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Items: 1 to 50 of 144

1.

Consent insufficient for data release-Response.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 May 3;364(6439):446. doi: 10.1126/science.aax7509. No abstract available.

PMID:
31048484
2.

The evolution of a super-swarm of foot-and-mouth disease virus in cattle.

Arzt J, Fish I, Pauszek SJ, Johnson SL, Chain PS, Rai DK, Rieder E, Goldberg TL, Rodriguez LL, Stenfeldt C.

PLoS One. 2019 Apr 25;14(4):e0210847. doi: 10.1371/journal.pone.0210847. eCollection 2019.

3.

Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus.

Kim WK, No JS, Lee D, Jung J, Park H, Yi Y, Kim JA, Lee SH, Kim Y, Park S, Cho S, Lee GY, Song DH, Gu SH, Park K, Kim HC, Wiley MR, Chain PSG, Jeong ST, Klein TA, Palacios G, Song JW.

Clin Infect Dis. 2019 Mar 20. pii: ciz234. doi: 10.1093/cid/ciz234. [Epub ahead of print]

PMID:
30891596
4.

Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in Serratia ureilytica and Resistance to Extreme Conditions.

Filippidou S, Junier T, Wunderlin T, Kooli WM, Palmieri I, Al-Dourobi A, Molina V, Lienhard R, Spangenberg JE, Johnson SL, Chain PSG, Dorador C, Junier P.

Front Microbiol. 2019 Feb 5;10:102. doi: 10.3389/fmicb.2019.00102. eCollection 2019.

5.

Bacterial spores, from ecology to biotechnology.

Paul C, Filippidou S, Jamil I, Kooli W, House GL, Estoppey A, Hayoz M, Junier T, Palmieri F, Wunderlin T, Lehmann A, Bindschedler S, Vennemann T, Chain PSG, Junier P.

Adv Appl Microbiol. 2019;106:79-111. doi: 10.1016/bs.aambs.2018.10.002. Epub 2018 Nov 27.

PMID:
30798805
6.

Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions.

Palmieri F, Estoppey A, House GL, Lohberger A, Bindschedler S, Chain PSG, Junier P.

Adv Appl Microbiol. 2019;106:49-77. doi: 10.1016/bs.aambs.2018.10.001. Epub 2018 Nov 27.

PMID:
30798804
7.

Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 Jan 25;363(6425):350-352. doi: 10.1126/science.aaw1280. No abstract available.

8.

Complete Genome Sequences of Historic Clostridioides difficile Food-Dwelling Ribotype 078 Strains in Canada Identical to That of the Historic Human Clinical Strain M120 in the United Kingdom.

Kumar A, Davenport KW, Vuyisich G, Kunde YA, Johnson SL, Chain PSG, Dichosa AEK, Rodriguez-Palacios A.

Microbiol Resour Announc. 2018 Sep 27;7(12). pii: e00853-18. doi: 10.1128/MRA.00853-18. eCollection 2018 Sep.

9.

Remedial Treatment of Corroded Iron Objects by Environmental Aeromonas Isolates.

Kooli WM, Junier T, Shakya M, Monachon M, Davenport KW, Vaideeswaran K, Vernudachi A, Marozau I, Monrouzeau T, Gleasner CD, McMurry K, Lienhard R, Rufener L, Perret JL, Sereda O, Chain PS, Joseph E, Junier P.

Appl Environ Microbiol. 2019 Jan 23;85(3). pii: e02042-18. doi: 10.1128/AEM.02042-18. Print 2019 Feb 1.

10.

Diagnostic targETEd seQuencing adjudicaTion (DETEQT): Algorithms for Adjudicating Targeted Infectious Disease Next-Generation Sequencing Panels.

Conrad TA, Lo CC, Koehler JW, Graham AS, Stefan CP, Hall AT, Douglas CE, Chain PS, Minogue TD.

J Mol Diagn. 2019 Jan;21(1):99-110. doi: 10.1016/j.jmoldx.2018.08.008. Epub 2018 Sep 28.

PMID:
30268944
11.

