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Development stage-specific proteomic profiling uncovers small, lineage specific proteins most abundant in the Aspergillus Fumigatus conidial proteome.

Suh MJ, Fedorova ND, Cagas SE, Hastings S, Fleischmann RD, Peterson SN, Perlin DS, Nierman WC, Pieper R, Momany M.

Proteome Sci. 2012 Apr 30;10(1):30. doi: 10.1186/1477-5956-10-30.


Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies.

Pieper R, Zhang Q, Clark DJ, Huang ST, Suh MJ, Braisted JC, Payne SH, Fleischmann RD, Peterson SN, Tzipori S.

PLoS One. 2011;6(11):e26554. doi: 10.1371/journal.pone.0026554. Epub 2011 Nov 7.


In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism.

Kuntumalla S, Zhang Q, Braisted JC, Fleischmann RD, Peterson SN, Donohue-Rolfe A, Tzipori S, Pieper R.

BMC Microbiol. 2011 Jun 24;11:147. doi: 10.1186/1471-2180-11-147.


Recombinant expression and functional analysis of proteases from Streptococcus pneumoniae, Bacillus anthracis, and Yersinia pestis.

Kwon K, Hasseman J, Latham S, Grose C, Do Y, Fleischmann RD, Pieper R, Peterson SN.

BMC Biochem. 2011 May 5;12:17. doi: 10.1186/1471-2091-12-17.


Investigating the genome diversity of B. cereus and evolutionary aspects of B. anthracis emergence.

Papazisi L, Rasko DA, Ratnayake S, Bock GR, Remortel BG, Appalla L, Liu J, Dracheva T, Braisted JC, Shallom S, Jarrahi B, Snesrud E, Ahn S, Sun Q, Rilstone J, Okstad OA, Kolstø AB, Fleischmann RD, Peterson SN.

Genomics. 2011 Jul;98(1):26-39. doi: 10.1016/j.ygeno.2011.03.008. Epub 2011 Apr 5.


Monitoring the long-term molecular epidemiology of the pneumococcus and detection of potential 'vaccine escape' strains.

Pandya GA, McEllistrem MC, Venepally P, Holmes MH, Jarrahi B, Sanka R, Liu J, Karamycheva SA, Bai Y, Fleischmann RD, Peterson SN.

PLoS One. 2011 Jan 10;6(1):e15950. doi: 10.1371/journal.pone.0015950.


Tracing phylogenomic events leading to diversity of Haemophilus influenzae and the emergence of Brazilian Purpuric Fever (BPF)-associated clones.

Papazisi L, Ratnayake S, Remortel BG, Bock GR, Liang W, Saeed AI, Liu J, Fleischmann RD, Kilian M, Peterson SN.

Genomics. 2010 Nov;96(5):290-302. doi: 10.1016/j.ygeno.2010.07.005. Epub 2010 Jul 30.


Using chemical derivatization and mass spectrometric analysis to characterize the post-translationally modified Staphylococcus aureus surface protein G.

Suh MJ, Clark DJ, Parmer PP, Fleischmann RD, Peterson SN, Pieper R.

Biochim Biophys Acta. 2010 Jun;1804(6):1394-404. doi: 10.1016/j.bbapap.2010.02.006. Epub 2010 Feb 20.


Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation.

Pieper R, Huang ST, Parmar PP, Clark DJ, Alami H, Fleischmann RD, Perry RD, Peterson SN.

BMC Microbiol. 2010 Jan 29;10:30. doi: 10.1186/1471-2180-10-30.


Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

Bucasas KL, Pandya GA, Pradhan S, Fleischmann RD, Peterson SN, Belmont JW.

BMC Genet. 2009 Dec 18;10:85. doi: 10.1186/1471-2156-10-85.


Allelic exchange and mutant selection demonstrate that common clinical embCAB gene mutations only modestly increase resistance to ethambutol in Mycobacterium tuberculosis.

Safi H, Fleischmann RD, Peterson SN, Jones MB, Jarrahi B, Alland D.

Antimicrob Agents Chemother. 2010 Jan;54(1):103-8. doi: 10.1128/AAC.01288-09. Epub 2009 Oct 12.


The Shigella dysenteriae serotype 1 proteome, profiled in the host intestinal environment, reveals major metabolic modifications and increased expression of invasive proteins.

Pieper R, Zhang Q, Parmar PP, Huang ST, Clark DJ, Alami H, Donohue-Rolfe A, Fleischmann RD, Peterson SN, Tzipori S.

Proteomics. 2009 Nov;9(22):5029-45. doi: 10.1002/pmic.200900196.


Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay.

Pandya GA, Holmes MH, Petersen JM, Pradhan S, Karamycheva SA, Wolcott MJ, Molins C, Jones M, Schriefer ME, Fleischmann RD, Peterson SN.

