Works by Paez-Espino, David

Results: 35

Erratum to: The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

Published in:

Standards in Genomic Sciences, 2016, v. 11, n. 1, p. 1, doi. 10.1186/s40793-016-0148-8

By:

Huntemann, Marcel;
Ivanova, Natalia;
Mavromatis, Konstantinos;
Tripp, H.;
Paez-Espino, David;
Palaniappan, Krishnaveni;
Szeto, Ernest;
Pillay, Manoj;
Chen, I-Min;
Pati, Amrita;
Nielsen, Torben;
Markowitz, Victor;
Kyrpides, Nikos

Publication type:

Article

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4).

Published in:

Standards in Genomic Sciences, 2016, v. 11, n. 1, p. 1, doi. 10.1186/s40793-016-0138-x

By:

Huntemann, Marcel;
Ivanova, Natalia;
Mavromatis, Konstantinos;
Tripp, H.;
Paez-Espino, David;
Tennessen, Kristin;
Palaniappan, Krishnaveni;
Szeto, Ernest;
Pillay, Manoj;
Chen, I-Min;
Pati, Amrita;
Nielsen, Torben;
Markowitz, Victor;
Kyrpides, Nikos

Publication type:

Article

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

Published in:

Standards in Genomic Sciences, 2015, v. 10, n. 1, p. 1, doi. 10.1186/s40793-015-0077-y

By:

Huntemann, Marcel;
Ivanova, Natalia;
Mavromatis, Konstantinos;
Tripp, H.;
Paez-Espino, David;
Palaniappan, Krishnaveni;
Szeto, Ernest;
Pillay, Manoj;
Chen, I-Min;
Pati, Amrita;
Nielsen, Torben;
Markowitz, Victor;
Kyrpides, Nikos

Publication type:

Article

A thermostable Cas9 with increased lifetime in human plasma.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01408-4

By:

Harrington, Lucas B.;
Paez-Espino, David;
Staahl, Brett T.;
Chen, Janice S.;
Ma, Enbo;
Kyrpides, Nikos C.;
Doudna, Jennifer A.

Publication type:

Article

VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-57500-7

By:

Zheng, Kaiyang;
Sun, Jianhua;
Liang, Yantao;
Kong, Liangliang;
Paez-Espino, David;
Mcminn, Andrew;
Wang, Min

Publication type:

Article

Pavlovian‐Type Learning in Environmental Bacteria: Regulation of Herbicide Resistance by Arsenic in Pseudomonas putida.

Published in:

Environmental Microbiology, 2024, v. 26, n. 12, p. 1, doi. 10.1111/1462-2920.70012

By:

Paez‐Espino, David;
Durante‐Rodríguez, Gonzalo;
Fernandes, Elena Alonso;
Carmona, Manuel;
de Lorenzo, Victor

Publication type:

Article

ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic.

Published in:

Environmental Microbiology, 2020, v. 22, n. 6, p. 2230, doi. 10.1111/1462-2920.14991

By:

Páez‐Espino, A. David;
Nikel, Pablo I.;
Chavarría, Max;
Lorenzo, Víctor

Publication type:

Article

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology.

Published in:

Environmental Microbiology, 2016, v. 18, n. 4, p. 1122, doi. 10.1111/1462-2920.13095

By:

Oulas, Anastasis;
Polymenakou, Paraskevi N.;
Seshadri, Rekha;
Tripp, H. James;
Mandalakis, Manolis;
Paez ‐ Espino, A. David;
Pati, Amrita;
Chain, Patrick;
Nomikou, Paraskevi;
Carey, Steven;
Kilias, Stephanos;
Christakis, Christos;
Kotoulas, Georgios;
Magoulas, Antonios;
Ivanova, Natalia N.;
Kyrpides, Nikos C.

Publication type:

Article

The two paralogue phoN (phosphinothricin acetyl transferase) genes of P seudomonas putida encode functionally different proteins.

Published in:

Environmental Microbiology, 2015, v. 17, n. 9, p. 3330, doi. 10.1111/1462-2920.12798

By:

Páez ‐ Espino, A. David;
Chavarría, Max;
Lorenzo, Víctor

Publication type:

Article

Functional coexistence of twin arsenic resistance systems in P seudomonas putida KT2440.

Published in:

Environmental Microbiology, 2015, v. 17, n. 1, p. 229, doi. 10.1111/1462-2920.12464

By:

Páez ‐ Espino, A. David;
Durante ‐ Rodríguez, Gonzalo;
Lorenzo, Víctor

Publication type:

Article

Monitoring biodegradative enzymes with nanobodies raised in Camelus dromedarius with mixtures of catabolic proteins.