Correction for Johnson et al., "Complete Genome Sequences for 35 Biothreat Assay-Relevant Bacillus Species".

Johnson SL, Daligault HE, Davenport KW, Jaissle J, Frey KG, Ladner JT, Broomall SM, Bishop-Lilly KA, Bruce DC, Gibbons HS, Coyne SR, Lo CC, Meincke L, Munk AC, Koroleva GI, Rosenzweig CN, Palacios GF, Redden CL, Minogue TD, Chain PS.

Genome Announc. 2018 Jan 18;6(3). pii: e01144-17. doi: 10.1128/genomeA.01144-17. No abstract available.

12.

Streptococcus mutans Displays Altered Stress Responses While Enhancing Biofilm Formation by Lactobacillus casei in Mixed-Species Consortium.

Wen ZT, Liao S, Bitoun JP, De A, Jorgensen A, Feng S, Xu X, Chain PSG, Caufield PW, Koo H, Li Y.

Front Cell Infect Microbiol. 2017 Dec 20;7:524. doi: 10.3389/fcimb.2017.00524. eCollection 2017.

13.

Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera.

Hayashi K, Busse HJ, Golke J, Anderson J, Wan X, Hou S, Chain PSG, Prescott RD, Donachie SP.

Int J Syst Evol Microbiol. 2018 Jan;68(1):35-41. doi: 10.1099/ijsem.0.002412. Epub 2017 Nov 7.

PMID:
29111971
14.

Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome.

Xie G, Johnson SL, Davenport KW, Rajavel M, Waldminghaus T, Detter JC, Chain PS, Sozhamannan S.

Int J Genomics. 2017;2017:8724304. doi: 10.1155/2017/8724304. Epub 2017 Aug 29.

15.

Ten Genome Sequences of Human and Livestock Isolates of Bacillus anthracis from the Country of Georgia.

Khmaladze E, Dzavashvili G, Chanturia G, Nikolich MP, Chain PSG, Johnson SL, Imnadze P.

Genome Announc. 2017 May 11;5(19). pii: e00256-17. doi: 10.1128/genomeA.00256-17.

16.

Draft Genome Sequence of Sorghum Grain Mold Fungus Epicoccum sorghinum, a Producer of Tenuazonic Acid.

Oliveira RC, Davenport KW, Hovde B, Silva D, Chain PS, Correa B, Rodrigues DF.

Genome Announc. 2017 Jan 26;5(4). pii: e01495-16. doi: 10.1128/genomeA.01495-16.

17.

Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages.

Li N, Hennelly SP, Stubben CJ, Micheva-Viteva S, Hu B, Shou Y, Vuyisich M, Tung CS, Chain PS, Sanbonmatsu KY, Hong-Geller E.

PLoS One. 2016 Dec 28;11(12):e0168915. doi: 10.1371/journal.pone.0168915. eCollection 2016.

18.

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform.

Li PE, Lo CC, Anderson JJ, Davenport KW, Bishop-Lilly KA, Xu Y, Ahmed S, Feng S, Mokashi VP, Chain PS.

Nucleic Acids Res. 2017 Jan 9;45(1):67-80. doi: 10.1093/nar/gkw1027. Epub 2016 Nov 28.

19.

Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6.

D'haeseleer P, Johnson SL, Davenport KW, Chain PS, Schoeniger J, Ray D, Sinha A, Williams KP, Peña J, Branda SS, El-Etr S.

Genome Announc. 2016 Jun 30;4(3). pii: e00649-16. doi: 10.1128/genomeA.00649-16.

20.

Culture-Independent Diagnostics for Health Security.

Doggett NA, Mukundan H, Lefkowitz EJ, Slezak TR, Chain PS, Morse S, Anderson K, Hodge DR, Pillai S.

Health Secur. 2016 May-Jun;14(3):122-42. doi: 10.1089/hs.2015.0074. Review.

PMID:
27314653
21.

Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258 Klebsiella pneumoniae Strains Isolated during a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones.

Ramirez MS, Xie G, Traglia GM, Johnson SL, Davenport KW, van Duin D, Ramazani A, Perez F, Jacobs MR, Sherratt DJ, Bonomo RA, Chain PS, Tolmasky ME.

Genome Biol Evol. 2016 Jul 3;8(6):2036-43. doi: 10.1093/gbe/evw135.

22.

Anoxybacillusgeothermalis sp. nov., a facultatively anaerobic, endospore-forming bacterium isolated from mineral deposits in a geothermal station.

Filippidou S, Jaussi M, Junier T, Wunderlin T, Jeanneret N, Palmieri F, Palmieri I, Roussel-Delif L, Vieth-Hillebrand A, Vetter A, Chain PS, Regenspurg S, Junier P.

Int J Syst Evol Microbiol. 2016 Aug;66(8):2944-51. doi: 10.1099/ijsem.0.001125. Epub 2016 Apr 28.

PMID:
27126386
23.

Correction for Johnson et al., Complete Genome Sequences for 59 Burkholderia Isolates, Both Pathogenic and Near Neighbor.

Johnson SL, Bishop-Lilly KA, Ladner JT, Daligault HE, Davenport KW, Jaissle J, Frey KG, Koroleva GI, Bruce DC, Coyne SR, Broomall SM, Ketheesan N, Mayo M, Hoffmaster A, Elrod MG, Wuthiekanun V, Tuanyok A, Norton R, Currie BJ, Wagner DM, Keim P, Li PE, Teshima H, Gibbons HS, Palacios GF, Rosenzweig CN, Redden CL, Xu Y, Minogue TD, Chain PS.

Genome Announc. 2016 Apr 21;4(2). pii: e00313-16. doi: 10.1128/genomeA.00313-16. No abstract available.

24.

ADEPT, a dynamic next generation sequencing data error-detection program with trimming.

Feng S, Lo CC, Li PE, Chain PS.

BMC Bioinformatics. 2016 Feb 29;17:109. doi: 10.1186/s12859-016-0967-z.

25.

Draft Genomes for Eight Burkholderia mallei Isolates from Turkey.

Daligault HE, Johnson SL, Davenport KW, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Munk C, Wolcott MJ, Palacios GF, Redden CL, Rosenzweig CN, Scholz MB, Chain PS.

Genome Announc. 2016 Jan 7;4(1). pii: e01234-15. doi: 10.1128/genomeA.01234-15.

26.

Building International Genomics Collaboration for Global Health Security.

Cui HH, Erkkila T, Chain PS, Vuyisich M.

Front Public Health. 2015 Dec 7;3:264. doi: 10.3389/fpubh.2015.00264. eCollection 2015.

27.

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.

Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JD, Wu L, He Z, Chain PS, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, Arkin AP, Zhou J.

Front Microbiol. 2015 Oct 31;6:1205. doi: 10.3389/fmicb.2015.01205. eCollection 2015.

28.

Finished Genome Assembly of Warm Spring Isolate Francisella novicida DPG 3A-IS.

Johnson SL, Minogue TD, Daligault HE, Wolcott MJ, Teshima H, Coyne SR, Davenport KW, Jaissle JG, Chain PS.

Genome Announc. 2015 Sep 17;3(5). pii: e01046-15. doi: 10.1128/genomeA.01046-15.

29.

Genome Assemblies for 11 Yersinia pestis Strains Isolated in the Caucasus Region.

Zhgenti E, Johnson SL, Davenport KW, Chanturia G, Daligault HE, Chain PS, Nikolich MP.

Genome Announc. 2015 Sep 17;3(5). pii: e01030-15. doi: 10.1128/genomeA.01030-15.

30.

Finished Genome Assembly of Yersinia pestis EV76D and KIM 10v.

Johnson SL, Minogue TD, Daligault HE, Wolcott MJ, Teshima H, Coyne SR, Davenport KW, Jaissle JG, Chain PS.

Genome Announc. 2015 Sep 17;3(5). pii: e01024-15. doi: 10.1128/genomeA.01024-15.

31.

Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4.

