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United States Department of Agriculture

Agricultural Research Service

Related Topics

David John Schneider (Dave)
Plant-Microbe Interactions Research
Computational Biologist

Phone: (607) 279-4446
Fax: (607) 255-2739
624 RHODES HALL - CORNELL UNIVERSITY
ITHACA, NY, 14853-2901

Projects
Analytic Frameworks for Infectious Diseases
General Cooperative Agreement (A)
  Accession Number: 425631
FRAMEWORKS FOR INFECTIOUS DISEASE DYNAMICS
Appropriated (D)
  Accession Number: 423063
ANALYTICAL FRAMEWORKS FOR INFECTIOUS DISEASE DYNAMICS
Reimbursable (R)
  Accession Number: 419077

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Analysis of the small RNA spf in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000 - (Peer Reviewed Journal)
Park, S., Bao, Z., Butcher, B., D'Amico, K.M., Xu, Y., Stodghill, P., Schneider, D.J., Cartinhour, S.W., Filiatrault, M.J. 2014. Analysis of the small RNA spf in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. Microbiology. 160(Pt 5):941-953.
Using multitype branching processes to quantify statistics of disease outbreaks in zoonotic epidemics - (Peer Reviewed Journal)
Singh, S., Schneider, D.J., Myers, C.R. 2014. Using multitype branching processes to quantify statistics of disease outbreaks in zoonotic epidemics. Physical Review E (PRE) - Statistical, Nonlinear, and Soft Matter Physics. 89:1-14.
Functional, structural and phylogenetic analysis of domains underlying the Al-sensitivity of the aluminium-activated malate/anion transporter, TaALMT1 Reprint Icon - (Peer Reviewed Journal)
Ligaba, A., Dreyer, I., Margaryan, A., Schneider, D.J., Kochian, L.V., Pineros, M. 2013. Functional, structural and phylogenetic analysis of domains underlying the Al-sensitivity of the aluminium-activated malate/anion transporter, TaALMT1. Plant Journal. 76(6):766-780. DOI: 10.1111/tpj.12332
Epidemic fronts in complex networks with metapopulation structure - (Peer Reviewed Journal)
Hindes, J., Singh, S., Myers, C.R., Schneider, D.J. 2013. Epidemic fronts in complex networks with metapopulation structure. Physical Review E (PRE) - Statistical, Nonlinear, and Soft Matter Physics. DOI: 10.1103/PhysRevE.88.012809.
Functional and computational analysis of amino acid patterns predictive of type III secretion system substrates in Pseudomonas syringae - (Peer Reviewed Journal)
Schechter, L.M., Valenta, J.C., Schneider, D.J., Collmer, A., Sakk, E. 2012. Functional and computational analysis of amino acid patterns predictive of type III secretion system substrates in Pseudomonas syringae. PLoS One. 7(4):1-13.
Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000 - (Peer Reviewed Journal)
Filiatrault, M.J., Stodghill, P., Myers, C.R., Bronstein, P.A., Butcher, B.G., Lam, H., Grills, G., Schweitzer, P., Wang, W., Schneider, D.J., Cartinhour, S.W. 2011. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS One. 6(12). Available: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029335.
HOPX1 Ea (Eop3) in Erwinia Amylovora functions as an avirulence gene in apple and is regulated by HRPL - (Peer Reviewed Journal)
Bocsanczy, A., Schneider, D.J., Declerck, G.A., Cartinhour, S.W., Beer, S.V. 2011. HOPX1 Ea (Eop3) in Erwinia Amylovora functions as an avirulence gene in apple and is regulated by HRPL. Journal of Bacteriology. 194:553-560.
Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000 - (Peer Reviewed Journal)
Butcher, B.G., Bronstein, P., Myers, C., Stodghill, P., Bolton, J.J., Markel, E.J., Filiatrault, M.J., Swingle, B.M., Gaballa, A., Helmann, J.D., Schneider, D.J., Cartinhour, S.W. 2011. Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000. Journal of Bacteriology. 193(18):4598-4611. Available: http://www.ncbi.nlm.nih.gov/pubmed/21784947.
An in vivo transcriptome for entomopathogenic fungus Metarhizium robertsii ARSEF 2575 - (Abstract Only)
Donzelli, B., Roe, B., Schneider, D.J., Declerck, G., Churchill, A.L., Gibson, D.M. 2011. An in vivo transcriptome for entomopathogenic fungus Metarhizium robertsii ARSEF 2575. Fungal Genetics Conference Proceedings. p. 118.
