Jaegil Kim

Jaegil Kim

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Jaegil Kim

Publications by authors named "Jaegil Kim"

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Racial Differences in Expression Levels of miRNA Machinery-Related Genes, Dicer, Drosha, DGCR8, and AGO2, in Asian Korean Papillary Thyroid Carcinoma and Comparative Validation Using the Cancer Genome Atlas.

Int J Genomics 2017 2;2017:5789769. Epub 2017 Mar 2.

Department of Immunology, School of Medicine & Institute of Medical Science, Keimyung University, 1095 Dalgubeol-daero, Dalseo-gu, Daegu 42601, Republic of Korea.

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http://dx.doi.org/10.1155/2017/5789769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5352891PMC
March 2017

Regulation of Transient Site-specific Copy Gain by MicroRNA.

J Biol Chem 2016 Mar 11;291(10):4862-71. Epub 2016 Jan 11.

From the Massachusetts General Hospital Cancer Center and Departments of Medicine and

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http://www.jbc.org/content/291/10/4862.full.pdf
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http://www.jbc.org/lookup/doi/10.1074/jbc.M115.711648
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http://dx.doi.org/10.1074/jbc.M115.711648DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777823PMC
March 2016

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair.

Cell 2016 Jan 21;164(3):538-49. Epub 2016 Jan 21.

Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.12.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4753048PMC
January 2016

Invasive Bladder Cancer: Genomic Insights and Therapeutic Promise.

Clin Cancer Res 2015 Oct;21(20):4514-24

The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts. Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1158/1078-0432.CCR-14-1215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610178PMC
October 2015

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers.

Nat Genet 2015 Sep 10;47(9):1067-72. Epub 2015 Aug 10.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA.

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http://dx.doi.org/10.1038/ng.3378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594173PMC
September 2015

The Cancer Genome Atlas Project on Muscle-invasive Bladder Cancer.

Eur Urol Focus 2015 Aug 6;1(1):94-95. Epub 2015 Jun 6.

Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.1016/j.euf.2014.11.002DOI Listing
August 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Entropic Description of Gas Hydrate Ice-Liquid Equilibrium via Enhanced Sampling of Coexisting Phases.

Phys Rev Lett 2015 May 28;114(17):170601. Epub 2015 Apr 28.

Department of Chemistry, Boston University, Boston, Massachusetts 02215-2521, USA.

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http://dx.doi.org/10.1103/PhysRevLett.114.170601DOI Listing
May 2015

Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method.

J Chem Phys 2014 Nov;141(18):18C525

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://aip.scitation.org/doi/10.1063/1.4896513
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http://dx.doi.org/10.1063/1.4896513DOI Listing
November 2014

Limit of metastability for liquid and vapor phases of water.

Phys Rev Lett 2014 Apr 16;112(15):157802. Epub 2014 Apr 16.

Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea.

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http://dx.doi.org/10.1103/PhysRevLett.112.157802DOI Listing
April 2014

Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients.

J Clin Oncol 2014 Jan 9;32(2):121-8. Epub 2013 Dec 9.

Youngwook Kim, Ji-ae Yoon, Yoomi Lee, Yeong Kyung Yoo, and Keunchil Park, Samsung Medical Center, Samsung Biomedical Research Institute; Jong-Mu Sun, Hong Kwan Kim, Yong Soo Choi, Kwhanmien Kim, Young Mog Shim, Yoon-La Choi, Jhingook Kim, Jin Seok Ahn, Myung-Ju Ahn, and Keunchil Park, Samsung Medical Center, Sungkyunkwan University School of Medicine; Sukki Cho, Seoul National University Bundang Hospital, College of Medicine, Seoul National University, Seoul; In-Jae Oh, Kyu-Sik Kim, Sang-Yun Song, Kook-Ju Na, and Young-Chul Kim, Chonnam National University Hwasun Hospital, Jeonnam, Republic of Korea; Peter S. Hammerman, Jaegil Kim, Chandra Sekhar Pedamallu, Kristian Cibulskis, Michael S. Lawrence, Petar Stojanov, Scott L. Carter, Aaron McKenna, Chip Stewart, Andrey Y. Sivachenko, Gad Getz, and Matthew Meyerson, Broad Institute of Harvard and MIT, Cambridge; Matthew Meyerson, Harvard Medical School; Peter S. Hammerman and Chandra Sekhar Pedamallu, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital Cancer Center, Boston, MA; and Matthew D. Wilkerson and D. Neil Hayes, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.

