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Items: 20

1.

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

Cotto KC, Wagner AH, Feng YY, Kiwala S, Coffman AC, Spies G, Wollam A, Spies NC, Griffith OL, Griffith M.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1068-D1073. doi: 10.1093/nar/gkx1143.

2.

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.

Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL.

Nat Genet. 2017 Jan 31;49(2):170-174. doi: 10.1038/ng.3774. No abstract available.

3.

Genome Sequence of Christensenella minuta DSM 22607T.

Rosa BA, Hallsworth-Pepin K, Martin J, Wollam A, Mitreva M.

Genome Announc. 2017 Jan 12;5(2). pii: e01451-16. doi: 10.1128/genomeA.01451-16.

4.

Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates.

Deitzler GE, Ruiz MJ, Lu W, Weimer C, Park S, Robinson LS, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG, Lewis AL.

Genome Announc. 2016 Sep 29;4(5). pii: e00889-16. doi: 10.1128/genomeA.00889-16.

5.

Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina.

Deitzler GE, Ruiz MJ, Weimer C, Park S, Robinson L, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis AL, Lewis WG.

Genome Announc. 2016 Sep 29;4(5). pii: e00888-16. doi: 10.1128/genomeA.00888-16.

6.

Genome Sequences of 11 Human Vaginal Actinobacteria Strains.

Lewis AL, Deitzler GE, Ruiz MJ, Weimer C, Park S, Robinson LS, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG.

Genome Announc. 2016 Sep 29;4(5). pii: e00887-16. doi: 10.1128/genomeA.00887-16.

7.

Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women.

Weimer CM, Deitzler GE, Robinson LS, Park S, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG, Lewis AL.

Genome Announc. 2016 Sep 29;4(5). pii: e00882-16. doi: 10.1128/genomeA.00882-16.

8.

Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis.

Robinson LS, Perry J, Lek S, Wollam A, Sodergren E, Weinstock G, Lewis WG, Lewis AL.

Genome Announc. 2016 Sep 29;4(5). pii: e00879-16. doi: 10.1128/genomeA.00879-16.

9.

Extreme Sensory Complexity Encoded in the 10-Megabase Draft Genome Sequence of the Chromatically Acclimating Cyanobacterium Tolypothrix sp. PCC 7601.

Yerrapragada S, Shukla A, Hallsworth-Pepin K, Choi K, Wollam A, Clifton S, Qin X, Muzny D, Raghuraman S, Ashki H, Uzman A, Highlander SK, Fryszczyn BG, Fox GE, Tirumalai MR, Liu Y, Kim S, Kehoe DM, Weinstock GM.

Genome Announc. 2015 May 7;3(3). pii: e00355-15. doi: 10.1128/genomeA.00355-15.

10.

Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study.

Zhou Y, Burnham CA, Hink T, Chen L, Shaikh N, Wollam A, Sodergren E, Weinstock GM, Tarr PI, Dubberke ER.

J Clin Microbiol. 2014 Dec;52(12):4260-6. doi: 10.1128/JCM.02115-14. Epub 2014 Oct 1.

11.

Whole-genome analyses of Enterococcus faecium isolates with diverse daptomycin MICs.

Diaz L, Tran TT, Munita JM, Miller WR, Rincon S, Carvajal LP, Wollam A, Reyes J, Panesso D, Rojas NL, Shamoo Y, Murray BE, Weinstock GM, Arias CA.

Antimicrob Agents Chemother. 2014 Aug;58(8):4527-34. doi: 10.1128/AAC.02686-14. Epub 2014 May 27.

12.

Transferable vancomycin resistance in a community-associated MRSA lineage.

Rossi F, Diaz L, Wollam A, Panesso D, Zhou Y, Rincon S, Narechania A, Xing G, Di Gioia TS, Doi A, Tran TT, Reyes J, Munita JM, Carvajal LP, Hernandez-Roldan A, Brandão D, van der Heijden IM, Murray BE, Planet PJ, Weinstock GM, Arias CA.

N Engl J Med. 2014 Apr 17;370(16):1524-31. doi: 10.1056/NEJMoa1303359. Erratum in: N Engl J Med. 2014 Jun 5;370(23):2253.

13.

Evolutionary Genomics of Salmonella enterica Subspecies.

Desai PT, Porwollik S, Long F, Cheng P, Wollam A, Bhonagiri-Palsikar V, Hallsworth-Pepin K, Clifton SW, Weinstock GM, McClelland M.

