Jong Bhak's CV

From Interactomics.org

Personal Details
Present Affiliation/Employer: KOBIC, KRIBB, Daejeon, (Korean BioInformation Center) 
Job Title: Director

Name
:
     English : Jong Bhak (Jong H. Park)

Address
Home Address: No 102, 306 Dong, Expo Apartment, Jeonmin-dong, Yuseong-gu, Daejeon, 305 - 390, South Korea.
Work  Address: KOBIC, KRIBB, 305-333, Yusung-Gu, DaeJeon, Korea 
Date of Birth: 1967. 05. 20. 
Contact Info : j@bio.cc, jong@kribb.re.kr (Korea 042-879 8500, Mobile: 010-7799-6754) 
Home page: http://jongbhak.com/
Marital Status: Married to Maryana Bhak

Education and military service (compulsory in Korea)
1990. 9 ~ 1994. 7 Aberdeen University, UK Biochemistry BSc. (1st class) Ann Glover 
1994. 10 ~ 1997. 7 MRC centre, Cambridge University, UK. Bioinformatics Ph.D. with Tim Hubbard & Cyrus Chothia Ph.D. 
                               Thesis : Genome sequence analysis and methods. 
                               Ph.D. supervisers: Tim Hubbard (MRC-CPE) & Cyrus Chothia (MRC-LMB) 
1997. 8 ~ 1997.12 MRC centre, Cambridge University, UK. Bioinformatics Postdoc with Cyrus Chothia

Employment and career experience 
1998. 1 ~1999. 4 Harvard Medical School, Genetics, George Church Lab. Research Fellow, Postdoc 
1999. 4 ~2000. 12 EBI (European Bioinformatics Institute) Research Fellow, Postdoc 
2000. 1 ~ 2003. 4. MRC-DUNN, Cambridge, UK, Group Leader(Faculty) 
2003. 4 ~ 2005. 3. Biosystems Dept. KAIST, Korea Associate Professor (Faculty) 
2005. 3 ~ Present: KOBIC, KRIBB, Daejeon, Korea (Director)
2006. 9 ~ Present: Korean University of Science and Technology (Associate Professor)

General Research Interests
Life time research interest: Ageing (Biological Gerontology)

Life time main occupation: Philosophy (Biosophy)

  • Pathogen-host interaction analysis at genomic/proteomic scale.

This work is on a large-scale pathogenic interaction studies using protein-protein interaction information.

  • Structural Interactomics (the whole biomolecular structural interaction network construction and analysis. Mainly proteins and their ligands). This is a high resolution structural analysis of interactome. It defines precisely the structural patterns and topologies of protein and chemical domains using computer algorithms developed by us. (Park, et al., 2001, JMB). (Http://interactomics.org/)
  • Network Biology (mapping and archiving biological entities such as sequences, structures and genomes using search algorithms and methodologies developed by my group). This is more toward evolutionary and computational analysis of biological spaces (protein space, etc). It is computational and mathematical. (Review article: Park, 2002, IEEE, Intelligent systems). (Http://networkbiology.org/)

 * Computational Bioenergetics (constructing databases for energy metabolism related genes and chemicals to analyze their networks and functions). We have been working on mitochondrial energy metabolism related proteins and their interactions and pathways to eventually model the biochemistry of energy metabolism.

  • Geronto-Genomics (bioinformatics research of gerontology). We are constructing the databases for ageing related genes and proteins to establish a new field of gerontology where computational and genomic infrastructure is used on biological ageing problems.
  • Protein Chemical (ligand) Interaction. I have been interested in the interaction between proteins and their ligands. No publishable or significant research results are available yet. However, I am quite interested in this topic and am currently negotiating a collaboration and grant with a research institute (symposium presentation: annual Korean Biochemistry society meeting, 2002. RNA and DNA binding proteins domains)
  • SNP (single nucleotide polymorphism) and SAP (small number amino acid polymorphism) analysis.
  • BioInfra (Construction of Bioinformatic infrastructure for large scale industrial biotechnology applications)
  • Molecular Anthropology. I have been interested in analyzing ancient DNA to track the origins and migrations of ethnic groups.
  • Protein and DNA chip development. I have been interested DNA chip data analysis for sometime. Now, I am interested developing and designing protein chips to detect proteins and map their interactions.


