David Paez-Espino
Joint Genome Institute
63 Papers
46 Citations
David Paez-Espino is an academic researcher from Joint Genome Institute. The author has contributed to research in topics: Metagenomics & Biology. The author has an hindex of 24, co-authored 52 publications. Previous affiliations of David Paez-Espino include University of California & Lawrence Berkeley National Laboratory.
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Papers
Uncovering Earth’s virome
David Paez-Espino,Emiley A. Eloe-Fadrosh,Georgios A. Pavlopoulos,Alex D. Thomas,Marcel Huntemann,Natalia Mikhailova,Edward M. Rubin,Edward M. Rubin,Natalia Ivanova,Nikos C. Kyrpides +9 more
TL;DR: Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups, and detailed insight into viral habitat distribution and host–virus interactions is provided.
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes.
Lucas B. Harrington,David Burstein,Janice S. Chen,David Paez-Espino,Enbo Ma,Isaac P. Witte,Joshua C Cofsky,Nikos C. Kyrpides,Jillian F. Banfield,Jennifer A. Doudna +9 more
TL;DR: Metagenomic data show that multiple CRISPR-Cas14 systems evolved independently and suggest a potential evolutionary origin of single-effector CRISpr-based adaptive immunity, as well as a fast and high-fidelity nucleic acid detection system that enabled detection ofsingle-nucleotide polymorphisms.
A genomic catalog of Earth’s microbiomes
Stephen Nayfach,Simon Roux,Rekha Seshadri,Daniel W. Udwary,Neha Varghese,Frederik Schulz,Dongying Wu,David Paez-Espino,I-Min Chen,Marcel Huntemann,Krishna Palaniappan,Joshua Ladau,Supratim Mukherjee,T. B. K. Reddy,Torben Nielsen,Edward Kirton,José P. Faria,Janaka N. Edirisinghe,Christopher S. Henry,Sean P. Jungbluth,Dylan Chivian,Paramvir S. Dehal,Elisha M. Wood-Charlson,Adam P. Arkin,Susannah G. Tringe,Axel Visel,Tanja Woyke,Nigel J Mouncey,Natalia Ivanova,Nikos C. Kyrpides,Emiley A. Eloe-Fadrosh +30 more
TL;DR: The utility of this collection of >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans is demonstrated for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses.
Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
Rekha Seshadri,Sinead C. Leahy,Graeme T. Attwood,Koon Hoong Teh,Suzanne C. Lambie,Adrian L. Cookson,Emiley A. Eloe-Fadrosh,Georgios A. Pavlopoulos,Michalis Hadjithomas,Neha Varghese,David Paez-Espino,Rechelle Perry,Gemma Henderson,Christopher J. Creevey,Nicolas Terrapon,Nicolas Terrapon,Pascal Lapébie,Pascal Lapébie,Elodie Drula,Elodie Drula,Vincent Lombard,Vincent Lombard,Edward M. Rubin,Nikos C. Kyrpides,Bernard Henrissat,Bernard Henrissat,Bernard Henrissat,Tanja Woyke,Natalia Ivanova,William J. Kelly +29 more
TL;DR: Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress.
Minimum information about an uncultivated virus genome (MIUVIG)
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,Arvind Varsani,Clara Amid,Ramy K. Aziz,Seth R. Bordenstein,Peer Bork,Mya Breitbart,Guy Cochrane,Rebecca A. Daly,Christelle Desnues,Melissa B. Duhaime,Joanne B. Emerson,François Enault,Jed A. Fuhrman,Pascal Hingamp,Philip Hugenholtz,Bonnie L. Hurwitz,Natalia Ivanova,Jessica M. Labonté,Kyung Bum Lee,Rex R. Malmstrom,Manuel Martinez-Garcia,Ilene Karsch Mizrachi,Hiroyuki Ogata,David Paez-Espino,Marie-Agnès Petit,Catherine Putonti,Thomas Rattei,Alejandro Reyes,Francisco Rodriguez-Valera,Karyna Rosario,Lynn M. Schriml,Frederik Schulz,Grieg F. Steward,Matthew B. Sullivan,Shinichi Sunagawa,Curtis A. Suttle,Ben Temperton,Susannah G. Tringe,Rebecca Vega Thurber,Nicole S. Webster,Nicole S. Webster,Katrine Whiteson,Steven W. Wilhelm,K. Eric Wommack,Tanja Woyke,Kelly C. Wrighton,Pelin Yilmaz,Takashi Yoshida,Mark J. Young,Natalya Yutin,Lisa Zeigler Allen,Lisa Zeigler Allen,Nikos C. Kyrpides,Emiley A. Eloe-Fadrosh +63 more
TL;DR: The MIUViG (Minimum Information about an Uncultivated Virus Genome) as mentioned in this paper standard was developed within the Genomic Standards Consortium framework and includes virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction.