Research Topics
| M McClellandSummaryAffiliation: Sidney Kimmel Cancer Center Country: USA Publications
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Publications
Host restriction of Salmonella enterica serotype Typhimurium pigeon isolates does not correlate with loss of discrete genesHelene L Andrews-Polymenis
Department of Medical Microbiology and Immunology, College of Medicine, Texas A and M University System Health Science Center, College Station, TX 77843, USA
J Bacteriol 186:2619-28. 2004..We conclude that serotype Typhimurium phage types with broad host range do not possess genetic islands influencing host restriction, which are absent from the host-restricted pigeon isolates...- Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chipShilpi Arora
Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
Genome Biol 9:R166. 2008..We examined the hypothesis that Egr1 regulates genes that mediate this process by use of a chip-on-chip protocol in human tumorigenic prostate M12 cells... - Genome-wide analysis of the PreA/PreB (QseB/QseC) regulon of Salmonella enterica serovar TyphimuriumMassimo Merighi
Department of Molecular Virology, Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210, USA
BMC Microbiol 9:42. 2009..Typhimurium) pmrAB operon, which encodes an important virulence-associated TCS... - Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: analysis of MX-treated SalmonellaWilliam O Ward
Environmental Carcinogenesis Division, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA
BMC Bioinformatics 8:378. 2007.... - Comparison of sample sequences of the Salmonella typhi genome to the sequence of the complete Escherichia coli K-12 genomeM McClelland
Sidney Kimmel Cancer Center, San Diego, California 92121, USA
Infect Immun 66:4305-12. 1998..typhi from E. coli K-12. The need for automatic methods to more effectively exploit sample sequences is discussed... 
Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoidMichael McClelland
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, California 92121, USA
Nat Genet 36:1268-74. 2004..Loss of function also occurs by mutation in different genes in the same pathway (e.g., in chemotaxis and in the production of fimbriae)...- Complete genome sequence of Salmonella enterica serovar Typhimurium LT2M McClelland
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, California 92121, USA
Nature 413:852-6. 2001..Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets... - Characterization of Salmonella enterica subspecies I genovars by use of microarraysS Porwollik
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92103, USA
J Bacteriol 186:5883-98. 2004..Just as serology has proved useful for understanding the host range and pathogenic manifestations of Salmonella, genovars are likely to further define previously unrecognized specific features of Salmonella infections... - The DeltauvrB mutations in the Ames strains of Salmonella span 15 to 119 genesS Porwollik
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92121, USA
Mutat Res 483:1-11. 2001..In general, microarrays will be useful for characterizing the extent and nature of deletion and amplification mutations... - Differences in gene content between Salmonella enterica serovar Enteritidis isolates and comparison to closely related serovars Gallinarum and DublinS Porwollik
Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, California 92121, USA
J Bacteriol 187:6545-55. 2005..These differences in gene content could be useful in DNA-based typing and in understanding the different phenotypes of these related serovars... 
WebArray: an online platform for microarray data analysisXiaoqin Xia
Genomic Core Facility, Sidney Kimmel Cancer Center, San Diego, CA 92121, USA
BMC Bioinformatics 6:306. 2005....- Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysisSteffen Porwollik
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92121, USA
Proc Natl Acad Sci U S A 99:8956-61. 2002..For example, at least 425 close homologues of LT2 genes may have been laterally transferred into Salmonella and then between Salmonella lineages... - WebArrayDB: cross-platform microarray data analysis and public data repositoryXiao Qin Xia
Vaccine Research Institute San Diego, San Diego, CA 92121, USA