Shetty AR, de Gannes V, Obi CC, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Teshima H, Han C, Tapia R, Land M, Hauser LJ, Kyrpides N, Ivanova N, Pagani I, Chain PS, Denef VJ, Woyke T, Hickey WJ.

Stand Genomic Sci. 2015 Aug 15;10:55. doi: 10.1186/s40793-015-0041-x. eCollection 2015.

32.

Genome Sequence of Bacillus alveayuensis Strain 24KAM51, a Halotolerant Thermophile Isolated from a Hydrothermal Vent.

Filippidou S, Wunderlin T, Junier T, Jeanneret N, Johnson S, McMurry K, Gleasner CD, Lo CC, Li PE, Vuyisich M, Chain PS, Junier P.

Genome Announc. 2015 Aug 27;3(4). pii: e00982-15. doi: 10.1128/genomeA.00982-15.

33.

Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir.

Filippidou S, Jaussi M, Junier T, Wunderlin T, Jeanneret N, Regenspurg S, Li PE, Lo CC, Johnson S, McMurry K, Gleasner CD, Vuyisich M, Chain PS, Junier P.

Genome Announc. 2015 Aug 27;3(4). pii: e00981-15. doi: 10.1128/genomeA.00981-15.

34.

CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA.

Willias SP, Chauhan S, Lo CC, Chain PS, Motin VL.

PLoS One. 2015 Aug 25;10(8):e0135481. doi: 10.1371/journal.pone.0135481. eCollection 2015.

35.

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial).

Howe A, Chain PS.

Front Microbiol. 2015 Jul 9;6:678. doi: 10.3389/fmicb.2015.00678. eCollection 2015. Review.

36.

Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species.

Filippidou S, Jaussi M, Junier T, Wunderlin T, Roussel-Delif L, Jeanneret N, Vieth-Hillebrand A, Vetter A, Regenspurg S, Johnson SL, McMurry K, Gleasner CD, Lo CC, Li P, Vuyisich M, Chain PS, Junier P.

Genome Announc. 2015 Jun 11;3(3). pii: e00575-15. doi: 10.1128/genomeA.00575-15.

37.

Under-detection of endospore-forming Firmicutes in metagenomic data.

Filippidou S, Junier T, Wunderlin T, Lo CC, Li PE, Chain PS, Junier P.

Comput Struct Biotechnol J. 2015 Apr 25;13:299-306. doi: 10.1016/j.csbj.2015.04.002. eCollection 2015.

38.

Complete genome sequences for 59 burkholderia isolates, both pathogenic and near neighbor.

Johnson SL, Bishop-Lilly KA, Ladner JT, Daligault HE, Davenport KW, Jaissle J, Frey KG, Koroleva GI, Bruce DC, Coyne SR, Broomall SM, Li PE, Teshima H, Gibbons HS, Palacios GF, Rosenzweig CN, Redden CL, Xu Y, Minogue TD, Chain PS.

Genome Announc. 2015 Apr 30;3(2). pii: e00159-15. doi: 10.1128/genomeA.00159-15. Erratum in: Genome Announc. 2016;4(2). pii: e00313-16. doi: 10.1128/genomeA.00313-16.

39.

Complete genome sequences for 35 biothreat assay-relevant bacillus species.

Johnson SL, Daligault HE, Davenport KW, Jaissle J, Frey KG, Ladner JT, Broomall SM, Bishop-Lilly KA, Bruce DC, Gibbons HS, Coyne SR, Lo CC, Meincke L, Munk AC, Koroleva GI, Rosenzweig CN, Palacios GF, Redden CL, Minogue TD, Chain PS.

Genome Announc. 2015 Apr 30;3(2). pii: e00151-15. doi: 10.1128/genomeA.00151-15. Erratum in: Genome Announc. 2018 Jan 18;6(3):.

40.

Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica.

Johnson SL, Daligault HE, Davenport KW, Jaissle J, Frey KG, Ladner JT, Broomall SM, Bishop-Lilly KA, Bruce DC, Coyne SR, Gibbons HS, Lo CC, Munk AC, Rosenzweig CN, Koroleva GI, Palacios GF, Redden CL, Xu Y, Minogue TD, Chain PS.

