Terry Gaasterland

Terry Gaasterland

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Terry Gaasterland

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The WNT target SP5 negatively regulates WNT transcriptional programs in human pluripotent stem cells.

Nat Commun 2017 10 18;8(1):1034. Epub 2017 Oct 18.

Department of Cellular & Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0695, USA.

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http://dx.doi.org/10.1038/s41467-017-01203-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647328PMC
October 2017

Top-Down Atmospheric Ionization Mass Spectrometry Microscopy Combined With Proteogenomics.

Anal Chem 2017 08 24;89(16):8251-8258. Epub 2017 Jul 24.

Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan.

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http://pubs.acs.org/doi/10.1021/acs.analchem.7b01096
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http://dx.doi.org/10.1021/acs.analchem.7b01096DOI Listing
August 2017

Age at natural menopause genetic risk score in relation to age at natural menopause and primary open-angle glaucoma in a US-based sample.

Menopause 2017 02;24(2):150-156

1Department of Ophthalmology, Massachusetts Eye and Ear Infirmary 2Channing Division of Network Medicine, Brigham and Women's Hospital 3Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, MA 4Department of Epidemiology and Biostatistics 5Institute of Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH 6Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 7Department of Ophthalmology 8Department of Medicine, Duke University, Duke University Medical Center, Durham, NC 9Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 10Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 11Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI 12Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, PA 13Departments of Ophthalmology and Anatomy/Cell Biology, University of Iowa, College of Medicine, Iowa City, IO 14Department of Ophthalmology, University of North Carolina, Chapel Hill, NC 15Department of Ophthalmology, WVU Eye Institute, Morgantown, WV 16Scripps Genome Center, University of California at San Diego, San Diego, CA 17Emmes Corporation, Chevy Chase, MD 18Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 19Department of Ophthalmology, Stanford University, Palo Alto, CA 20Department of Ophthalmology, Mayo Clinic, Rochester, MN 21Wills Eye Institute, Philadelphia, PA 22Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, NY 23Department of Ophthalmology, Case Western Reserve University School of Medicine, Cleveland, OH 24Department of Ophthalmology & Visual Sciences, University of Nebraska Medical Center, Omaha, NE 25Department of Genetics; Stanford University, Palo Alto, CA 26Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, MD 27Department of Ophthalmology, Hamilton Eye Center; University of California at San Diego, San Diego, CA 28Department of Cellular Biology & Anatomy, Augusta University, Augusta, GA.

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http://dx.doi.org/10.1097/GME.0000000000000741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5266624PMC
February 2017

Genome-wide association analysis identifies TXNRD2, ATXN2 and FOXC1 as susceptibility loci for primary open-angle glaucoma.

Nat Genet 2016 Feb 11;48(2):189-94. Epub 2016 Jan 11.

Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA.

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http://search.proquest.com/openview/9583d4c1af74c01602d422b2
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http://www.nature.com/doifinder/10.1038/ng.3482
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http://dx.doi.org/10.1038/ng.3482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731307PMC
February 2016

Analysis of SOX2-expressing cell populations derived from human pluripotent stem cells.

Stem Cell Reports 2013 31;1(5):464-78. Epub 2013 Oct 31.

Stem Cell Program, Department of Cellular and Molecular Medicine, UCSD, 9500 Gilman Drive, La Jolla, CA 92093-0695, USA.

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http://dx.doi.org/10.1016/j.stemcr.2013.09.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841266PMC
October 2015

Endogenous WNT signaling regulates hPSC-derived neural progenitor cell heterogeneity and specifies their regional identity.

Stem Cell Reports 2014 Dec 13;3(6):1015-28. Epub 2014 Nov 13.

Department of Cellular and Molecular Medicine, Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0695, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287-9709, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2014.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264562PMC
December 2014

Let-7 coordinately suppresses components of the amino acid sensing pathway to repress mTORC1 and induce autophagy.

Cell Metab 2014 Oct;20(4):626-38

Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Hospital, San Diego, CA 92123, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2014.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245205PMC
October 2014

WNT5A encodes two isoforms with distinct functions in cancers.

PLoS One 2013 18;8(11):e80526. Epub 2013 Nov 18.

