Girke Lab Research and Teaching Site

Publications

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  1. Zillikens et al. (2017) Large meta-analysis of genome-wide association studies identifies five loci for lean body mass. Nature Communications: 8, 1-13. PubMed
  2. Zhang X, Aksoy E, Girke T, Raikhel AS, Karginov FV (2017) Transcriptome-wide microRNA and target dynamics in the fat body during the gonadotrophic cycle of Aedes aegypti. PNAS: 114, E1895-E1903. PubMed
  3. Backman T, Evans D, Girke T (2017) Large-scale Bioactivity Analysis of the Small-Molecule Assayed Proteome. PLoS ONE, 12: e0171413. PubMed
  4. Arnold N, Girke T, Sureshchandra S, Messaoudi I (2016) Acute simian varicella infection causes robust and sustained changes in gene expression in the sensory ganglia. J Virol: 90, 10823-10843. PubMed
  5. Arnold N, Girke T, Sureshchandra S, Nguyen C, Rais M, Messaoudi I (2016) Genomic and functional analysis of the host response to acute simian varicella infection in the lung. Sci Rep: 6, 34164. PubMed
  6. Backman TW, Girke T (2016) systemPipeR: NGS workflow and report generation environment. BMC Bioinformatics: 17, 1-8. PubMed
  7. Backman TW, Girke T (2016) bioassayR: Cross-Target Analysis of Small Molecule Bioactivity. J Chem Inf Model: 56, 1237-1242. PubMed
  8. 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 (2016) Transcriptomes of eight Arabidopsis thaliana accessions reveal core conserved, genotype- and organ-specific responses to flooding stress. Plant Physiol: 172, 668-689. PubMed
  9. Teixeira M, Sela N, Ng J, Casteel CL, Peng H-C, Bekal S, Girke T, Ghanim M, Kaloshian I (2016) A novel virus from Macrosiphum euphorbiae with similarities to members of the family Flaviviridae. J Gen Virol: 97, 1261-1271. PubMed
  10. Saha TT, Shin SW, Dou W, Roy S, Zhao B, Hou Y, Wang X-L, Zou Z, Girke T, Raikhel AS (2016) Hairy and Groucho mediate the action of juvenile hormone receptor Methoprene-tolerant in gene repression. PNAS: 113, E735-743. PubMed
  11. Barr T, Girke T, Sureshchandra S, Nguyen C, Grant K, Messaoudi I (2016) Alcohol Consumption Modulates Host Defense in Rhesus Macaques by Altering Gene Expression in Circulating Leukocytes. J Immunol: 196, 182-195. PubMed
  12. Roy S, Saha TT, Johnson L, Zhao B, Ha J, White KP, Girke T, Zou Z, Raikhel AS (2015) Regulation of Gene Expression Patterns in Mosquito Reproduction. PLoS Genet: 11, e1005450. PubMed
  13. Huber W, Carey V, Gentleman R, Carlson M, Carvalho B, Corrada Bravo H, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen K, Irizarry R, Lawrence M, Love M, MacDonald J, Obenchain V, Oleś A, Pagès H, Reyes A, Anders S, Shannon P, Smyth G, Tenenbaum D, Waldron L, Morgan M (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods: 12, 115-121. PubMed
  14. Engelmann F, Josset L, Girke T, Byung P, Barron A, Haberthur K, Dewane J, Hammarlund E, Lewis A, Axthelm M, Slifka M, Messaoudi I (2014) Pathophysiologic and transcriptomic analysis of lethal yellow fever viscerotropic disease in a rhesus macaque model. PLOS Neglected Tropical Diseases: 8, e3295. PubMed
  15. Yadav RK, Tavakkoli M, Xie M, Girke T, Reddy GV (2014) A high-resolution gene expression map of the Arabidopsis shoot meristem stem cell niche. Development: 141, 2735–2744. PubMed
