Reference paper list for Bioinformatics

 

 

Genome Biology.2014, 15:R55  DOI: 10.1186/gb-2014-15-4-r55

http://genomebiology.com/2014/15/4/R55

 

 

 

Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq Park KD, Park J, Ko J, Kim BC, Kim HS, Ahn K, Do KT, Choi H, Kim HM, Song S, Lee S, Jho S, Kong HS, Yang YM, Jhun BH, Kim C,Kim TH, Hwang S, Bhak J, Lee HK, Cho BW.

 

 

A public resource facilitating clinical use of genomes. Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM,Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K,Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM. Proc Natl Acad Sci USA. 2012 Jul 13.

 

Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion. Xu S, Pugach I, Stoneking M, Kayser M, Jin L; HUGO Pan-Asian SNP Consortium. Proc Natl Acad Sci USA. 2012 Mar 20;109(12):4574-9. Epub 2012 Mar 6.

 

MetaBase--the wiki-database of biological databases. Bolser DM, Chibon PY, Palopoli N, Gong S, Jacob D, Del Angel VD, Swan D, Bassi S, González V, Suravajhala P, Hwang S, Romano P, Edwards R, Bishop B, Eargle J, Shtatland T, Provart NJ, Clements D, Renfro DP, Bhak D, Bhak J. Nucleic Acids Res. 2012 Jan;40(Database issue):D1250-4. Epub 2011 Dec 1.

 

Liverome: a curated database of liver cancer-related gene signatures with self-contained context information. Lee L, Wang K, Li G, Xie Z, Wang Y, Xu J, Sun S, Pocalyko D, Bhak J, Kim C, Lee KH, Jang YJ, Yeom YI, Yoo HS, Hwang S. BMC Genomics 2011 Nov 30;12 Suppl 3:S3. Epub 2011 Nov 30..

 

Identification of close relatives in the HUGO Pan-Asian SNP database. Yang X, Xu S; HUGO Pan-Asian SNP Consortium.Indian Genome Variation Consortium. PLoS One. 2011;6(12):e29502. Epub 2011 Dec 29.

 

De novo transcriptome sequencing of Momordica cochinchinensis to identify genes involved in the carotenoid biosynthesis. Hyun TK, Rim Y, Jang HJ, Kim CH, Park J, Kumar R, Lee S, Kim BC, Bhak J, Nguyen-Quoc B, Kim SW, Lee SY, Kim JY. Plant Mol Biol 2012 Jul;79(4-5):413-27. Epub 2012 May 12..

 

Mutational hotspots in the mitochondrial genome of lung cancer. Choi SJ, Kim SH, Kang HY, Lee J, Bhak JH, Sohn I, Jung SH, Choi YS, Kim HK, Han J, Huh N, Lee G, Kim BC, Kim J. Biochem Biophys Res Commun. 2011 Apr 1;407(1):23-7. Epub 2011 Feb 18.

 

Population genetic structure of peninsular Malaysia Malay sub-ethnic groups. Hatin WI, Nur-Shafawati AR, Zahri MK, Xu S, Jin L, Tan SG, Rizman-Idid M, Zilfalil BA; HUGO Pan-Asian SNP Consortium. PLoS One. 2011 Apr 5;6(4):e18312.

 

BetaDock: shape-priority docking method based on beta-complex. Kim DS, Kim CM, Won CI, Kim JK, Ryu J, Cho Y, Lee C, Bhak J. J Biomol Struct Dyn. 2011 Aug;29(1):219-42.

 

PanSNPdb: the Pan-Asian SNP genotyping database. Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, Bhak J, Liu E, Tongsima S; HUGO Pan-Asian SNP Consortium. PLoS One. 2011;6(6):e21451. Epub 2011 Jun 23.

 

Gene expression pattern in transmitochondrial cytoplasmic hybrid cells harboring type 2 diabetes-associated mitochondrial DNA haplogroups. Hwang S, Kwak SH, Bhak J, Kang HS, Lee YR, Koo BK, Park KS, Lee HK, Cho YM. PLoS One. 2011;6(7):e22116. Epub 2011 Jul 13.

 

Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. Flórez AF, Park D, Bhak J, Kim BC, Kuchinsky A, Morris JH, Espinosa J, Muskus C. 

BMC Bioinformatics. 2010 Sep 27;11:484.

