Thomas Girke

Thomas Girke

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Genetic Support for Longevity-Enhancing Drug Targets: Issues, Preliminary Data, and Future Directions.

J Gerontol A Biol Sci Med Sci 2019 Nov;74(Supplement_1):S61-S71

Department of Quantitative Medicine and Systems Biology, The Translational Genomics Research Institute (TGen), Phoenix, Arizona.

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http://dx.doi.org/10.1093/gerona/glz206DOI Listing
November 2019

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

Oncotarget 2018 May 4;9(34):23670-23680. Epub 2018 May 4.

Department of Biochemistry, University of California at Riverside, Riverside, CA, USA.

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http://dx.doi.org/10.18632/oncotarget.25330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5955119PMC
May 2018

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

Authors:
M Carola Zillikens Serkalem Demissie Yi-Hsiang Hsu Laura M Yerges-Armstrong Wen-Chi Chou Lisette Stolk Gregory Livshits Linda Broer Toby Johnson Daniel L Koller Zoltán Kutalik Jian'an Luan Ida Malkin Janina S Ried Albert V Smith Gudmar Thorleifsson Liesbeth Vandenput Jing Hua Zhao Weihua Zhang Ali Aghdassi Kristina Åkesson Najaf Amin Leslie J Baier Inês Barroso David A Bennett Lars Bertram Rainer Biffar Murielle Bochud Michael Boehnke Ingrid B Borecki Aron S Buchman Liisa Byberg Harry Campbell Natalia Campos Obanda Jane A Cauley Peggy M Cawthon Henna Cederberg Zhao Chen Nam H Cho Hyung Jin Choi Melina Claussnitzer Francis Collins Steven R Cummings Philip L De Jager Ilja Demuth Rosalie A M Dhonukshe-Rutten Luda Diatchenko Gudny Eiriksdottir Anke W Enneman Mike Erdos Johan G Eriksson Joel Eriksson Karol Estrada Daniel S Evans Mary F Feitosa Mao Fu Melissa Garcia Christian Gieger Thomas Girke Nicole L Glazer Harald Grallert Jagvir Grewal Bok-Ghee Han Robert L Hanson Caroline Hayward Albert Hofman Eric P Hoffman Georg Homuth Wen-Chi Hsueh Monica J Hubal Alan Hubbard Kim M Huffman Lise B Husted Thomas Illig Erik Ingelsson Till Ittermann John-Olov Jansson Joanne M Jordan Antti Jula Magnus Karlsson Kay-Tee Khaw Tuomas O Kilpeläinen Norman Klopp Jacqueline S L Kloth Heikki A Koistinen William E Kraus Stephen Kritchevsky Teemu Kuulasmaa Johanna Kuusisto Markku Laakso Jari Lahti Thomas Lang Bente L Langdahl Lenore J Launer Jong-Young Lee Markus M Lerch Joshua R Lewis Lars Lind Cecilia Lindgren Yongmei Liu Tian Liu Youfang Liu Östen Ljunggren Mattias Lorentzon Robert N Luben William Maixner Fiona E McGuigan Carolina Medina-Gomez Thomas Meitinger Håkan Melhus Dan Mellström Simon Melov Karl Michaëlsson Braxton D Mitchell Andrew P Morris Leif Mosekilde Anne Newman Carrie M Nielson Jeffrey R O'Connell Ben A Oostra Eric S Orwoll Aarno Palotie Stephen C J Parker Munro Peacock Markus Perola Annette Peters Ozren Polasek Richard L Prince Katri Räikkönen Stuart H Ralston Samuli Ripatti John A Robbins Jerome I Rotter Igor Rudan Veikko Salomaa Suzanne Satterfield Eric E Schadt Sabine Schipf Laura Scott Joban Sehmi Jian Shen Chan Soo Shin Gunnar Sigurdsson Shad Smith Nicole Soranzo Alena Stančáková Elisabeth Steinhagen-Thiessen Elizabeth A Streeten Unnur Styrkarsdottir Karin M A Swart Sian-Tsung Tan Mark A Tarnopolsky Patricia Thompson Cynthia A Thomson Unnur Thorsteinsdottir Emmi Tikkanen Gregory J Tranah Jaakko Tuomilehto Natasja M van Schoor Arjun Verma Peter Vollenweider Henry Völzke Jean Wactawski-Wende Mark Walker Michael N Weedon Ryan Welch H-Erich Wichmann Elisabeth Widen Frances M K Williams James F Wilson Nicole C Wright Weijia Xie Lei Yu Yanhua Zhou John C Chambers Angela Döring Cornelia M van Duijn Michael J Econs Vilmundur Gudnason Jaspal S Kooner Bruce M Psaty Timothy D Spector Kari Stefansson Fernando Rivadeneira André G Uitterlinden Nicholas J Wareham Vicky Ossowski Dawn Waterworth Ruth J F Loos David Karasik Tamara B Harris Claes Ohlsson Douglas P Kiel

