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Items: 1 to 50 of 72

1.

Proposal for assignment of allele numbers for mobile colistin resistance (mcr) genes.

Partridge SR, Di Pilato V, Doi Y, Feldgarden M, Haft DH, Klimke W, Kumar-Singh S, Liu JH, Malhotra-Kumar S, Prasad A, Rossolini GM, Schwarz S, Shen J, Walsh T, Wang Y, Xavier BB.

J Antimicrob Chemother. 2018 Oct 1;73(10):2625-2630. doi: 10.1093/jac/dky262.

PMID:
30053115
2.

Both widespread PEP-CTERM proteins and exopolysaccharides are required for floc formation of Zoogloea resiniphila and other activated sludge bacteria.

Gao N, Xia M, Dai J, Yu D, An W, Li S, Liu S, He P, Zhang L, Wu Z, Bi X, Chen S, Haft DH, Qiu D.

Environ Microbiol. 2018 May;20(5):1677-1692. doi: 10.1111/1462-2920.14080. Epub 2018 Mar 26.

PMID:
29473278
3.

RefSeq: an update on prokaryotic genome annotation and curation.

Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O'Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu F, Marchler GH, Song JS, Thanki N, Yamashita RA, Zheng C, Thibaud-Nissen F, Geer LY, Marchler-Bauer A, Pruitt KD.

Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860. doi: 10.1093/nar/gkx1068.

4.

A comprehensive software suite for protein family construction and functional site prediction.

Haft DR, Haft DH.

PLoS One. 2017 Feb 9;12(2):e0171758. doi: 10.1371/journal.pone.0171758. eCollection 2017.

5.

Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors.

Haft DH, Pierce PG, Mayclin SJ, Sullivan A, Gardberg AS, Abendroth J, Begley DW, Phan IQ, Staker BL, Myler PJ, Marathias VM, Lorimer DD, Edwards TE.

Sci Rep. 2017 Jan 25;7:41074. doi: 10.1038/srep41074.

6.

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA Jr, Yang XF, Zhang JJ, Vinetz JM.

PLoS Negl Trop Dis. 2016 Feb 18;10(2):e0004403. doi: 10.1371/journal.pntd.0004403. eCollection 2016 Feb.

7.

Permuting the PGF Signature Motif Blocks both Archaeosortase-Dependent C-Terminal Cleavage and Prenyl Lipid Attachment for the Haloferax volcanii S-Layer Glycoprotein.

Abdul Halim MF, Karch KR, Zhou Y, Haft DH, Garcia BA, Pohlschroder M.

J Bacteriol. 2015 Dec 28;198(5):808-15. doi: 10.1128/JB.00849-15.

8.

An updated evolutionary classification of CRISPR-Cas systems.

Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV.

Nat Rev Microbiol. 2015 Nov;13(11):722-36. doi: 10.1038/nrmicro3569. Epub 2015 Sep 28. Review.

9.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G.

Database (Oxford). 2015 Jul 11;2015:bav063. doi: 10.1093/database/bav063. eCollection 2015.

10.

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.

11.

Using comparative genomics to drive new discoveries in microbiology.

Haft DH.

Curr Opin Microbiol. 2015 Feb;23:189-96. doi: 10.1016/j.mib.2014.11.017. Epub 2015 Jan 21. Review.

12.

Simultaneous non-contiguous deletions using large synthetic DNA and site-specific recombinases.

Krishnakumar R, Grose C, Haft DH, Zaveri J, Alperovich N, Gibson DG, Merryman C, Glass JI.

Nucleic Acids Res. 2014 Aug;42(14):e111. doi: 10.1093/nar/gku509. Epub 2014 Jun 9.

13.

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.

14.

Pathogenomic inference of virulence-associated genes in Leptospira interrogans.

Lehmann JS, Fouts DE, Haft DH, Cannella AP, Ricaldi JN, Brinkac L, Harkins D, Durkin S, Sanka R, Sutton G, Moreno A, Vinetz JM, Matthias MA.

PLoS Negl Trop Dis. 2013 Oct 3;7(10):e2468. doi: 10.1371/journal.pntd.0002468. eCollection 2013.

15.

Methanobactin and MmoD work in concert to act as the 'copper-switch' in methanotrophs.

Semrau JD, Jagadevan S, DiSpirito AA, Khalifa A, Scanlan J, Bergman BH, Freemeier BC, Baral BS, Bandow NL, Vorobev A, Haft DH, Vuilleumier S, Murrell JC.

Environ Microbiol. 2013 Nov;15(11):3077-86. doi: 10.1111/1462-2920.12150. Epub 2013 May 20.

16.

Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis.

Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S, Smith RD, Adkins JN, Grundner C, Wright AT.

Chem Biol. 2013 Jan 24;20(1):123-33. doi: 10.1016/j.chembiol.2012.11.008.

17.

TIGRFAMs and Genome Properties in 2013.

Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E.

Nucleic Acids Res. 2013 Jan;41(Database issue):D387-95. doi: 10.1093/nar/gks1234. Epub 2012 Nov 28.

18.

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature.

Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJ, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA.

Nat Prod Rep. 2013 Jan;30(1):108-60. doi: 10.1039/c2np20085f. Review.

19.

High-speed microbial community profiling.

Haft DH, Tovchigrechko A.

Nat Methods. 2012 Jun 10;9(8):793-4. doi: 10.1038/nmeth.2080. No abstract available.

PMID:
22688412
20.

Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism.

Pathak DT, Wei X, Bucuvalas A, Haft DH, Gerloff DL, Wall D.

PLoS Genet. 2012;8(4):e1002626. doi: 10.1371/journal.pgen.1002626. Epub 2012 Apr 12.

