Jeong-Hyeon Choi

Jeong-Hyeon Choi

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Jeong-Hyeon Choi

Jeong-Hyeon Choi

Publications by authors named "Jeong-Hyeon Choi"

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61Publications

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MYC deregulates TET1 and TET2 expression to control global DNA (hydroxy)methylation and gene expression to maintain a neoplastic phenotype in T-ALL.

Epigenetics Chromatin 2019 Jul 2;12(1):41. Epub 2019 Jul 2.

Department of Biochemistry and Molecular Biology, Augusta University, 1410 Laney-Walker Blvd., Augusta, GA, 30912, USA.

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http://dx.doi.org/10.1186/s13072-019-0278-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6604319PMC
July 2019

Discovery and Validation of a Novel Neutrophil Activation Marker Associated with Obesity.

Sci Rep 2019 Mar 5;9(1):3433. Epub 2019 Mar 5.

Georgia Prevention Institute, Augusta University, Augusta, Gerogia, USA.

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http://dx.doi.org/10.1038/s41598-019-39764-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400958PMC
March 2019

Long non-coding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function.

Nucleic Acids Res 2017 05;45(8):4479-4492

Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA.

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http://dx.doi.org/10.1093/nar/gkx055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5416847PMC
May 2017

High fat diet and exercise lead to a disrupted and pathogenic DNA methylome in mouse liver.

Epigenetics 2017 01 18;12(1):55-69. Epub 2016 Nov 18.

a Department of Molecular Pharmacology and Experimental Therapeutics , Mayo Clinic , Rochester , MN , USA.

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http://dx.doi.org/10.1080/15592294.2016.1261239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5270632PMC
January 2017

Targeted next generation sequencing approach identifies eighteen new candidate genes in normosmic hypogonadotropic hypogonadism and Kallmann syndrome.

Mol Cell Endocrinol 2016 12 5;437:86-96. Epub 2016 Aug 5.

Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, GA, United States; Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States; Department of Physiology, Medical College of Georgia, Augusta University, Augusta, GA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.mce.2016.08.007DOI Listing
December 2016

CD133+CD24lo defines a 5-Fluorouracil-resistant colon cancer stem cell-like phenotype.

Oncotarget 2016 Nov;7(48):78698-78712

Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.

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http://dx.doi.org/10.18632/oncotarget.12168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5346671PMC
November 2016

Transcriptional Profiling Reveals a Common Metabolic Program in High-Risk Human Neuroblastoma and Mouse Neuroblastoma Sphere-Forming Cells.

Cell Rep 2016 10;17(2):609-623

The Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.09.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536348PMC
October 2016

OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis.

BMC Genomics 2016 08 25;17:678. Epub 2016 Aug 25.

Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, UK.

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http://dx.doi.org/10.1186/s12864-016-2886-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000498PMC
August 2016

Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth.

Cancer Res 2016 06 5;76(11):3224-35. Epub 2016 Apr 5.

Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia. CRU Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia.

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http://dx.doi.org/10.1158/0008-5472.CAN-15-2249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891240PMC
June 2016

Dynamic reprogramming of DNA methylation in SETD2-deregulated renal cell carcinoma.

Oncotarget 2016 Jan;7(2):1927-46

Department of Molecular Pharmacology and Experimental Therapeutics and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA.

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http://dx.doi.org/10.18632/oncotarget.6481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811507PMC
January 2016

KDM4C and ATF4 Cooperate in Transcriptional Control of Amino Acid Metabolism.

Cell Rep 2016 Jan 7;14(3):506-519. Epub 2016 Jan 7.

Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA. Electronic address:

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http://www.cell.com/cell-reports/pdf/S2211-1247(15)01494-1.p
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http://www.cell.com/cms/attachment/2043257326/2055827387/mmc
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http://linkinghub.elsevier.com/retrieve/pii/S221112471501494
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http://dx.doi.org/10.1016/j.celrep.2015.12.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731315PMC
January 2016

H3K9 Trimethylation Silences Fas Expression To Confer Colon Carcinoma Immune Escape and 5-Fluorouracil Chemoresistance.

J Immunol 2015 Aug 1;195(4):1868-82. Epub 2015 Jul 1.

Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912; Cancer Center, Georgia Regents University, Augusta, GA 30912; Charlie Norwood Veterans Affairs Medical Center, Augusta, GA 30904;

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http://dx.doi.org/10.4049/jimmunol.1402243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530033PMC
August 2015

Sequencing the cancer methylome.

Methods Mol Biol 2015 ;1238:627-51

GRU Cancer Center, Georgia Regents University, Augusta, GA, 30912, USA.

