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Items: 21

1.

OMeta: an ontology-based, data-driven metadata tracking system.

Singh I, Kuscuoglu M, Harkins DM, Sutton G, Fouts DE, Nelson KE.

BMC Bioinformatics. 2019 Jan 7;20(1):8. doi: 10.1186/s12859-018-2580-9.

2.

Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.

Espinoza JL, Harkins DM, Torralba M, Gomez A, Highlander SK, Jones MB, Leong P, Saffery R, Bockmann M, Kuelbs C, Inman JM, Hughes T, Craig JM, Nelson KE, Dupont CL.

MBio. 2018 Nov 27;9(6). pii: e01631-18. doi: 10.1128/mBio.01631-18.

3.

A draft genome sequence for the Ixodes scapularis cell line, ISE6.

Miller JR, Koren S, Dilley KA, Harkins DM, Stockwell TB, Shabman RS, Sutton GG.

F1000Res. 2018 Mar 8;7:297. doi: 10.12688/f1000research.13635.1. eCollection 2018.

4.

A host subtraction database for virus discovery in human cell line sequencing data.

Miller JR, Dilley KA, Harkins DM, Stockwell TB, Shabman RS, Sutton GG.

Version 3. F1000Res. 2018 Jan 23 [revised 2019 Jan 1];7:98. doi: 10.12688/f1000research.13580.3. eCollection 2018.

5.

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation.

Miller JR, Koren S, Dilley KA, Puri V, Brown DM, Harkins DM, Thibaud-Nissen F, Rosen B, Chen XG, Tu Z, Sharakhov IV, Sharakhova MV, Sebra R, Stockwell TB, Bergman NH, Sutton GG, Phillippy AM, Piermarini PM, Shabman RS.

Gigascience. 2018 Mar 1;7(3):1-13. doi: 10.1093/gigascience/gix135.

6.

Host Genetic Control of the Oral Microbiome in Health and Disease.

Gomez A, Espinoza JL, Harkins DM, Leong P, Saffery R, Bockmann M, Torralba M, Kuelbs C, Kodukula R, Inman J, Hughes T, Craig JM, Highlander SK, Jones MB, Dupont CL, Nelson KE.

Cell Host Microbe. 2017 Sep 13;22(3):269-278.e3. doi: 10.1016/j.chom.2017.08.013.

7.

Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function.

Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R.

Theranostics. 2017 Jul 7;7(10):2704-2717. doi: 10.7150/thno.19679. eCollection 2017.

8.

Initial genome sequencing of the sugarcane CP 96-1252 complex hybrid.

Miller JR, Dilley KA, Harkins DM, Torralba MG, Moncera KJ, Beeri K, Goglin K, Stockwell TB, Sutton GG, Shabman RS.

F1000Res. 2017 May 17;6:688. doi: 10.12688/f1000research.11629.1. eCollection 2017.

9.

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.

Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, Tovchigrechko A, Highlander SK, Pieper R, Sender L, Nelson KE.

BMC Genomics. 2016 Aug 15;17(1):635. doi: 10.1186/s12864-016-2965-y.

10.

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection.

Yooseph S, Kirkness EF, Tran TM, Harkins DM, Jones MB, Torralba MG, O'Connell E, Nutman TB, Doumbo S, Doumbo OK, Traore B, Crompton PD, Nelson KE.

BMC Genomics. 2015 Aug 22;16:631. doi: 10.1186/s12864-015-1819-3.

11.

A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii.

Chan AP, Sutton G, DePew J, Krishnakumar R, Choi Y, Huang XZ, Beck E, Harkins DM, Kim M, Lesho EP, Nikolich MP, Fouts DE.

Genome Biol. 2015 Jul 21;16:143. doi: 10.1186/s13059-015-0701-6.

12.

Erratum for "New Insights into Dissemination and Variation of the Health Care-Associated Pathogen Acinetobacter baumannii from Genomic Analysis".

Wright MS, Haft DH, Harkins DM, Perez F, Hujer KM, Bajaksouzian S, Benard MF, Jacobs MR, Bonomo RA, Adams MD.

MBio. 2015 Jun 4;6(3):e00585. doi: 10.1128/mBio.00585-15. No abstract available.

13.

Draft Genome Sequence of Enterococcus faecium PC4.1, a Clade B Strain Isolated from Human Feces.

O Cuív P, Klaassens ES, Smith WJ, Mondot S, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M.

Genome Announc. 2014 Feb 6;2(1). pii: e00022-14. doi: 10.1128/genomeA.00022-14.

14.

New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis.

Wright MS, Haft DH, Harkins DM, Perez F, Hujer KM, Bajaksouzian S, Benard MF, Jacobs MR, Bonomo RA, Adams MD.

MBio. 2014 Jan 21;5(1):e00963-13. doi: 10.1128/mBio.00963-13. Erratum in: MBio. 2015;6(3):e00585.

15.

Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces.

O Cuív P, Klaassens ES, Smith WJ, Mondot S, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M.

Genome Announc. 2013 Jan;1(1). pii: e00160-12. doi: 10.1128/genomeA.00160-12. Epub 2013 Feb 21.

16.

Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.

Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M, Webster NJ, Vinetz JM, Matthias MA.

PLoS Negl Trop Dis. 2012;6(10):e1853. doi: 10.1371/journal.pntd.0001853. Epub 2012 Oct 25.

17.

Draft genome sequence of Bacteroides vulgatus PC510, a strain isolated from human feces.

Cuív PÓ, Klaassens ES, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M.

J Bacteriol. 2011 Aug;193(15):4025-6. doi: 10.1128/JB.05256-11. Epub 2011 May 27.

18.

Draft genome sequence of Turicibacter sanguinis PC909, isolated from human feces.

Cuív PÓ, Klaassens ES, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M.

J Bacteriol. 2011 Mar;193(5):1288-9. doi: 10.1128/JB.01328-10. Epub 2010 Dec 23.

19.

The Protein Naming Utility: a rules database for protein nomenclature.

Goll J, Montgomery R, Brinkac LM, Schobel S, Harkins DM, Sebastian Y, Shrivastava S, Durkin S, Sutton G.

Nucleic Acids Res. 2010 Jan;38(Database issue):D336-9. doi: 10.1093/nar/gkp958. Epub 2009 Dec 8.

20.

Pathema: a clade-specific bioinformatics resource center for pathogen research.

Brinkac LM, Davidsen T, Beck E, Ganapathy A, Caler E, Dodson RJ, Durkin AS, Harkins DM, Lorenzi H, Madupu R, Sebastian Y, Shrivastava S, Thiagarajan M, Orvis J, Sundaram JP, Crabtree J, Galens K, Zhao Y, Inman JM, Montgomery R, Schobel S, Galinsky K, Tanenbaum DM, Resnick A, Zafar N, White O, Sutton G.

Nucleic Acids Res. 2010 Jan;38(Database issue):D408-14. doi: 10.1093/nar/gkp850. Epub 2009 Oct 20.

21.

Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5.

Fricke WF, Wright MS, Lindell AH, Harkins DM, Baker-Austin C, Ravel J, Stepanauskas R.

J Bacteriol. 2008 Oct;190(20):6779-94. doi: 10.1128/JB.00661-08. Epub 2008 Aug 15.

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