  16. Bao E, Jiang T, Girke T (2014) AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references. Bioinformatics: 30, i319-i328. PubMed. Presentation at the 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 11-15, Boston, Massachusetts. ISMB
  17. Worden N, Girke T, Drakakaki G (2014) Endomembrane dissection using chemically induced bioactive clusters. Methods Mol Biol: 1056, 159-168. PubMed
  18. Backman TW, Girke T (2014) Cheminformatic analysis of high-throughput compound screens. Methods Mol Biol: 1056, 145-157. PubMed
  19. Juntawonga P, Girke T, Bazin J,  Bailey-Serres S (2014) Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. PNAS: 111, E203-212. PubMed
  20. Scranton MA, Fowler JH, Girke T, Walling LL (2013) Microarray Analysis of Tomato’s Early and Late Wound Response Reveals New Regulatory Targets for Leucine Aminopeptidase A. PLoS ONE: 8, e77889. PubMed
  21. Choy A, Severo MS, Sun R, Girke S, Gillespie JJ, Pedra J (2013) Decoding the Ubiquitin-Mediated Pathway of Arthropod Disease Vectors. PLoS ONE: 8, e78077. PubMed
  22. Wang Y, Backman T, Horan K, Girke T (2013) fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R. Bioinformatics: 29, 2792-2794. PubMed
  23. Yang EW, Girke T, Jiang T (2013) Differential Gene Expression Analysis Using Coexpression and RNA-Seq Data. Bioinformatics: 29, 2153-2161. PubMed
  24. Zou Z, Saha TT, Roy S, Shin SW, Backman TW, Girke T, White KP, Raikhel AS (2013) Juvenile hormone and its receptor, methoprene-tolerant, control the dynamics of mosquito gene expression. PNAS: 110, E2173-2181. PubMed
  25. Yadav RK, Perales M, Gruel J, Ohno C, Heisler M, Girke T, Jönsson H, Reddy GV (2013) Plant stem cell maintenance involves direct transcriptional repression of differentiation program. Mol Syst Biol: 9, 654ff. PubMed
  26. 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, Bailey-Serres J, Stevenson RA, Zhu JK, Mittler R (2013) Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening. Physiol Plant: 148, 322-333. PubMed
  27. Bao E, Jiang T, Girke T (2013) BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences. Bioinformatics: 29, 1250-1259. PubMed 
  28. Atamian HS, Chaudhary R, Cin VD, Bao E, Girke T, Kaloshian I (2013) In planta expression or delivery of potato aphid Macrosiphum euphorbiae effectors Me10 and Me23 enhances aphid fecundity. Mol Plant Microbe Interact: 26, 67-74. PubMed
  29. Yadav RK, Snipes S, Girke T, Reddy GV (2013) Gene expression analysis of shoot apical meristem cell types. Methods Mol Biol: 959, 235-245. PubMed
  30. Mustroph A, Zanetti ME, Girke T, Bailey-Serres J (2013) Isolation and Analysis of mRNAs from Specific Cell Types of Plants by Ribosome Immunopurification. Methods Mol Biol: 959, 277-302. PubMed
  31. Zhao H, Sun R, Albrecht U, Padmanabhan C, Wang A, Coffey MD, Girke T, Wang Z, Close TJ, Roose M, Yokomi RK, Folimonova S, Vidalakis G, Rouse R, Bowman KD, Jin H (2013) Small RNA profiling reveals phosphorus deficiency as a contributing factor in symptom expression for citrus Huanglongbing disease. Mol Plant: 6, 301-310. PubMed
  32. Bell EM, Lin WC, Husbands AY, Yu L, Jaganatha V, Jablonska B, Mangeon A, Neff MM, Girke T, Springer PS (2012) Arabidopsis lateral organ boundaries negatively regulates brassinosteroid accumulation to limit growth in organ boundaries. PNAS: 109, 21146-21151. PubMed
  33. Dinh TT, Girke T, Liu X, Yant L, Schmid M, Chen X (2012) The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element. Development: 139, 1978-1986. PubMed
