Publications by authors named "Jongmin Nam"

15Publications

Multiplex cis-regulatory analysis.

Authors:
Jongmin Nam

Methods Cell Biol 2019 20;151:159-176. Epub 2019 Mar 20.

Department of Biology and Center for Computational & Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States. Electronic address:

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http://dx.doi.org/10.1016/bs.mcb.2019.01.009DOI Listing
July 2019

Single embryo-resolution quantitative analysis of reporters permits multiplex spatial cis-regulatory analysis.

Dev Biol 2017 02 16;422(2):92-104. Epub 2017 Jan 16.

Center for Computational & Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ 08102, USA; Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ 08102, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2017.01.010DOI Listing
February 2017

Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.

PLoS One 2012 26;7(4):e35934. Epub 2012 Apr 26.

Division of Biology, California Institute of Technology, Pasadena, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035934PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339872PMC
September 2012

High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development.

Gene Expr Patterns 2010 Jun 14;10(4-5):177-84. Epub 2010 Apr 14.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.gep.2010.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902461PMC
June 2010

Functional cis-regulatory genomics for systems biology.

Proc Natl Acad Sci U S A 2010 Feb 8;107(8):3930-5. Epub 2010 Feb 8.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.1000147107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840491PMC
February 2010

Exclusive developmental functions of gatae cis-regulatory modules in the Strongylocentrorus purpuratus embryo.

Dev Biol 2007 Jul 10;307(2):434-45. Epub 2007 May 10.

Division of Biology, California Institute of Technology, 1200 E. California Blvd., Mail Code 156-29, Pasadena, CA 9112, USA.

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http://dx.doi.org/10.1016/j.ydbio.2007.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2031225PMC
July 2007

Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network.

Dev Biol 2007 Jun 28;306(2):860-9. Epub 2007 Mar 28.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.ydbio.2007.03.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063469PMC
June 2007

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

Genome Res 2007 Feb 8;17(2):175-83. Epub 2007 Jan 8.

Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.

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http://dx.doi.org/10.1101/gr.5509507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781349PMC
February 2007

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

Evolutionary change of the numbers of homeobox genes in bilateral animals.

Mol Biol Evol 2005 Dec 3;22(12):2386-94. Epub 2005 Aug 3.

Institute of Molecular Evolutionary Genetics, Department of Biology, Pennsylvania State University, USA.

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http://dx.doi.org/10.1093/molbev/msi229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1464090PMC
December 2005

A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes.

Nucleic Acids Res 2005 Jan 19;33(2):e12. Epub 2005 Jan 19.

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University University Park, PA 16802, USA.

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http://dx.doi.org/10.1093/nar/gni003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548370PMC
January 2005

Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms.

Proc Natl Acad Sci U S A 2004 Feb 5;101(7):1910-5. Epub 2004 Feb 5.

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1073/pnas.0308430100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC357026PMC
February 2004

Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case.

Plant Cell Physiol 2003 Dec;44(12):1403-11

National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Republic of Korea.

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http://dx.doi.org/10.1093/pcp/pcg156DOI Listing
December 2003

Antiquity and evolution of the MADS-box gene family controlling flower development in plants.

Mol Biol Evol 2003 Sep 30;20(9):1435-47. Epub 2003 May 30.

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, USA.

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http://dx.doi.org/10.1093/molbev/msg152DOI Listing
September 2003