Nat Commun 2017 11 7;8(1):1414. Epub 2017 Nov 7.

Hebrew SeniorLife, Institute for Aging Research, Roslindale, MA, 02131, USA.

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http://dx.doi.org/10.1038/s41467-017-01008-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676783PMC
November 2017

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

PLoS One 2017 8;12(2):e0171413. Epub 2017 Feb 8.

Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0171413PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5298297PMC
August 2017

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

Authors:
M Carola Zillikens Serkalem Demissie Yi-Hsiang Hsu Laura M Yerges-Armstrong Wen-Chi Chou Lisette Stolk Gregory Livshits Linda Broer Toby Johnson Daniel L Koller Zoltán Kutalik Jian'an Luan Ida Malkin Janina S Ried Albert V Smith Gudmar Thorleifsson Liesbeth Vandenput Jing Hua Zhao Weihua Zhang Ali Aghdassi Kristina Åkesson Najaf Amin Leslie J Baier Inês Barroso David A Bennett Lars Bertram Rainer Biffar Murielle Bochud Michael Boehnke Ingrid B Borecki Aron S Buchman Liisa Byberg Harry Campbell Natalia Campos Obanda Jane A Cauley Peggy M Cawthon Henna Cederberg Zhao Chen Nam H Cho Hyung Jin Choi Melina Claussnitzer Francis Collins Steven R Cummings Philip L De Jager Ilja Demuth Rosalie A M Dhonukshe-Rutten Luda Diatchenko Gudny Eiriksdottir Anke W Enneman Mike Erdos Johan G Eriksson Joel Eriksson Karol Estrada Daniel S Evans Mary F Feitosa Mao Fu Melissa Garcia Christian Gieger Thomas Girke Nicole L Glazer Harald Grallert Jagvir Grewal Bok-Ghee Han Robert L Hanson Caroline Hayward Albert Hofman Eric P Hoffman Georg Homuth Wen-Chi Hsueh Monica J Hubal Alan Hubbard Kim M Huffman Lise B Husted Thomas Illig Erik Ingelsson Till Ittermann John-Olov Jansson Joanne M Jordan Antti Jula Magnus Karlsson Kay-Tee Khaw Tuomas O Kilpeläinen Norman Klopp Jacqueline S L Kloth Heikki A Koistinen William E Kraus Stephen Kritchevsky Teemu Kuulasmaa Johanna Kuusisto Markku Laakso Jari Lahti Thomas Lang Bente L Langdahl Lenore J Launer Jong-Young Lee Markus M Lerch Joshua R Lewis Lars Lind Cecilia Lindgren Yongmei Liu Tian Liu Youfang Liu Östen Ljunggren Mattias Lorentzon Robert N Luben William Maixner Fiona E McGuigan Carolina Medina-Gomez Thomas Meitinger Håkan Melhus Dan Mellström Simon Melov Karl Michaëlsson Braxton D Mitchell Andrew P Morris Leif Mosekilde Anne Newman Carrie M Nielson Jeffrey R O'Connell Ben A Oostra Eric S Orwoll Aarno Palotie Stephen C J Parker Munro Peacock Markus Perola Annette Peters Ozren Polasek Richard L Prince Katri Räikkönen Stuart H Ralston Samuli Ripatti John A Robbins Jerome I Rotter Igor Rudan Veikko Salomaa Suzanne Satterfield Eric E Schadt Sabine Schipf Laura Scott Joban Sehmi Jian Shen Chan Soo Shin Gunnar Sigurdsson Shad Smith Nicole Soranzo Alena Stančáková Elisabeth Steinhagen-Thiessen Elizabeth A Streeten Unnur Styrkarsdottir Karin M A Swart Sian-Tsung Tan Mark A Tarnopolsky Patricia Thompson Cynthia A Thomson Unnur Thorsteinsdottir Emmi Tikkanen Gregory J Tranah Jaakko Tuomilehto Natasja M van Schoor Arjun Verma Peter Vollenweider Henry Völzke Jean Wactawski-Wende Mark Walker Michael N Weedon Ryan Welch H-Erich Wichmann Elisabeth Widen Frances M K Williams James F Wilson Nicole C Wright Weijia Xie Lei Yu Yanhua Zhou John C Chambers Angela Döring Cornelia M van Duijn Michael J Econs Vilmundur Gudnason Jaspal S Kooner Bruce M Psaty Timothy D Spector Kari Stefansson Fernando Rivadeneira André G Uitterlinden Nicholas J Wareham Vicky Ossowski Dawn Waterworth Ruth J F Loos David Karasik Tamara B Harris Claes Ohlsson Douglas P Kiel