Genome Announc. 2015 Apr 30;3(2). pii: e00148-15. doi: 10.1128/genomeA.00148-15.

41.

Genome sequencing of 18 francisella strains to aid in assay development and testing.

Johnson SL, Daligault HE, Davenport KW, Coyne SR, Frey KG, Koroleva GI, Broomall SM, Bishop-Lilly KA, Bruce DC, Chertkov O, Freitas T, Jaissle J, Ladner JT, Rosenzweig CN, Gibbons HS, Palacios GF, Redden CL, Xu Y, Minogue TD, Chain PS.

Genome Announc. 2015 Apr 30;3(2). pii: e00147-15. doi: 10.1128/genomeA.00147-15.

42.

Genome Sequence of Kosakonia radicincitans Strain YD4, a Plant Growth-Promoting Rhizobacterium Isolated from Yerba Mate (Ilex paraguariensis St. Hill.).

Bergottini VM, Filippidou S, Junier T, Johnson S, Chain PS, Otegui MB, Zapata PD, Junier P.

Genome Announc. 2015 Apr 2;3(2). pii: e00239-15. doi: 10.1128/genomeA.00239-15.

43.

Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity.

Chapman C, Henry M, Bishop-Lilly KA, Awosika J, Briska A, Ptashkin RN, Wagner T, Rajanna C, Tsang H, Johnson SL, Mokashi VP, Chain PS, Sozhamannan S.

PLoS One. 2015 Mar 20;10(3):e0120311. doi: 10.1371/journal.pone.0120311. eCollection 2015.

44.

Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets.

Dichosa AE, Davenport KW, Li PE, Ahmed SA, Daligault H, Gleasner CD, Kunde Y, McMurry K, Lo CC, Reitenga KG, Daughton AR, Shen X, Frietze S, Wang D, Johnson SL, Drautz-Moses DI, Schuster S, Chain PS, Han C.

Genome Announc. 2015 Mar 19;3(2). pii: e00132-15. doi: 10.1128/genomeA.00132-15.

45.

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures.

Freitas TA, Li PE, Scholz MB, Chain PS.

Nucleic Acids Res. 2015 May 26;43(10):e69. doi: 10.1093/nar/gkv180. Epub 2015 Mar 12.

46.

Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei.

Johnson SL, Baker AL, Chain PS, Currie BJ, Daligault HE, Davenport KW, Davis CB, Inglis TJ, Kaestli M, Koren S, Mayo M, Merritt AJ, Price EP, Sarovich DS, Warner J, Rosovitz MJ.

Genome Announc. 2015 Feb 12;3(1). pii: e01282-14. doi: 10.1128/genomeA.01282-14.

47.

Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes.

Johnson SL, Minogue TD, Teshima H, Davenport KW, Shea AA, Miner HL, Wolcott MJ, Chain PS.

Genome Announc. 2015 Jan 15;3(1). pii: e01446-14. doi: 10.1128/genomeA.01446-14.

48.

Adaptation genomics of a small-colony variant in a Pseudomonas chlororaphis 30-84 biofilm.

Wang D, Dorosky RJ, Han CS, Lo CC, Dichosa AE, Chain PS, Yu JM, Pierson LS 3rd, Pierson EA.

Appl Environ Microbiol. 2015 Feb;81(3):890-9. doi: 10.1128/AEM.02617-14. Epub 2014 Nov 21.

49.

Whole-genome assemblies of 56 burkholderia species.

Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Munk C, Palacios GF, Redden CL, Rosenzweig CN, Scholz MB, Johnson SL.

Genome Announc. 2014 Nov 20;2(6). pii: e01106-14. doi: 10.1128/genomeA.01106-14.

50.

Rapid evaluation and quality control of next generation sequencing data with FaQCs.

Lo CC, Chain PS.

BMC Bioinformatics. 2014 Nov 19;15:366. doi: 10.1186/s12859-014-0366-2.

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