  34. 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 (2011) Clusters of bioactive compounds target dynamic endomembrane networks in vivo. PNAS: 108, 17850-17855. PubMed
  35. Yadav RK, Perales M, Gruel J, Girke T, Jonsson H, Reddy GV (2011) WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis. Genes & Development: 25, 2025-2030. PubMed
  36. Bao E, Jiang T, Kaloshian I, Girke T (2011) SEED: Efficient Clustering of Next Generation Sequences. Bioinformatics: 27, 2502-2509. PubMed
  37. Backman T, Cao Y, Girke T (2011) ChemMine Tools: an online service for analyzing and clustering small molecules. Nucleic Acids Research: 39, W486-491. PubMed
  38. Cui X, You N, Girke T, Michelmore R, Van Deynze A (2010) Using Recombinant Inbred Line Microarray Expression Data. Bioinformatics: 15, 1983-1989. PubMed
  39. Horan K, Shelton CR, Girke T (2010) Predicting conserved protein motifs with Sub-HMMs. BMC Bioinformatics: 11, 205. PubMed
  40. Cao Y, Jiang T, Girke T (2010) Accelerated Similarity Searching and Clustering of Large Compound Sets by Geometric Embedding and Locality Sensitive Hashing. Bioinformatics: 26, 953-959. PubMed [Selected for Faculty of 1000 Biology]
  41. Agee, A, Surpin, M, Ju Sohn, E, Girke, T, Rosado, A, Kram, B, Carter, C, Wentzell, A, Kliebenstein, D, Chul Jin, H, Park, O, Jin, H, Hicks, G, Raikhel, N (2009) MODIFIED VACUOLE PHENOTYPE1 Is an Arabidopsis Myrosinase-Associated Protein Involved in Endomembrane Protein Trafficking. Plant Physiol: 152,120-132. PubMed
  42. Mustroph A, Zanetti M, Jang C, Holtan H, Repetti P, Galbraith D, Girke T, Bailey-Serres J (2009) Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. PNAS: 106, 18843-18848. PubMed
  43. Yadav RK, Girke T, Pasala S, Xie M, Reddy GV (2009) Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. PNAS: 106, 4941-4946. PubMed
  44. Knoth C, Salus M, Girke T, Eulgem T (2009) The synthetic elicitor 3,5-Dichloroanthranillic acid (DCA) induces NPR1-dependent and NPR1-independent mechanisms of disease resistance in Arabidopsis thaliana. Plant Physiol: 150, 333-347.  PubMed
  45. Cao Y, Charisi A, Cheng LC, Jiang T, Girke T (2008) ChemmineR: A Compound Mining Framework for R. Bioinformatics: 24, 1733-1734. PubMed
  46. Cao Y, Jiang T, Girke T (2008) A maximum common substructure-based algorithm for searching and predicting drug-like compounds. Bioinformatics: 24, i366-374. PubMed
  47. Bhattarai KK, Xie QG, Mantelin S, Bishnoi U, Girke T, Navarre DA, Kaloshian I (2008) Tomato susceptibility to root-knot nematodes requires an intact jasmonic Acid signaling pathway. Mol Plant Microbe Interact: 21, 1205-1214. PubMed
  48. Ponts N, Yang J, Chung DWD, Prudhomme J, Girke T, Horrocks P, Le Roch K (2008) Deciphering the Ubiquitin-Mediated Pathway in Apicomplexan Parasites: A Potential Strategy to Interfere with Parasite Virulence. PLoS ONE: 3, e2386. PubMed
  49. Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu JK, Cushman JJ, Gollery M, Girke T (2008) Annotating Genes of Known and Unknown Function by Large-Scale Co-Expression Analysis. Plant Physiol: 147, 41-57. PubMed
  50. Cao Y, Jiang T, Girke T (2008) A maximum common substructure-based algorithm for searching and predicting drug-like compounds. Presented at the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 19-23, Toronto, Canada. ISMB
  51. Jin H, Vacic V, Girke T, Lonardi S, Zhu JK (2008) Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol: 9, 6. PubMed
