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Thomas Girke - Publications

Affiliations: 
University of California, Riverside, Riverside, CA, United States 
Area:
Bioinformatics
Website:
https://profiles.ucr.edu/app/home/profile/tgirke

42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Arnold N, Girke T, Sureshchandra S, Nguyen C, Rais M, Messaoudi I. Genomic and functional analysis of the host response to acute simian varicella infection in the lung. Scientific Reports. 6: 34164. PMID 27677639 DOI: 10.1038/srep34164  0.64
2016 Van Veen H, Vashisht D, Akman M, Girke T, Mustroph A, Reinen E, Hartman S, Kooiker M, van Tienderen P, Schranz ME, Bailey-Serres J, Voesenek LA, Sasidharan R. Transcriptomes of eight Arabidopsis thaliana accessions reveal core conserved, genotype- and organ-specific responses to flooding stress. Plant Physiology. PMID 27208254 DOI: 10.1104/pp.16.00472  0.32
2016 Teixeira M, Sela N, Ng J, Casteel CL, Peng HC, Bekal S, Girke T, Ghanim M, Kaloshian I. A novel virus from Macrosiphum euphorbiae with similarities to members of the family Flaviviridae. The Journal of General Virology. PMID 26822322 DOI: 10.1099/jgv.0.000414  0.64
2016 Saha TT, Shin SW, Dou W, Roy S, Zhao B, Hou Y, Wang XL, Zou Z, Girke T, Raikhel AS. Hairy and Groucho mediate the action of juvenile hormone receptor Methoprene-tolerant in gene repression. Proceedings of the National Academy of Sciences of the United States of America. PMID 26744312 DOI: 10.1073/pnas.1523838113  0.64
2015 Barr T, Girke T, Sureshchandra S, Nguyen C, Grant K, Messaoudi I. Alcohol Consumption Modulates Host Defense in Rhesus Macaques by Altering Gene Expression in Circulating Leukocytes. Journal of Immunology (Baltimore, Md. : 1950). PMID 26621857 DOI: 10.4049/jimmunol.1501527  0.64
2015 Roy S, Saha TT, Johnson L, Zhao B, Ha J, White KP, Girke T, Zou Z, Raikhel AS. Regulation of Gene Expression Patterns in Mosquito Reproduction. Plos Genetics. 11: e1005450. PMID 26274815 DOI: 10.1371/journal.pgen.1005450  0.64
2015 Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. 12: 115-21. PMID 25633503 DOI: 10.1038/nmeth.3252  0.64
2014 Engelmann F, Josset L, Girke T, Park B, Barron A, Dewane J, Hammarlund E, Lewis A, Axthelm MK, Slifka MK, Messaoudi I. Pathophysiologic and transcriptomic analyses of viscerotropic yellow fever in a rhesus macaque model. Plos Neglected Tropical Diseases. 8: e3295. PMID 25412185 DOI: 10.1371/journal.pntd.0003295  0.64
2014 Bao E, Jiang T, Girke T. AlignGraph: Algorithm for secondary de novo genome assembly guided by closely related references Bioinformatics. 30. PMID 24932000 DOI: 10.1093/bioinformatics/btu291  0.64
2014 Juntawong P, Girke T, Bazin J, Bailey-Serres J. Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 111: E203-12. PMID 24367078 DOI: 10.1073/pnas.1317811111  0.64
2014 Worden N, Girke T, Drakakaki G. Endomembrane dissection using chemically induced bioactive clusters. Methods in Molecular Biology (Clifton, N.J.). 1056: 159-68. PMID 24306872 DOI: 10.1007/978-1-62703-592-7_16  0.88
2013 Choy A, Severo MS, Sun R, Girke T, Gillespie JJ, Pedra JH. Decoding the ubiquitin-mediated pathway of arthropod disease vectors. Plos One. 8: e78077. PMID 24205097 DOI: 10.1371/journal.pone.0078077  0.64
2013 Scranton MA, Fowler JH, Girke T, Walling LL. Microarray analysis of tomato's early and late wound response reveals new regulatory targets for Leucine aminopeptidase A. Plos One. 8: e77889. PMID 24205013 DOI: 10.1371/journal.pone.0077889  0.64
2013 Wang Y, Backman TW, Horan K, Girke T. fmcsR: mismatch tolerant maximum common substructure searching in R. Bioinformatics (Oxford, England). 29: 2792-4. PMID 23962615 DOI: 10.1093/bioinformatics/btt475  0.32
2013 Zou Z, Saha TT, Roy S, Shin SW, Backman TW, Girke T, White KP, Raikhel AS. Juvenile hormone and its receptor, methoprene-tolerant, control the dynamics of mosquito gene expression. Proceedings of the National Academy of Sciences of the United States of America. 110: E2173-81. PMID 23633570 DOI: 10.1073/pnas.1305293110  0.64
2013 Yadav RK, Perales M, Gruel J, Ohno C, Heisler M, Girke T, Jönsson H, Reddy GV. Plant stem cell maintenance involves direct transcriptional repression of differentiation program. Molecular Systems Biology. 9: 654. PMID 23549482 DOI: 10.1038/msb.2013.8  0.64
2013 Luhua S, Hegie A, Suzuki N, Shulaev E, Luo X, Cenariu D, Ma V, Kao S, Lim J, Gunay MB, Oosumi T, Lee SC, Harper J, Cushman J, Gollery M, ... Girke T, et al. Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening. Physiologia Plantarum. 148: 322-33. PMID 23517122 DOI: 10.1111/ppl.12013  0.64
2013 Bao E, Jiang T, Girke T. BRANCH: Boosting RNA-Seq assemblies with partial or related genomic sequences Bioinformatics. 29: 1250-1259. PMID 23493323 DOI: 10.1093/bioinformatics/btt127  0.64
2013 Mustroph A, Zanetti ME, Girke T, Bailey-Serres J. Isolation and analysis of mRNAs from specific cell types of plants by ribosome immunopurification. Methods in Molecular Biology (Clifton, N.J.). 959: 277-302. PMID 23299683 DOI: 10.1007/978-1-62703-221-6_19  0.64
2013 Atamian HS, Chaudhary R, Cin VD, Bao E, Girke T, Kaloshian I. In planta expression or delivery of potato aphid Macrosiphum euphorbiae effectors Me10 and Me23 enhances aphid fecundity. Molecular Plant-Microbe Interactions : Mpmi. 26: 67-74. PMID 23194342 DOI: 10.1094/MPMI-06-12-0144-FI  0.64
2012 Bell EM, Lin WC, Husbands AY, Yu L, Jaganatha V, Jablonska B, Mangeon A, Neff MM, Girke T, Springer PS. Arabidopsis lateral organ boundaries negatively regulates brassinosteroid accumulation to limit growth in organ boundaries. Proceedings of the National Academy of Sciences of the United States of America. 109: 21146-51. PMID 23213252 DOI: 10.1073/pnas.1210789109  0.64
2011 Drakakaki G, Robert S, Szatmari AM, Brown MQ, Nagawa S, Van Damme D, Leonard M, Yang Z, Girke T, Schmid SL, Russinova E, Friml J, Raikhel NV, Hicks GR. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. Proceedings of the National Academy of Sciences of the United States of America. 108: 17850-5. PMID 22006339 DOI: 10.1073/pnas.1108581108  0.64
2011 Yadav RK, Perales M, Gruel J, Girke T, Jönsson H, Reddy GV. WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex. Genes & Development. 25: 2025-30. PMID 21979915 DOI: 10.1101/gad.17258511  0.64
2011 Bao E, Jiang T, Kaloshian I, Girke T. SEED: efficient clustering of next-generation sequences. Bioinformatics (Oxford, England). 27: 2502-9. PMID 21810899 DOI: 10.1093/bioinformatics/btr447  0.64
2010 Horan K, Shelton CR, Girke T. Predicting conserved protein motifs with Sub-HMMs. Bmc Bioinformatics. 11: 205. PMID 20420695 DOI: 10.1186/1471-2105-11-205  0.64
2010 Agee AE, Surpin M, Sohn EJ, Girke T, Rosado A, Kram BW, Carter C, Wentzell AM, Kliebenstein DJ, Jin HC, Park OK, Jin H, Hicks GR, Raikhel NV. MODIFIED VACUOLE PHENOTYPE1 is an Arabidopsis myrosinase-associated protein involved in endomembrane protein trafficking. Plant Physiology. 152: 120-32. PMID 19880612 DOI: 10.1104/pp.109.145078  0.64