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http://dx.doi.org/10.1007/978-1-4939-1804-1_33DOI Listing
July 2015

iTagPlot: an accurate computation and interactive drawing tool for tag density plot.

Bioinformatics 2015 Jul 19;31(14):2384-7. Epub 2015 Mar 19.

Cancer Center and Department of Biostatistics and Epidemiology, Medical College of Georgia, Georgia Regents University, Augusta, GA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495303PMC
July 2015

Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells.

J Genet Genomics 2015 Jul 24;42(7):355-71. Epub 2015 Jun 24.

GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Georgia Regents University, Augusta, GA 30912, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jgg.2015.06.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4648292PMC
July 2015

Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome.

Cell Rep 2014 Nov 6;9(4):1554-66. Epub 2014 Nov 6.

Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA; Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.10.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254561PMC
November 2014

Impact of human MLL/COMPASS and polycomb complexes on the DNA methylome.

Oncotarget 2014 Aug;5(15):6338-52

Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4171634PMC
http://dx.doi.org/10.18632/oncotarget.2215DOI Listing
August 2014

Function and evolution of DNA methylation in Nasonia vitripennis.

PLoS Genet 2013 10;9(10):e1003872. Epub 2013 Oct 10.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America ; Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003872DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3794928PMC
March 2014

Potential for sexual conflict assessed via testosterone-mediated transcriptional changes in liver and muscle of a songbird.

J Exp Biol 2014 Feb 6;217(Pt 4):507-17. Epub 2013 Nov 6.

Department of Biology, Center for Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1242/jeb.089813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3922831PMC
February 2014

Preparation of normalized cDNA libraries for 454 Titanium transcriptome sequencing.

Methods Mol Biol 2012 ;888:119-33

The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1007/978-1-61779-870-2_8DOI Listing
September 2012

ESTclean: a cleaning tool for next-gen transcriptome shotgun sequencing.

BMC Bioinformatics 2012 Sep 26;13:247. Epub 2012 Sep 26.

The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47401, USA.

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http://dx.doi.org/10.1186/1471-2105-13-247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630001PMC
September 2012

GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis.

Bioinformatics 2012 Jun 11;28(11):1527-9. Epub 2012 Apr 11.

School of Informatics and Computing, Indiana University Bloomington, IN 47404, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356842PMC
June 2012

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.

Nucleic Acids Res 2011 Oct 23;39(19):e127. Epub 2011 Jul 23.

GHSU Cancer Center, Department of Biochemistry and Molecular Biology, Georgia Health Sciences University, Augusta, GA 30912, USA.

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http://dx.doi.org/10.1093/nar/gkr598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201883PMC
October 2011

RAPSearch: a fast protein similarity search tool for short reads.

BMC Bioinformatics 2011 May 15;12:159. Epub 2011 May 15.

School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA.

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http://dx.doi.org/10.1186/1471-2105-12-159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113943PMC
May 2011

The ecoresponsive genome of Daphnia pulex.

Science 2011 Feb;331(6017):555-61

Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA.

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http://www3.nd.edu/~mpfrende/PDFs/Science-2011-Colbourne-555
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http://www.sciencemag.org/cgi/doi/10.1126/science.1197761
Publisher Site
http://dx.doi.org/10.1126/science.1197761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529199PMC
February 2011

A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences.

BMC Genomics 2010 Dec 7;11:694. Epub 2010 Dec 7.

Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1186/1471-2164-11-694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014983PMC
December 2010

Gene discovery in the horned beetle Onthophagus taurus.

BMC Genomics 2010 Dec 14;11:703. Epub 2010 Dec 14.

Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1186/1471-2164-11-703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019233PMC
December 2010

