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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
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53 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
2019 McCorrison J, Girke T, Goetz LH, Miller RA, Schork NJ. Genetic Support for Longevity-Enhancing Drug Targets: Issues, Preliminary Data, and Future Directions. The Journals of Gerontology. Series a, Biological Sciences and Medical Sciences. 74: S61-S71. PMID 31724058 DOI: 10.1093/Gerona/Glz206  0.315
2018 Hamilton MJ, Girke T, Martinez E. Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma. Oncotarget. 9: 23670-23680. PMID 29805765 DOI: 10.18632/Oncotarget.25330  0.366
2018 Teixeira MA, Sela N, Atamian HS, Bao E, Chaudhary R, MacWilliams J, He J, Mantelin S, Girke T, Kaloshian I. Sequence analysis of the potato aphid Macrosiphum euphorbiae transcriptome identified two new viruses. Plos One. 13: e0193239. PMID 29596449 DOI: 10.1371/Journal.Pone.0193239  0.76
2016 Arnold N, Girke T, Sureshchandra S, Messaoudi I. Acute Simian Varicella Virus Infection Causes Robust and Sustained Changes in Gene Expression in the Sensory Ganglia. Journal of Virology. 90: 10823-10843. PMID 27681124 DOI: 10.1128/Jvi.01272-16  0.308
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  0.338
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  0.393
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  0.331
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  0.319
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  0.31
2014 Yadav RK, Tavakkoli M, Xie M, Girke T, Reddy GV. A high-resolution gene expression map of the Arabidopsis shoot meristem stem cell niche. Development (Cambridge, England). 141: 2735-44. PMID 24961803 DOI: 10.1242/Dev.106104  0.314
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  0.746
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  0.349
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  0.382
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  0.311
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  0.319
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  0.315
2013 Yang EW, Girke T, Jiang T. Differential gene expression analysis using coexpression and RNA-Seq data. Bioinformatics (Oxford, England). 29: 2153-61. PMID 23793751 DOI: 10.1093/Bioinformatics/Btt363  0.419
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  0.344
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  0.303
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  0.316
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  0.753
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  0.337
2013 Yadav RK, Snipes S, Girke T, Reddy GV. Gene expression analysis of shoot apical meristem cell types. Methods in Molecular Biology (Clifton, N.J.). 959: 235-45. PMID 23299680 DOI: 10.1007/978-1-62703-221-6_16  0.36
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  0.742
2012 Dinh TT, Girke T, Liu X, Yant L, Schmid M, Chen X. The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element. Development (Cambridge, England). 139: 1978-86. PMID 22513376 DOI: 10.1242/Dev.077073  0.368
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  0.534
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  0.733
2010 Cao Y, Jiang T, Girke T. Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing. Bioinformatics (Oxford, England). 26: 953-9. PMID 20179075 DOI: 10.1093/Bioinformatics/Btq067  0.379
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  0.537
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  0.318
2009 Knoth C, Salus MS, Girke T, Eulgem T. The synthetic elicitor 3,5-dichloroanthranilic acid induces NPR1-dependent and NPR1-independent mechanisms of disease resistance in Arabidopsis. Plant Physiology. 150: 333-47. PMID 19304930 DOI: 10.1104/Pp.108.133678  0.368
2009 Yadav RK, Girke T, Pasala S, Xie M, Reddy GV. Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proceedings of the National Academy of Sciences of the United States of America. 106: 4941-6. PMID 19258454 DOI: 10.1073/Pnas.0900843106  0.355
2008 Cao Y, Charisi A, Cheng LC, Jiang T, Girke T. ChemmineR: a compound mining framework for R. Bioinformatics (Oxford, England). 24: 1733-4. PMID 18596077 DOI: 10.1093/Bioinformatics/Btn307  0.385
2008 Ponts N, Yang J, Chung DW, Prudhomme J, Girke T, Horrocks P, Le Roch KG. Deciphering the ubiquitin-mediated pathway in apicomplexan parasites: a potential strategy to interfere with parasite virulence. Plos One. 3: e2386. PMID 18545708 DOI: 10.1371/Journal.Pone.0002386  0.366
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  0.6
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  0.403
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  0.369
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  0.363
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  0.381
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  0.579
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  0.587
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  0.522
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  0.538
2004 Heilmann I, Pidkowich MS, Girke T, Shanklin J. Switching desaturase enzyme specificity by alternate subcellular targeting. Proceedings of the National Academy of Sciences of the United States of America. 101: 10266-71. PMID 15240892 DOI: 10.1073/Pnas.0402200101  0.308
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  0.367
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  0.543
2003 Ohlrogge J, Ruuska S, Mekhedov S, Girke T, Benning C. Functional genomics from a plant biochemist's perspective Acta Agriculturae Scandinavica - Section B: Soil and Plant Science. 53: 41-50. DOI: 10.1080/16519140310015175  0.629
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  0.578
2000 Ohlrogge J, Pollard M, Bao X, Focke M, Girke T, Ruuska S, Mekhedov S, Benning C. Fatty acid synthesis: from CO2 to functional genomics. Biochemical Society Transactions. 28: 567-73. PMID 11171129 DOI: 10.1042/Bst0280567  0.701
2000 White JA, Todd J, Newman T, Focks N, Girke T, de Ilárduya OM, Jaworski JG, Ohlrogge JB, Benning C. A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil. Plant Physiology. 124: 1582-94. PMID 11115876 DOI: 10.1104/Pp.124.4.1582  0.623
2000 Girke T, Todd J, Ruuska S, White J, Benning C, Ohlrogge J. Microarray analysis of developing arabidopsis seeds Plant Physiology. 124: 1570-1581. PMID 11115875 DOI: 10.1104/Pp.124.4.1570  0.602
2000 Sperling P, Lee M, Girke T, Zähringer U, Stymne S, Heinz E. A bifunctional Δ6‐fatty acyl acetylenase/desaturase from the moss Ceratodon purpureus Febs Journal. 267: 3801-3811. PMID 10848999 DOI: 10.1046/J.1432-1327.2000.01418.X  0.615
1998 Girke T, Schmidt H, Zahringer U, Reski R, Heinz E. Identification of a novel D6‐acyl‐group desaturase by targeted gene disruption in Physcomitrella patens Plant Journal. 15: 39-48. PMID 9744093 DOI: 10.1046/J.1365-313X.1998.00178.X  0.654
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