  52. Avila EL, Brown M, Pan S, Desikan R, Neill SJ, Girke T, Surpin M, Raikhel NV (2008) Expression analysis of Arabidopsis vacuolar sorting receptor 3 reveals a putative function in guard cells. J Exp Bot: 59, 1149-1161. PubMed
  53. Gollery M, Harper J, Cushman J, Mittler T, Girke T, Zhu JK, Bailey-Serres J, Mittler R (2006) What makes species unique? The contribution of proteins with obscure features. Genome Biol: 7, R57. PubMed
  54. Girke T, Cheng LC, Raikhel N (2005) ChemMine: A compound mining database for chemical genomics. Plant Physiol: 138, 573-577. PubMed
  55. Sunkar R, Girke T, Zhu JK (2005) Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Res: 33, 4443-4454. PubMed
  56. Horan K, Lauricha J, Bailey-Serres J, Raikhel N, Girke T (2005) Genome cluster database. A sequence family analysis platform for Arabidopsis and rice. Plant Physiol: 138, 47-54. PubMed
  57. Sunkar R, Girke T, Jain PK, Zhu JK (2005) Cloning and characterization of microRNAs from rice. Plant Cell: 17, 1397-1411. PubMed
  58. Carter C, Pan S, Zouhar J, Avila EL, Girke T, Raikhel NV (2004) The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins. Plant Cell: 16, 3285-3303. PubMed
  59. Girke T, Lauricha J, Tran H, Keegstra K, Raikhel N (2004) The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiol: 136, 3003-3008. PubMed
  60. Heilmann I, Pidkowich MS, Girke T, Shanklin J (2004) Switching desaturase enzyme specificity by alternate subcellular targeting. Proc Natl Acad Sci U S A: 101, 10266-10271. PubMed
  61. Gibbons R, Dugaiczyk LJ, Girke T, Duistermars B, Zielinski R, Dugaiczyk A (2004) Distinguishing humans from great apes with AluYb8 repeats. J Mol Biol: 339, 721-729. PubMed
  62. Kawaguchi R, Girke T, Bray EA, Bailey-Serres J (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J: 38, 823-839. PubMed
  63. Girke T, Ozkan M, Carter D, Raikhel NV (2003) Towards a modeling infrastructure for studying plant cells. Plant Physiol: 132, 410-414. PubMed
  64. Girke, T (2003) Genome Scale mRNA Profiling in Agricultural Genomics, p. 115-130. In G Hardiman, ed, Microarray Methods and Applications - Nuts & Bolts, DNA Press, LLC, Mountain View. Amazon
  65. Ruuska SA, Girke T, Benning C, Ohlrogge JB (2002) Contrapuntal networks of gene expression during Arabidopsis seed filling. Plant Cell: 14, 1191-1206. PubMed
  66. Ohlrogge J, Pollard M, Bao X, Focke M, Girke T, Ruuska S, Mekhedov S, Benning C (2000) Fatty acid synthesis: from CO2 to functional genomics. Biochem Soc Trans: 28, 567-573. PubMed
  67. White JA, Todd J, Newman T, Focks N, Girke T, de Ilarduya OM, Jaworski JG, Ohlrogge JB, Benning C (2000) A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil. Plant Physiol: 124, 1582-1594. PubMed
  68. Girke T, Todd J, Ruuska S, White J, Benning C, Ohlrogge J (2000) Microarray analysis of developing Arabidopsis seeds. Plant Physiol: 124, 1570-1581. PubMed
  69. Sperling P, Lee M, Girke T, Zahringer U, Stymne S, Heinz E (2000) A bifunctional delta-fatty acyl acetylenase/desaturase from the moss Ceratodon purpureus. A new member of the cytochrome b5 superfamily. Eur J Biochem: 267, 3801-3811. PubMed
  70. Girke T, Schmidt H, Zahringer U, Reski R, Heinz E (1998) Identification of a novel delta 6-acyl-group desaturase by targeted gene disruption in Physcomitrella patens. Plant J: 15, 39-48. PubMed