Bioinformatics 25:2425-9. 2009..Cross-platform microarray analysis is an increasingly important research tool, but researchers still lack open source tools for storing, integrating and analyzing large amounts of microarray data obtained from different array platforms... - Lateral gene transfer in SalmonellaSteffen Porwollik
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92121, USA
Microbes Infect 5:977-89. 2003..Therefore, lateral gene transfer (LGT) plays an important role in diversity among Salmonella. Overall, almost one quarter of the entire S. enterica sv Typhimurium genome may have been introduced by LGT... - Differences in gene content among Salmonella enterica serovar typhi isolatesE F Boyd
Sidney Kimmel Cancer Center, San Diego, California 92121, USA
J Clin Microbiol 41:3823-8. 2003..Overall, these differences in gene content indicate that even within a highly clonal bacterial population the genomic reservoir is unstable... - Evaluating oligonucleotide properties for DNA microarray probe designXiao Qin Xia
Lechner Haag Genomics Core, Vaccine Research Institute of San Diego, 10835 Road to the Cure, Suite 150, San Diego, CA 92121, USA
Nucleic Acids Res 38:e121. 2010..Programs and correlation parameters from this study are freely available to facilitate the design of DNA microarray oligonucleotide probes... - TabSQL: a MySQL tool to facilitate mapping user data to public databasesXiao Qin Xia
Vaccine Research Institute of San Diego, 10835 Road to the Cure, San Diego, CA 92121, USA
BMC Bioinformatics 11:342. 2010..With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases... - Vertical arrays: microarrays of complex mixtures of nucleic acidsRosana Risques
Department of Molecular Biology and Cancer Genetics, Sidney Kimmel Cancer Center, San Diego, CA, USA
Methods Mol Biol 317:99-109. 2006..In cases where the number of genes is limited, but the number of experiments is very large, vertical arrays may be advantageous... - Analysis of pools of targeted Salmonella deletion mutants identifies novel genes affecting fitness during competitive infection in miceCarlos A Santiviago
Sidney Kimmel Cancer Center, San Diego, CA, USA
PLoS Pathog 5:e1000477. 2009..We refer to the method as Array-based analysis of cistrons under selection (ABACUS)... - Determination of the gene content of Salmonella genomes by microarray analysisSteffen Porwollik
Sidney Kimmel Cancer Center, San Diego, CA, USA
Methods Mol Biol 394:89-103. 2007.... - DNA amplification and rearrangements in archival Salmonella enterica serovar Typhimurium LT2 culturesSteffen Porwollik
Sidney Kimmel Cancer Center, San Diego, California 92121, USA
J Bacteriol 186:1678-82. 2004..These results demonstrate that storage in stabs over time at room temperature not only allows for further bacterial growth but also may produce an environment that selects for a variety of mutations, including genomic rearrangements... - A non-redundant microarray of genes for two related bacteriaSteffen Porwollik
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92121, USA
Nucleic Acids Res 31:1869-76. 2003..Non-redundant DNA arrays could be constructed for any group of closely related organisms that differ by the presence and absence of a few genes... - Enhanced microarray performance using low complexity representations of the transcriptomeGaelle Rondeau
Sidney Kimmel Cancer Center 10835 Altman Row, San Diego, CA 92121, USA
Nucleic Acids Res 33:e100. 2005..Thus, this target preparation strategy considerably increases the sensitivity of cDNA microarrays... - Assessment of gene expression in many samples using vertical arraysRosa Ana Risques
Sidney Kimmel Cancer Center, 10905 Road to the Cure, San Diego, CA 92121, USA
Nucleic Acids Res 36:e60. 2008..Here, we demonstrate the quantitative capabilities of vertical arrays, including the sensitivity and accuracy of the method and the number of subsets needed to achieve this accuracy for most expressed genes... - Identification of new flagellar genes of Salmonella enterica serovar TyphimuriumJonathan Frye
Sidney Kimmel Cancer Center, San Diego, California 92121, USA
J Bacteriol 188:2233-43. 2006..Null alleles in cheV, mcpA, mcpB, mcpC, and srfB did not affect motility, while deletion of yhjH did result in reduced motility compared to that of the wild type... - Messenger RNAs under differential translational control in Ki-ras-transformed cellsJean Spence
Sidney Kimmel Cancer Center, San Diego, CA, USA
Mol Cancer Res 4:47-60. 2006.... 