BMC Microbiol. 2009 Oct 7;9:213. doi: 10.1186/1471-2180-9-213.


High quality protein microarray using in situ protein purification.

Kwon K, Grose C, Pieper R, Pandya GA, Fleischmann RD, Peterson SN.

BMC Biotechnol. 2009 Aug 23;9:72. doi: 10.1186/1472-6750-9-72.


Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome.

Kuntumalla S, Braisted JC, Huang ST, Parmar PP, Clark DJ, Alami H, Zhang Q, Donohue-Rolfe A, Tzipori S, Fleischmann RD, Peterson SN, Pieper R.

Proteome Sci. 2009 Jun 29;7:22. doi: 10.1186/1477-5956-7-22.


Integral and peripheral association of proteins and protein complexes with Yersinia pestis inner and outer membranes.

Pieper R, Huang ST, Clark DJ, Robinson JM, Alami H, Parmar PP, Suh MJ, Kuntumalla S, Bunai CL, Perry RD, Fleischmann RD, Peterson SN.

Proteome Sci. 2009 Feb 19;7:5. doi: 10.1186/1477-5956-7-5.


Temperature and growth phase influence the outer-membrane proteome and the expression of a type VI secretion system in Yersinia pestis.

Pieper R, Huang ST, Robinson JM, Clark DJ, Alami H, Parmar PP, Perry RD, Fleischmann RD, Peterson SN.

Microbiology. 2009 Feb;155(Pt 2):498-512. doi: 10.1099/mic.0.022160-0.


The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results.

Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R.

BMC Bioinformatics. 2008 Dec 9;9:529. doi: 10.1186/1471-2105-9-529.


Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change.

Pieper R, Huang ST, Clark DJ, Robinson JM, Parmar PP, Alami H, Bunai CL, Perry RD, Fleischmann RD, Peterson SN.

Proteomics. 2008 Apr;8(7):1442-58. doi: 10.1002/pmic.200700923.


Widespread Occurrence of Non-Enzymatic Deamidations of Asparagine Residues in Yersinia pestis Proteins Resulting from Alkaline pH Membrane Extraction Conditions.

Suh MJ, Alami H, Clark DJ, Parmar PP, Robinson JM, Huang ST, Fleischmann RD, Peterson SN, Pieper R.

Open Proteomics J. 2008 Jan 1;1:106-115.


A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform.

Pandya GA, Holmes MH, Sunkara S, Sparks A, Bai Y, Verratti K, Saeed K, Venepally P, Jarrahi B, Fleischmann RD, Peterson SN.

Nucleic Acids Res. 2007;35(21):e148. Epub 2007 Nov 15.


Transcriptional regulation of multi-drug tolerance and antibiotic-induced responses by the histone-like protein Lsr2 in M. tuberculosis.

Colangeli R, Helb D, Vilchèze C, Hazbón MH, Lee CG, Safi H, Sayers B, Sardone I, Jones MB, Fleischmann RD, Peterson SN, Jacobs WR Jr, Alland D.

PLoS Pathog. 2007 Jun;3(6):e87.


Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis.

Alland D, Lacher DW, Hazbón MH, Motiwala AS, Qi W, Fleischmann RD, Whittam TS.

J Clin Microbiol. 2007 Jan;45(1):39-46. Epub 2006 Nov 1.


Comparative proteomic analysis of Staphylococcus aureus strains with differences in resistance to the cell wall-targeting antibiotic vancomycin.

Pieper R, Gatlin-Bunai CL, Mongodin EF, Parmar PP, Huang ST, Clark DJ, Fleischmann RD, Gill SR, Peterson SN.

Proteomics. 2006 Aug;6(15):4246-58.


Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus.

Gatlin CL, Pieper R, Huang ST, Mongodin E, Gebregeorgis E, Parmar PP, Clark DJ, Alami H, Papazisi L, Fleischmann RD, Gill SR, Peterson SN.

Proteomics. 2006 Mar;6(5):1530-49.


Comparative whole-genome analysis of virulent and avirulent strains of Porphyromonas gingivalis.

Chen T, Hosogi Y, Nishikawa K, Abbey K, Fleischmann RD, Walling J, Duncan MJ.

J Bacteriol. 2004 Aug;186(16):5473-9.


Attenuation of late-stage disease in mice infected by the Mycobacterium tuberculosis mutant lacking the SigF alternate sigma factor and identification of SigF-dependent genes by microarray analysis.

Geiman DE, Kaushal D, Ko C, Tyagi S, Manabe YC, Schroeder BG, Fleischmann RD, Morrison NE, Converse PJ, Chen P, Bishai WR.

Infect Immun. 2004 Mar;72(3):1733-45.


Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays.