Nat Commun 2017 07 19;8(1):80. Epub 2017 Jul 19.

Hebrew SeniorLife, Institute for Aging Research, Roslindale, MA, 02131, USA.

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http://dx.doi.org/10.1038/s41467-017-00031-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517526PMC
July 2017

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

Proc Natl Acad Sci U S A 2017 03 21;114(10):E1895-E1903. Epub 2017 Feb 21.

Institute of Integrative Genome Biology, University of California, Riverside, CA 92521;

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http://dx.doi.org/10.1073/pnas.1701474114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5347622PMC
March 2017

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

J Virol 2016 Dec 14;90(23):10823-10843. Epub 2016 Nov 14.

Graduate Program in Microbiology, University of California-Riverside, Riverside, California, USA

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http://dx.doi.org/10.1128/JVI.01272-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5110160PMC
December 2016

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

Plant Physiol 2016 10 15;172(2):668-689. Epub 2016 May 15.

Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.)

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047075PMC
http://dx.doi.org/10.1104/pp.16.00472DOI Listing
October 2016

systemPipeR: NGS workflow and report generation environment.

BMC Bioinformatics 2016 Sep 20;17:388. Epub 2016 Sep 20.

Institute for Integrative Genome Biology, University of California, Riverside, 1207F Genomics Building, 3401 Watkins Drive, Riverside, 92521, CA, USA.

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http://dx.doi.org/10.1186/s12859-016-1241-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5029110PMC
September 2016

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

Sci Rep 2016 Sep 28;6:34164. Epub 2016 Sep 28.

Graduate Program in Microbiology, University of California-Riverside, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039758PMC
http://dx.doi.org/10.1038/srep34164DOI Listing
September 2016

bioassayR: Cross-Target Analysis of Small Molecule Bioactivity.

J Chem Inf Model 2016 07 12;56(7):1237-42. Epub 2016 Jul 12.

Institute for Integrative Genome Biology, University of California, Riverside , Riverside, California 92521, United States.

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http://dx.doi.org/10.1021/acs.jcim.6b00109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330305PMC
July 2016

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

PLoS Negl Trop Dis 2014 20;8(11):e3295. Epub 2014 Nov 20.

Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California, United States of America; Division of Pathobiology and Immunology, Oregon National Primate Research Center, Portland, Oregon, United States of America; Division of Neuroscience, Oregon National Primate Research Center, Portland, Oregon, United States of America.

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https://www.plos.org/wp-content/uploads/2014/11/pntd.0003295
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http://dx.plos.org/10.1371/journal.pntd.0003295
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http://dx.doi.org/10.1371/journal.pntd.0003295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238990PMC
May 2016

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

J Gen Virol 2016 05 27;97(5):1261-71. Epub 2016 Jan 27.

4​ Institute of Integrative Genome Biology,University of California, Riverside, California,USA 1​ Department of Nematology,University of California, Riverside, California,USA.

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http://dx.doi.org/10.1099/jgv.0.000414DOI Listing
May 2016

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

Proc Natl Acad Sci U S A 2016 Feb 7;113(6):E735-43. Epub 2016 Jan 7.

Department of Entomology, University of California, Riverside, CA 92521; The Institute for Integrative Genome Biology, University of California, Riverside, CA 92521;

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http://dx.doi.org/10.1073/pnas.1523838113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760797PMC
February 2016

Regulation of Gene Expression Patterns in Mosquito Reproduction.

PLoS Genet 2015 Aug 14;11(8):e1005450. Epub 2015 Aug 14.

Department of Entomology, University of California, Riverside, Riverside, California, United States of America; Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537244PMC
August 2015

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

PLoS One 2013 24;8(10):e77889. Epub 2013 Oct 24.

Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, Riverside, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077889PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812031PMC
September 2014

Decoding the ubiquitin-mediated pathway of arthropod disease vectors.

PLoS One 2013 21;8(10):e78077. Epub 2013 Oct 21.

Institute for Integrative Genome Biology, Center for Disease Vector Research and Department of Entomology, University of California Riverside, Riverside, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078077PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804464PMC
September 2014

Cheminformatic analysis of high-throughput compound screens.

Methods Mol Biol 2014 ;1056:145-57

Department of Bioengineering, University of California Riverside, Riverside, CA, USA.

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http://dx.doi.org/10.1007/978-1-62703-592-7_15DOI Listing
July 2014

Endomembrane dissection using chemically induced bioactive clusters.

Methods Mol Biol 2014 ;1056:159-68

Department of Plant Sciences, University of California, Davis, CA, USA.

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http://dx.doi.org/10.1007/978-1-62703-592-7_16DOI Listing
July 2014

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

Development 2014 Jul;141(13):2735-44

Department of Botany and Plant Sciences, Center for Plant Cell Biology (CEPCEB), Institute of Integrative Genome Biology (IIGB), University of California, Riverside, CA 92521, USA

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http://dx.doi.org/10.1242/dev.106104DOI Listing
July 2014

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

Bioinformatics 2014 Jun;30(12):i319-i328

Department of Computer Science and Engineering and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058956PMC
June 2014

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

Proc Natl Acad Sci U S A 2014 Jan 23;111(1):E203-12. Epub 2013 Dec 23.

Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521.

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http://dx.doi.org/10.1073/pnas.1317811111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890782PMC
January 2014

fmcsR: mismatch tolerant maximum common substructure searching in R.

Bioinformatics 2013 Nov 20;29(21):2792-4. Epub 2013 Aug 20.

Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt475DOI Listing
November 2013

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

Mol Syst Biol 2013 ;9:654

Department of Botany and Plant Sciences, Center for Plant Cell Biology (CEPCEB), Institute of Integrative Genome Biology (IIGB), University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1038/msb.2013.8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658276PMC
September 2013

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

Bioinformatics 2013 Sep 21;29(17):2153-61. Epub 2013 Jun 21.

