· Genome-Wide Screen for Salmonella Genes Required for Long-Term Systemic Infection of the Mouse

· Trevor D. Lawley, Kaman Chan, Lucinda J. Thompson, Charles C. Kim, Gregory R. Govoni, Denise M. Monack


· Supplementary Figure 1.pdf

· Supplementary Table 1

· Supplementary Table 2

· Supplementary data from Figure 1 for TreeView.txt


· Microarray-based detection of S. enterica sv. Typhimurium transposon mutants that cannot survive in macrophages and mice

· Kaman Chan, Charles C. Kim, and Stanley Falkow


· Appendices: Supplementary table legends and supplementary Figure A1

· Table A1: RAW 264.7 macrophage SGL

· Table A2: Balb/cJ mouse SGL


· Chronic Helicobacter pylori infection in C57BL/6 and BALB/c mice using SS1 and a newly identified mouse-adapted strain (SS2000) (in review)

· Lucinda J. Thompson, Stephen J. Danon, John E. Wilson, Jani L. O'Rourke, Nina R. Salama, Stanley Falkow, Hazel Mitchell, and Adrian Lee


· Genes differing between SS1 and SS2000


· A High Throughput Method For Detecting Genomic Deletion Polymorhpisms

· Y.-O.L. Goguet de la Salmonière, C.C. Kim, A.G. Tsolaki, A.S. Pym, M.S. Siegrist, P.M. Small

· Algorithm description

· Software


· Phosphorylation-Independent Effects of CagA during Interaction between Helicobacter pylori and T84 Polarized Monolayers

· S.H. El-Etr, A. Mueller, L.S. Tompkins, S. Falkow and D.S. Merrell

· J Infect Dis. 2004 Oct 15;190(8):1516-23

· All files

· PAI-dependent genes.xls

· PAI-independent genes.CNV

· PAI-independent genes.xls

· T84 and AGS comparison.xls

· T84 and AGS comparisons.CNV

· WT H. pylori Gene Lists.xls


· Profiling of microdissected gastric epithelial cells reveals a cell type specific response to Helicobacter pylori infection

· Mueller A, Merrell DS, Grimm J, Falkow S

· Chief, Mucus and Pareital Cell Signatures

· Comparison of study I and II_changes at 28 days pi

· Gene expression changes in parietal cells in response to 7 days of omeprazole treatment

· Genes that are differentially expressed in infected compared to mock-infected mice (mucus producing cells)


· Disruption of the epithelial apical-junctional complex by Helicobacter pylori CagA

· Amieva MR, Vogelmann R, Covacci A, Tompkins LS, Nelson WJ, Falkow S

· Science. 2003 May 30;300(5624):1430-4

· Significance Analysis of Lexical Bias in Microarray Data

· Charles C. Kim and S. Falkow

· BMC Bioinformatics. 2003 Apr 3;4(1):12 (Biomed Central) BMC Bioinformatics. 2003 Apr 3;4(1):12 (PubMed Central)


· Software and example data (also available at above manuscript links)



· Live Imaging of Salmonella and Yersinia Induced Macrophage Death

· D.M. Monack and S. Falkow


· Chapter 4 from Monack Thesis

· Salmonella Movie (requires Quicktime Player)

· Yersinia Movie (requires Quicktime Player)



· Gene expression profiling of Helicobacter pylori reveals a growth phase dependent switch in virulence gene expression

· L.J. Thompson, D.S. Merrell, B.A. Neilan, H. Mitchell, A. Lee and S. Falkow

· Infect Immun. 2003 May;71(5):2643-55


· Supplementary table 1 (Mac users should save these files and open manually from Excel)

· Supplementary table 2



· Genomic Comparison of Salmonella enterica serovars and Salmonella bongori using a Typhimurium DNA Microarray

· Kaman Chan, Stephen Baker, Charles C. Kim, Corrella S. Detweiler, Gordon Dougan, and Stanley Falkow

· Journal of Bacteriology, January 2003, p. 553-563, Vol. 185, No. 2

· Note: The following appendix files were updated May 2004.

· Appendix 1

· Appendix 2

· Appendix 3

· Appendix 4

· Appendix 5



· pH regulated Gene Expression of the Gastric Pathogen Helicobacter pylori

· D. Scott Merrell, Maria L. Goodrich, Glen Otto, Lucy Tompkins, and Stanley Falkow

· Infect Immun. 2003 Jun;71(6):3529-39


· Download Movies for PC or Mac (requires Quicktime Player)

· Supplementary Table 1



· Improved Analytical Methods for Microarray-Based Genome Composition Analysis

· Charles C. Kim, Elizabeth A. Joyce, Kaman Chan, Stanley Falkow

· Genome Biology 2002 3(11):research0065.1-0065.17

· All tables are in tab-delimited text format, following the .pcl format headers.

· Table 1: Raw C. jejuni log(2) ratios (tab-delimited, .pcl format)

· Table 2: C. jejuni GACKed trinary output (tab-delimited, .pcl format)

· Table 3: Raw H. pylori log(2) ratios (tab-delimited, .pcl format)

· Table 4: H. pylori GACKed trinary output (tab-delimited, .pcl format)

· Table 5: C. jejuni divergent genes (Excel format)

· Table 6: H. pylori divergent genes (Excel format)


Software and manual are available here


Falkow Main Page