Names of Referees
Dr. Tim Hubbard: th@sanger.ac.uk, The Sanger Centre Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK, Tel: +44 1223 496886 , Fax: +44 1223 494919
(http://www.sanger.ac.uk/Users/th/)
Dr. Cyrus Chothia: chc1@mrc-lmb.cam.ac.uk, MRC-LMB, Cambridge, Hills Road, CB22QH, UK ,+44 (0)1223 402221 
Dr. George Churchhttp://arep.med.harvard.edu/ Genetics Dept. Harvard Med. School, Longwood Ave. Boston, MA, USA, (617) 432-1278
(http://arep.med.harvard.edu)
Prof. Liisa Holm: liisa.holm@helsinki.fi, or holm@ebi.ac.uk, Department of Biosciences, P.O.Box 56 (Viikinkaari 9), FIN-00014 University of Helsinki, Finland, phone: +358 9191 59117 , fax: +358-9-191-58754 
Prof. Michael Schroeder: michael.schroeder @ biotec.tu-dresden.de. http://www.biotec.tu-dresden.de/schroeder, since 2003 Professor in Bioinformatics, Biotec and Dept. of
Computing, TU Dresden  ,
+49-351-463-40062
Prof. Shoba Ranganathan, Ph.D. Chair of Bioinformatics, Dept. of Chemistry and Biomolecular Sciences, Macquarie University, Sydney. Australia, Tel +61 2 9850 6262, Fax: +61 2 9850 8313, Email: shoba.ranganathan  @  mq.edu.au, http://bioinfo.org/people/shoba.html

List of publication (Jong Bhak is the same person as Jong H. Park) 

Most recent ones are here: Jong's Research Articles

43) CONSORF: a consensus prediction system for prokaryotic coding sequences Sungsoo Kang, Sung-Jin Yang, Sangsoo Kim and Jong Bhak, Bioinformatics 2007; doi: 10.1093/bioinformatics/btm512

42) SynechoNET: integrated protein-protein interaction database of a model cyanobacterium /Synechocystis/ sp. PCC 6803.BMC Bioinformatics, (accepted, 2007) Woo-Yeon Kim*, Sungsoo Kang*, Byoung-Chul Kim, Jeehyun Oh, Seongwoong Cho, Jong Bhak§ , and Jong-Soon Choi§ 

41) Proteomic approaches for the analysis of atopic dermatitis and new insights from interactomics., PROTEOMICS, the 2008 Annual Reviews issue (Accepted)., Yong-Doo Park, Daeui Park, Jong Bhak* and Jun-Mo Yang*

40) SNP@Promoter: A database of human SNPs (Single Nucleotide Polymorphisms) within putative promoter region. BMC Bioinformatics, (accepted, 2007). Byoung-Chul Kim, Woo-Yeon Kim, Daeui Park, Won-Hyong Chung, Kwang-sik Shin and Jong Bhak*. 

39) Impact of transcriptional properties on essentiality and evolutionary rate. Genetics. 175:199-206 (2007) Jung Kyoon Choi, Sang Cheol Kim, Jungmin Seo, Sangsoo Kim*, and Jong Bhak*

38) Functional annotation and analysis of Korean patented biological sequences using bioinformatics Byungwook Lee, Tae Hyung Kim, Seon Kyu Kim, Sang Soo Kim, Gee Chan Ryu and Jong BhakMolecules and Cells 2006 Feb. 21, p.269-275

37)  Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information, Lee SungHoon, Lee ByungWook, Jang Insoo, Kim Sangsoo, and Jong BhakNAR, 2006

36)  Interaction Interfaces in Proteins via the Voronoi Diagram of Atoms   Computer-Aided Design    Chong-Min Kim, Chung-In Won,  Youngsong Cho, Donguk Kim, Sunghoon Lee, Jong Bhak, and Deok-Soo Kim, (2007) 

35) Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Yang TJ, Kim JS, Kwon SJ, Lim KB, Choi BS, Kim JA, Jin M, Park JY, Lim MH, Kim HI, Lim YP, Kang JJ, Hong JH, Kim CB, Bhak J, Bancroft I, and Park BS.(2006). Plant Cell.18(6):1339-1347. 