Saturation mutagenesis of a CepR binding site as a means to identify new quorum-regulated promoters in Burkholderia cenocepacia - (Peer Reviewed Journal)
Wei, Y., Flores-Mireles, A.L., Costa, E.D., Ryan, G.T., Schneider, D.J., Winans, S.C. 2010. Saturation mutagenesis of a CepR binding site as a means to identify new quorum-regulated promoters in Burkholderia cenocepacia. Molecular Microbiology. 79(3):616-632.
Studying plant-pathogen interactions in the genomics era: beyond molecular Koch’s postulates to systems biology - (Review Article)
Schneider, D.J., Collmer, A. 2010. Studying plant-pathogen interactions in the genomics era: beyond molecular Koch’s postulates to systems biology. Annual Review of Phytopathology. 48:457-479.
Construction of an rsmX co-variance model and identification of five rsmX-like ncRNAs in Pseudomonas syringae pv. tomato DC3000 - (Peer Reviewed Journal)
Moll, S., Schneider, D.J., Stodghill, P., Myers, C.R., Cartinhour, S.W., Filiatrault, M.J. 2010. Construction of an rsmX co-variance model and identification of five rsmX-like ncRNAs in Pseudomonas syringae pv. tomato DC3000. RNA Biology. 7(5):1-10.
Analyzing the transcriptome of Pseudomonas syringae using high-throughput sequencing methodologies - (Abstract Only)
Filiatrault, M.J., Bronstein, P., Stodghill, P., Moll, S., Schneider, D.J., Cartinhour, S.W. 2010. Analyzing the transcriptome of Pseudomonas syringae using high-throughput sequencing methodologies. Meeting Abstract. p. 31.
Transcriptome analysis of Pseudomonas syringae identifies new genes, ncRNAs, and antisense activity - (Peer Reviewed Journal)
Filiatrault, M.J., Stodghill, P., Bronstein, P., Moll, S., Lindeberg, M., Grills, G., Schweitzer, P., Wang, W., Schroth, G., Luo, S., Khrebtukova, I., Thannhauser, T.W., Yang, Y., Butcher, B.G., Cartinhour, S.W., Schneider, D.J. 2010. Transcriptome analysis of Pseudomonas syringae identifies new genes, ncRNAs, and antisense activity. Journal of Bacteriology. 192(9):2359-2372.
Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946 - (Peer Reviewed Journal)
Sebaihia, M., Bocsanczy, A.M., Biehl, B.S., Quail, M.A., Perna, N.T., Glasner, J.D., Declerck, G.A., Cartinhour, S.W., Schneider, D.J., Bentley, S.D., Parkhill, J., Beer, S.V. 2010. Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946. Journal of Bacteriology. 192(7):2020-2021.
Magnetic resonance spectra and statistical geometry - (Peer Reviewed Journal)
Earle, K.A., Sahu, I., Mainali, L., Schneider, D.J. 2009. Magnetic resonance spectra and statistical geometry. Applied Magnetic Resonance. 37:865-880.
Lifestyles of the effector-rich: genome-enabled characterization of bacterial plant pathogens - (Peer Reviewed Journal)
Collmer, A., Schneider, D.J., Lindeberg, M. 2009. Lifestyles of the effector-rich: genome-enabled characterization of bacterial plant pathogens. Plant Physiology. 150:1623-1630.
Deletions in the repertoire of Pseudomonas syringae pv. tomato DC3000 type III secretion effector genes reveal functional overlap among effectors - (Peer Reviewed Journal)
Kvitko, B.H., Velasquez, A.C., Wei, C., Russell, A.B., Martin, G.B., Schneider, D.J., Collmer, A. 2009. Deletions in the repertoire of Pseudomonas syringae pv. tomato DC3000 type III secretion effector genes reveal functional overlap among effectors. PLoS Pathogens. 5(4):1-16.
Iron concentration limits growth rate and the expression of virulence factors in hrp-inducing minimal medium with Pseudomonas syringae - (Peer Reviewed Journal)
Kim, B., Park, J., Park, T., Bronstein, P., Schneider, D.J., Cartinhour, S.W., Shuler, M.L. 2009. Iron concentration limits growth rate and the expression of virulence factors in hrp-inducing minimal medium with Pseudomonas syringae. Applied and Environmental Microbiology. 25(9):2720-2726.
Investigating the role of two iron-regulated small RNAs of Pseudomonas syringae - (Abstract Only)
Bronstein, P., Filiatrault, M.J., Stodghill, P., Schneider, D.J., Cartinhour, S.W. 2009. Investigating the role of two iron-regulated small RNAs of Pseudomonas syringae. American Society for Microbiology. p. 20.
