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Robert Fleischmann

Research Profile

Genes & Molecular Sequences

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Oligonucleotide Array Sequence Analysis

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Moo-Jin Suh; Steven E Cagas; Natalie Fedorova Abrams; Robert D Fleischmann; Susan Hastings; William C Nierman; David S Perlin; Scott N Peterson; Rembert Pieper; Michelle Momany
Development stage-specific proteomic profiling uncovers small, lineage specific proteins most abundant in the Aspergillus Fumigatus conidial proteome.
Leka Papazisi; David Rasko; Shashikala Ratnayake; Brian G Remortel; Jennifer Rilstone; Shamira Shallom; Erik Snesrud; Qiang Sun; Susie Ahn; Lakshmi Appalla; Geoff R Bock; John C Braisted; Tatiana Dracheva; Robert D Fleischmann; Behnam Jarrahi; Anne-Brit Kolstø; Jia Liu; OA Okstad; Scott N Peterson
Investigating the genome diversity of B. cereus and evolutionary aspects of B. anthracis emergence.
Rembert Pieper; Moo-Jin Suh; Quanshun Zhang; John C Braisted; David J Clark; Robert D Fleischmann; Shih-Ting Huang; Samuel H Payne; Scott N Peterson; Saul Tzipori
Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies.

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All Publications

2012: Moo-Jin Suh; Steven E Cagas; Natalie Fedorova Abrams; Robert D Fleischmann; Susan Hastings; William C Nierman; David S Perlin; Scott N Peterson; Rembert Pieper; Michelle Momany
Development stage-specific proteomic profiling uncovers small, lineage specific proteins most abundant in the Aspergillus Fumigatus conidial proteome.
Proteome science 2012;10(1):30.
2011: Leka Papazisi; David Rasko; Shashikala Ratnayake; Brian G Remortel; Jennifer Rilstone; Shamira Shallom; Erik Snesrud; Qiang Sun; Susie Ahn; Lakshmi Appalla; Geoff R Bock; John C Braisted; Tatiana Dracheva; Robert D Fleischmann; Behnam Jarrahi; Anne-Brit Kolstø; Jia Liu; OA Okstad; Scott N Peterson
Investigating the genome diversity of B. cereus and evolutionary aspects of B. anthracis emergence.
Genomics 2011;98(1):26-39.
2011: Rembert Pieper; Moo-Jin Suh; Quanshun Zhang; John C Braisted; David J Clark; Robert D Fleischmann; Shih-Ting Huang; Samuel H Payne; Scott N Peterson; Saul Tzipori
Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies.
PloS one 2011;6(11):e26554.
2011: Keehwan Kwon; Saeeda Latham; Rembert Pieper; Yu Do; Robert D Fleischmann; Carissa Grose; Jeremy Hasseman; Scott N Peterson
Recombinant expression and functional analysis of proteases from Streptococcus pneumoniae, Bacillus anthracis, and Yersinia pestis.
BMC biochemistry 2011;12():17.
2011: Gagan A Pandya; M Catherine McEllistrem; Pratap Venepally; Michael H Holmes; Behnam Jarrahi; Ravi Sanka; Jia Liu; Svetlana A Karamycheva; Yun Bai; Robert D Fleischmann; Scott N Peterson
Monitoring the long-term molecular epidemiology of the pneumococcus and detection of potential 'vaccine escape' strains.
PloS one 2011;6(1):e15950.
2010: Leka Papazisi; Shashikala Ratnayake; Brian G Remortel; Geoffrey R Bock; Wei Liang; Alexander I Saeed; Jia Liu; Robert D Fleischmann; Mogens Kilian; Scott N Peterson
Tracing phylogenomic events leading to diversity of Haemophilus influenzae and the emergence of Brazilian Purpuric Fever (BPF)-associated clones.
Genomics 2010;96(5):290-302.
2010: Moo-Jin Suh; David J Clark; Prashanth P Parmer; Robert D Fleischmann; Scott N Peterson; Rembert Pieper
Using chemical derivatization and mass spectrometric analysis to characterize the post-translationally modified Staphylococcus aureus surface protein G.
Biochimica et biophysica acta 2010;1804(6):1394-404.
2010: Rembert Pieper; Shih-Ting Huang; Prashanth P Parmar; David J Clark; Hamid Alami; Robert D Fleischmann; Robert D Perry; Scott N Peterson
Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation.
BMC microbiology 2010;10():30.