34) Functional annotation and analysis of Korean patented biological sequences using bioinformatics  Molecules and Cells 2006 Feb. 21, p.269-275, PMID: 16682823 [PubMed - in process]  Byungwook Lee, Tae Hyung Kim, Seon Kyu Kim, Sang Soo Kim, Gee Chan Ryu and Jong Bhak

33) A protein domain interaction interface database: InterPare Sungsam Gong, Changbum Park, Hansol Choi, Junsu Ko, Insoo Jang, Jungsul Lee, Dan M Bolser, Donghoon Oh, Deok-Soo Kim and Jong Bhak, BMC Bioinformatics 2005, 6:207 doi:10.1186/1471-2105-6-207

32) Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map). Park D, Lee S, Bolser D, Schroeder M, Lappe M, Oh D, Bhak J. Bioinformatics. 2005 Aug 1;21(15):3234-40. Epub 2005 May 24.

31) PSIbase: a database of Protein Structural Interactome map (PSIMAP). Gong S, Yoon G, Jang I, Bolser D, Dafas P, Schroeder M, Choi H, Cho Y, Han K, Lee S, Choi H, Lappe M, Holm L, Kim S, Oh D, Bhak J. Bioinformatics. 2005 May 15;21(10):2541-3. Epub 2005 Mar 3.

30) Architecture of basic building blocks in protein and domain structural interaction networks. Moon HS, Bhak J, Lee KH, Lee D. Bioinformatics. 2005 Apr 15;21(8):1479-86. 

29) The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3’ untranslated regions. Hyeong Jun An, Doheon Lee, Kwang Hyung Lee, and J. Bhak. BMC Genomics. 2004 Dec 21;5(1):97.

28) High correlation between Alu elements and the conversion of 3 UTR of mRNAs processed pseudogenes. Hyeong Jun An, Dokyun Na, Doheon Lee, Kwang Hyung Lee and Jonghwa Bhak, Genomics & Informatics, June 2004, 2(2):86-91.

27) HPID: the Human Protein Interaction Database. Han K, Park B, Kim H, Hong J, and Park J. Bioinformatics. 2004 Oct 12;20(15):2466-2470.

26) Large scale co-evolution analysis of Protein Structural Interlogues using the global Protein Structural Interactome Map(PSIMAP). WanKyu Kim, Dan Bolser and Jong H. Park, Bioinformatics, 2004, 1;20(7):1138-1150.

25) Using convex hulls to extract interaction interfaces from known structures. Panos Dafas, Dan Bolser, Jacek Gomoluch, Jong Park and Michael Schroeder, Bioinformatics. 10 July 2004. 20(10):1486-1490.

24) Biological Network Evolution Hypothesis Applied to Protein Structural Interactome. Dan M. Bolser and Jong H. Park, Genomics & Informatics, Vol. 1(1) 7-19, September 2003.

23) Visualisation and Graph-theoretic Analysis of a Large-scale Protein Structural Interactome. Dan M Bolser, Panos Dafas, Richard Harrington, Jong H Park, Michael Schroeder BMC Bioinformatics 2003, 4:45 (8 October 2003)

22) Visualization and Analysis of Protein Interactions, B.-H. Ju, B. Park, J. H. Park, and K. Han, Bioinformatics, Vol.19, 317-318, 2003.

21) Predicting Protein Interactions in Human by Homologous Interactions in Yeast, H. Kim, J. Park, and K. Han, Lecture Notes in Computer Science, Vol.2637, 159-169, 2003.

20) Large Scale Statistical Prediction of Protein-Protein Interaction by Potentially Interacting Domain (PID) Pair. Wan Kyu Kim, Jong Park & Jung Keun Suh. Genome Informatics, 13, 42-50 (2002)

19) InterViewer: Dynamic Visualization of Protein-Protein Interactions, K. Han, B.-H. Ju, and J. H. Park, Lecture Notes in Computer Science, Vol.2528, 364-365, 2002.