High-throughput identification of transcriptional start sites in Pseudomonas syringae - (Abstract Only)
Filiatrault, M.J., Stodghill, P., Wang, W., Schweitzer, P., Grills, G., Cartinhour, S.W., Schneider, D.J. 2009. High-throughput identification of transcriptional start sites in Pseudomonas syringae. American Society for Microbiology. p. 251.
Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro - (Peer Reviewed Journal)
Bronstein, P., Filiatrault, M.J., Myers, C., Rutzke, M., Schneider, D.J., Cartinhour, S.W. 2008. Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro. BMC Microbiology. 8:209.
A draft genome sequence of Pseudomonas syringae pv. tomato strain T1 reveals a repertoire of type III related genes significantly divergent from that of Pseudomonas syringae pv tomato strain DC3000 - (Peer Reviewed Journal)
Almeida, N.F., Yan, S., Lindeberg, M., Studholme, D., Schneider, D.J., Condon, B., Liu, H., Viana, C.J., Warren, A., Evans, C., Kemen, E., Maclean, D., Angot, A., Martin, G.B., Jones, J.D., Collmer, A., Setubal, J.C., Vinatzer, B.A. 2009. A draft genome sequence of Pseudomonas syringae pv. tomato strain T1 reveals a repertoire of type III related genes significantly divergent from that of Pseudomonas syringae pv tomato strain DC3000 . Molecular Plant-Microbe Interactions. 22(1):52-62.
Characterization of the Promoter Motif Regulated by PSPTO_1209 a FecI-like ECF Sigma Factor of Pseudomonas syringae pv. tomato DC3000 - (Abstract Only)
Swingle, B.M., Schneider, D.J. 2008. Characterization of the Promoter Motif Regulated by PSPTO_1209 a FecI-like ECF Sigma Factor of Pseudomonas syringae pv. tomato DC3000. American Society for Microbiology. H-039:p.128.
Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads - (Peer Reviewed Journal)
Swingle, B.M., Thete, D., Moll, M., Myers, C., Schneider, D.J., Cartinhour, S.W. 2008. Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads. Molecular Microbiology. 68(4):871-889.
Roadmap to new virulence determinants in Pseudomonas syringae: Insights from Comparative Genomics and Genome Organization - (Review Article)
Lindeberg, M., Myers, C., Collmer, A., Schneider, D.J. 2008. Roadmap to new virulence determinants in Pseudomonas syringae: Insights from Comparative Genomics and Genome Organization. Molecular Plant-Microbe Interactions. 21:685-700.
Extracytoplasmic Function (ECF) Sigma Factor Gene Regulation in Pseudomonas syringae: Integrated Molecular and Computational Characterization of PvdS-Regulated Promoters - (Abstract Only)
Swingle, B.M., Thete,, D., Moll, M., Myers,, C., Schneider, D.J., Cartinhour, S.W. 2007. Extracytoplasmic Function (ECF) Sigma Factor Gene Regulation in Pseudomonas syringae: Integrated Molecular and Computational Characterization of PvdS-Regulated Promoters. Molecular Genetics of Bacteria and Phage. p. 262.
Pyoverdine and beyond: PvdS dependent gene regulation in Pseudomonas syringae - (Abstract Only)
Swingle, B.M., Thete,, D., Moll, M., Myers,, C., Schneider, D.J., Cartinhour, S.W. Pyoverdine and beyond: PvdS dependent gene regulation in Pseudomonas syringae. American Society for Microbiology Conference. 159A:p. 90.
Shotgun Sequencing of the Pseudomonas syringae DC3000 Transcriptome - (Abstract Only)
Filiatrault, M.J., Bronstein, P., Stodghill, P., Declerck, G.A., Schneider, D.J., Cartinhour, S.W. 2007. Shotgun Sequencing of the Pseudomonas syringae DC3000 Transcriptome. American Society for Microbiology Conference. p. 20.
Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro - (Abstract Only)
Bronstein, P., Filiatrault, M.J., Kim, B., Moll, M., Rutzke, M., Shuler, M., Schneider, D.J., Cartinhour, S.W. 2007. Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro. American Society for Microbiology. p. 20.
Closing the circle on the discovery of genes encoding Hrp regulon members and type III secretion system effectors in the genomes of three model Pseudomonas syringae strains - (Review Article)
Lindeberg, M., Cartinhour, S.W., Myers, C., Schechter, L., Schneider, D.J., Collmer, A. 2006. Closing the circle on the discovery of genes encoding Hrp regulon members and type III secretion system effectors in the genomes of three model Pseudomonas syringae strains. Molecular Plant-Microbe Interactions. 19(11):1151-1158.
Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A - (Peer Reviewed Journal)
Vencato, M., Tian, F., Alfano, J.R., Buell, C., Cartinhour, S.W., Declerck, G.A., Guttman, D.S., Stavrinides, J., Joardar, V., Lindeberg, M., Bronstein, P., Mansfield, J.W., Myers, C.R., Collmer, A., Schneider, D.J. 2006. Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A. Molecular Plant-Microbe Interactions. 19(11):1193-1206.
WHOLE-GENOME EXPRESSION PROFILING DEFINES THE HRPL REGULON OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000, ALLOWS DE NOVO RECONSTRUCTION OF THE HRP CIS ELEMENT, AND IDENTIFIES NOVEL CO-REGULATED GENES - (Peer Reviewed Journal)
Fereirra, A.O., Myers, C.R., Gordon, J., Martin, G.B., Vencato, M., Collmer, A., Wehling, M.D., Alfano, J.R., Moreno-Hagelsieb, G., Lamboy, W.F., Declerck, G.A., Schneider, D.J., Cartinhour, S.W. 2006. Whole-genome expression profiling defines the hrpl regulon of pseudomonas syringae pv. tomato dc3000, allows de novo reconstruction of the hrp cis element, and identifies novel co-regulated genes. Molecular Plant-Microbe Interactions. 19(11):1167-1179.
IDENTIFICATION OF TWIN-ARGININE TRANSLOCATION SYSTEM IN PSEUDOMONAS SYRINGAE AND ITS CONTRIBUTION TO PATHOGENICITY AND FITNESS - (Peer Reviewed Journal)
Bronstein, P., Marrichi, M., Cartinhour, S.W., Schneider, D.J., Delisa, M.P. 2005. Identification of twin-arginine translocation system in pseudomonas syringae and its contribution to pathogenicity and fitness. Journal of Bacteriology. 187(24):8450-8461.
WHOLE GENOME SEQUENCE ANALYSIS OF PSEUDOMONAS SYRINGAE PV. PHASEOLICOLA 1448A REVEALS DIVERGENCE AMONG PATHOVARS IN GENES INVOLVED IN VIRULENCE AND TRANSPOSITION - (Peer Reviewed Journal)
Joardar, V., Lindeberg, M., Jackson, R.W., Fraser, C.M., Chatterjee, A.K., Cartinhour, S.W., Schneider, D.J., Mansfield, J., Collmer, A., Buell, C.R. 2005. Whole genome sequence analysis of pseudomonas syringae pv. phaseolicola 1448a reveals divergence among pathovars in genes involved in virulence and transposition. Journal of Bacteriology. 187:6488-6498.
COMPLETE GENOME SEQUENCE OF THE PLANT COMMENSAL PSEUDOMONAS FLUORESCENS PF-5: INSIGHTS INTO THE BIOLOGICAL CONTROL OF PLANT DISEASE - (Peer Reviewed Journal)
Paulsen, I.T., Press, C.M., Ravel, J., Kobayashi, D.Y., Myers, G., Mavrodi, D.V., Deboy, R.T., Seshadri, R., Ren, Q., Madupu, R., Dodson, R.J., Durkin, A.S., Brinkac, L.M., Daugherty, S.C., Sullivan, S.A., Rosovitz, M.J., Gwinn, M.L., Zhou, L., Schneider, D.J., Cartinhour, S.W., Nelson, W.C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E.A., Pierson, L.S., Thomashow, L.S., Loper, J.E. 2005. Complete genome sequence of the plant commensal pseudomonas fluorescens pf-5: insights into the biological control of plant disease. Nature Biotechnology. 23:873-878.
LINEAGE SPECIFIC REGIONS IN PSEUDOMONAS SYRINGAE PV TOMATO DC3000 - (Peer Reviewed Journal)
Joardar, V., Lindeberg, M., Schneider, D.J., Collmer, A., Buell, C. 2005. Lineage specific regions in pseudomonas syringae pv tomato dc3000. Molecular Plant Pathology. 6(1):53-64.
GENOMIC MINING FOR SUBSTRATES OF THE TYPE III SECRETION SYSTEM IN PSEUDOMONAS SYRINGAE PV. TOMATO DC3000: NEW INSIGHTS INTO MECHANISMS OF PATHOGENESIS - (Book / Chapter)
Alfano, J.R., Buell, C.R., Collmer, A., Shan, L., Tang, X., Schneider, D.J. 2004. Genomic mining for substrates of the type iii secretion system in pseudomonas syringae pv. tomato dc3000: new insights into mechanisms of pathogenesis. In: Iacobellis, N.S., Ullrich, M.S., Collmer, A., Hutcheson, S.W., Mansfield, J.W., Morris, C.E., Murillo, J., Schaad, N.W., Stead, D.E., Surico, G.,editors. Pseudomonas syringae and Related Pathogens: Biology and Genetics. Springer-Verlag. pp.363-371.