Published in:

Environmental Microbiology, 2011, v. 13, n. 4, p. 960, doi. 10.1111/j.1462-2920.2010.02401.x

By:

Zafra, Olga;
Fraile, Sofía;
Gutiérrez, Carlos;
Haro, Amparo;
Páez-Espino, A. David;
Jiménez, Jose I.;
de Lorenzo, Víctor

Publication type:

Article

Author Correction: A genomic catalog of Earth's microbiomes.

Published in:

2021

By:

Nayfach, Stephen;
Roux, Simon;
Seshadri, Rekha;
Udwary, Daniel;
Varghese, Neha;
Schulz, Frederik;
Wu, Dongying;
Paez-Espino, David;
Chen, I-Min;
Huntemann, Marcel;
Palaniappan, Krishna;
Ladau, Joshua;
Mukherjee, Supratim;
Reddy, T. B. K.;
Nielsen, Torben;
Kirton, Edward;
Faria, José P.;
Edirisinghe, Janaka N.;
Henry, Christopher S.;
Jungbluth, Sean P.

Publication type:

Correction Notice

Publisher Correction: A genomic catalog of Earth's microbiomes.

Published in:

2021

By:

Nayfach, Stephen;
Roux, Simon;
Seshadri, Rekha;
Udwary, Daniel;
Varghese, Neha;
Schulz, Frederik;
Wu, Dongying;
Paez-Espino, David;
Chen, I-Min;
Huntemann, Marcel;
Palaniappan, Krishna;
Ladau, Joshua;
Mukherjee, Supratim;
Reddy, T. B. K.;
Nielsen, Torben;
Kirton, Edward;
Faria, José P.;
Edirisinghe, Janaka N.;
Henry, Christopher S.;
Jungbluth, Sean P.

Publication type:

Correction Notice

A genomic catalog of Earth's microbiomes.

Published in:

Nature Biotechnology, 2021, v. 39, n. 4, p. 499, doi. 10.1038/s41587-020-0718-6

By:

Nayfach, Stephen;
Roux, Simon;
Seshadri, Rekha;
Udwary, Daniel;
Varghese, Neha;
Schulz, Frederik;
Wu, Dongying;
Paez-Espino, David;
Chen, I-Min;
Huntemann, Marcel;
Palaniappan, Krishna;
Ladau, Joshua;
Mukherjee, Supratim;
Reddy, T. B. K.;
Nielsen, Torben;
Kirton, Edward;
Faria, José P.;
Edirisinghe, Janaka N.;
Henry, Christopher S.;
Jungbluth, Sean P.

Publication type:

Article

Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

Published in:

Nature Biotechnology, 2018, v. 36, n. 4, p. 368, doi. 10.1038/nbt0418-368c

By:

Mukherjee, Supratim;
Seshadri, Rekha;
Varghese, Neha J;
Eloe-Fadrosh, Emiley A;
Meier-Kolthoff, Jan P;
Göker, Markus;
Coates, R Cameron;
Hadjithomas, Michalis;
Pavlopoulos, Georgios A;
Paez-Espino, David;
Yoshikuni, Yasuo;
Visel, Axel;
Whitman, William B;
Garrity, George M;
Eisen, Jonathan A;
Hugenholtz, Philip;
Pati, Amrita;
Ivanova, Natalia N;
Woyke, Tanja;
Klenk, Hans-Peter

Publication type:

Article

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.

Published in:

Nature Biotechnology, 2018, v. 36, n. 4, p. 359, doi. 10.1038/nbt.4110

By:

Seshadri, Rekha;
Leahy, Sinead C;
Attwood, Graeme T;
Teh, Koon Hoong;
Lambie, Suzanne C;
Cookson, Adrian L;
Eloe-Fadrosh, Emiley A;
Pavlopoulos, Georgios A;
Hadjithomas, Michalis;
Varghese, Neha J;
Paez-Espino, David;
Perry, Rechelle;
Henderson, Gemma;
Creevey, Christopher J;
Terrapon, Nicolas;
Lapebie, Pascal;
Drula, Elodie;
Lombard, Vincent;
Rubin, Edward;
Kyrpides, Nikos C

Publication type:

Article

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

Published in:

Nature Biotechnology, 2017, v. 35, n. 7, p. 676, doi. 10.1038/nbt.3886

By:

