Bong-Hyun Kim

Curriculum vitae

UMass Medical School

*** ********** **. ****** ******* Center

4th floor room 1079

Worcester, MA 01605

214-***-****

acpcf0@r.postjobfree.com

acpcf0@r.postjobfree.com

Education:

U.T. Southwestern Medical Center at Dallas, Texas, USA

Ph.D. in Molecular Biophysics (Computational Biology), Nov 2009

Handong University, Pohang, Republic of Korea

B.S. majors in Biology and in Food engineering,

minor in Computer Science, Sep 2002

Professional Experience:

3/97 - 9/98. Undergraduate Research Program, Handong University.

Mentor: Dr. Jong-Bae Kim

Project: Identifying active compound from mistletoe extracts

8/00 - 8/02. Research Assistant. Handong University, Institute of Biomedical Research

Mentor: Dr. Kwan-Hee Lee

Project: Homology modeling of a lectin protein

9/02 - 7/03. Bioinformatics Researcher, Seoul National University

Advisor: Dr. Jongsik Chun

Project: Developing a multiple RNA sequence alignment program

9/03 - 11/09. Graduate Student, Biophysics Graduate Program, UT Southwestern Medical

Center.

Advisor: Dr. Nick Grishin.

Thesis Project: Automatic Classification of Proteins using Sequence and Structure

11/09 – 04/12. Postdoctoral Researcher, Department of Biochemistry, UT Southwestern Medical

Center.

Advisor: Dr. Nick Grishin

07/12 – 06/14 Postdoctoral Researcher, Bioinformatics and Integrative Biology, UMass Medical

School

Advisor: Dr. Zhiping Weng

Bong-Hyun Kim C.V.

07/14 – Current Researcher, Bioinformatics and Integrative Biology, UMass Medical School

Advisor: Dr. Manuel Garber

Publications:

Kim BH Garber M. MSNAP: A Fast Bisulfite Sequencing Read Mapper with SNAP (manuscript in preparation)

1.

Kim BH, Garber M. ME-Plot: A QC package for Bisulfite Sequencing Reads (manuscript submitted)

2.

Kim BH, Juang J, Wang W, Weng Z. Factorbook Motif Pipeline: A ChIP-Seq Motif Discovery Server

3.

(manuscript submitted)

Cheng H, Schaeffer RD, Liao Y, Kinch LN, Pei J, Shi S, Kim BH, Grishin NV. ECOD: an evolutionary

4.

classification of protein domains. PLOS Comput Biol 2014, Dec

Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, The mouse ENCODE Consortium, Weng Z.

5.

Hardison RC and Snyder MP. Principles of regulatory information conservation revealed by comparing mouse

and human transcription factor binding profiles, Nature, 2014, Nov 20

Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z. ZDOCK server: interactive docking prediction of

6.

pretein-protein complexes and symmetric multimers. Bioinformatics. 2014 Mar 12.

Wang J*, Zhuang J*, Iyer S*, Lin XY*, Greven MC*, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E,

7.

Hung JH, Weng Z. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by

the ENCODE consortium. Nucleic Acids Res. 2013 Jan;41(Database Issue):D171-6.

Kim BH, Chituri S, Grishin NV. Self consistency grouping, a stringent clustering method. BMC Bioinformatics

8.

2012;13 Suppl 13:S3.

Cong Q, Kinch LN, Kim BH, Grishin NV. Predictive sequence analysis of the Candidatus Liberibacter asiaticus

9.

proteome. PLoS One. 2012;7(7):e41071.

10. Kim BH, Cong Q, Grishin NV. HangOut: generating clean PSI-BLAST profiles for domains with long insertions.

Bioinformatics. 2010 Apr 22. [Epub ahead of print] PubMed PMID: 20413635.

11. Cong Q*, Kim BH*, Kinch L, Grishin NV. Structural Differences Between Proteins With Similar Sequences

2010, 10th IEEE International conference on Bioinformatics and Bioengineering

12. Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L,

Sheffler W, Kim BH, Das R, Grishin NV, Baker D. Structure prediction for CASP8 with all-atom refinement

using Rosetta. Proteins. 2009;77 Suppl 9:89-99. PubMed PMID: 19701941.

13. Shi S, Pei J, Sadreyev RI, Kinch LN, Majumdar I, Tong J, Cheng H, Kim BH, Grishin NV. Analysis of CASP8

targets, predictions and assessment methods. Database (Oxford). 2009;2009:bap003. Epub 2009 Apr 14.

PubMed PMID: 20157476.

14. Sadreyev RI, Kim BH, Grishin NV. Discrete-continuous duality of protein structure space. Curr Opin Struct Biol.

2009 Jun;19(3):321-8. Epub 2009 May 29.

15. Sadreyev RI, Tang M, Kim BH, Grishin NV. COMPASS server for homology detection: improved statistical

accuracy, speed and functionality. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W90-4. Epub 2009 May

12.

16. Kim BH, Cheng H, Grishin NV. HorA web server to infer homology between proteins using sequence and

structural similarity. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W532-8. Epub 2009 May 5.

17. Xie CQ, Jeong Y, Fu M, Bookout AL, Garcia-Barrio MT, Sun T, Kim BH, Xie Y, Root S, Zhang J, Xu RH, Chen

YE, Mangelsdorf DJ. Expression profiling of nuclear receptors in human and mouse embryonic stem cells. Mol

Endocrinol. 2009 May;23(5):724-33. Epub 2009 Feb 5.

Bong-Hyun Kim C.V.

18. Cheng H, Kim BH, Grishin NV. Discrimination between distant homologs and structural analogs: lessons from

manually constructed, reliable data sets. J Mol Biol. 2008 Apr 4;377(4):1265-78. Epub 2008 Jan 5.

