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The ECF sigma factor, PSPTO_1043, in Pseudomonas syringae pv. tomato DC3000 is induced by oxidative stress and regulates genes involved in oxidative stress response.

Butcher BG, Bao Z, Wilson J, Stodghill P, Swingle B, Filiatrault M, Schneider D, Cartinhour S.

PLoS One. 2017 Jul 12;12(7):e0180340. doi: 10.1371/journal.pone.0180340. eCollection 2017.


Global analysis of the HrpL regulon in the plant pathogen Pseudomonas syringae pv. tomato DC3000 reveals new regulon members with diverse functions.

Lam HN, Chakravarthy S, Wei HL, BuiNguyen H, Stodghill PV, Collmer A, Swingle BM, Cartinhour SW.

PLoS One. 2014 Aug 29;9(8):e106115. doi: 10.1371/journal.pone.0106115. eCollection 2014.


Analysis of the small RNA spf in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000.

Park SH, Bao Z, Butcher BG, D'Amico K, Xu Y, Stodghill P, Schneider DJ, Cartinhour S, Filiatrault MJ.

Microbiology. 2014 May;160(Pt 5):941-53. doi: 10.1099/mic.0.076497-0. Epub 2014 Mar 5.


Genomic plasticity enables phenotypic variation of Pseudomonas syringae pv. tomato DC3000.

Bao Z, Stodghill PV, Myers CR, Lam H, Wei HL, Chakravarthy S, Kvitko BH, Collmer A, Cartinhour SW, Schweitzer P, Swingle B.

PLoS One. 2014 Feb 6;9(2):e86628. doi: 10.1371/journal.pone.0086628. eCollection 2014.


CrcZ and CrcX regulate carbon source utilization in Pseudomonas syringae pathovar tomato strain DC3000.

Filiatrault MJ, Stodghill PV, Wilson J, Butcher BG, Chen H, Myers CR, Cartinhour SW.

RNA Biol. 2013 Feb;10(2):245-55. doi: 10.4161/rna.23019. Epub 2013 Jan 25.


Substrate and target sequence length influence RecTE(Psy) recombineering efficiency in Pseudomonas syringae.

Bao Z, Cartinhour S, Swingle B.

PLoS One. 2012;7(11):e50617. doi: 10.1371/journal.pone.0050617. Epub 2012 Nov 30.


Regulons of three Pseudomonas syringae pv. tomato DC3000 iron starvation sigma factors.

Markel E, Butcher BG, Myers CR, Stodghill P, Cartinhour S, Swingle B.

Appl Environ Microbiol. 2013 Jan;79(2):725-7. doi: 10.1128/AEM.02801-12. Epub 2012 Nov 2.


Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000.

Filiatrault MJ, Stodghill PV, Myers CR, Bronstein PA, Butcher BG, Lam H, Grills G, Schweitzer P, Wang W, Schneider DJ, Cartinhour SW.

PLoS One. 2011;6(12):e29335. doi: 10.1371/journal.pone.0029335. Epub 2011 Dec 28.


HopX1 in Erwinia amylovora functions as an avirulence protein in apple and is regulated by HrpL.

Bocsanczy AM, Schneider DJ, DeClerck GA, Cartinhour S, Beer SV.

J Bacteriol. 2012 Feb;194(3):553-60. doi: 10.1128/JB.05065-11. Epub 2011 Nov 28.


An extracytoplasmic function sigma factor-mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores.

Markel E, Maciak C, Butcher BG, Myers CR, Stodghill P, Bao Z, Cartinhour S, Swingle B.

J Bacteriol. 2011 Oct;193(20):5775-83. doi: 10.1128/JB.05114-11. Epub 2011 Aug 12.


Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000.

Butcher BG, Bronstein PA, Myers CR, Stodghill PV, Bolton JJ, Markel EJ, Filiatrault MJ, Swingle B, Gaballa A, Helmann JD, Schneider DJ, Cartinhour SW.

J Bacteriol. 2011 Sep;193(18):4598-611. doi: 10.1128/JB.00340-11. Epub 2011 Jul 22.


Oligonucleotide recombination: a hidden treasure.

Swingle B, Markel E, Cartinhour S.

Bioeng Bugs. 2010 Jul-Aug;1(4):263-6. doi: 10.4161/bbug.1.4.12098. Epub 2010 May 19.


Construction of an rsmX co-variance model and identification of five rsmX non-coding RNAs in Pseudomonas syringae pv. tomato DC3000.

Moll S, Schneider DJ, Stodghill P, Myers CR, Cartinhour SW, Filiatrault MJ.

RNA Biol. 2010 Sep-Oct;7(5):508-16. Epub 2010 Sep 1.