Mukherjee, Supratim;
Seshadri, Rekha;
Varghese, Neha J;
Eloe-Fadrosh, Emiley A;
Meier-Kolthoff, Jan P;
Göker, Markus;
Coates, R Cameron;
Hadjithomas, Michalis;
Pavlopoulos, Georgios A;
Paez-Espino, David;
Yoshikuni, Yasuo;
Visel, Axel;
Whitman, William B;
Garrity, George M;
Eisen, Jonathan A;
Hugenholtz, Philip;
Pati, Amrita;
Ivanova, Natalia N;
Woyke, Tanja;
Klenk, Hans-Peter

Publication type:

Article

Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 3, p. 1, doi. 10.1371/journal.pcbi.1008841

By:

Pavlova, Yekaterina S.;
Paez-Espino, David;
Morozov, Andrew Yu.;
Belalov, Ilya S.

Publication type:

Article

VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families.

Published in:

Bioinformatics, 2021, v. 37, n. 13, p. 1805, doi. 10.1093/bioinformatics/btab026

By:

Pons, Joan Carles;
Paez-Espino, David;
Riera, Gabriel;
Ivanova, Natalia;
Kyrpides, Nikos C;
Llabrés, Mercè

Publication type:

Article

Investigation of recombination-intense viral groups and their genes in the Earth’s virome.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-29272-2

By:

Meier-Kolthoff, Jan P.;
Uchiyama, Jumpei;
Yahara, Hiroko;
Paez-Espino, David;
Yahara, Koji

Publication type:

Article

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes.

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D678, doi. 10.1093/nar/gky1127

By:

Paez-Espino, David;
Roux, Simon;
Chen, I-Min A;
Palaniappan, Krishna;
Ratner, Anna;
Chu, Ken;
Huntemann, Marcel;
Reddy, T B K;
Pons, Joan Carles;
Llabrés, Mercè;
Eloe-Fadrosh, Emiley A;
Ivanova, Natalia N;
Kyrpides, Nikos C

Publication type:

Article

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Published in:

Nucleic Acids Research, 2017, v. 45, n. D1, p. D457, doi. 10.1093/nar/gkw1030

By:

Paez-Espino, David;
Chen, I.-Min A.;
Palaniappan, Krishna;
Ratner, Anna;
Ken Chu;
Szeto, Ernest;
Pillay, Manoj;
Jinghua Huang;
Markowitz, Victor M.;
Nielsen, Torben;
Huntemann, Marcel;
Reddy, T. B. K.;
Pavlopoulos, Georgios A.;
Sullivan, Matthew B.;
Campbell, Barbara J.;
Feng Chen;
McMahon, Katherine;
Hallam, Steve J.;
Denef, Vincent;
Cavicchioli, Ricardo

Publication type:

Article

The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes.

Published in:

Nucleic Acids Research, 2013, v. 41, p. D666, doi. 10.1093/nar/gks1119

By:

Silva-Rocha, Rafael;
Martínez-García, Esteban;
Calles, Belén;
Chavarría, Max;
Arce-Rodríguez, Alejandro;
de las Heras, Aitor;
Páez-Espino, A. David;
Durante-Rodríguez, Gonzalo;
Juhyun Kim;
Nikel, Pablo I.;
Platero, Raúl;
de Lorenzo, Víctor

Publication type:

Article

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.

Published in:

Nature Communications, 2016, v. 7, n. 1, p. 10476, doi. 10.1038/ncomms10476

By:

Eloe-Fadrosh, Emiley A.;
Paez-Espino, David;
Jarett, Jessica;
Dunfield, Peter F.;
Hedlund, Brian P.;
Dekas, Anne E.;
Grasby, Stephen E.;
Brady, Allyson L.;
Dong, Hailiang;
Briggs, Brandon R.;
Li, Wen-Jun;
Goudeau, Danielle;
Malmstrom, Rex;
Pati, Amrita;
Pett-Ridge, Jennifer;
Rubin, Edward M.;
Woyke, Tanja;
Kyrpides, Nikos C.;
Ivanova, Natalia N.

Publication type:

Article

Strong bias in the bacterial CRISPR elements that confer immunity to phage.

Published in:

Nature Communications, 2013, v. 4, n. 2, p. 1430, doi. 10.1038/ncomms2440

By:

Paez-Espino, David;
Morovic, Wesley;
Sun, Christine L.;
Thomas, Brian C.;
Ueda, Ken-ichi;
Stahl, Buffy;
Barrangou, Rodolphe;
Banfield, Jillian F.