Department of Computer Science and Engineering, Department of Botany and Plant Sciences and Institute of Integative Genome Biology, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt363DOI Listing
September 2013

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

Physiol Plant 2013 Jul 20;148(3):322-33. Epub 2013 Mar 20.

Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle, #305220, Denton, TX 76203-5017, USA.

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http://dx.doi.org/10.1111/ppl.12013DOI Listing
July 2013

Gene expression analysis of shoot apical meristem cell types.

Methods Mol Biol 2013 ;959:235-45

Department of Botany and Plant Sciences, Center for Plant Cell Biology (CEPCEB), Institute of Integrative Genome Biology (IIGB), University of California, Riverside, CA, USA.

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http://dx.doi.org/10.1007/978-1-62703-221-6_16DOI Listing
June 2013

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

Methods Mol Biol 2013 ;959:277-302

Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany.

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http://dx.doi.org/10.1007/978-1-62703-221-6_19DOI Listing
June 2013

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

Proc Natl Acad Sci U S A 2013 Jun 30;110(24):E2173-81. Epub 2013 Apr 30.

Departments of Entomology and Botany and Plant Sciences, Institute for Integrative Genome Biology, and Graduate Program in Genetics, Genomics and Bioinformatics, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1073/pnas.1305293110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683779PMC
June 2013

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

Bioinformatics 2013 May 14;29(10):1250-9. Epub 2013 Mar 14.

Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt127DOI Listing
May 2013

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

Proc Natl Acad Sci U S A 2012 Dec 4;109(51):21146-51. Epub 2012 Dec 4.

Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1073/pnas.1210789109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529045PMC
December 2012

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

Development 2012 Jun 18;139(11):1978-86. Epub 2012 Apr 18.

Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1242/dev.077073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3347690PMC
June 2012

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

Genes Dev 2011 Oct;25(19):2025-30

Department of Botany and Plant Sciences, Center for Plant Cell Biology (CEPCEB), Institute of Integrative Genome Biology (IIGB), University of California at Riverside, Riverside, California 92521, USA.

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http://dx.doi.org/10.1101/gad.17258511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197201PMC
October 2011

Clusters of bioactive compounds target dynamic endomembrane networks in vivo.

Proc Natl Acad Sci U S A 2011 Oct 17;108(43):17850-5. Epub 2011 Oct 17.

Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1073/pnas.1108581108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203817PMC
October 2011

SEED: efficient clustering of next-generation sequences.

Bioinformatics 2011 Sep 2;27(18):2502-9. Epub 2011 Aug 2.

Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167058PMC
September 2011

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

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

Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1093/nar/gkr320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125754PMC
July 2011

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

Bioinformatics 2010 Aug 23;26(16):1983-9. Epub 2010 Jun 23.

Department of Statistics, University of California, Riverside, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq316DOI Listing
August 2010

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

Bioinformatics 2010 Apr 23;26(7):953-9. Epub 2010 Feb 23.

Department of Computer Science & Engineering and Department of Botany & Plant Sciences, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844998PMC
April 2010

Predicting conserved protein motifs with Sub-HMMs.

BMC Bioinformatics 2010 Apr 26;11:205. Epub 2010 Apr 26.

Department of Computer Science and Engineering, University of California Riverside, Riverside, California, USA.

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http://dx.doi.org/10.1186/1471-2105-11-205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879284PMC
April 2010

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

Proc Natl Acad Sci U S A 2009 Nov 20;106(44):18843-8. Epub 2009 Oct 20.

Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1073/pnas.0906131106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764735PMC
November 2009

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

Plant Physiol 2009 May 20;150(1):333-47. Epub 2009 Mar 20.

Center for Plant Cell Biology, Institute for Integrative Genome Biology, Department of Botany and Plant Sciences, University of California at Riverside, Riverside, California 92521, USA.

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http://dx.doi.org/10.1104/pp.108.133678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675713PMC
May 2009

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

Proc Natl Acad Sci U S A 2009 Mar 3;106(12):4941-6. Epub 2009 Mar 3.

