Literature DB >> 31748692

Detecting contamination in viromes using ViromeQC.

Moreno Zolfo1, Federica Pinto1, Francesco Asnicar1, Paolo Manghi1, Adrian Tett1, Frederic D Bushman2, Nicola Segata3.   

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Year:  2019        PMID： 31748692     DOI： 10.1038/s41587-019-0334-5

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  27 in total

1.  Cenote-Taker 2 democratizes virus discovery and sequence annotation.

Authors:  Michael J Tisza; Anna K Belford; Guillermo Domínguez-Huerta; Benjamin Bolduc; Christopher B Buck
Journal:  Virus Evol       Date:  2020-12-30

2.  grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories.

Authors:  Louis J Taylor; Arwa Abbas; Frederic D Bushman
Journal:  Bioinformatics       Date:  2020-06-01       Impact factor: 6.937

Review 3.  Mutualistic interplay between bacteriophages and bacteria in the human gut.

Authors:  Andrey N Shkoporov; Christopher J Turkington; Colin Hill
Journal:  Nat Rev Microbiol       Date:  2022-06-30       Impact factor: 60.633

4.  RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data.

Authors:  Xubo Tang; Jiayu Shang; Yanni Sun
Journal:  Brief Bioinform       Date:  2022-03-10       Impact factor: 11.622

5.  Viral biogeography of the mammalian gut and parenchymal organs.

Authors:  Andrey N Shkoporov; Stephen R Stockdale; Aonghus Lavelle; Ivanela Kondova; Cara Heuston; Aditya Upadrasta; Ekaterina V Khokhlova; Imme van der Kamp; Boudewijn Ouwerling; Lorraine A Draper; Jan A M Langermans; R Paul Ross; Colin Hill
Journal:  Nat Microbiol       Date:  2022-08-02       Impact factor: 30.964

6.  Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.

Authors:  Francesco Beghini; Lauren J McIver; Aitor Blanco-Míguez; Leonard Dubois; Francesco Asnicar; Sagun Maharjan; Ana Mailyan; Paolo Manghi; Matthias Scholz; Andrew Maltez Thomas; Mireia Valles-Colomer; George Weingart; Yancong Zhang; Moreno Zolfo; Curtis Huttenhower; Eric A Franzosa; Nicola Segata
Journal:  Elife       Date:  2021-05-04       Impact factor: 8.140

7.  Discovery of several thousand highly diverse circular DNA viruses.

Authors:  Michael J Tisza; Diana V Pastrana; Nicole L Welch; Brittany Stewart; Alberto Peretti; Gabriel J Starrett; Yuk-Ying S Pang; Siddharth R Krishnamurthy; Patricia A Pesavento; David H McDermott; Philip M Murphy; Jessica L Whited; Bess Miller; Jason Brenchley; Stephan P Rosshart; Barbara Rehermann; John Doorbar; Blake A Ta'ala; Olga Pletnikova; Juan C Troncoso; Susan M Resnick; Ben Bolduc; Matthew B Sullivan; Arvind Varsani; Anca M Segall; Christopher B Buck
Journal:  Elife       Date:  2020-02-04       Impact factor: 8.140

8.  Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.

Authors:  Stephen Nayfach; David Páez-Espino; Lee Call; Soo Jen Low; Hila Sberro; Natalia N Ivanova; Amy D Proal; Michael A Fischbach; Ami S Bhatt; Philip Hugenholtz; Nikos C Kyrpides
Journal:  Nat Microbiol       Date:  2021-06-24       Impact factor: 17.745

9.  Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly.

Authors:  Nicolai Karcher; Eleonora Nigro; Mireia Valles-Colomer; Willem M de Vos; Nicola Segata; Michal Punčochář; Aitor Blanco-Míguez; Matteo Ciciani; Paolo Manghi; Moreno Zolfo; Fabio Cumbo; Serena Manara; Davide Golzato; Anna Cereseto; Manimozhiyan Arumugam; Thi Phuong Nam Bui; Hanne L P Tytgat
Journal:  Genome Biol       Date:  2021-07-14       Impact factor: 13.583

10.  Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation.

Authors:  Akbar Adjie Pratama; Benjamin Bolduc; Ahmed A Zayed; Zhi-Ping Zhong; Jiarong Guo; Dean R Vik; Maria Consuelo Gazitúa; James M Wainaina; Simon Roux; Matthew B Sullivan
Journal:  PeerJ       Date:  2021-06-14       Impact factor: 2.984
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