin Steinegger, Johannes Söding
Pubblicato in: Nature Communications, Numero 9/1, 2018, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-018-04964-5

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

Autori: Milot Mirdita, Martin Steinegger, Johannes Söding
Pubblicato in: Bioinformatics, Numero 35/16, 2019, Pagina/e 2856-2858, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/bty1057

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

Autori: Eli Levy Karin, Milot Mirdita, Johannes Söding
Pubblicato in: Microbiome, Numero 8/1, 2020, ISSN 2049-2618
Editore: Springer Nature
DOI: 10.1186/s40168-020-00808-x

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

Autori: 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
Pubblicato in: Acta Crystallographica Section D Structural Biology, Numero 75/11, 2019, Pagina/e 1028-1039, ISSN 2059-7983
Editore: 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

Autori: Daniel Bruce, Emily Cardew, Stefanie Freitag-Pohl, Ehmke Pohl
Pubblicato in: Journal of Visualized Experiments, Numero 144, 2019, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/58666

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Autori: 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
Pubblicato in: Nature Biotechnology, Numero 37/1, 2019, Pagina/e 29-37, ISSN 1087-0156
Editore: 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

Autori: Magdalena Plotka, Malgorzata Kapusta, Sebastian Dorawa, Anna-Karina Kaczorowska, Tadeusz Kaczorowski
Pubblicato in: Viruses, Numero 11/7, 2019, Pagina/e 657, ISSN 1999-4915
Editore: 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

Autori: Ruth-Anne Sandaa, Julia E. Storesund, Emily Olesin, Maria Lund Paulsen, Aud Larsen, Gunnar Bratbak, Jessica Ray
Pubblicato in: Viruses, Numero 10/12, 2018, Pagina/e 715, ISSN 1999-4915
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v10120715

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

Autori: Martin Steinegger, Milot Mirdita, Johannes Söding
Pubblicato in: Nature Methods, Numero 16/7, 2019, Pagina/e 603-606, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-019-0437-4

New CRISPR-Cas9 vectors for genetic modifications of Bacillus species

Autori: Anna A Toymentseva, Josef Altenbuchner
Pubblicato in: FEMS Microbiology Letters, Numero 366/1, 2018, ISSN 1574-6968
Editore: Oxford University Press
DOI: 10.1093/femsle/fny284

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

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

A packing for A-form DNA in an icosahedral virus

Autori: 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
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 116/45, 2019, Pagina/e 22591-22597, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.1908242116

Clustering huge protein sequence sets in linear time.

Autori: Martin Steinegger and Johannes Soeding
Pubblicato in: Nature Communications, Numero 9(1), 2018, Pagina/e 2542
Editore: Nature press
DOI: 10.1101/104034

Les virus à la source

Autori: Arnthor Ævarsson
Pubblicato in: La Recherche, 2018, ISSN 0029-5671
Editore: Societe d'Editions Scientifiques

Posters

Autori: 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.
Pubblicato in: FEBS Open Bio, Numero 9/S1, 2019, Pagina/e 65-431, ISSN 2211-5463
Editore: Elsevier BV
DOI: 10.1002/2211-5463.12675

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