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Items: 1 to 50 of 72

1.

Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma.

Hamilton MJ, Girke T, Martinez E.

Oncotarget. 2018 May 4;9(34):23670-23680. doi: 10.18632/oncotarget.25330. eCollection 2018 May 4.

2.

Sequence analysis of the potato aphid Macrosiphum euphorbiae transcriptome identified two new viruses.

Teixeira MA, Sela N, Atamian HS, Bao E, Chaudhary R, MacWilliams J, He J, Mantelin S, Girke T, Kaloshian I.

PLoS One. 2018 Mar 29;13(3):e0193239. doi: 10.1371/journal.pone.0193239. eCollection 2018.

3.

Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.

Zillikens MC, Demissie S, Hsu YH, Yerges-Armstrong LM, Chou WC, Stolk L, Livshits G, Broer L, Johnson T, Koller DL, Kutalik Z, Luan J, Malkin I, Ried JS, Smith AV, Thorleifsson G, Vandenput L, Hua Zhao J, Zhang W, Aghdassi A, Åkesson K, Amin N, Baier LJ, Barroso I, Bennett DA, Bertram L, Biffar R, Bochud M, Boehnke M, Borecki IB, Buchman AS, Byberg L, Campbell H, Campos Obanda N, Cauley JA, Cawthon PM, Cederberg H, Chen Z, Cho NH, Jin Choi H, Claussnitzer M, Collins F, Cummings SR, De Jager PL, Demuth I, Dhonukshe-Rutten RAM, Diatchenko L, Eiriksdottir G, Enneman AW, Erdos M, Eriksson JG, Eriksson J, Estrada K, Evans DS, Feitosa MF, Fu M, Garcia M, Gieger C, Girke T, Glazer NL, Grallert H, Grewal J, Han BG, Hanson RL, Hayward C, Hofman A, Hoffman EP, Homuth G, Hsueh WC, Hubal MJ, Hubbard A, Huffman KM, Husted LB, Illig T, Ingelsson E, Ittermann T, Jansson JO, Jordan JM, Jula A, Karlsson M, Khaw KT, Kilpeläinen TO, Klopp N, Kloth JSL, Koistinen HA, Kraus WE, Kritchevsky S, Kuulasmaa T, Kuusisto J, Laakso M, Lahti J, Lang T, Langdahl BL, Launer LJ, Lee JY, Lerch MM, Lewis JR, Lind L, Lindgren C, Liu Y, Liu T, Liu Y, Ljunggren Ö, Lorentzon M, Luben RN, Maixner W, McGuigan FE, Medina-Gomez C, Meitinger T, Melhus H, Mellström D, Melov S, Michaëlsson K, Mitchell BD, Morris AP, Mosekilde L, Newman A, Nielson CM, O'Connell JR, Oostra BA, Orwoll ES, Palotie A, Parker SCJ, Peacock M, Perola M, Peters A, Polasek O, Prince RL, Räikkönen K, Ralston SH, Ripatti S, Robbins JA, Rotter JI, Rudan I, Salomaa V, Satterfield S, Schadt EE, Schipf S, Scott L, Sehmi J, Shen J, Soo Shin C, Sigurdsson G, Smith S, Soranzo N, Stančáková A, Steinhagen-Thiessen E, Streeten EA, Styrkarsdottir U, Swart KMA, Tan ST, Tarnopolsky MA, Thompson P, Thomson CA, Thorsteinsdottir U, Tikkanen E, Tranah GJ, Tuomilehto J, van Schoor NM, Verma A, Vollenweider P, Völzke H, Wactawski-Wende J, Walker M, Weedon MN, Welch R, Wichmann HE, Widen E, Williams FMK, Wilson JF, Wright NC, Xie W, Yu L, Zhou Y, Chambers JC, Döring A, van Duijn CM, Econs MJ, Gudnason V, Kooner JS, Psaty BM, Spector TD, Stefansson K, Rivadeneira F, Uitterlinden AG, Wareham NJ, Ossowski V, Waterworth D, Loos RJF, Karasik D, Harris TB, Ohlsson C, Kiel DP.

Nat Commun. 2017 Nov 7;8(1):1414. doi: 10.1038/s41467-017-01008-2.