2009 Mustroph A, Zanetti ME, Jang CJ, Holtan HE, Repetti PP, Galbraith DW, Girke T, Bailey-Serres J. Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 106: 18843-8. PMID 19843695 DOI: 10.1073/pnas.0906131106  0.64
2008 Bhattarai KK, Xie QG, Mantelin S, Bishnoi U, Girke T, Navarre DA, Kaloshian I. Tomato susceptibility to root-knot nematodes requires an intact jasmonic acid signaling pathway. Molecular Plant-Microbe Interactions : Mpmi. 21: 1205-14. PMID 18700825 DOI: 10.1094/MPMI-21-9-1205  0.64
2008 Avila EL, Brown M, Pan S, Desikan R, Neill SJ, Girke T, Surpin M, Raikhel NV. Expression analysis of Arabidopsis vacuolar sorting receptor 3 reveals a putative function in guard cells. Journal of Experimental Botany. 59: 1149-61. PMID 18436547 DOI: 10.1093/jxb/ern025  0.64
2008 Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu JK, Cushman JC, Gollery M, Girke T. Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiology. 147: 41-57. PMID 18354039 DOI: 10.1104/pp.108.117366  0.64
2008 Jin H, Vacic V, Girke T, Lonardi S, Zhu JK. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. Bmc Molecular Biology. 9: 6. PMID 18194570 DOI: 10.1186/1471-2199-9-6  0.64
2006 Gollery M, Harper J, Cushman J, Mittler T, Girke T, Zhu JK, Bailey-Serres J, Mittler R. What makes species unique? The contribution of proteins with obscure features. Genome Biology. 7: R57. PMID 16859532 DOI: 10.1186/gb-2006-7-7-r57  0.64
2005 Sunkar R, Girke T, Zhu JK. Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Research. 33: 4443-54. PMID 16077027 DOI: 10.1093/nar/gki758  0.64
2005 Girke T, Cheng LC, Raikhel N. ChemMine. A compound mining database for chemical genomics. Plant Physiology. 138: 573-7. PMID 15955920 DOI: 10.1104/pp.105.062687  0.56
2005 Horan K, Lauricha J, Bailey-Serres J, Raikhel N, Girke T. Genome cluster database. A sequence family analysis platform for Arabidopsis and rice. Plant Physiology. 138: 47-54. PMID 15888677 DOI: 10.1104/pp.104.059048  0.64
2005 Sunkar R, Girke T, Jain PK, Zhu JK. Cloning and characterization of microRNAs from rice. The Plant Cell. 17: 1397-411. PMID 15805478 DOI: 10.1105/tpc.105.031682  0.64
2004 Carter C, Pan S, Zouhar J, Avila EL, Girke T, Raikhel NV. The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins. The Plant Cell. 16: 3285-303. PMID 15539469 DOI: 10.1105/tpc.104.027078  0.64
2004 Girke T, Lauricha J, Tran H, Keegstra K, Raikhel N. The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiology. 136: 3003-8; discussion 3. PMID 15489283 DOI: 10.1104/pp.104.049965  0.64
2004 Gibbons R, Dugaiczyk LJ, Girke T, Duistermars B, Zielinski R, Dugaiczyk A. Distinguishing humans from great apes with AluYb8 repeats Journal of Molecular Biology. 339: 721-729. PMID 15165846 DOI: 10.1016/j.jmb.2004.04.033  0.64
2004 Kawaguchi R, Girke T, Bray EA, Bailey-Serres J. Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. The Plant Journal : For Cell and Molecular Biology. 38: 823-39. PMID 15144383 DOI: 10.1111/j.1365-313X.2004.02090.x  0.64
2003 Girke T, Ozkan M, Carter D, Raikhel NV. Towards a modeling infrastructure for studying plant cells. Plant Physiology. 132: 410-4. PMID 12805570 DOI: 10.1104/pp.103.022103  0.64
2002 Ruuska SA, Girke T, Benning C, Ohlrogge JB. Contrapuntal networks of gene expression during Arabidopsis seed filling. The Plant Cell. 14: 1191-206. PMID 12084821 DOI: 10.1105/tpc.000877  0.64
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