Recombineering using RecTE from Pseudomonas syringae.

Swingle B, Bao Z, Markel E, Chambers A, Cartinhour S.

Appl Environ Microbiol. 2010 Aug;76(15):4960-8. doi: 10.1128/AEM.00911-10. Epub 2010 Jun 11.


Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity.

Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, Lindeberg M, Grills G, Schweitzer P, Wang W, Schroth GP, Luo S, Khrebtukova I, Yang Y, Thannhauser T, Butcher BG, Cartinhour S, Schneider DJ.

J Bacteriol. 2010 May;192(9):2359-72. doi: 10.1128/JB.01445-09. Epub 2010 Feb 26.


Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946.

Sebaihia M, Bocsanczy AM, Biehl BS, Quail MA, Perna NT, Glasner JD, DeClerck GA, Cartinhour S, Schneider DJ, Bentley SD, Parkhill J, Beer SV.

J Bacteriol. 2010 Apr;192(7):2020-1. doi: 10.1128/JB.00022-10. Epub 2010 Jan 29.


Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs.

Oliver HF, Orsi RH, Ponnala L, Keich U, Wang W, Sun Q, Cartinhour SW, Filiatrault MJ, Wiedmann M, Boor KJ.

BMC Genomics. 2009 Dec 30;10:641. doi: 10.1186/1471-2164-10-641.


Complex responses to culture conditions in Pseudomonas syringae pv. tomato DC3000 continuous cultures: the role of iron in cell growth and virulence factor induction.

Kim BJ, Schneider DJ, Cartinhour SW, Shuler ML.

Biotechnol Bioeng. 2010 Apr 1;105(5):955-64. doi: 10.1002/bit.22609.


Oligonucleotide recombination in Gram-negative bacteria.

Swingle B, Markel E, Costantino N, Bubunenko MG, Cartinhour S, Court DL.

Mol Microbiol. 2010 Jan;75(1):138-48. doi: 10.1111/j.1365-2958.2009.06976.x. Epub 2009 Nov 25.


The effect of target vector selection on the invariance of classifier performance measures.

Sakk E, Schneider DJ, Myers CR, Cartinhour SW.

IEEE Trans Neural Netw. 2009 May;20(5):745-57. doi: 10.1109/TNN.2008.2011809. Epub 2009 Mar 31.


Effect of iron concentration on the growth rate of Pseudomonas syringae and the expression of virulence factors in hrp-inducing minimal medium.

Kim BJ, Park JH, Park TH, Bronstein PA, Schneider DJ, Cartinhour SW, Shuler ML.

Appl Environ Microbiol. 2009 May;75(9):2720-6. doi: 10.1128/AEM.02738-08. Epub 2009 Mar 6.


Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro.

Bronstein PA, Filiatrault MJ, Myers CR, Rutzke M, Schneider DJ, Cartinhour SW.

BMC Microbiol. 2008 Dec 2;8:209. doi: 10.1186/1471-2180-8-209.


Gramene: development and integration of trait and gene ontologies for rice.

Jaiswal P, Ware D, Ni J, Chang K, Zhao W, Schmidt S, Pan X, Clark K, Teytelman L, Cartinhour S, Stein L, McCouch S.

Comp Funct Genomics. 2002;3(2):132-6. doi: 10.1002/cfg.156.


Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads.

Swingle B, Thete D, Moll M, Myers CR, Schneider DJ, Cartinhour S.

Mol Microbiol. 2008 May;68(4):871-89. doi: 10.1111/j.1365-2958.2008.06209.x. Epub 2008 Mar 19.


Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A.

Vencato M, Tian F, Alfano JR, Buell CR, Cartinhour S, DeClerck GA, Guttman DS, Stavrinides J, Joardar V, Lindeberg M, Bronstein PA, Mansfield JW, Myers CR, Collmer A, Schneider DJ.

Mol Plant Microbe Interact. 2006 Nov;19(11):1193-206.


Whole-genome expression profiling defines the HrpL regulon of Pseudomonas syringae pv. tomato DC3000, allows de novo reconstruction of the Hrp cis clement, and identifies novel coregulated genes.

Ferreira AO, Myers CR, Gordon JS, Martin GB, Vencato M, Collmer A, Wehling MD, Alfano JR, Moreno-Hagelsieb G, Lamboy WF, DeClerck G, Schneider DJ, Cartinhour SW.

Mol Plant Microbe Interact. 2006 Nov;19(11):1167-79.


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.

Lindeberg M, Cartinhour S, Myers CR, Schechter LM, Schneider DJ, Collmer A.

Mol Plant Microbe Interact. 2006 Nov;19(11):1151-8. Review.


Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition.

Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR.

J Bacteriol. 2005 Sep;187(18):6488-98.


Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5.

Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GS, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson LS 3rd, Thomashow LS, Loper JE.

Nat Biotechnol. 2005 Jul;23(7):873-8. Epub 2005 Jun 26. Erratum in: Nat Biotechnol. 2006 Apr;24(4):466.


A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps.

Yap IV, Schneider D, Kleinberg J, Matthews D, Cartinhour S, McCouch SR.

Genetics. 2003 Dec;165(4):2235-47.


The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000.

Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT, Gwinn ML, Dodson RJ, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Daugherty S, Brinkac L, Beanan MJ, Haft DH, Nelson WC, Davidsen T, Zafar N, Zhou L, Liu J, Yuan Q, Khouri H, Fedorova N, Tran B, Russell D, Berry K, Utterback T, Van Aken SE, Feldblyum TV, D'Ascenzo M, Deng WL, Ramos AR, Alfano JR, Cartinhour S, Chatterjee AK, Delaney TP, Lazarowitz SG, Martin GB, Schneider DJ, Tang X, Bender CL, White O, Fraser CM, Collmer A.

Proc Natl Acad Sci U S A. 2003 Sep 2;100(18):10181-6. Epub 2003 Aug 19.


Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) (supplement).

McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L.

DNA Res. 2002 Dec 31;9(6):257-79. No abstract available.


Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.).

McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L.

DNA Res. 2002 Dec 31;9(6):199-207.


Gramene, a tool for grass genomics.

Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR.

Plant Physiol. 2002 Dec;130(4):1606-13. Review.


Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor.

Fouts DE, Abramovitch RB, Alfano JR, Baldo AM, Buell CR, Cartinhour S, Chatterjee AK, D'Ascenzo M, Gwinn ML, Lazarowitz SG, Lin NC, Martin GB, Rehm AH, Schneider DJ, van Dijk K, Tang X, Collmer A.

Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2275-80.


Gramene: a resource for comparative grass genomics.

Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L.

Nucleic Acids Res. 2002 Jan 1;30(1):103-5.


A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map.

Klein PE, Klein RR, Cartinhour SW, Ulanch PE, Dong J, Obert JA, Morishige DT, Schlueter SD, Childs KL, Ale M, Mullet JE.

Genome Res. 2000 Jun;10(6):789-807.


UK CropNet: a collection of databases and bioinformatics resources for crop plant genomics.

Dicks J, Anderson M, Cardle L, Cartinhour S, Couchman M, Davenport G, Dickson J, Gale M, Marshall D, May S, McWilliam H, O'Malia A, Ougham H, Trick M, Walsh S, Waugh R.

Nucleic Acids Res. 2000 Jan 1;28(1):104-7.


ACEDB: a database for genome information.

Walsh S, Anderson M, Cartinhour SW.

Methods Biochem Anal. 1998;39:299-318. No abstract available.


JADE: an approach for interconnecting bioinformatics databases.

Stein LD, Cartinhour S, Thierry-Mieg D, Thierry-Mieg J.

Gene. 1998 Mar 16;209(1-2):GC39-GC43.


JADE: An approach for interconnecting bioinformatics databases

Stein LD, Cartinhour S, Thierry-Mieg D, Thierry-Mieg J.

Gene. 1998 Mar 16;209(1-2):39-43.


Public informatics resources for rice and other grasses.

Cartinhour SW.

Plant Mol Biol. 1997 Sep;35(1-2):241-51. Review.


Precise excision of telomere-bearing transposons during Oxytricha fallax macronuclear development.

Hunter DJ, Williams K, Cartinhour S, Herrick G.

Genes Dev. 1989 Dec;3(12B):2101-12.


Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family.

Herrick G, Cartinhour SW, Williams KR, Kotter KP.

J Protozool. 1987 Nov;34(4):429-34. Review.


A genetic linkage map of the human genome.

Donis-Keller H, Green P, Helms C, Cartinhour S, Weiffenbach B, Stephens K, Keith TP, Bowden DW, Smith DR, Lander ES, et al.

Cell. 1987 Oct 23;51(2):319-37.


Mobile elements bounded by C4A4 telomeric repeats in Oxytricha fallax.

Herrick G, Cartinhour S, Dawson D, Ang D, Sheets R, Lee A, Williams K.

Cell. 1985 Dec;43(3 Pt 2):759-68.


Elimination of germ-line tandemly repeated sequences from the somatic genome of the ciliate Oxytricha fallax.

Dawson D, Buckley B, Cartinhour S, Myers R, Herrick G.

Chromosoma. 1984;90(4):289-94.


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