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http://dx.doi.org/10.1200/JCO.2013.50.8556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4062710PMC
January 2014

Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method.

J Chem Phys 2013 Mar;138(10):104119

Division of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, USA.

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http://dx.doi.org/10.1063/1.4794786DOI Listing
March 2013

Exploring the solid-liquid phase change of an adapted Dzugutov model using generalized replica exchange method.

J Phys Chem B 2012 Jul 10;116(29):8654-61. Epub 2012 Apr 10.

Division of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, United States.

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http://pubs.acs.org/doi/10.1021/jp300406c
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http://dx.doi.org/10.1021/jp300406cDOI Listing
July 2012

Replica exchange statistical temperature molecular dynamics algorithm.

J Phys Chem B 2012 Jul 15;116(29):8646-53. Epub 2012 May 15.

Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States.

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http://pubs.acs.org/doi/10.1021/jp300366j
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http://dx.doi.org/10.1021/jp300366jDOI Listing
July 2012

Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables.

J Chem Phys 2011 Aug;135(6):061103

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://aip.scitation.org/doi/10.1063/1.3626150
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http://dx.doi.org/10.1063/1.3626150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166335PMC
August 2011

Generalized simulated tempering for exploring strong phase transitions.

J Chem Phys 2010 Oct;133(15):154101

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://aip.scitation.org/doi/10.1063/1.3503503
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http://dx.doi.org/10.1063/1.3503503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2973984PMC
October 2010

Generalized replica exchange method.

J Chem Phys 2010 Jun;132(22):224107

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1063/1.3432176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896417PMC
June 2010

Optimal replica exchange method combined with Tsallis weight sampling.

J Chem Phys 2009 Apr;130(14):144114

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1063/1.3108523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736612PMC
April 2009

Replica exchange statistical temperature Monte Carlo.

J Chem Phys 2009 Mar;130(12):124112

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1063/1.3095422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736574PMC
March 2009

Relationship between protein folding thermodynamics and the energy landscape.

Phys Rev E Stat Nonlin Soft Matter Phys 2009 Mar 4;79(3 Pt 1):030902. Epub 2009 Mar 4.

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1103/PhysRevE.79.030902DOI Listing
March 2009

Influence of Go-like interactions on global shapes of energy landscapes in beta-barrel forming model proteins: inherent structure analysis and statistical temperature molecular dynamics simulation.

J Phys Chem B 2008 Jan 19;112(3):954-66. Epub 2007 Dec 19.

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1021/jp072872uDOI Listing
January 2008

Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing.

Phys Rev E Stat Nonlin Soft Matter Phys 2007 Jul 18;76(1 Pt 1):011913. Epub 2007 Jul 18.

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1103/PhysRevE.76.011913DOI Listing
July 2007

Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models.

J Chem Phys 2007 Apr;126(13):135101

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1063/1.2711812DOI Listing
April 2007

Inherent structure analysis of protein folding.

J Phys Chem B 2007 Mar 21;111(10):2647-57. Epub 2007 Feb 21.

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1021/jp0665776DOI Listing
March 2007

Statistical-temperature Monte Carlo and molecular dynamics algorithms.

Phys Rev Lett 2006 Aug 1;97(5):050601. Epub 2006 Aug 1.

Department of Chemistry, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1103/PhysRevLett.97.050601DOI Listing
August 2006