4.

Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.

Zillikens MC, Demissie S, Hsu YH, Yerges-Armstrong LM, Chou WC, Stolk L, Livshits G, Broer L, Johnson T, Koller DL, Kutalik Z, Luan J, Malkin I, Ried JS, Smith AV, Thorleifsson G, Vandenput L, Hua Zhao J, Zhang W, Aghdassi A, Åkesson K, Amin N, Baier LJ, Barroso I, Bennett DA, Bertram L, Biffar R, Bochud M, Boehnke M, Borecki IB, Buchman AS, Byberg L, Campbell H, Campos Obanda N, Cauley JA, Cawthon PM, Cederberg H, Chen Z, Cho NH, Jin Choi H, Claussnitzer M, Collins F, Cummings SR, De Jager PL, Demuth I, Dhonukshe-Rutten RAM, Diatchenko L, Eiriksdottir G, Enneman AW, Erdos M, Eriksson JG, Eriksson J, Estrada K, Evans DS, Feitosa MF, Fu M, Garcia M, Gieger C, Girke T, Glazer NL, Grallert H, Grewal J, Han BG, Hanson RL, Hayward C, Hofman A, Hoffman EP, Homuth G, Hsueh WC, Hubal MJ, Hubbard A, Huffman KM, Husted LB, Illig T, Ingelsson E, Ittermann T, Jansson JO, Jordan JM, Jula A, Karlsson M, Khaw KT, Kilpeläinen TO, Klopp N, Kloth JSL, Koistinen HA, Kraus WE, Kritchevsky S, Kuulasmaa T, Kuusisto J, Laakso M, Lahti J, Lang T, Langdahl BL, Launer LJ, Lee JY, Lerch MM, Lewis JR, Lind L, Lindgren C, Liu Y, Liu T, Liu Y, Ljunggren Ö, Lorentzon M, Luben RN, Maixner W, McGuigan FE, Medina-Gomez C, Meitinger T, Melhus H, Mellström D, Melov S, Michaëlsson K, Mitchell BD, Morris AP, Mosekilde L, Newman A, Nielson CM, O'Connell JR, Oostra BA, Orwoll ES, Palotie A, Parker SCJ, Peacock M, Perola M, Peters A, Polasek O, Prince RL, Räikkönen K, Ralston SH, Ripatti S, Robbins JA, Rotter JI, Rudan I, Salomaa V, Satterfield S, Schadt EE, Schipf S, Scott L, Sehmi J, Shen J, Soo Shin C, Sigurdsson G, Smith S, Soranzo N, Stančáková A, Steinhagen-Thiessen E, Streeten EA, Styrkarsdottir U, Swart KMA, Tan ST, Tarnopolsky MA, Thompson P, Thomson CA, Thorsteinsdottir U, Tikkanen E, Tranah GJ, Tuomilehto J, van Schoor NM, Verma A, Vollenweider P, Völzke H, Wactawski-Wende J, Walker M, Weedon MN, Welch R, Wichmann HE, Widen E, Williams FMK, Wilson JF, Wright NC, Xie W, Yu L, Zhou Y, Chambers JC, Döring A, van Duijn CM, Econs MJ, Gudnason V, Kooner JS, Psaty BM, Spector TD, Stefansson K, Rivadeneira F, Uitterlinden AG, Wareham NJ, Ossowski V, Waterworth D, Loos RJF, Karasik D, Harris TB, Ohlsson C, Kiel DP.

Nat Commun. 2017 Jul 19;8(1):80. doi: 10.1038/s41467-017-00031-7. Erratum in: Nat Commun. 2017 Nov 7;8(1):1414.

5.

Transcriptome-wide microRNA and target dynamics in the fat body during the gonadotrophic cycle of Aedes aegypti.

Zhang X, Aksoy E, Girke T, Raikhel AS, Karginov FV.

Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E1895-E1903. doi: 10.1073/pnas.1701474114. Epub 2017 Feb 21.

6.

Large-scale bioactivity analysis of the small-molecule assayed proteome.

Backman TW, Evans DS, Girke T.

PLoS One. 2017 Feb 8;12(2):e0171413. doi: 10.1371/journal.pone.0171413. eCollection 2017.