2010: Hassan Safi; Robert D Fleischmann; Scott N Peterson; Marcus B Jones; Behnam Jarrahi; David Alland
Allelic exchange and mutant selection demonstrate that common clinical embCAB gene mutations only modestly increase resistance to ethambutol in Mycobacterium tuberculosis.
Antimicrobial agents and chemotherapy 2010;54(1):103-8.
2009: Rembert Pieper; Quanshun Zhang; Prashanth P Parmar; Shih-Ting Huang; David J Clark; Hamid Alami; Arthur Donohue-Rolfe; Robert D Fleischmann; Scott N Peterson; Saul Tzipori
The Shigella dysenteriae serotype 1 proteome, profiled in the host intestinal environment, reveals major metabolic modifications and increased expression of invasive proteins.
Proteomics 2009;9(22):5029-45.
2009: Rembert Pieper; Shih-Ting Huang; Jeffrey M Robinson; David J Clark; Hamid Alami; Prashanth P Parmar; Robert D Perry; Robert D Fleischmann; Scott N Peterson
Temperature and growth phase influence the outer-membrane proteome and the expression of a type VI secretion system in Yersinia pestis.
Microbiology (Reading, England) 2009;155(Pt 2):498-512.
2009: Gagan A Pandya; Michael H Holmes; Jeannine M Petersen; Sonal Pradhan; Svetlana A Karamycheva; Mark J Wolcott; Claudia Molins; Marcus Jones; Martin E Schriefer; Robert D Fleischmann; Scott N Peterson
Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay.
BMC microbiology 2009;9():213.
2009: Keehwan Kwon; Carissa Grose; Rembert Pieper; Gagan A Pandya; Robert D Fleischmann; Scott N Peterson
High quality protein microarray using in situ protein purification.
BMC biotechnology 2009;9():72.
2009: Srilatha Kuntumalla; John C Braisted; Shih-Ting Huang; Prashanth P Parmar; David J Clark; Hamid Alami; Quanshun Zhang; Arthur Donohue-Rolfe; Saul Tzipori; Robert D Fleischmann; Scott N Peterson; Rembert Pieper
Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome.
Proteome science 2009;7():22.
2009: Rembert Pieper; Shih-Ting Huang; David J Clark; Jeffrey M Robinson; Hamid Alami; Prashanth P Parmar; Moo-Jin Suh; Srilatha Kuntumalla; Christine L Bunai; Robert D Perry; Robert D Fleischmann; Scott N Peterson
Integral and peripheral association of proteins and protein complexes with Yersinia pestis inner and outer membranes.
Proteome science 2009;7():5.
2008: Rembert Pieper; Shih-Ting Huang; David J Clark; Jeffrey M Robinson; Prashanth P Parmar; Hamid Alami; Christine L Bunai; Robert D Perry; Robert D Fleischmann; Scott N Peterson
Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change.
Proteomics 2008;8(7):1442-58.
2008: John C Braisted; Srilatha Kuntumalla; Christine Vogel; Edward M Marcotte; Alan R Rodrigues; Rong Wang; Shih-Ting Huang; Erik S Ferlanti; Alexander I Saeed; Robert D Fleischmann; Scott N Peterson; Rembert Pieper
The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results.
BMC bioinformatics 2008;9():529.
2007: Keehwan Kwon; Rembert Pieper; Shamira Shallom; Carissa Grose; Erika Kwon; Yu Do; Saeeda Latham; Hamid Alami; Shih-Ting Huang; Christine L Gatlin; Leka Papazisi; Robert D Fleischmann; Scott Peterson
A correlation analysis of protein characteristics associated with genome-wide high throughput expression and solubility of Streptococcus pneumoniae proteins.
Protein expression and purification 2007;55(2):368-78.
2007: Roberto Colangeli; danica helb; Catherine Vilchèze; Manzour Hernando Hazbón; Chee-Gun Lee; Hassan Safi; Brendan Sayers; Irene Sardone; Marcus B Jones; Robert D Fleischmann; Scott N Peterson; William R. Jacobs Jr.; David Alland
Transcriptional regulation of multi-drug tolerance and antibiotic-induced responses by the histone-like protein Lsr2 in M. tuberculosis.
PLoS pathogens 2007;3(6):e87.
2007: Gagan A Pandya; Michael H Holmes; Sirisha Sunkara; Andrew Sparks; Yun Bai; Kathleen Verratti; Kelly Saeed; Pratap Venepally; Behnam Jarrahi; Robert D Fleischmann; Scott N Peterson
A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform.
Nucleic acids research 2007;35(21):e148.