Publication type:

Article

Microbial responses to environmental arsenic.

Published in:

BioMetals, 2009, v. 22, n. 1, p. 117, doi. 10.1007/s10534-008-9195-y

By:

David Páez-Espino;
Javier Tamames;
Víctor de Lorenzo;
David Cánovas

Publication type:

Article

Remarkably coherent population structure for a dominant Antarctic Chlorobium species.

Published in:

Microbiome, 2021, v. 9, n. 1, p. 1, doi. 10.1186/s40168-021-01173-z

By:

Panwar, Pratibha;
Allen, Michelle A.;
Williams, Timothy J.;
Haque, Sabrina;
Brazendale, Sarah;
Hancock, Alyce M.;
Paez-Espino, David;
Cavicchioli, Ricardo

Publication type:

Article

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community.

Published in:

Microbiome, 2020, v. 8, n. 1, p. 1, doi. 10.1186/s40168-020-00889-8

By:

Panwar, Pratibha;
Allen, Michelle A.;
Williams, Timothy J.;
Hancock, Alyce M.;
Brazendale, Sarah;
Bevington, James;
Roux, Simon;
Páez-Espino, David;
Nayfach, Stephen;
Berg, Maureen;
Schulz, Frederik;
Chen, I-Min A.;
Huntemann, Marcel;
Shapiro, Nicole;
Kyrpides, Nikos C.;
Woyke, Tanja;
Eloe-Fadrosh, Emiley A.;
Cavicchioli, Ricardo

Publication type:

Article

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis.

Published in:

Advances in Bioinformatics, 2017, p. 1, doi. 10.1155/2017/1278932

By:

Pavlopoulos, Georgios A.;
Paez-Espino, David;
Kyrpides, Nikos C.;
Iliopoulos, Ioannis

Publication type:

Article

A Bifan Motif Shaped by ArsR1, ArsR2, and Their Cognate Promoters Frames Arsenic Tolerance of Pseudomonas putida.

Published in:

Frontiers in Microbiology, 2021, v. 11, p. N.PAG, doi. 10.3389/fmicb.2021.641440

By:

Durante-Rodríguez, Gonzalo;
Páez-Espino, David;
de Lorenzo, Víctor

Publication type:

Article

Diversity, evolution, and classification of virophages uncovered through global metagenomics.

Published in:

Microbiome, 2019, v. 7, n. 1, p. 1, doi. 10.1186/s40168-019-0768-5

By:

Paez-Espino, David;
Zhou, Jinglie;
Roux, Simon;
Nayfach, Stephen;
Pavlopoulos, Georgios A.;
Schulz, Frederik;
McMahon, Katherine D.;
Walsh, David;
Woyke, Tanja;
Ivanova, Natalia N.;
Eloe-Fadrosh, Emiley A.;
Tringe, Susannah G.;
Kyrpides, Nikos C.

Publication type:

Article

Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-30049-5

By:

Gao, Shaoming;
Paez-Espino, David;
Li, Jintian;
Ai, Hongxia;
Liang, Jieliang;
Luo, Zhenhao;
Zheng, Jin;
Chen, Hao;
Shu, Wensheng;
Huang, Linan

Publication type:

Article

Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25678-1

By:

Chen, Yiqiang;
Wang, Yulin;
Paez-Espino, David;
Polz, Martin F.;
Zhang, Tong

Publication type:

Article

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2020, v. 14, n. 10, p. 2527, doi. 10.1038/s41396-020-0705-4

By:

Jarett, Jessica K.;
Džunková, Mária;
Schulz, Frederik;
Roux, Simon;
Paez-Espino, David;
Eloe-Fadrosh, Emiley;
Jungbluth, Sean P.;
Ivanova, Natalia;
Spear, John R.;
Carr, Stephanie A.;
Trivedi, Christopher B.;
Corsetti, Frank A.;
Johnson, Hope A.;
Becraft, Eric;
Kyrpides, Nikos;
Stepanauskas, Ramunas;
Woyke, Tanja

Publication type:

Article

Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2015, v. 9, n. 9, p. 2094, doi. 10.1038/ismej.2015.110

By:

Tschitschko, Bernhard;
Williams, Timothy J;
Allen, Michelle A;
Páez-Espino, David;
Kyrpides, Nikos;
Zhong, Ling;
Raftery, Mark J;
Cavicchioli, Ricardo

Publication type:

Article