Salmonella promoters preferentially activated inside tumorsNabil Arrach
Sidney Kimmel Cancer Center, AntiCancer, Inc, and Department of Surgery, University of California, San Diego, San Diego, California, USA
Cancer Res 68:4827-32. 2008..The expression of therapeutics in Salmonella under the regulation of one or more promoters that are activated preferentially in tumors has the potential to improve the targeting of drug delivery...- Survey of differentially methylated promoters in prostate cancer cell linesYipeng Wang
Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
Neoplasia 7:748-60. 2005.... - High-throughput screening for salmonella avirulent mutants that retain targeting of solid tumorsNabil Arrach
Sanford Burnham Medical Research Institute, La Jolla, California 92121, USA
Cancer Res 70:2165-70. 2010..In addition, an STM3120 mutant successfully targeted tumors after intragastric delivery, opening up the oral route as an option for therapy administration... - Distinct DNA methylation profiles between adenocarcinoma and squamous cell carcinoma of human uterine cervixEun Ju Lee
Vaccine Research Institute of San Diego, San Diego, CA, USA
Oncol Res 18:401-8. 2010..Therefore, we have identified the 21 genes with differential methylation pattern between ACA and SCC and, furthermore, we found that PAK6 and NOGOR could be useful markers of ACA to be distinct from SCC... - Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced tree knotsAna Maria Rojas
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92121, USA
Int J Syst Evol Microbiol 54:2217-22. 2004..nov. is proposed. The isolates are available at CFBP, CECT and ATCC. The G+C content is 52+/-0.5 mol%. The type strain is CFBP 6631(T) (=A37(T)=ATCC 700880(T)=CECT 5263(T))... - Identification of promoters bound by c-Jun/ATF2 during rapid large-scale gene activation following genotoxic stressJun Hayakawa
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, California 92121, USA
Mol Cell 16:521-35. 2004..Thus, the genotoxic stress response occurs at least partly via activation of ATF2 and c-Jun, leading to large-scale coordinate gene expression dominated by genes of DNA repair... - Host gene expression changes and DNA amplification during temperate phage inductionJonathan G Frye
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92121, USA
J Bacteriol 187:1485-92. 2005..Escape replication is probably widespread; large regions of host genome amplification were also observed after phage induction in serovar Typhimurium strains SL1344 and 14028s at the suspected integration site of prophage genomes... - Major transcript variants of VAV3, a new member of the VAV family of guanine nucleotide exchange factorsT Trenkle
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA, USA
Gene 245:139-49. 2000..TGF-beta and EGF reversibly down-regulate the abundance of the VAV3. 1 transcript in HaCaT keratinocytes, representing the first observation of transcript regulation of a member of the VAV family by a growth factor... - Microarray analysis using RNA arbitrarily primed PCRSteven Ringquist
Sidney Kimmel Cancer Center, San Diego, CA, USA
Methods Mol Biol 226:245-54. 2003 - Salmonella serovar identification using PCR-based detection of gene presence and absenceNabil Arrach
Sidney Kimmel Cancer Center, 10905 Road to the Cure, San Diego, CA 92121, USA
J Clin Microbiol 46:2581-9. 2008..Thus, a typing methodology based on these predictive genes would generally alert users if there is an error, an unexpected polymorphism, or a potential new genovar... - DNA microarray-based typing of an atypical monophasic Salmonella enterica serovarJavier Garaizar
Sidney Kimmel Cancer Center, San Diego, California 92121, USA
J Clin Microbiol 40:2074-8. 2002..Recent isolates have acquired a more-complete subset of homologues to this virulence plasmid. In general, microarrays can provide useful complementary data to other typing methods... - The wisdom of the commons: ensemble tree classifiers for prostate cancer prognosisJames A Koziol
The Scripps Research Institute, La Jolla, San Diego, CA, USA
Bioinformatics 25:54-60. 2009..Moreover, the consensus classifications were independent predictors of time to progression compared to known clinical prognostic factors... - EnteriX 2003: Visualization tools for genome alignments of EnterobacteriaceaeLiliana Florea
Informatics Research, Celera Applied Biosystems, 45 W Gude Drive, Rockville, MD 20850, USA
Nucleic Acids Res 31:3527-32. 2003..The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments... - Global regulation by CsrA in Salmonella typhimuriumSara D Lawhon
College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh 27606, USA