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Authors:
John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne Leo W Beukeboom Claude Desplan Christine G Elsik Cornelis J P Grimmelikhuijzen Paul Kitts Jeremy A Lynch Terence Murphy Deodoro C S G Oliveira Christopher D Smith Louis van de Zande Kim C Worley Evgeny M Zdobnov Maarten Aerts Stefan Albert Victor H Anaya Juan M Anzola Angel R Barchuk Susanta K Behura Agata N Bera May R Berenbaum Rinaldo C Bertossa Márcia M G Bitondi Seth R Bordenstein Peer Bork Erich Bornberg-Bauer Marleen Brunain Giuseppe Cazzamali Lesley Chaboub Joseph Chacko Dean Chavez Christopher P Childers Jeong-Hyeon Choi Michael E Clark Charles Claudianos Rochelle A Clinton Andrew G Cree Alexandre S Cristino Phat M Dang Alistair C Darby Dirk C de Graaf Bart Devreese Huyen H Dinh Rachel Edwards Navin Elango Eran Elhaik Olga Ermolaeva Jay D Evans Sylvain Foret Gerald R Fowler Daniel Gerlach Joshua D Gibson Donald G Gilbert Dan Graur Stefan Gründer Darren E Hagen Yi Han Frank Hauser Da Hultmark Henry C Hunter Gregory D D Hurst Shalini N Jhangian Huaiyang Jiang Reed M Johnson Andrew K Jones Thomas Junier Tatsuhiko Kadowaki Albert Kamping Yuri Kapustin Bobak Kechavarzi Jaebum Kim Jay Kim Boris Kiryutin Tosca Koevoets Christie L Kovar Evgenia V Kriventseva Robert Kucharski Heewook Lee Sandra L Lee Kristin Lees Lora R Lewis David W Loehlin John M Logsdon Jacqueline A Lopez Ryan J Lozado Donna Maglott Ryszard Maleszka Anoop Mayampurath Danielle J Mazur Marcella A McClure Andrew D Moore Margaret B Morgan Jean Muller Monica C Munoz-Torres Donna M Muzny Lynne V Nazareth Susanne Neupert Ngoc B Nguyen Francis M F Nunes John G Oakeshott Geoffrey O Okwuonu Bart A Pannebakker Vikas R Pejaver Zuogang Peng Stephen C Pratt Reinhard Predel Ling-Ling Pu Hilary Ranson Rhitoban Raychoudhury Andreas Rechtsteiner Justin T Reese Jeffrey G Reid Megan Riddle Hugh M Robertson Jeanne Romero-Severson Miriam Rosenberg Timothy B Sackton David B Sattelle Helge Schlüns Thomas Schmitt Martina Schneider Andreas Schüler Andrew M Schurko David M Shuker Zilá L P Simões Saurabh Sinha Zachary Smith Victor Solovyev Alexandre Souvorov Andreas Springauf Elisabeth Stafflinger Deborah E Stage Mario Stanke Yoshiaki Tanaka Arndt Telschow Carol Trent Selina Vattathil Eveline C Verhulst Lumi Viljakainen Kevin W Wanner Robert M Waterhouse James B Whitfield Timothy E Wilkes Michael Williamson Judith H Willis Florian Wolschin Stefan Wyder Takuji Yamada Soojin V Yi Courtney N Zecher Lan Zhang Richard A Gibbs

ESTPiper--a web-based analysis pipeline for expressed sequence tags.

BMC Genomics 2009 Apr 21;10:174. Epub 2009 Apr 21.

The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA.

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http://dx.doi.org/10.1186/1471-2164-10-174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2676306PMC
April 2009

A machine-learning approach to combined evidence validation of genome assemblies.

Bioinformatics 2008 Mar 18;24(6):744-50. Epub 2008 Jan 18.

The Center for Genomics and Bioinformatics, School of Informatics and Department of Biology, Indiana University, IN 47405, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm608DOI Listing
March 2008

Gene teams with relaxed proximity constraint.

Proc IEEE Comput Syst Bioinform Conf 2005 :44-55

School of Informatics, Center for Genomics and Bioinformatics, Indiana University, IN 47408, USA.

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May 2007

De novo identification of LTR retrotransposons in eukaryotic genomes.

BMC Genomics 2007 Apr 3;8:90. Epub 2007 Apr 3.

Department of Computer Science, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1186/1471-2164-8-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858694PMC
April 2007

ARCS: an aggregated related column scoring scheme for aligned sequences.

Bioinformatics 2006 Oct 26;22(19):2326-32. Epub 2006 Jul 26.

Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl398DOI Listing
October 2006

A hybrid gene team model and its application to genome analysis.

J Bioinform Comput Biol 2006 Apr;4(2):171-96

School of Informatics and Center for Genomics and Bioinformatics, Indiana University Bloomington, Indiana 47408, USA.

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April 2006

COMPAM :visualization of combining pairwise alignments for multiple genomes.

Bioinformatics 2006 Jan 3;22(2):242-4. Epub 2005 Nov 3.

School of Computer Engineering, Miryang National University Miryang, Kyungnam 627-702, Korea.

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http://dx.doi.org/10.1093/bioinformatics/bti759DOI Listing
January 2006

GAME: a simple and efficient whole genome alignment method using maximal exact match filtering.

Comput Biol Chem 2005 Jun;29(3):244-53

School of Informatics, Indiana University, Bloomington, IN 47408, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2005.04.004DOI Listing
June 2005

Analysis of common k-mers for whole genome sequences using SSB-tree.

Genome Inform 2002 ;13:30-41

ALGORIGENE Bioinformatics Lab., Department of Computer Science, Pusan National University, Kum-Jung-Ku, Pusan 609-735, Korea.

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November 2003