Centre National de Recherche Scientifique-Université Paris, Institut de Cancérologie Gustave Roussy, Villejuif, France ; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080526PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832467PMC
August 2014

Vespucci: a system for building annotated databases of nascent transcripts.

Nucleic Acids Res 2014 Feb 4;42(4):2433-47. Epub 2013 Dec 4.

Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA, Department of Bioinformatics and Systems Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA, San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0375, USA, A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, P.O. Box 1627, 70120 Kuopio, Finland, Institute for Genomic Medicine and Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA and Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.

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http://dx.doi.org/10.1093/nar/gkt1237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3936758PMC
February 2014

The WNT receptor FZD7 is required for maintenance of the pluripotent state in human embryonic stem cells.

Proc Natl Acad Sci U S A 2014 Jan 13;111(4):1409-14. Epub 2014 Jan 13.

Department of Cellular and Molecular Medicine, Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0695.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1323697111
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http://dx.doi.org/10.1073/pnas.1323697111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910637PMC
January 2014

Mild iron overload in an African American man with SLC40A1 D270V.

Acta Haematol 2012 15;128(1):28-32. Epub 2012 May 15.

Department of Molecular and Experimental Medicine, Scripps Research Institute, University of California-San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1159/000337034DOI Listing
September 2012

Biomedical impact of splicing mutations revealed through exome sequencing.

Mol Med 2012 Mar 30;18:314-9. Epub 2012 Mar 30.

Institute of Public Health Genomics, Department of Genetics and Cell Biology, Research Institutes CAPHRI and GROW, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands.

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http://dx.doi.org/10.2119/molmed.2011.00126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324954PMC
March 2012

The medicinal leech genome encodes 21 innexin genes: different combinations are expressed by identified central neurons.

Dev Genes Evol 2012 Mar 23;222(1):29-44. Epub 2012 Feb 23.

Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1007/s00427-011-0387-zDOI Listing
March 2012

Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana.

PLoS One 2011 12;6(8):e22870. Epub 2011 Aug 12.

Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022870PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155517PMC
February 2012

Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination.

Nucleic Acids Res 2012 Feb 29;40(3):e24. Epub 2011 Nov 29.

Laboratory of Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium.

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http://dx.doi.org/10.1093/nar/gkr1000DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273786PMC
February 2012

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm.

BMC Bioinformatics 2008 Oct 7;9:419. Epub 2008 Oct 7.

Marine Biology Research Division, Scripps Institution of Oceanography University of California at San Diego, La Jolla, CA 92093 USA.

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http://dx.doi.org/10.1186/1471-2105-9-419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2573894PMC
October 2008

Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1.

Appl Environ Microbiol 2008 May 14;74(9):2646-58. Epub 2008 Mar 14.

Department of Environmental and Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Sciences University, 20000 NW Walker Rd., Beaverton, OR 97006, USA.

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http://aem.asm.org/content/74/9/2646.full.pdf
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http://aem.asm.org/cgi/doi/10.1128/AEM.01656-07
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http://dx.doi.org/10.1128/AEM.01656-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394881PMC
May 2008

Computational prediction and experimental validation of Ciona intestinalis microRNA genes.

BMC Genomics 2007 Nov 29;8:445. Epub 2007 Nov 29.

Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, MSC 0202, La Jolla, CA 92093 USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-8-445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2243180PMC
November 2007

Prediction of cyclin-dependent kinase phosphorylation substrates.

PLoS One 2007 Aug 1;2(7):e656. Epub 2007 Aug 1.

Department of Chemistry, York College of the City University of New York, Jamaica, New York, United States of America; Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000656PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1924601PMC
August 2007

DarkHorse: a method for genome-wide prediction of horizontal gene transfer.

Genome Biol 2007 ;8(2):R16

Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, Gilman Drive, La Jolla, CA 92093-0202, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2007-8-2-r16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852411PMC
July 2007

Spliced leader RNA trans-splicing in dinoflagellates.

Proc Natl Acad Sci U S A 2007 Mar 2;104(11):4618-23. Epub 2007 Mar 2.

Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, Groton, CT 06340, USA.

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http://dx.doi.org/10.1073/pnas.0700258104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838650PMC
March 2007

An RNA map predicting Nova-dependent splicing regulation.

Nature 2006 Nov 25;444(7119):580-6. Epub 2006 Oct 25.