18) Network Biology: Datamining biological networks. Jong Park, IEEE Trends and controversies, May/June, 2002 (Vol. 17, No. 3) p66-80. (A review article)

17) The Conservation of Protein Interaction Network in Evolution Jong Park & Dan Bolser, Genome Informatics, 2001;12:135-140.

16) Generating protein interaction maps from incomplete data: application to Fold assignment. Lappe M, Park J, Niggemann O, and Holm L. Bioinformatics 2001: S149-S156 (ISMB 2001 paper printed in Bioinformatics)

15) Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. Park J, Lappe M, and Teichmann SA. J Mol Biol. 2001 Mar 30;307(3):929-38.

14) PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Qian J, Stenger B, Wilson CA, Lin J, Jansen R, Teichmann SA, Park J, Krebs WG, Yu H, Alexandrov V, Echols N, & Gerstein M. Nucleic Acids Res 2001, 15;29(8):1750-64

13) A fully automatic evolutionary classification of protein folds: Dali domain dictionary version 3. Dietmann S, Park Jong, Notredame C, Heger A, Lappe M, and Holm L. (Nucleic Acids Res. Jan;29(1):55-57, 2001)

12) Estimating the significance of sequence order in protein secondary structure prediction, Jong Park, Sabine Dietmann, Andreas Heger, and Liisa Holm. (2000, Bioinformatics, In press for Issue 9, 2000)

11) Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Sarah A. Teichmann, Cyrus Chothia, George M. Church, and Jong Park Bioinformatics, 16, 117-124 (2000)

10) DaliLite: A standalone program for Dali structure comparison server. Liisa Holm and Jong Park, Bioinformatics, Issue 6, p566-667, (2000)

9) RSDB: representative sequence databases with high information content. Jong Park, Liisa Holm, Andreas Heger and Cyrus Chothia, Bioinformatics, (2000), May, Vol 16. Issue No. 5. 458-464

8) Sequence Search Algorithm Assessment and Testing Toolkit (SAT) Jong Park, Liisa Holm, and Cyrus Chothia, Bioinformatics, (2000), Vol 16. No.2, 104-110.

7) Sequence Comparisons Using Multiple Sequences Detect Three Times as Many Remote Homologues as Pairwise Methods. Jong Park, Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T. & Chothia, C., Journal of Molecular Biology, 1998, Dec 11;284(4):1201-1210

6) Structural assignments to the proteins of Mycoplasma genitalium show that they have been formed by extensive gene duplications and domain rearrangements, Sarah Teichmann, Jong Park & Cyrus Chothia, PNAS., 1998, Dec 8;95(25):14658-14663.

5) DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics. 1998 ;14(2):144-50. Jong Park & Sarah Teichmann

4) Intermediate sequences find distant sequence homologues, Jong Park, Sarah A. Teichmann, Tim Hubbard, & Cyrus Chothia, Journal of Molecular Biology . 1997 Oct 17;273(1):349-54.

3) Protein structure prediction: Playing the fold. Hubbard T, Jong Park, Lahm A, Leplae R, & Tramontano A., TIBS, 1996 Aug;21(8):279-281, (1996)

2) Hubbard,T., Tramontano,A., Barton,G., Jones,D., Sippl,M., Valencia,A., Lesk,A., Moult,J., Rost,B., Sander,C., Schneider,R., Lahm,A., Leplae,R., Buta,C., Eisenstein,M., Fjellstr^m,O., Floeckner,H., Grossman,G., Hansen,J., Helmer Citterich,M., Joergensen,F.S., Marchler-Bauer, A., Osuna,J., Jong Park, Reinhardt,A., Ribas de Pouplana,L., Rojo-Dominguez,A., Saudek,V., Sinclair,J., Sturrock,S., Venclovas,C., Vinals,C. (1996). Update on protein structure prediction: results of the IRBM 1995 workshop. Folding and Design, 1, 55-63.

1) Fold recognition and ab initio structure predictions using Hidden Markov Models and beta-strand pair potentials. Tim Hubbard & Jong Park, Proteins, Nov. 23(3): 398-402, (1995