2007: David Alland; David W Lacher; Manzour Hernando Hazbón; Alifiya Motiwala; Weihong Qi; Robert D Fleischmann; Thomas S Whittam
Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis.
Journal of clinical microbiology 2007;45(1):39-46.
2006: Rembert Pieper; Christine L Gatlin-Bunai; Emmanuel F Mongodin; Prashanth P Parmar; Shih-Ting Huang; David J Clark; Robert D Fleischmann; Steven R Gill; Scott N Peterson
Comparative proteomic analysis of Staphylococcus aureus strains with differences in resistance to the cell wall-targeting antibiotic vancomycin.
Proteomics 2006;6(15):4246-58.
2006: Christine L Gatlin; Rembert Pieper; Shih-Ting Huang; Emmanuel F Mongodin; Elizabeth Gebregeorgis; Prashanth P Parmar; David J Clark; Hamid Alami; Leka Papazisi; Robert D Fleischmann; Steven R Gill; Scott N Peterson
Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus.
Proteomics 2006;6(5):1530-49.
2006: Ingrid Filliol; Alifiya Motiwala; Magali Cavatore; Weihong Qi; Manzour Hernando Hazbón; Miriam Bobadilla Del Valle; Janet Fyfe; Lourdes García-García; Nalin Rastogi; Christophe Sola; Thierry Zozio; martha guerrero; Clara Inés León; Jonathan Crabtree; Samuel V Angiuoli; Kathleen D Eisenach; Riza Durmaz; Moses L Joloba; Adrian Rendón; José Sifuentes-Osornio; Alfredo Ponce-De-León; M Donald Cave; Robert D Fleischmann; Thomas S Whittam; David Alland
Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set.
Journal of bacteriology 2006;188(2):759-72.
2004: Tsute Chen; Yumiko Hosogi; Kiyoshi Nishikawa; Kevin Abbey; Robert D Fleischmann; Jennifer Walling; Margaret J Duncan
Comparative whole-genome analysis of virulent and avirulent strains of Porphyromonas gingivalis.
Journal of bacteriology 2004;186(16):5473-9.
2004: Deborah E Geiman; Deepak Kaushal; Chiew Ko; Sandeep Tyagi; Yukari C Manabe; Benjamin G Schroeder; Robert D Fleischmann; Norman E Morrison; Paul J Converse; Ping Chen; William R Bishai
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.
Infection and immunity 2004;72(3):1733-45.
2004: Scott N Peterson; Chang Kyoo Sung; Robin Cline; Bhushan Vijay Desai; Erik C Snesrud; Ping Luo; Jennifer Walling; Haiying Li; Michelle Mintz; Getahun Tsegaye; Patrick C Burr; Yu Do; Susie Ahn; Joseph Gilbert; Robert D Fleischmann; Donald A Morrison
Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays.
Molecular microbiology 2004;51(4):1051-70.
2003: Karen E Nelson; Robert D Fleischmann; Robert T Deboy; Ian Paulsen; Derrick E Fouts; Jonathan Eisen; Sean C Daugherty; Robert J Dodson; A Scott Durkin; Michelle G Giglio; Daniel H Haft; James F Kolonay; William C Nelson; Tanya Mason; Luke J Tallon; Jessica Gray; David Granger; Hervé Tettelin; Hong Dong; Jamie L Galvin; Margaret J Duncan; Floyd E Dewhirst; Claire M Fraser-Liggett
Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83.
Journal of bacteriology 2003;185(18):5591-601.
2003: David Alland; Thomas S Whittam; Megan B Murray; M Donald Cave; Manzour H Hazbon; Kim Dix; Mark Kokoris; Andreas Duesterhoeft; Jonathan Eisen; Claire M Fraser-Liggett; Robert D Fleischmann
Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis.
Journal of bacteriology 2003;185(11):3392-9.
2002: Robert D Fleischmann; David Alland; Jonathan Eisen; L Carpenter; Owen R White; J Peterson; Robert T Deboy; Robert J Dodson; Michelle G Giglio; Daniel H Haft; EK Hickey; James F Kolonay; William C Nelson; Lowell Umayam; Maria D Ermolaeva; Steven L Salzberg; Arthur L Delcher; Teresa Utterback; Janice Weidman; Hoda Khouri; J Gill; A Mikula; William R Bishai; W R Jacobs Jr; J Craig Venter; Claire M Fraser-Liggett
Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.
Journal of bacteriology 2002;184(19):5479-90.