THE COMPLETE GENOME SEQUENCE OF THE ARABIDOPSIS AND TOMATO PATHOGEN PSEUDOMONAS SYRINGAE PV. TOMATODC3000 - (Peer Reviewed Journal)
BUELL, C.R., JOARDAR, V., D'ASCENZO, M., DEGN, W.L., RAMOS, A.R., ALFANO, J.R., CARTINHOUR, S.W., DELANEY, T.P., LAZAROWITZ, S.G., MARTIN, G.B., SCHNEIDER, D.J., COLLMER, A. THE COMPLETE GENOME SEQUENCE OF THE ARABIDOPSIS AND TOMATO PATHOGEN PSEUDOMONAS SYRINGAE PV. TOMATODC3000. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. 2003. v. 100(18). p. 10181-10186.
A GRAPH-THEORETIC APPROACH TO COMPARING AND INTEGRATING GENETIC, PHYSICAL AND SEQUENCE-BASED MAPS - (Peer Reviewed Journal)
YAP, I.V., SCHNEIDER, D.J., KLEINBERG, J., MATTHEWS, D.E., CARTINHOUR, S.W., MCCOUCH, S.R. A GRAPH-THEORETIC APPROACH TO COMPARING AND INTEGRATING GENETIC, PHYSICAL AND SEQUENCE-BASED MAPS. GENETICS. 2003. V. 165. P. 2235-2247.
DEVELOPMENT AND MAPPING OF 2240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA L.) - (Peer Reviewed Journal)
MCCOUCH, S.R., TEYTELMAN, L., XU, Y., LOBOS, K.B., CLARE, K., WALTON, M., FU, B., MAGHIRANG, R., LI, Z., XING, Y., ZHANG, Q., KONO, I., YANO, M., FJELLSTROM, R.G., DECLERCK, G.A., CARTINHOUR, S.W., SCHNEIDER, D.J., WARE, D., STEIN, L. DEVELOPMENT AND MAPPING OF 2240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA L.). DNA Research 9:199-207. 2002.
DEVELOPMENT OF 2,240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA) - (Peer Reviewed Journal)
MCCOUGH, S.R., TEYTELMAN, L., KONO, I., YANO, M., FJELLSTROM, R.G., DECLERCK, G.A., SCHNEIDER, D.J., CARTINHOUR, S.W., WARE, D., STEIN, L. DEVELOPMENT OF 2,240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA). GENOME RESEARCH. 2002.
GENOMIC MINING TYPE III SECRETION SYSTEM EFFECTORS IN PSEUDOMONAS SYRINGAE YIELDS NEW PICKS FOR ALL TTSS PROSPECTORS - (Review Article)
SCHNEIDER, D.J. GENOMIC MINING TYPE III SECRETION SYSTEM EFFECTORS IN PSEUDOMONAS SYRINGAE YIELDS NEW PICKS FOR ALL TTSS PROSPECTORS. TRENDS IN MICROBIOLOGY. 2002.
GENOME-WIDE IDENTIFICATION OF PROTEINS SECRETED BY THE HRP TYPE III SECRETION SYSTEM OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 - (Peer Reviewed Journal)
SCHNEIDER, D.J., PETNICKI-OCWIEJA, T., TAM, V., CHANCEY, S., SHAN, L., JAMIR, Y., SCHECHTER, L., TANG, X., COLLMER, A., ALFANO, J.R. GENOME-WIDE IDENTIFICATION OF PROTEINS SECRETED BY THE HRP TYPE III SECRETION SYSTEM OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. 2002.
GENOME-WIDE IDENTIFICATION OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 PROMOTERS CONTROLLED BY THE HRPL ALTERNATIVE SIGMA FACTOR - (Peer Reviewed Journal)
FOUTS, D.E., BALDO, A.M., CARTINHOUR, S.W., LAZAROWITZ, S.G., MARTIN, G.B., REHM, A.H., SCHNEIDER, D.J., VAN DIJK, K., TANG, X., COLLMER, A. GENOME-WIDE IDENTIFICATION OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 PROMOTERS CONTROLLED BY THE HRPL ALTERNATIVE SIGMA FACTOR. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. 2002. v. 99(4). p. 2275-2280.
Last Modified: 9/1/2014
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