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Items: 26

1.

A Guide to Conquer the Biological Network Era Using Graph Theory.

Koutrouli M, Karatzas E, Paez-Espino D, Pavlopoulos GA.

Front Bioeng Biotechnol. 2020 Jan 31;8:34. doi: 10.3389/fbioe.2020.00034. eCollection 2020. Review.

2.

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

Sierra-Garcia IN, Belgini DRB, Torres-Ballesteros A, Paez-Espino D, Capilla R, Santos Neto EV, Gray N, de Oliveira VM.

Sci Total Environ. 2020 May 1;715:136646. doi: 10.1016/j.scitotenv.2020.136646. Epub 2020 Jan 15.

PMID:
32014760
3.

Giant virus diversity and host interactions through global metagenomics.

Schulz F, Roux S, Paez-Espino D, Jungbluth S, Walsh DA, Denef VJ, McMahon KD, Konstantinidis KT, Eloe-Fadrosh EA, Kyrpides NC, Woyke T.

Nature. 2020 Feb;578(7795):432-436. doi: 10.1038/s41586-020-1957-x. Epub 2020 Jan 22.

PMID:
31968354
4.

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

Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC.

Microbiome. 2019 Dec 10;7(1):157. doi: 10.1186/s40168-019-0768-5.

5.

A Functional Mini-Integrase in a Two-Protein-type V-C CRISPR System.

Wright AV, Wang JY, Burstein D, Harrington LB, Paez-Espino D, Kyrpides NC, Iavarone AT, Banfield JF, Doudna JA.

Mol Cell. 2019 Feb 21;73(4):727-737.e3. doi: 10.1016/j.molcel.2018.12.015. Epub 2019 Jan 29.

6.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.

Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.

7.

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

Paez-Espino D, Roux S, Chen IA, Palaniappan K, Ratner A, Chu K, Huntemann M, Reddy TBK, Pons JC, Llabrés M, Eloe-Fadrosh EA, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2019 Jan 8;47(D1):D678-D686. doi: 10.1093/nar/gky1127.

8.

Programmed DNA destruction by miniature CRISPR-Cas14 enzymes.

Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA.

Science. 2018 Nov 16;362(6416):839-842. doi: 10.1126/science.aav4294. Epub 2018 Oct 18.

9.

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

Meier-Kolthoff JP, Uchiyama J, Yahara H, Paez-Espino D, Yahara K.

Sci Rep. 2018 Jul 31;8(1):11496. doi: 10.1038/s41598-018-29272-2.

10.

Murine colitis reveals a disease-associated bacteriophage community.

Duerkop BA, Kleiner M, Paez-Espino D, Zhu W, Bushnell B, Hassell B, Winter SE, Kyrpides NC, Hooper LV.

Nat Microbiol. 2018 Sep;3(9):1023-1031. doi: 10.1038/s41564-018-0210-y. Epub 2018 Jul 23.

11.

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

Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators, Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ.

Nat Biotechnol. 2018 Apr;36(4):359-367. doi: 10.1038/nbt.4110. Epub 2018 Mar 19.

12.

A thermostable Cas9 with increased lifetime in human plasma.

Harrington LB, Paez-Espino D, Staahl BT, Chen JS, Ma E, Kyrpides NC, Doudna JA.

Nat Commun. 2017 Nov 10;8(1):1424. doi: 10.1038/s41467-017-01408-4.

13.

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

Pavlopoulos GA, Paez-Espino D, Kyrpides NC, Iliopoulos I.

Adv Bioinformatics. 2017;2017:1278932. doi: 10.1155/2017/1278932. Epub 2017 Jul 18. Review.

14.

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data.

Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC.

Nat Protoc. 2017 Aug;12(8):1673-1682. doi: 10.1038/nprot.2017.063. Epub 2017 Jul 27.

15.

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

Silas S, Makarova KS, Shmakov S, Páez-Espino D, Mohr G, Liu Y, Davison M, Roux S, Krishnamurthy SR, Fu BXH, Hansen LL, Wang D, Sullivan MB, Millard A, Clokie MR, Bhaya D, Lambowitz AM, Kyrpides NC, Koonin EV, Fire AZ.

mBio. 2017 Jul 11;8(4). pii: e00897-17. doi: 10.1128/mBio.00897-17.

16.

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

Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC.

Nat Biotechnol. 2017 Jul;35(7):676-683. doi: 10.1038/nbt.3886. Epub 2017 Jun 12.

17.

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

Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.

18.

Uncovering Earth's virome.

Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC.

Nature. 2016 Aug 25;536(7617):425-30. Epub 2016 Aug 17.

19.

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

Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Palaniappan K, Szeto E, Pillay M, Chen IM, Pati A, Nielsen T, Markowitz VM, Kyrpides NC.

Stand Genomic Sci. 2016 Mar 21;11:27. doi: 10.1186/s40793-016-0148-8. eCollection 2016.

20.

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

Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Tennessen K, Palaniappan K, Szeto E, Pillay M, Chen IM, Pati A, Nielsen T, Markowitz VM, Kyrpides NC.

Stand Genomic Sci. 2016 Feb 24;11:17. doi: 10.1186/s40793-016-0138-x. eCollection 2016.

21.

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

Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Dekas AE, Grasby SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmstrom R, Pati A, Pett-Ridge J, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN.

Nat Commun. 2016 Jan 27;7:10476. doi: 10.1038/ncomms10476.

22.

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

Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Palaniappan K, Szeto E, Pillay M, Chen IM, Pati A, Nielsen T, Markowitz VM, Kyrpides NC.

Stand Genomic Sci. 2015 Oct 26;10:86. doi: 10.1186/s40793-015-0077-y. eCollection 2015. Erratum in: Stand Genomic Sci. 2016;11:27.

23.

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

Tschitschko B, Williams TJ, Allen MA, Páez-Espino D, Kyrpides N, Zhong L, Raftery MJ, Cavicchioli R.

ISME J. 2015 Sep;9(9):2094-107. doi: 10.1038/ismej.2015.110. Epub 2015 Jun 30.

24.

CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus.

Paez-Espino D, Sharon I, Morovic W, Stahl B, Thomas BC, Barrangou R, Banfield JF.

mBio. 2015 Apr 21;6(2). pii: e00262-15. doi: 10.1128/mBio.00262-15.

25.

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

Paez-Espino D, Morovic W, Sun CL, Thomas BC, Ueda K, Stahl B, Barrangou R, Banfield JF.

Nat Commun. 2013;4:1430. doi: 10.1038/ncomms2440.

PMID:
23385575
26.

Microbial responses to environmental arsenic.

Páez-Espino D, Tamames J, de Lorenzo V, Cánovas D.

Biometals. 2009 Feb;22(1):117-30. doi: 10.1007/s10534-008-9195-y. Epub 2009 Jan 7. Review.

PMID:
19130261

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