 

 

 

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Moon Young Kima,1, Sunghoon Leeb,1,2, Kyujung Vana,1, Tae-Hyung Kimb,1,2, Soon-Chun Jeongc, Ik-Young Choid, Dae-Soo Kimb, Yong-Seok Leeb, Daeui Parkb, Jianxin Mae, Woo-Yeon Kimb, Byoung-Chul Kimb, Sungjin Parkb, Kyung-A Leeb, Dong Hyun Kima, Kil Hyun Kima, Jin Hee Shina, Young Eun Janga, Kyung Do Kima, Wei Xian Liua, Tanapon Chaisana, Yang Jae Kanga, Yeong-Ho Leea, Kook-Hyung Kimf, Jung-Kyung Moong, Jeremy Schmutzh, Scott A. Jacksone, Jong Bhak* and Suk-Ha Lee*. Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22032-7. Epub 2010 Dec 3.

87) Gene Flow between the Korean Peninsula and Its Neighboring Countries. Jongsun Jung, Hoyoung Kang, Yoon Shin Cho, Ji Hee Oh, Min Hyung Ryu, Hye Won Chung, Jeong-Sun Seo, Jong-Eun Lee, Bermseok Oh, Jong Bhak, and Hyung-Lae Kim*. PLoS ONE 5(7):e11855. doi:10.1371/journal.pone.0011855. 20100729

86) PDBWiki: added value through community annotation of the Protein Data Bank. Henning Stehr,*, Jose M. Duarte1, Michael Lappe1, Jong Bhak,* and Dan M. Bolser. Database, Vol. 2010:baq009; doi:10.1093/database/baq009.
 
85) Mapping Human Genetic Diversity in Asia. The HUGO Pan-Asian SNP Consortium. Science. 2009. Dec. 11th. (As the Korean Principal Investigator) http://www.ncbi.nlm.nih.gov/pubmed/20007900

84) PDbase: a database of Parkinson's Disease-related genes and genetic variation using substantia nigra ESTs.Yang JO, Kim WY, Jeong SY, Oh JH, Jho S, Bhak J*, and Kim NS*. BMC Genomics 2009, 10(Suppl 3):S32 (3 December 2009).

83) MitoInteractome: Mitochondrial protein interactome database, and its application in 'aging network' analysis. Reja R, Venkatakrishnan AJ, Lee J, Kim BC, Ryu JW, Gong S, Bhak J*, and  Park D*. BMC Genomics 2009, 10(Suppl 3):S20 (3 December 2009).

82) PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440.Park SJ, Choi JS, Kim BC, Jho SW, Ryu JW, Park D, Lee KA, Bhak J*, and Kim SI*. BMC Genomics 2009, 10(Suppl 3):S18 (3 December 2009).

81) The Korean Bird Information System (KBIS) through open and public participation. Paik IH, Lim J, Chun BS, Jin SD, Yu JP, Lee JW, Bhak J, and Paek WK. BMC Bioinformatics 2009, 10(Suppl 15):S11 (3 December 2009).

80) Gevab: a prototype genome variation analysis browsing server. Kim WY, Kim SY, Kim TH, Ahn SM, Byun HN, Kim D, Kim DS, Lee YS, Ghang H, Park D, Kim BC, Kim C, Lee S, Kim SJ, and Bhak J*. BMC Bioinformatics 2009, 10(Suppl 15):S3 (3 December 2009). 

79) MitoVariome: a variome database of human mitochondrial DNA. Lee YS, Kim WY, Ji M, Kim JH, and Bhak J*. BMC Genomics 2009, 10(Suppl 3):S12 (3 December 2009).

78) COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.
Jho S, Kim BC, Ghang H, Kim JH, Park D, Kim HM, Jung S, Yoo K, Kim HJ, Lee S, and Bhak J*. BMC Genomics 2009, 10(Suppl 3):S35 (3 December 2009).

77) BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources.Lim J, Kim SY, Kim S, Eo HS, Kim CB, Paek WK, Kim W*, and Bhak J*. BMC Genomics 2009, 10(Suppl 3):S8 (3 December 2009).

76) ssSNPTarget: Genome-Wide Splice-Site Single Nucleotide Polymorphism Database. Ok Yang J, Kim WY, and Bhak J. Human mutation, 2009 Sep. 16th, PMID: 19760752.