Peterson SN, Sung CK, Cline R, Desai BV, Snesrud EC, Luo P, Walling J, Li H, Mintz M, Tsegaye G, Burr PC, Do Y, Ahn S, Gilbert J, Fleischmann RD, Morrison DA.

Mol Microbiol. 2004 Feb;51(4):1051-70.


Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83.

Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM.

J Bacteriol. 2003 Sep;185(18):5591-601. Erratum in: J Bacteriol. 2004 Jan;186(2):593.


Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis.

Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, Eisen JA, Fraser CM, Fleischmann RD.

J Bacteriol. 2003 Jun;185(11):3392-9.


Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.

Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs WR Jr, Venter JC, Fraser CM.

J Bacteriol. 2002 Oct;184(19):5479-90.


Reduced immunopathology and mortality despite tissue persistence in a Mycobacterium tuberculosis mutant lacking alternative sigma factor, SigH.

Kaushal D, Schroeder BG, Tyagi S, Yoshimatsu T, Scott C, Ko C, Carpenter L, Mehrotra J, Manabe YC, Fleischmann RD, Bishai WR.

Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8330-5.


Improved quantitation and reproducibility in Mycobacterium tuberculosis DNA microarrays.

Schroeder BG, Peterson LM, Fleischmann RD.

J Mol Microbiol Biotechnol. 2002 Mar;4(2):123-6.


Comparative genomics and understanding of microbial biology.

Fraser CM, Eisen J, Fleischmann RD, Ketchum KA, Peterson S.

Emerg Infect Dis. 2000 Sep-Oct;6(5):505-12. Review.


Characterization of Porphyromonas gingivalis insertion sequence-like element ISPg5.

Califano JV, Kitten T, Lewis JP, Macrina FL, Fleischmann RD, Fraser CM, Duncan MJ, Dewhirst FE.

Infect Immun. 2000 Sep;68(9):5247-53.


Genome data: what do we learn?

Nierman WC, Eisen JA, Fleischmann RD, Fraser CM.

Curr Opin Struct Biol. 2000 Jun;10(3):343-8. Review.


Complete genome sequence of Neisseria meningitidis serogroup B strain MC58.

Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Venter JC.

Science. 2000 Mar 10;287(5459):1809-15.


Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.

White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg S, Smith HO, Venter JC, Fraser CM.

Science. 1999 Nov 19;286(5444):1571-7.


Genomic loci of the Porphyromonas gingivalis insertion element IS1126.

Dong H, Chen T, Dewhirst FE, Fleischmann RD, Fraser CM, Duncan MJ.

Infect Immun. 1999 Jul;67(7):3416-23.


Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.

Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM.

Nature. 1999 May 27;399(6734):323-9.


Alignment of whole genomes.

Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL.

Nucleic Acids Res. 1999 Jun 1;27(11):2369-76.


Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.

Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, Gwinn M, Dougherty B, Tomb JF, Fleischmann RD, Richardson D, Peterson J, Kerlavage AR, Quackenbush J, Salzberg S, Hanson M, van Vugt R, Palmer N, Adams MD, Gocayne J, Weidman J, Utterback T, Watthey L, McDonald L, Artiach P, Bowman C, Garland S, Fuji C, Cotton MD, Horst K, Roberts K, Hatch B, Smith HO, Venter JC.

Nature. 1997 Dec 11;390(6660):580-6.


DNA-PKcs: a T-cell tumour suppressor encoded at the mouse scid locus.

Jhappan C, Morse HC 3rd, Fleischmann RD, Gottesman MM, Merlino G.

Nat Genet. 1997 Dec;17(4):483-6.


The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.

Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC.

Nature. 1997 Nov 27;390(6658):364-70. Erratum in: Nature 1998 Jul 2;394(6688):101.


The complete genome sequence of the gastric pathogen Helicobacter pylori.

Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC.

Nature. 1997 Aug 7;388(6642):539-47. Erratum in: Nature 1997 Sep 25;389(6649):412.


Strategies for whole microbial genome sequencing and analysis.

Fraser CM, Fleischmann RD.

Electrophoresis. 1997 Aug;18(8):1207-16. Review.


DNA repeats identify novel virulence genes in Haemophilus influenzae.

Hood DW, Deadman ME, Jennings MP, Bisercic M, Fleischmann RD, Venter JC, Moxon ER.

Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):11121-5.


Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii.

Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NS, Venter JC.

Science. 1996 Aug 23;273(5278):1058-73.


The minimal gene complement of Mycoplasma genitalium.

Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison CA 3rd, Venter JC.

Science. 1995 Oct 20;270(5235):397-403.


Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence.

Adams MD, Kerlavage AR, Fleischmann RD, Fuldner RA, Bult CJ, Lee NH, Kirkness EF, Weinstock KG, Gocayne JD, White O, et al.

Nature. 1995 Sep 28;377(6547 Suppl):3-174.


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