MBio. 2013 Mar 5;4(2). pii: e00579-12. doi: 10.1128/mBio.00579-12. Erratum in: MBio. 2013;4(2):e00198-13. Bhonagiri-Palsikar, Veena [added]; Hallsworth-Pepin, Kymberlie [added].

14.

Modernizing reference genome assemblies.

Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala R, McLaren WM, Ritchie GR, Albracht D, Kremitzki M, Rock S, Kotkiewicz H, Kremitzki C, Wollam A, Trani L, Fulton L, Fulton R, Matthews L, Whitehead S, Chow W, Torrance J, Dunn M, Harden G, Threadgold G, Wood J, Collins J, Heath P, Griffiths G, Pelan S, Grafham D, Eichler EE, Weinstock G, Mardis ER, Wilson RK, Howe K, Flicek P, Hubbard T.

PLoS Biol. 2011 Jul;9(7):e1001091. doi: 10.1371/journal.pbio.1001091. Epub 2011 Jul 5. No abstract available.

15.

A catalog of reference genomes from the human microbiome.

Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D.

Science. 2010 May 21;328(5981):994-9. doi: 10.1126/science.1183605.

16.

Genome sequence of Cronobacter sakazakii BAA-894 and comparative genomic hybridization analysis with other Cronobacter species.

Kucerova E, Clifton SW, Xia XQ, Long F, Porwollik S, Fulton L, Fronick C, Minx P, Kyung K, Warren W, Fulton R, Feng D, Wollam A, Shah N, Bhonagiri V, Nash WE, Hallsworth-Pepin K, Wilson RK, McClelland M, Forsythe SJ.

PLoS One. 2010 Mar 8;5(3):e9556. doi: 10.1371/journal.pone.0009556.

17.

Genomics. Genome project standards in a new era of sequencing.

Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A; Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC.

Science. 2009 Oct 9;326(5950):236-7. doi: 10.1126/science.1180614. No abstract available.

18.

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.

Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI.

Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5859-64. doi: 10.1073/pnas.0901529106. Epub 2009 Mar 24.

19.

The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle.

Welsh EA, Liberton M, Stöckel J, Loh T, Elvitigala T, Wang C, Wollam A, Fulton RS, Clifton SW, Jacobs JM, Aurora R, Ghosh BK, Sherman LA, Smith RD, Wilson RK, Pakrasi HB.

Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):15094-9. doi: 10.1073/pnas.0805418105. Epub 2008 Sep 23.

20.

Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.

Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T, Hosouchi T, Kawashima K, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Naruo K, Okumura S, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Sato S, de la Bastide M, Huang E, Spiegel L, Gnoj L, O'Shaughnessy A, Preston R, Habermann K, Murray J, Johnson D, Rohlfing T, Nelson J, Stoneking T, Pepin K, Spieth J, Sekhon M, Armstrong J, Becker M, Belter E, Cordum H, Cordes M, Courtney L, Courtney W, Dante M, Du H, Edwards J, Fryman J, Haakensen B, Lamar E, Latreille P, Leonard S, Meyer R, Mulvaney E, Ozersky P, Riley A, Strowmatt C, Wagner-McPherson C, Wollam A, Yoakum M, Bell M, Dedhia N, Parnell L, Shah R, Rodriguez M, See LH, Vil D, Baker J, Kirchoff K, Toth K, King L, Bahret A, Miller B, Marra M, Martienssen R, McCombie WR, Wilson RK, Murphy G, Bancroft I, Volckaert G, Wambutt R, Düsterhöft A, Stiekema W, Pohl T, Entian KD, Terryn N, Hartley N, Bent E, Johnson S, Langham SA, McCullagh B, Robben J, Grymonprez B, Zimmermann W, Ramsperger U, Wedler H, Balke K, Wedler E, Peters S, van Staveren M, Dirkse W, Mooijman P, Lankhorst RK, Weitzenegger T, Bothe G, Rose M, Hauf J, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Villarroel R, Gielen J, Ardiles W, Bents O, Lemcke K, Kolesov G, Mayer K, Rudd S, Schoof H, Schueller C, Zaccaria P, Mewes HW, Bevan M, Fransz P; Kazusa DNA Research Institute; Cold Spring Harbor and Washington University in St Louis Sequencing Consortium; European Union Arabidopsis Genome Sequencing Consortium.

Nature. 2000 Dec 14;408(6814):823-6.

PMID:
11130714

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