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Items: 1 to 20 of 43

1.

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.

2.

IMG/M: integrated genome and metagenome comparative data analysis system.

Chen IA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, Ratner A, Huang J, Andersen E, Huntemann M, Varghese N, Hadjithomas M, Tennessen K, Nielsen T, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D507-D516. doi: 10.1093/nar/gkw929. Epub 2016 Oct 13.

3.

Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system.

Chen IM, Markowitz VM, Palaniappan K, Szeto E, Chu K, Huang J, Ratner A, Pillay M, Hadjithomas M, Huntemann M, Mikhailova N, Ovchinnikova G, Ivanova NN, Kyrpides NC.

BMC Genomics. 2016 Apr 26;17:307. doi: 10.1186/s12864-016-2629-y.

4.

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.

5.

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.

6.

Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland.

Susanti D, Johnson EF, Lapidus A, Han J, Reddy TB, Pilay M, Ivanova NN, Markowitz VM, Woyke T, Kyrpides NC, Mukhopadhyay B.

Stand Genomic Sci. 2016 Jan 13;11:3. doi: 10.1186/s40793-015-0128-4. eCollection 2016.

7.

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.

8.

Ten years of maintaining and expanding a microbial genome and metagenome analysis system.

Markowitz VM, Chen IM, Chu K, Pati A, Ivanova NN, Kyrpides NC.

Trends Microbiol. 2015 Nov;23(11):730-41. doi: 10.1016/j.tim.2015.07.012. Epub 2015 Oct 14. Review.

PMID:
26439299
9.

High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea.

Ntougias S, Lapidus A, Copeland A, Reddy TB, Pati A, Ivanova NN, Markowitz VM, Klenk HP, Woyke T, Fasseas C, Kyrpides NC, Zervakis GI.

Stand Genomic Sci. 2015 Aug 13;10:52. doi: 10.1186/s40793-015-0052-7. eCollection 2015.

10.

High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum.

Sakamoto M, Lapidus AL, Han J, Trong S, Haynes M, Reddy TB, Mikhailova N, Huntemann M, Pati A, Ivanova NN, Pukall R, Markowitz VM, Woyke T, Klenk HP, Kyrpides NC, Ohkuma M.

Stand Genomic Sci. 2015 Aug 2;10:48. doi: 10.1186/s40793-015-0045-6. eCollection 2015.

11.

Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a.

Rooney EA, Rowe KT, Guseva A, Huntemann M, Han JK, Chen A, Kyrpides NC, Mavromatis K, Markowitz VM, Palaniappan K, Ivanova N, Pati A, Liolios K, Nordberg HP, Cantor MN, Hua SX, Shapiro N, Woyke T, Lynd LR, Izquierdo JA.

Genome Announc. 2015 Jul 23;3(4). pii: e00797-15. doi: 10.1128/genomeA.00797-15.

12.

High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass.

Laviad S, Lapidus A, Copeland A, Reddy T, Huntemann M, Pati A, Ivanova NN, Markowitz VM, Pukall R, Klenk HP, Woyke T, Kyrpides NC, Halpern M.

Stand Genomic Sci. 2015 May 8;10:21. doi: 10.1186/s40793-015-0003-3. eCollection 2015.

13.

IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites.

Hadjithomas M, Chen IM, Chu K, Ratner A, Palaniappan K, Szeto E, Huang J, Reddy TB, Cimermančič P, Fischbach MA, Ivanova NN, Markowitz VM, Kyrpides NC, Pati A.

MBio. 2015 Jul 14;6(4):e00932. doi: 10.1128/mBio.00932-15.

14.

Draft genome sequences of 10 strains of the genus exiguobacterium.

Vishnivetskaya TA, Chauhan A, Layton AC, Pfiffner SM, Huntemann M, Copeland A, Chen A, Kyrpides NC, Markowitz VM, Palaniappan K, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen EW, Pati A, Stamatis D, Reddy TB, Shapiro N, Nordberg HP, Cantor MN, Hua XS, Woyke T.

Genome Announc. 2014 Oct 16;2(5). pii: e01058-14. doi: 10.1128/genomeA.01058-14.

15.

IMG 4 version of the integrated microbial genomes comparative analysis system.

Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2014 Jan;42(Database issue):D560-7. doi: 10.1093/nar/gkt963. Epub 2013 Oct 27.

16.

IMG/M 4 version of the integrated metagenome comparative analysis system.

Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2014 Jan;42(Database issue):D568-73. doi: 10.1093/nar/gkt919. Epub 2013 Oct 16.

17.

Improving microbial genome annotations in an integrated database context.

Chen IM, Markowitz VM, Chu K, Anderson I, Mavromatis K, Kyrpides NC, Ivanova NN.

PLoS One. 2013;8(2):e54859. doi: 10.1371/journal.pone.0054859. Epub 2013 Feb 12.

18.

IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project.

Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Jacob B, Ratner A, Liolios K, Pagani I, Huntemann M, Mavromatis K, Ivanova NN, Kyrpides NC.

PLoS One. 2012;7(7):e40151. doi: 10.1371/journal.pone.0040151. Epub 2012 Jul 5.

19.

A framework for human microbiome research.

Human Microbiome Project Consortium.

Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209.

20.

Structure, function and diversity of the healthy human microbiome.

Human Microbiome Project Consortium.

Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234.

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