Center for Plant Cell Biology and Department of Botany and Plant Sciences, 2150 Batchelor Hall, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1073/pnas.0900843106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660727PMC
March 2009

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

Mol Plant Microbe Interact 2008 Sep;21(9):1205-14

Department of Nematology, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA.

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http://apsjournals.apsnet.org/doi/10.1094/MPMI-21-9-1205
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http://dx.doi.org/10.1094/MPMI-21-9-1205DOI Listing
September 2008

ChemmineR: a compound mining framework for R.

Bioinformatics 2008 Aug 2;24(15):1733-4. Epub 2008 Jul 2.

Department of Computer Science and Engineering, University of California, Riverside, California, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638865PMC
August 2008

A maximum common substructure-based algorithm for searching and predicting drug-like compounds.

Bioinformatics 2008 Jul;24(13):i366-74

Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718661PMC
July 2008

Deciphering the ubiquitin-mediated pathway in apicomplexan parasites: a potential strategy to interfere with parasite virulence.

PLoS One 2008 Jun 11;3(6):e2386. Epub 2008 Jun 11.

Department of Cell Biology and Neurosciences, University of California at Riverside, Riverside, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408969PMC
June 2008

Annotating genes of known and unknown function by large-scale coexpression analysis.

Plant Physiol 2008 May 19;147(1):41-57. Epub 2008 Mar 19.

Department of Botany and Plant Sciences , University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1104/pp.108.117366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2330292PMC
May 2008

Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis.

BMC Mol Biol 2008 Jan 14;9. Epub 2008 Jan 14.

Department of Plant Pathology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1186/1471-2199-9-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2262095PMC
January 2008

What makes species unique? The contribution of proteins with obscure features.

Genome Biol 2006 ;7(7):R57

Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779552PMC
May 2007

Identification and characterization of endogenous small interfering RNAs from rice.

Nucleic Acids Res 2005 2;33(14):4443-54. Epub 2005 Aug 2.

Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, 2150 Batchelor Hall, University of California, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1093/nar/gki758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182700PMC
August 2005

ChemMine. A compound mining database for chemical genomics.

Plant Physiol 2005 Jun;138(2):573-7

Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA.

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http://dx.doi.org/10.1104/pp.105.062687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1150377PMC
June 2005

Cloning and characterization of microRNAs from rice.

Plant Cell 2005 May 1;17(5):1397-411. Epub 2005 Apr 1.

Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1091763PMC
May 2005

Genome cluster database. A sequence family analysis platform for Arabidopsis and rice.

Plant Physiol 2005 May;138(1):47-54

Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA.

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http://dx.doi.org/10.1104/pp.104.059048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1104159PMC
May 2005

The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins.

Plant Cell 2004 Dec 11;16(12):3285-303. Epub 2004 Nov 11.

Center for Plant Cell Biology, Botany and Plant Sciences, University of California, Riverside, California 92521, USA.

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http://dx.doi.org/10.1105/tpc.104.027078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC535874PMC
December 2004

The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism.

Plant Physiol 2004 Oct;136(2):3003-8; discussion 3001

Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC523362PMC
October 2004

Switching desaturase enzyme specificity by alternate subcellular targeting.

Proc Natl Acad Sci U S A 2004 Jul 6;101(28):10266-71. Epub 2004 Jul 6.

Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC478599PMC
July 2004

Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana.

Plant J 2004 Jun;38(5):823-39

Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521-0124, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2004.02090.xDOI Listing
June 2004

Distinguishing humans from great apes with AluYb8 repeats.

J Mol Biol 2004 Jun;339(4):721-9

Department of Biochemistry, University of California, Riverside, CA 92521, USA.

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June 2004

Contrapuntal networks of gene expression during Arabidopsis seed filling.

Plant Cell 2002 Jun;14(6):1191-206

Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.

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http://dx.doi.org/10.1105/tpc.000877DOI Listing
June 2002