21.

AntiFam: a tool to help identify spurious ORFs in protein annotation.

Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A.

Database (Oxford). 2012 Mar 20;2012:bas003. doi: 10.1093/database/bas003. Print 2012.

22.
23.

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.

Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Venter JC.

ISME J. 2012 Jun;6(6):1186-99. doi: 10.1038/ismej.2011.189. Epub 2011 Dec 15.

24.

ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.

Basu MK, Selengut JD, Haft DH.

BMC Bioinformatics. 2011 Nov 9;12:434. doi: 10.1186/1471-2105-12-434.

25.

Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.

Haft DH, Payne SH, Selengut JD.

J Bacteriol. 2012 Jan;194(1):36-48. doi: 10.1128/JB.06026-11. Epub 2011 Oct 28.

26.

Evolution and classification of the CRISPR-Cas systems.

Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV.

Nat Rev Microbiol. 2011 Jun;9(6):467-77. doi: 10.1038/nrmicro2577. Epub 2011 May 9. Review.

27.
29.

A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.

Krentz BD, Mulheron HJ, Semrau JD, Dispirito AA, Bandow NL, Haft DH, Vuilleumier S, Murrell JC, McEllistrem MT, Hartsel SC, Gallagher WH.

Biochemistry. 2010 Nov 30;49(47):10117-30. doi: 10.1021/bi1014375. Epub 2010 Nov 4.

30.

Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.

Selengut JD, Haft DH.

J Bacteriol. 2010 Nov;192(21):5788-98. doi: 10.1128/JB.00425-10. Epub 2010 Jul 30.

31.

Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family.

Haft DH, Basu MK, Mitchell DA.

BMC Biol. 2010 May 25;8:70. doi: 10.1186/1741-7007-8-70.

33.
34.

Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.

Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR.

Appl Environ Microbiol. 2009 Apr;75(7):2046-56. doi: 10.1128/AEM.02294-08. Epub 2009 Feb 5.

35.

Orphan SelD proteins and selenium-dependent molybdenum hydroxylases.

Haft DH, Self WT.

Biol Direct. 2008 Feb 20;3:4. doi: 10.1186/1745-6150-3-4.

36.

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.

Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O.

Nucleic Acids Res. 2007 Jan;35(Database issue):D260-4. Epub 2006 Dec 6.

37.

Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus.

Badger JH, Hoover TR, Brun YV, Weiner RM, Laub MT, Alexandre G, Mrázek J, Ren Q, Paulsen IT, Nelson KE, Khouri HM, Radune D, Sosa J, Dodson RJ, Sullivan SA, Rosovitz MJ, Madupu R, Brinkac LM, Durkin AS, Daugherty SC, Kothari SP, Giglio MG, Zhou L, Haft DH, Selengut JD, Davidsen TM, Yang Q, Zafar N, Ward NL.

J Bacteriol. 2006 Oct;188(19):6841-50.

39.

Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens.

Myers GS, Rasko DA, Cheung JK, Ravel J, Seshadri R, DeBoy RT, Ren Q, Varga J, Awad MM, Brinkac LM, Daugherty SC, Haft DH, Dodson RJ, Madupu R, Nelson WC, Rosovitz MJ, Sullivan SA, Khouri H, Dimitrov GI, Watkins KL, Mulligan S, Benton J, Radune D, Fisher DJ, Atkins HS, Hiscox T, Jost BH, Billington SJ, Songer JG, McClane BA, Titball RW, Rood JI, Melville SB, Paulsen IT.

Genome Res. 2006 Aug;16(8):1031-40. Epub 2006 Jul 6.

40.

Comparative genomics of emerging human ehrlichiosis agents.

Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H.

PLoS Genet. 2006 Feb;2(2):e21. Epub 2006 Feb 17. Erratum in: PLoS Genet. 2006 Dec;2(12):e213. Eisen, Jonathan [corrected to Eisen, Jonathan A].

41.

Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.

Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA.

PLoS Genet. 2005 Nov;1(5):e65. Epub 2005 Nov 25. Erratum in: PLoS Genet. 2006 Apr;2(4):e60. Haft, Daniel H [added].

42.

A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.

Haft DH, Selengut J, Mongodin EF, Nelson KE.

PLoS Comput Biol. 2005 Nov;1(6):e60. Epub 2005 Nov 11.

43.

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".

Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM.

Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13950-5. Epub 2005 Sep 19. Erratum in: Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16530.

44.

Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition.

Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR.

J Bacteriol. 2005 Sep;187(18):6488-98.

45.

Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.

Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM.

J Bacteriol. 2005 Apr;187(7):2426-38.

46.

Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.

Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N.

Nature. 2004 Dec 16;432(7019):910-3.

PMID:
15602564
47.

Structural flexibility in the Burkholderia mallei genome.

Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC, Davidsen TD, Deboy RT, Dimitrov G, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Khouri H, Kolonay JF, Madupu R, Mohammoud Y, Nelson WC, Radune D, Romero CM, Sarria S, Selengut J, Shamblin C, Sullivan SA, White O, Yu Y, Zafar N, Zhou L, Fraser CM.

Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14246-51. Epub 2004 Sep 17.

48.

Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics.

Haft DH, Selengut JD, Brinkac LM, Zafar N, White O.

Bioinformatics. 2005 Feb 1;21(3):293-306. Epub 2004 Sep 3.

PMID:
15347579
49.

Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species.

Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM.

Nucleic Acids Res. 2004 Apr 28;32(8):2386-95. Print 2004.

50.

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM.

Nat Biotechnol. 2004 May;22(5):554-9. Epub 2004 Apr 11.

PMID:
15077118

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