Medical Information Technology
Resume:
Bong-Hyun Kim
Curriculum vitae
UMass Medical School
*** ********** **. ****** ******* Center
4th floor room 1079
Worcester, MA 01605
*********@*****.***
***@****.*****.***
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-***-****
*******@****.*****.***
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-***-****
******.******@********.***
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-***-****
************@*******.***
Additional References:
Zbyszek Otwinowski, PhD
Professor
Biochemistry Department
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, TX 75390
Voice: 214-***-**** Fax: 214-***-****
*******.**********@**************.***
Rama Ranganathan, PhD
Professor
Pharmacology Department
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, TX 75390
Voice: 214-***-**** Fax: 214-***-****
****.***********@**************.***
Steve Altschuler, PhD
Associate Professor
Pharmacology Department
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, TX 75390
Voice: 214-***-**** Fax: 214-***-****
******.**********@**************.***
Zhiping Weng, PhD
Professor
Program in Bioinformatics and Integrative Biology
UMASS Medical School
368 Plantation St. Albert Sherman Center
Worcester, MA 01605
Voice: 508-***-****
*******.****@********.***
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