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1

Uncovering Earth’s virome

Paez-Espino, David, Eloe-Fadrosh, Emiley A., Pavlopoulos, Georgios A., Thomas, Alex D., Huntemann, Marcel, Mikhailova, Natalia, Rubin, Edward, Ivanova, Natalia N., Kyrpides, Nikos C.

Journal:

Year:

2016

Language:

english

File:

PDF, 12.67 MB

english, 2016

2

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

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

Journal:

The ISME Journal

Year:

2015

Language:

english

File:

PDF, 2.58 MB

english, 2015

3

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

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, Emil

Journal:

Year:

2019

Language:

english

File:

PDF, 2.29 MB

english, 2019

4

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

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, Emil

Journal:

Year:

2019

File:

PDF, 2.29 MB

2019

5

Giant virus diversity and host interactions through global metagenomics

Schulz, Frederik, Roux, Simon, Paez-Espino, David, Jungbluth, Sean, Walsh, David A., Denef, Vincent J., McMahon, Katherine D., Konstantinidis, Konstantinos T., Eloe-Fadrosh, Emiley A., Kyrpides, Nikos

Journal:

Year:

2020

File:

PDF, 8.05 MB

2020

6

Microbial responses to environmental arsenic

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

Journal:

Year:

2009

Language:

english

File:

PDF, 472 KB

english, 2009

7

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

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

Journal:

Environmental Microbiology

Year:

2011

Language:

english

File:

PDF, 1.05 MB

english, 2011

8

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

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

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 1.38 MB

english, 2013

9

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

Páez-Espino, A. David, Durante-Rodríguez, Gonzalo, de Lorenzo, Víctor

Journal:

Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 614 KB

english, 2015

10

CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus

Paez-Espino, David, Sharon, Itai, Morovic, Wesley, Stahl, Buffy, Thomas, Brian C., Barrangou, Rodolphe, Banfield, Jillian F.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.08 MB

english, 2015

11

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

Páez-Espino, A. David, Chavarría, Max, de Lorenzo, Víctor

Journal:

Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 3.09 MB

english, 2015

12

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

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-

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 1.62 MB

english, 2016

13

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

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, Steph

Journal:

Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 1.34 MB

english, 2015

14

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

Huntemann, Marcel, Ivanova, Natalia N., Mavromatis, Konstantinos, Tripp, H. James, Paez-Espino, David, Palaniappan, Krishnaveni, Szeto, Ernest, Pillay, Manoj, Chen, I-Min A., Pati, Amrita, Nielsen, To

Journal:

Standards in Genomic Sciences

Year:

2016

Language:

english

File:

PDF, 335 KB

english, 2016

15

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

Huntemann, Marcel, Ivanova, Natalia N., Mavromatis, Konstantinos, Tripp, H. James, Paez-Espino, David, Palaniappan, Krishnaveni, Szeto, Ernest, Pillay, Manoj, Chen, I-Min A., Pati, Amrita, Nielsen, To

Journal:

Standards in Genomic Sciences

Year:

2015

Language:

english

File:

PDF, 839 KB

english, 2015

16

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

Huntemann, Marcel, Ivanova, Natalia N., Mavromatis, Konstantinos, Tripp, H. James, Paez-Espino, David, Tennessen, Kristin, Palaniappan, Krishnaveni, Szeto, Ernest, Pillay, Manoj, Chen, I-Min A., Pati,

Journal:

Standards in Genomic Sciences

Year:

2016

Language:

english

File:

PDF, 1.29 MB

english, 2016

17

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

Paez-Espino, David, Chen, I.-Min A., Palaniappan, Krishna, Ratner, Anna, Chu, Ken, Szeto, Ernest, Pillay, Manoj, Huang, Jinghua, Markowitz, Victor M., Nielsen, Torben, Huntemann, Marcel, K. Reddy, T.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 5.69 MB

english, 2016

18

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

Silas, Sukrit, Makarova, Kira S., Shmakov, Sergey, Páez-Espino, David, Mohr, Georg, Liu, Yi, Davison, Michelle, Roux, Simon, Krishnamurthy, Siddharth R., Fu, Becky Xu Hua, Hansen, Loren L., Wang, Davi

Journal:

Year:

2017

Language:

english

File:

PDF, 1.49 MB

english, 2017

19

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

Paez-Espino, David, Pavlopoulos, Georgios A, Ivanova, Natalia N, Kyrpides, Nikos C

Journal:

Nature Protocols

Year:

2017

Language:

english

File:

PDF, 2.17 MB

english, 2017

20

A thermostable Cas9 with increased lifetime in human plasma

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

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 910 KB

english, 2017

21

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

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

Journal:

Advances in Bioinformatics

Year:

2017

Language:

english

File:

PDF, 2.31 MB

english, 2017

22

Murine colitis reveals a disease-associated bacteriophage community

Duerkop, Breck A., Kleiner, Manuel, Paez-Espino, David, Zhu, Wenhan, Bushnell, Brian, Hassell, Brian, Winter, Sebastian E., Kyrpides, Nikos C., Hooper, Lora V.

Journal:

Nature Microbiology

Year:

2018

Language:

english

File:

PDF, 1.42 MB

english, 2018

23

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

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

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 2.31 MB

english, 2018

24

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

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, Natal

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 3.43 MB

english, 2018

25

In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs

Sierra-Garcia, Isabel Natalia, Belgini, Daiane R.B., Torres-Ballesteros, Adriana, Paez-Espino, David, Capilla, RamsÃ©s, Santos Neto, Eugenio V., Gray, Neil, de Oliveira, Valeria Maia

Journal:

Science of The Total Environment

Year:

2020

Language:

english

File:

PDF, 4.03 MB

english, 2020

26

A Guide to Conquer the Biological Network Era Using Graph Theory

Koutrouli, Mikaela, Karatzas, Evangelos, Paez-Espino, David, Pavlopoulos, Georgios A.

Journal:

Frontiers in Bioengineering and Biotechnology

Year:

2020

File:

PDF, 5.31 MB

2020

27

A scoutRNA Is Required for Some Type V CRISPR-Cas Systems

Harrington, Lucas B., Ma, Enbo, Chen, Janice S., Witte, Isaac P., Gertz, Dov, Paez-Espino, David, Al-Shayeb, Basem, Kyrpides, Nikos C., Burstein, David, Banfield, Jillian F., Doudna, Jennifer A.

Journal:

Year:

2020

File:

PDF, 1.57 MB

2020

28

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

Jarett, Jessica K., DÅ¾unkovÃ¡, MÃ¡ria, Schulz, Frederik, Roux, Simon, Paez-Espino, David, Eloe-Fadrosh, Emiley, Jungbluth, Sean P., Ivanova, Natalia, Spear, John R., Carr, Stephanie A., Trivedi, Chri

Journal:

The ISME Journal

Year:

2020

File:

PDF, 2.18 MB

2020

29

A genomic catalog of Earthâs microbiomes

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,

Journal:

Nature Biotechnology

Year:

2020

File:

PDF, 9.36 MB

2020

30

Publisher Correction: A genomic catalog of Earthâs microbiomes

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,

Journal:

Nature Biotechnology

Year:

2020

File:

PDF, 697 KB

2020

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