2002: Deepak Kaushal; Benjamin G Schroeder; Sandeep Tyagi; Tetsuyuki Yoshimatsu; Cherise Scott; Chiew Ko; Liane Carpenter; Jyoti Mehrotra; Yukari C Manabe; Robert D Fleischmann; William R Bishai
Reduced immunopathology and mortality despite tissue persistence in a Mycobacterium tuberculosis mutant lacking alternative sigma factor, SigH.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(12):8330-5.
2002: Benjamin G Schroeder; Liane M Peterson; Robert D Fleischmann
Improved quantitation and reproducibility in Mycobacterium tuberculosis DNA microarrays.
Journal of molecular microbiology and biotechnology 2002;4(2):123-6.
2000: Claire M Fraser-Liggett; Jonathan Eisen; Robert D Fleischmann; KA Ketchum; S Peterson
Comparative genomics and understanding of microbial biology.
Emerging infectious diseases 2000;6(5):505-12.
2000: Joseph Vincent Califano; Todd Kitten; Janina P Lewis; Francis L Macrina; Robert D Fleischmann; Claire M Fraser-Liggett; Margaret J Duncan; Floyd E Dewhirst
Characterization of Porphyromonas gingivalis insertion sequence-like element ISPg5.
Infection and immunity 2000;68(9):5247-53.
2000: William C Nierman; Jonathan Eisen; Robert D Fleischmann; Claire M Fraser-Liggett
Genome data: what do we learn?
Current opinion in structural biology 2000;10(3):343-8.
1999: H Dong; Tsute Chen; Floyd E Dewhirst; Robert D Fleischmann; Claire M Fraser-Liggett; Margaret J Duncan
Genomic loci of the Porphyromonas gingivalis insertion element IS1126.
Infection and immunity 1999;67(7):3416-23.
1999: Arthur L Delcher; S Kasif; Robert D Fleischmann; J Peterson; Owen R White; Steven L Salzberg
Alignment of whole genomes.
Nucleic acids research 1999;27(11):2369-76.
1999: Karen E Nelson; RA Clayton; Steven R Gill; Michelle G Giglio; Robert J Dodson; Daniel H Haft; EK Hickey; J D Peterson; William C Nelson; KA Ketchum; L McDonald; Teresa Utterback; JA Malek; K D Linher; M M Garrett; A M Stewart; M D Cotton; M S Pratt; C A Phillips; D Richardson; John F Heidelberg; Granger Sutton; Robert D Fleischmann; Jonathan Eisen; Owen R White; Steven L Salzberg; Hamilton O Smith; J Craig Venter; Claire M Fraser-Liggett
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
Nature 1999;399(6734):323-9.
1996: Carol Bult; Owen R White; Gary J Olsen; L Zhou; Robert D Fleischmann; Granger Sutton; J A Blake; L M FitzGerald; R A Clayton; J D Gocayne; A R Kerlavage; B A Dougherty; J F Tomb; Mark D Adams; C I Reich; Ross Overbeek; Ewen F Kirkness; K G Weinstock; J M Merrick; A Glodek; J L Scott; N S Geoghagen; J Craig Venter
Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii.
Science (New York, N.Y.) 1996;273(5278):1058-73.
1995: Claire M Fraser-Liggett; J D Gocayne; Owen R White; Mark D Adams; R A Clayton; Robert D Fleischmann; Carol Bult; A R Kerlavage; G Sutton; J M Kelley; R D Fritchman; J F Weidman; K V Small; M Sandusky; J Fuhrmann; D Nguyen; T R Utterback; D M Saudek; C A Phillips; J M Merrick; J F Tomb; B A Dougherty; Kenneth Bott; P C Hu; T S Lucier; S N Peterson; Hamilton O Smith; Clyde A Hutchison; J Craig Venter
The minimal gene complement of Mycoplasma genitalium.
Science (New York, N.Y.) 1995;270(5235):397-403.
1995: Mark D Adams; A R Kerlavage; Robert D Fleischmann; R A Fuldner; Carol Bult; N H Lee; Ewen F Kirkness; K G Weinstock; J D Gocayne; Owen R White
Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence.
Nature 1995;377(6547 Suppl):3-174.
1995: Hamilton O Smith; J F Tomb; B A Dougherty; Robert D Fleischmann; J Craig Venter
Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome.
Science (New York, N.Y.) 1995;269(5223):538-40.
1995: Robert D Fleischmann; Mark D Adams; Owen R White; R A Clayton; Ewen F Kirkness; A R Kerlavage; Carol Bult; J F Tomb; B A Dougherty; J M Merrick
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Science (New York, N.Y.) 1995;269(5223):496-512.