Mol Microbiol 48:1633-45. 2003.... - Selective silencing of foreign DNA with low GC content by the H-NS protein in SalmonellaWilliam Wiley Navarre
Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
Science 313:236-8. 2006..Characteristic GC/AT ratios of bacterial genomes may facilitate discrimination between a cell's own DNA and foreign DNA... - Transcriptome of Salmonella enterica serovar Typhi within macrophages revealed through the selective capture of transcribed sequencesSebastien P Faucher
Department of Microbiology and Immunology, University of Montreal, C P 6128 Succursale Centre Ville, Montreal, QC, Canada H3C 3J7
Proc Natl Acad Sci U S A 103:1906-11. 2006.... - Identification of specific gene sequences conserved in contemporary epidemic strains of Salmonella entericaMin-Su Kang
Department of Veterinary Microbiology and Pathology, Washington State University, 402 Bustad Hall, Pullman, WA 99164-7040, USA
Appl Environ Microbiol 72:6938-47. 2006..The emergence of epidemic MDR strains may therefore be associated with the presence of fitness-associated genetic factors in addition to their antimicrobial resistance genes... - Microarray for molecular typing of Salmonella enterica serovarsJoy Scaria
Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
Mol Cell Probes 22:238-43. 2008.... - Microarray analysis identifies Salmonella genes belonging to the low-shear modeled microgravity regulonJames W Wilson
Tulane U, New Orleans, LA
Proc Natl Acad Sci U S A 99:13807-12. 2002..The results provide important insight about the Salmonella LSMMG response and could provide clues for the functioning of known Salmonella virulence systems or the identification of uncharacterized bacterial virulence strategies... - Nitric oxide antagonizes the acid tolerance response that protects Salmonella against innate gastric defensesTravis J Bourret
Department of Microbiology, University of Colorado Health Sciences Center, Aurora, Colorado, United States of America
PLoS ONE 3:e1833. 2008..The mechanisms by which these reactive species exert antimicrobial activity in the gastric lumen are, however, poorly understood... - Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-ChipClaudia Hoemme
Department of Medicine, Hematology and Oncology and Interdisciplinary Center for Clinical Research IZKF, University of Munster, Domagkstrasse 3, Munster, Germany
Blood 111:2887-95. 2008..Taken together, our results reveal that the transcription factor PML-RARalpha regulates key cancer-related genes and pathways by inducing a repressed chromatin formation on its direct genomic target genes... - Low-Shear modeled microgravity alters the Salmonella enterica serovar typhimurium stress response in an RpoS-independent mannerJames W Wilson
Tulane U Med Ctr, New Orleans, LA
Appl Environ Microbiol 68:5408-16. 2002..Moreover, our studies also indicate that low-shear MMG can be added to a short list of growth conditions that can serve to preadapt an rpoS mutant for resistance to multiple environmental stresses... - Microarray analysis of Mu transposition in Salmonella enterica, serovar Typhimurium: transposon exclusion by high-density DNA binding proteinsDipankar Manna
Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Mol Microbiol 66:315-28. 2007..Our data show that competition between cellular proteins and transposition proteins on plasmids and the chromosome is a dominant factor controlling the genetic footprint of transposons in living cells... - In silico dissection of cell-type-associated patterns of gene expression in prostate cancerRobert O Stuart
Veterans Affairs San Diego Healthcare System, and Department of Medicine and John and Rebecca Moores UCSD Cancer Center, University of California at San Diego, La Jolla, USA
Proc Natl Acad Sci U S A 101:615-20. 2004..The results provide patterns of gene expression for these three lineages with relevance to pathogenetic, diagnostic, and therapeutic considerations... - Alternative sigma factor interactions in Salmonella: sigma and sigma promote antioxidant defences by enhancing sigma levelsIel Soo Bang
Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
Mol Microbiol 56:811-23. 2005..Interactions between alternative sigma factors permit the integration of diverse stress signals to produce coordinated genetic responses... - Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimuriumPieter Monsieurs
ESAT-SCD, K.U. Leuven, Kasteelpark Arenberg 10, 3001, Leuven-Heverlee, Belgium
J Mol Evol 60:462-74. 2005..g., pathogenesis in S. typhimurium)... - Gene expression patterns during swarming in Salmonella typhimurium: genes specific to surface growth and putative new motility and pathogenicity genesQingfeng Wang