7.

Acute Simian Varicella Virus Infection Causes Robust and Sustained Changes in Gene Expression in the Sensory Ganglia.

Arnold N, Girke T, Sureshchandra S, Messaoudi I.

J Virol. 2016 Nov 14;90(23):10823-10843. doi: 10.1128/JVI.01272-16. Print 2016 Dec 1.

8.

Genomic and functional analysis of the host response to acute simian varicella infection in the lung.

Arnold N, Girke T, Sureshchandra S, Nguyen C, Rais M, Messaoudi I.

Sci Rep. 2016 Sep 28;6:34164. doi: 10.1038/srep34164.

9.

systemPipeR: NGS workflow and report generation environment.

H Backman TW, Girke T.

BMC Bioinformatics. 2016 Sep 20;17:388. doi: 10.1186/s12859-016-1241-0.

10.

bioassayR: Cross-Target Analysis of Small Molecule Bioactivity.

Backman TW, Girke T.

J Chem Inf Model. 2016 Jul 25;56(7):1237-42. doi: 10.1021/acs.jcim.6b00109. Epub 2016 Jul 12.

11.

Transcriptomes of Eight Arabidopsis thaliana Accessions Reveal Core Conserved, Genotype- and Organ-Specific Responses to Flooding Stress.

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.

Plant Physiol. 2016 Oct;172(2):668-689. Epub 2016 May 15.

12.

A novel virus from Macrosiphum euphorbiae with similarities to members of the family Flaviviridae.

Teixeira M, Sela N, Ng J, Casteel CL, Peng HC, Bekal S, Girke T, Ghanim M, Kaloshian I.

J Gen Virol. 2016 May;97(5):1261-71. doi: 10.1099/jgv.0.000414. Epub 2016 Jan 27.

13.

Hairy and Groucho mediate the action of juvenile hormone receptor Methoprene-tolerant in gene repression.

Saha TT, Shin SW, Dou W, Roy S, Zhao B, Hou Y, Wang XL, Zou Z, Girke T, Raikhel AS.

Proc Natl Acad Sci U S A. 2016 Feb 9;113(6):E735-43. doi: 10.1073/pnas.1523838113. Epub 2016 Jan 7.

14.

Alcohol Consumption Modulates Host Defense in Rhesus Macaques by Altering Gene Expression in Circulating Leukocytes.

Barr T, Girke T, Sureshchandra S, Nguyen C, Grant K, Messaoudi I.

J Immunol. 2016 Jan 1;196(1):182-95. doi: 10.4049/jimmunol.1501527. Epub 2015 Nov 30.

15.

Regulation of Gene Expression Patterns in Mosquito Reproduction.

Roy S, Saha TT, Johnson L, Zhao B, Ha J, White KP, Girke T, Zou Z, Raikhel AS.

PLoS Genet. 2015 Aug 14;11(8):e1005450. doi: 10.1371/journal.pgen.1005450. eCollection 2015 Aug.

16.

Clinical characteristics and mental health outcomes for women admitted to an Australian Mother-Baby Unit: a focus on borderline personality disorder and emotional dysregulation?

Yelland C, Girke T, Tottman C, Williams AS.

Australas Psychiatry. 2015 Dec;23(6):683-7. doi: 10.1177/1039856215590251. Epub 2015 Jun 11.

PMID:
26070637
17.

Orchestrating high-throughput genomic analysis with Bioconductor.

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, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.

Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Review.

18.

Pathophysiologic and transcriptomic analyses of viscerotropic yellow fever in a rhesus macaque model.

Engelmann F, Josset L, Girke T, Park B, Barron A, Dewane J, Hammarlund E, Lewis A, Axthelm MK, Slifka MK, Messaoudi I.

PLoS Negl Trop Dis. 2014 Nov 20;8(11):e3295. doi: 10.1371/journal.pntd.0003295. eCollection 2014.

19.

A high-resolution gene expression map of the Arabidopsis shoot meristem stem cell niche.

Yadav RK, Tavakkoli M, Xie M, Girke T, Reddy GV.

Development. 2014 Jul;141(13):2735-44. doi: 10.1242/dev.106104.

20.

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.

Bao E, Jiang T, Girke T.