Howard Hughes Medical Institute, New York, New York 10021, USA.

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http://dx.doi.org/10.1038/nature05304DOI Listing
November 2006

The genome of the sea urchin Strongylocentrotus purpuratus.

Authors:
Erica Sodergren George M Weinstock Eric H Davidson R Andrew Cameron Richard A Gibbs Robert C Angerer Lynne M Angerer Maria Ina Arnone David R Burgess Robert D Burke James A Coffman Michael Dean Maurice R Elphick Charles A Ettensohn Kathy R Foltz Amro Hamdoun Richard O Hynes William H Klein William Marzluff David R McClay Robert L Morris Arcady Mushegian Jonathan P Rast L Courtney Smith Michael C Thorndyke Victor D Vacquier Gary M Wessel Greg Wray Lan Zhang Christine G Elsik Olga Ermolaeva Wratko Hlavina Gretchen Hofmann Paul Kitts Melissa J Landrum Aaron J Mackey Donna Maglott Georgia Panopoulou Albert J Poustka Kim Pruitt Victor Sapojnikov Xingzhi Song Alexandre Souvorov Victor Solovyev Zheng Wei Charles A Whittaker Kim Worley K James Durbin Yufeng Shen Olivier Fedrigo David Garfield Ralph Haygood Alexander Primus Rahul Satija Tonya Severson Manuel L Gonzalez-Garay Andrew R Jackson Aleksandar Milosavljevic Mark Tong Christopher E Killian Brian T Livingston Fred H Wilt Nikki Adams Robert Bellé Seth Carbonneau Rocky Cheung Patrick Cormier Bertrand Cosson Jenifer Croce Antonio Fernandez-Guerra Anne-Marie Genevière Manisha Goel Hemant Kelkar Julia Morales Odile Mulner-Lorillon Anthony J Robertson Jared V Goldstone Bryan Cole David Epel Bert Gold Mark E Hahn Meredith Howard-Ashby Mark Scally John J Stegeman Erin L Allgood Jonah Cool Kyle M Judkins Shawn S McCafferty Ashlan M Musante Robert A Obar Amanda P Rawson Blair J Rossetti Ian R Gibbons Matthew P Hoffman Andrew Leone Sorin Istrail Stefan C Materna Manoj P Samanta Viktor Stolc Waraporn Tongprasit Qiang Tu Karl-Frederik Bergeron Bruce P Brandhorst James Whittle Kevin Berney David J Bottjer Cristina Calestani Kevin Peterson Elly Chow Qiu Autumn Yuan Eran Elhaik Dan Graur Justin T Reese Ian Bosdet Shin Heesun Marco A Marra Jacqueline Schein Michele K Anderson Virginia Brockton Katherine M Buckley Avis H Cohen Sebastian D Fugmann Taku Hibino Mariano Loza-Coll Audrey J Majeske Cynthia Messier Sham V Nair Zeev Pancer David P Terwilliger Cavit Agca Enrique Arboleda Nansheng Chen Allison M Churcher F Hallböök Glen W Humphrey Mohammed M Idris Takae Kiyama Shuguang Liang Dan Mellott Xiuqian Mu Greg Murray Robert P Olinski Florian Raible Matthew Rowe John S Taylor Kristin Tessmar-Raible D Wang Karen H Wilson Shunsuke Yaguchi Terry Gaasterland Blanca E Galindo Herath J Gunaratne Celina Juliano Masashi Kinukawa Gary W Moy Anna T Neill Mamoru Nomura Michael Raisch Anna Reade Michelle M Roux Jia L Song Yi-Hsien Su Ian K Townley Ekaterina Voronina Julian L Wong Gabriele Amore Margherita Branno Euan R Brown Vincenzo Cavalieri Véronique Duboc Louise Duloquin Constantin Flytzanis Christian Gache François Lapraz Thierry Lepage Annamaria Locascio Pedro Martinez Giorgio Matassi Valeria Matranga Ryan Range Francesca Rizzo Eric Röttinger Wendy Beane Cynthia Bradham Christine Byrum Tom Glenn Sofia Hussain Gerard Manning Esther Miranda Rebecca Thomason Katherine Walton Athula Wikramanayke Shu-Yu Wu Ronghui Xu C Titus Brown Lili Chen Rachel F Gray Pei Yun Lee Jongmin Nam Paola Oliveri Joel Smith Donna Muzny Stephanie Bell Joseph Chacko Andrew Cree Stacey Curry Clay Davis Huyen Dinh Shannon Dugan-Rocha Jerry Fowler Rachel Gill Cerrissa Hamilton Judith Hernandez Sandra Hines Jennifer Hume Laronda Jackson Angela Jolivet Christie Kovar Sandra Lee Lora Lewis George Miner Margaret Morgan Lynne V Nazareth Geoffrey Okwuonu David Parker Ling-Ling Pu Rachel Thorn Rita Wright