19. Pei J, Kim BH, Grishin NV. PROMALS3D: a tool for multiple protein sequence and structure alignments.

Nucleic Acids Res. 2008 Apr;36(7):2295-300. Epub 2008 Feb 20.

20. Cheng H, Kim BH, Grishin NV. MALIDUP: a database of manually constructed structure alignments for

duplicated domain pairs. Proteins. 2008 Mar;70(4):1162-6.

21. Cheng H, Kim BH, Grishin NV. MALISAM: a database of structurally analogous motifs in proteins. Nucleic

Acids Res. 2008 Jan;36 (Database issue):D211-7. Epub 2007 Sep 12.

22. Qi Y, Sadreyev RI, Wang Y, Kim BH, Grishin NV. A comprehensive system for evaluation of remote sequence

similarity detection. BMC Bioinformatics. 2007 Aug 28;8:314.

23. Sadreyev RI, Tang M, Kim BH, Grishin NV. COMPASS server for remote homology inference. Nucleic Acids

Res. 2007 Jul;35(Web Server issue):W653-8. Epub 2007 May 21.

24. Pei J, Kim BH, Tang M, Grishin NV. PROMALS web server for accurate multiple protein sequence alignments.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W649-52. Epub 2007 Apr 22.

25. Kim BH, Sadreyev R, Grishin NV. COG4849 is a novel family of nucleotidyltransferases. J Mol Recognit. 2005

Sep-Oct;18(5):422-5.

Reviewed Journals and Conferences :

Science, Genome Research, Bioinformatics, PLoS One, Database, BMC Evolutionary Biology,

BMC Bioinformatics, BMC Research Note, BMC Biology and IEEE 10 th International Conference

on BioInformatics & BioEngineering

Memberships and Honors:

Member, Editorial Board of The Scientific World Journal, 2010-Present

Member, Scientific Steering Board of KOSEN (The Global Network of Scientist & Engineers) at

Korea Institute of Science and Technology Information 2009–2012

Member, International Society for Computation Biology

Member, Web committee of Post-Doctoral Association at UT Southwestern

Best Poster Award, Annual Biochemistry Research Symposium 2007

Information Technology Fellowship for Academic Excellence, Ministry of Information Technology

and Communications (S. Korea), 2001

Undergraduate Fellowship for Excellence, Handong University, 1996-1997

Research Interests:

Personalized medicine by understanding gene expression regulation through chromosome

folding, Epigenetic regulation of gene expression, DNA-protein/protein-protein interaction

network in biological processes

Developing computation algorithms for various biological problems and developing novel

insights by combining various sources of datasets

Bong-Hyun Kim C.V.

Computational Skills:

Computer languages: C/C++, Java, Perl, Python, Visual Basic, Java Script and ASP

Statistical/mathematical Softwares: R, Matlab & Mathematica

Operating Systems: Windows, Mac OS X, and Linux/Unix

Web developments: HTML, CSS, PHP, python/Cherrypy and Jinja2

Database: MySQL & MS Access

Big Data Technology: Hadoop, Pig, & Spark

Conferences and Talks:

Annual Biochemistry Research Symposium, UT Southwestern (2008)

Bioinformatics Conference at Dallas (2007)

International conference on bioinformatics and information technology, UT Arlington (2008)

Teaching Experiences:

Computational biology courses:

topics about protein structure comparisons (2008 & 2009)

Research Mentoring for graduate students (with the guidance of Dr. Nick Grishin):

Qian Cong (2009), Druba Deb (2009), and Rui Zhong (2010)

Research Mentoring for undergraduate students (with the guidance of Dr. Nick Grishin):

Ivan Huang (an undergraduate student, Rice Univ. 2010)

UTeach mentoring program at UTSW:

Adam Haraburda (an undergraduate student, UT Dallas, 2010)

References:

Nick Grishin, PhD

Professor

Biochemistry Department

UT Southwestern Medical Center

5323 Harry Hines Blvd.

Dallas, TX 75390

Voice: 214-***-**** Fax: 214-***-****

acpcf0@r.postjobfree.com

Manuel Garber, PhD

Professor

Program in Bioinformatics and Integrative Biology

UMASS Medical School

368 Plantation St. Albert Sherman Center

Bong-Hyun Kim C.V.

Worcester, MA 01605

Voice: 508-***-****

acpcf0@r.postjobfree.com

Alexander Pertsemlidis, PhD

Associate Professor

Division of Pediatric hematology-Oncology

UT Health Science Center at San Antonio

8403 Floyd Curl Drive

San Antonio, TX 78229

Voice: 210-***-****

acpcf0@r.postjobfree.com

Additional References:

Zbyszek Otwinowski, PhD

Professor

Biochemistry Department

UT Southwestern Medical Center

5323 Harry Hines Blvd.

Dallas, TX 75390

Voice: 214-***-**** Fax: 214-***-****

acpcf0@r.postjobfree.com

Rama Ranganathan, PhD

Professor

Pharmacology Department

UT Southwestern Medical Center

5323 Harry Hines Blvd.

Dallas, TX 75390

Voice: 214-***-**** Fax: 214-***-****

acpcf0@r.postjobfree.com

Steve Altschuler, PhD

Associate Professor

Pharmacology Department

UT Southwestern Medical Center

5323 Harry Hines Blvd.

Dallas, TX 75390

Voice: 214-***-**** Fax: 214-***-****

acpcf0@r.postjobfree.com

Zhiping Weng, PhD

Professor

Program in Bioinformatics and Integrative Biology

UMASS Medical School

368 Plantation St. Albert Sherman Center

Worcester, MA 01605

Voice: 508-***-****

acpcf0@r.postjobfree.com

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