Section of Molecular Genetics and Microbiology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
Mol Microbiol 52:169-87. 2004..Based on cluster analysis of distinctive expression patterns, we report here the identification of putative new genes involved in motility and virulence... - Correlation of phenotype with the genotype of egg-contaminating Salmonella enterica serovar EnteritidisCesar A Morales
Egg Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 950 College Station Rd, Athens, GA 30605, USA
Appl Environ Microbiol 71:4388-99. 2005..These results strongly suggest that the pandemic of egg-associated human salmonellosis that came into prominence in the 1980s is primarily an example of bacterial adaptive radiation that affects the safety of the food supply... - Egr1 signaling in prostate cancerEileen Adamson
The Burnham Institute, Cancer Research Center, La Jolla, California 92037, USA
Cancer Biol Ther 2:617-22. 2003..Expression microarray analyses combined with binding data promise new ways to identify stage specific cancer markers, to aid in patient risk assessment and in therapeutic choices... - Detection of a Salmonella enterica serovar California strain spreading in spanish feed mills and genetic characterization with DNA microarraysJuan Alvarez
Department of Immunology, Microbiology, and Parasitology, School of Pharmacy, University of the Basque Country, 01006 Vitoria-Gasteiz, Spain
Appl Environ Microbiol 69:7531-4. 2003..enterica serovar Typhimurium LT2 gene clusters that are absent from serovar California... - Regulation of Salmonella typhimurium virulence gene expression by cationic antimicrobial peptidesMartin W Bader
Departments of Microbiology and Laboratory Medicine, University of Washington Medical School, Seattle, WA 98195, USA
Mol Microbiol 50:219-30. 2003..Because bacterial resistance to oxidative stress and CAMP are induced during infection of animals, CAMP may be an important signal recognized by bacteria on colonization of animal tissues... - "Promoter array" studies identify cohorts of genes directly regulated by methylation, copy number change, or transcription factor binding in human cancer cellsYipeng Wang
Stanley Kimmel Cancer Center, San Diego California 92121, USA
Ann N Y Acad Sci 1058:162-85. 2005.... - DNA microarray detection of antimicrobial resistance genes in diverse bacteriaJonathan G Frye
Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U S Department of Agriculture, Agriculture Research Service, Richard B Russell Research Center, 950 College Station Road, Athens, GA 30605, USA
Int J Antimicrob Agents 27:138-51. 2006..These results demonstrate that this approach could be used to construct a microarray to detect all sequenced antimicrobial resistance genes in nearly all bacteria... - [Salmonella transcriptome during macrophage infection]Sebastien P Faucher
Med Sci (Paris) 22:792-3. 2006 - FNR is a global regulator of virulence and anaerobic metabolism in Salmonella enterica serovar Typhimurium (ATCC 14028s)Ryan C Fink
Department of Microbiology, North Carolina State University, Raleigh, NC 27695 7615, USA
J Bacteriol 189:2262-73. 2007..The inability of the mutant to survive inside macrophages is likely due to its sensitivity to the reactive oxygen species generated by NADPH phagocyte oxidase... - Delineation of the Salmonella enterica serovar Typhimurium HilA regulon through genome-wide location and transcript analysisInge M V Thijs
Centre of Microbial and Plant Genetics, K U Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
J Bacteriol 189:4587-96. 2007..Finally, the interactions of HilA with the SPI-2 secretion system gene ssaH and the flagellar gene flhD imply a repressor function for HilA under invasion-inducing conditions... - Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNAWilliam Wiley Navarre
Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
Genes Dev 21:1456-71. 2007..The possibility that microorganisms maintain and exploit their characteristic genomic GC ratios for the purpose of self/non-self-discrimination is discussed... - Salmonella enterica serovar Typhi strains from which SPI7, a 134-kilobase island with genes for Vi exopolysaccharide and other functions, has been deletedSatheesh Nair
Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
J Bacteriol 186:3214-23. 2004..We propose that these deletions occurred during storage following isolation...
Research Grants
- Salmonella Gene Expression in Complex EnvironmentsMichael McClelland; Fiscal Year: 2004..As a class, these methods should be applicable to studying gene expression in any bacterial or eukaryotic microbial community. ..