Bioinformatics. 2014 Jun 15;30(12):i319-i328. doi: 10.1093/bioinformatics/btu291.

21.

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis.

Juntawong P, Girke T, Bazin J, Bailey-Serres J.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):E203-12. doi: 10.1073/pnas.1317811111. Epub 2013 Dec 23.

22.

Endomembrane dissection using chemically induced bioactive clusters.

Worden N, Girke T, Drakakaki G.

Methods Mol Biol. 2014;1056:159-68. doi: 10.1007/978-1-62703-592-7_16.

PMID:
24306872
23.

Cheminformatic analysis of high-throughput compound screens.

Backman TW, Girke T.

Methods Mol Biol. 2014;1056:145-57. doi: 10.1007/978-1-62703-592-7_15.

PMID:
24306871
24.

Decoding the ubiquitin-mediated pathway of arthropod disease vectors.

Choy A, Severo MS, Sun R, Girke T, Gillespie JJ, Pedra JH.

PLoS One. 2013 Oct 21;8(10):e78077. doi: 10.1371/journal.pone.0078077. eCollection 2013.

25.

Microarray analysis of tomato's early and late wound response reveals new regulatory targets for Leucine aminopeptidase A.

Scranton MA, Fowler JH, Girke T, Walling LL.

PLoS One. 2013 Oct 24;8(10):e77889. doi: 10.1371/journal.pone.0077889. eCollection 2013.

26.

fmcsR: mismatch tolerant maximum common substructure searching in R.

Wang Y, Backman TW, Horan K, Girke T.

Bioinformatics. 2013 Nov 1;29(21):2792-4. doi: 10.1093/bioinformatics/btt475. Epub 2013 Aug 20.

PMID:
23962615
27.

Differential gene expression analysis using coexpression and RNA-Seq data.

Yang EW, Girke T, Jiang T.

Bioinformatics. 2013 Sep 1;29(17):2153-61. doi: 10.1093/bioinformatics/btt363. Epub 2013 Jun 21.

PMID:
23793751
28.

Juvenile hormone and its receptor, methoprene-tolerant, control the dynamics of mosquito gene expression.

Zou Z, Saha TT, Roy S, Shin SW, Backman TW, Girke T, White KP, Raikhel AS.

Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):E2173-81. doi: 10.1073/pnas.1305293110. Epub 2013 Apr 30.

29.

Plant stem cell maintenance involves direct transcriptional repression of differentiation program.

Yadav RK, Perales M, Gruel J, Ohno C, Heisler M, Girke T, Jönsson H, Reddy GV.

Mol Syst Biol. 2013;9:654. doi: 10.1038/msb.2013.8.

30.

Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening.

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.

Physiol Plant. 2013 Jul;148(3):322-33. doi: 10.1111/ppl.12013. Epub 2013 Mar 20.

PMID:
23517122
31.

BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences.

Bao E, Jiang T, Girke T.

Bioinformatics. 2013 May 15;29(10):1250-9. doi: 10.1093/bioinformatics/btt127. Epub 2013 Mar 14.

PMID:
23493323
32.

Isolation and analysis of mRNAs from specific cell types of plants by ribosome immunopurification.

Mustroph A, Zanetti ME, Girke T, Bailey-Serres J.

Methods Mol Biol. 2013;959:277-302. doi: 10.1007/978-1-62703-221-6_19.

PMID:
23299683
33.

Gene expression analysis of shoot apical meristem cell types.

Yadav RK, Snipes S, Girke T, Reddy GV.

Methods Mol Biol. 2013;959:235-45. doi: 10.1007/978-1-62703-221-6_16.

PMID:
23299680
34.

Small RNA profiling reveals phosphorus deficiency as a contributing factor in symptom expression for citrus huanglongbing disease.

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.

Mol Plant. 2013 Mar;6(2):301-10. doi: 10.1093/mp/sst002. Epub 2013 Jan 5.

35.

Arabidopsis lateral organ boundaries negatively regulates brassinosteroid accumulation to limit growth in organ boundaries.

Bell EM, Lin WC, Husbands AY, Yu L, Jaganatha V, Jablonska B, Mangeon A, Neff MM, Girke T, Springer PS.

Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):21146-51. doi: 10.1073/pnas.1210789109. Epub 2012 Dec 4.

36.

In planta expression or delivery of potato aphid Macrosiphum euphorbiae effectors Me10 and Me23 enhances aphid fecundity.

Atamian HS, Chaudhary R, Cin VD, Bao E, Girke T, Kaloshian I.

Mol Plant Microbe Interact. 2013 Jan;26(1):67-74. doi: 10.1094/MPMI-06-12-0144-FI.

37.

The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element.

Dinh TT, Girke T, Liu X, Yant L, Schmid M, Chen X.

Development. 2012 Jun;139(11):1978-86. doi: 10.1242/dev.077073. Epub 2012 Apr 18.

38.

Clusters of bioactive compounds target dynamic endomembrane networks in vivo.

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.

Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17850-5. doi: 10.1073/pnas.1108581108. Epub 2011 Oct 17.

39.

WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex.

Yadav RK, Perales M, Gruel J, Girke T, Jönsson H, Reddy GV.

Genes Dev. 2011 Oct 1;25(19):2025-30. doi: 10.1101/gad.17258511.

40.

SEED: efficient clustering of next-generation sequences.

Bao E, Jiang T, Kaloshian I, Girke T.

Bioinformatics. 2011 Sep 15;27(18):2502-9. doi: 10.1093/bioinformatics/btr447. Epub 2011 Aug 2.

41.

ChemMine tools: an online service for analyzing and clustering small molecules.

Backman TW, Cao Y, Girke T.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W486-91. doi: 10.1093/nar/gkr320. Epub 2011 May 16.

42.

Single feature polymorphism detection using recombinant inbred line microarray expression data.

Cui X, You N, Girke T, Michelmore R, Van Deynze A.

Bioinformatics. 2010 Aug 15;26(16):1983-9. doi: 10.1093/bioinformatics/btq316. Epub 2010 Jun 23.

PMID:
20576626
43.

Predicting conserved protein motifs with Sub-HMMs.

Horan K, Shelton CR, Girke T.

BMC Bioinformatics. 2010 Apr 26;11:205. doi: 10.1186/1471-2105-11-205.

44.

Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing.

Cao Y, Jiang T, Girke T.

Bioinformatics. 2010 Apr 1;26(7):953-9. doi: 10.1093/bioinformatics/btq067. Epub 2010 Feb 23.

45.

MODIFIED VACUOLE PHENOTYPE1 is an Arabidopsis myrosinase-associated protein involved in endomembrane protein trafficking.

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.

Plant Physiol. 2010 Jan;152(1):120-32. doi: 10.1104/pp.109.145078. Epub 2009 Oct 30.

46.

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis.

Mustroph A, Zanetti ME, Jang CJ, Holtan HE, Repetti PP, Galbraith DW, Girke T, Bailey-Serres J.

Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18843-8. doi: 10.1073/pnas.0906131106. Epub 2009 Oct 20.

47.

The synthetic elicitor 3,5-dichloroanthranilic acid induces NPR1-dependent and NPR1-independent mechanisms of disease resistance in Arabidopsis.

Knoth C, Salus MS, Girke T, Eulgem T.

Plant Physiol. 2009 May;150(1):333-47. doi: 10.1104/pp.108.133678. Epub 2009 Mar 20.

48.

Gene expression map of the Arabidopsis shoot apical meristem stem cell niche.

Yadav RK, Girke T, Pasala S, Xie M, Reddy GV.

Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4941-6. doi: 10.1073/pnas.0900843106. Epub 2009 Mar 3.

49.

Tomato susceptibility to root-knot nematodes requires an intact jasmonic acid signaling pathway.

Bhattarai KK, Xie QG, Mantelin S, Bishnoi U, Girke T, Navarre DA, Kaloshian I.

Mol Plant Microbe Interact. 2008 Sep;21(9):1205-14. doi: 10.1094/MPMI-21-9-1205.

50.

ChemmineR: a compound mining framework for R.

Cao Y, Charisi A, Cheng LC, Jiang T, Girke T.

Bioinformatics. 2008 Aug 1;24(15):1733-4. doi: 10.1093/bioinformatics/btn307. Epub 2008 Jul 2.

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