Science 2006 Nov;314(5801):941-52

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http://dx.doi.org/10.1126/science.1133609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423PMC
November 2006

Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana.

Genome Biol 2005 15;6(4):R30. Epub 2005 Mar 15.

Laboratory of Computational Genomics, The Rockefeller University, New York, NY 10021, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2005-6-4-r30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088958PMC
August 2006

A computational investigation of kinetoplastid trans-splicing.

Genome Biol 2005 17;6(11):R95. Epub 2005 Oct 17.

Laboratory of Computational Genomics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

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http://dx.doi.org/10.1186/gb-2005-6-11-r95DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1297651PMC
June 2006

Prediction and identification of herpes simplex virus 1-encoded microRNAs.

J Virol 2006 Jun;80(11):5499-508

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1128/JVI.00200-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1472173PMC
June 2006

Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific.

Genome Biol 2004 30;5(10):R75. Epub 2004 Sep 30.

The Laboratory of Computational Genomics, The Rockefeller University, New York, NY 10021, USA.

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http://dx.doi.org/10.1186/gb-2004-5-10-r75DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545595PMC
July 2005

Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets.

Genome Biol 2004 31;5(9):R65. Epub 2004 Aug 31.

Laboratory of Computational Genomics, The Rockefeller University, New York, NY 10021, USA.

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http://dx.doi.org/10.1186/gb-2004-5-9-r65DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC522872PMC
May 2005

Monitoring genome-wide changes in gene expression in response to endogenous cytokinin reveals targets in Arabidopsis thaliana.

FEBS Lett 2003 Nov;554(3):373-80

Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

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http://dx.doi.org/10.1016/s0014-5793(03)01194-3DOI Listing
November 2003

An organism-specific method to rank predicted coding regions in Trypanosoma brucei.

Nucleic Acids Res 2003 Oct;31(20):5877-85

Laboratory of Computational Genomics, The Rockefeller University, 1230 York Avenue, Box 250, New York, NY 10021, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC219476PMC
http://dx.doi.org/10.1093/nar/gkg798DOI Listing
October 2003

The small RNA profile during Drosophila melanogaster development.

Dev Cell 2003 Aug;5(2):337-50

Department of Animal Molecular Genetics, Institute of Molecular Genetics, Kurchatov sq. 2, 123182, Moscow, Russia.

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http://dx.doi.org/10.1016/s1534-5807(03)00228-4DOI Listing
August 2003

Identification of transcription coactivator OCA-B-dependent genes involved in antigen-dependent B cell differentiation by cDNA array analyses.

Proc Natl Acad Sci U S A 2003 Jul 11;100(15):8868-73. Epub 2003 Jul 11.

Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

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http://dx.doi.org/10.1073/pnas.1033108100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC166405PMC
July 2003

The phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1alpha and EF-2.

J Eukaryot Microbiol 2002 Jan-Feb;49(1):1-10

Department of Biosystems Science, Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, Japan.

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http://dx.doi.org/10.1111/j.1550-7408.2002.tb00332.xDOI Listing
November 2002

Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome.

Genome Res 2002 Sep;12(9):1377-85

Laboratory for Computational Genomics, The Rockefeller University, New York, New York 10021, USA.

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http://dx.doi.org/10.1101/gr.191702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186662PMC
September 2002

Genomic insights into evolution.

Curr Opin Struct Biol 2002 Jun;12(3):345-7

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http://dx.doi.org/10.1016/s0959-440x(02)00329-9DOI Listing
June 2002