75) The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Sung-Min Ahn, Tae-Hyung Kim, Sunghoon Lee, Deokhoon Kim, Ho Ghang, Daesoo Kim, Byoung-Chul Kim, Sang-Yoon Kim, Woo-Yeon Kim, Chulhong Kim, Daeui Park, Yong Seok Lee, Sangsoo Kim, Rohit Reja, Sungwoong Jho, Chang Geun Kim, Ji-Young Cha, Kyung-Hee Kim, Bonghee Lee, Jong Bhak*, and Seong-Jin Kim*. Genome Research, May 26, 2009. PMID: 19470904.

74) Planning the Human Variome Project: The Spain report. Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, Dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS; on behalf of contributors to the Human Variome Project Planning Meeting. Hum Mutat. 2009 March 20; 30(4):496-510.  PMID: 19306394 [PubMed - indexed for MEDLINE].

73) Kinetics of Zn2+ -induced Brain Type Creatine Kinase Unfolding and Aggregation. Mu H, Lü ZR, Park D, Kim BC, Bhak J, Zou F, Yang JM, Li S, Park YD, Zou HC, Zhou HM. Appl Biochem Biotechnol. 2009 Mar 11.

72) Profiling the dysregulated genes of keratinocytes in atopic dermatitis patients: cDNA microarray and interactomic analyses. Lü ZR, Park D, Lee KA, Ryu JW, Bhak J, Shi L, Lee DY, Park YD, Zou F, Yang JM. J Dermatol Sci. 2009 Jan 19.

71) The effects of acrylamide on brain creatine kinase: Inhibition kinetics and computational docking simulation. Zhi-Rong Lüa, He-Chang Zou, Seong Jin Park, Daeui Park, Long Shi, Sang Ho Oh, Yong-Doo Park, Jong Bhak, and Fei Zou, INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 2009, 44(2):128-132.

70) Dysregulated genes of extrinsic type of atopic dermatitis: 34K microarray and interactomic analyses. Zhi-Rong Lü1, a, Tae-Ho Park1, b, Eil-Soo Leec, Kea-Jeung Kimb, Daeui Parkd, Byoung-Chul Kim, Seong-Woong Chod, Jong Bhak, Yong-Doo Park, Fei Zoua, and Jun-Mo Yang. Journal of Dermatological Science, 2009, 53(2):146-165.

69) Personal Genomics, Bioinformatics, and Variomics. Jong Bhak, Ho Ghang, Rohit Reja, and Sangsoo Kim. Genomics & Informatics, 2008, 6(4):161-165.

68) An integrated korean biodiversity and genetic information retrieval system. Jeongheui Lim, Jong Bhak, Hee-Mock Oh, Chang-Bae Kim, Yong-Ha Park, and Woon Kee Paek. BMC Bioinformatics, 2008, 9(12):S24.

67) An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases. Jin Ok Yang, Sohyun Hwang, Jeongsu Oh, Jong Bhak, and Tae-Kwon Sohn. BMC Bioinformatics, 2008, 9(12):S19.

66) Prediction and evaluation of protein-protein interaction in keratinocyte differentiation. Hyun Kyung Yoon, Kyung-Cheol Sohn, Jung-Suk Lee, Yu Jin Kim, Jong Bhak, Jun-Mo Yang, Kwan-Hee You, Chang-Deok Kim, Jeung-Hoon Lee. BBRC, 2008,377(2):662-667.

65) Transcriptome analysis and identification of regulators for long-term plasticity in Aplysia kurodai. Yong-seok Lee, Sun-Lim Choi, Tae-Hyung Kim, Jin-A Lee, Hyong Kyu Kim, Hyoung Kim, Deok-Jin Jang, Jennifer J. Lee, Sunghoon Lee, Gwang Sik Sin, Chang-Bae Kim, Yutaka Suzuki, Sumio Sugano, Tai Kubo, Leonid L. Moroz, Eric R. Kandel, Jong Bhak, and Bong-Kiun Kaang. PNAS, 2008, 105(47):18602-18607.

64) The Effect of Histidine Residue Modification on Tyrosinase Activity and Conformation: Inhibition Kinetics and Computational Prediction. Lin Gou, Zhi-Rong Lu, Daeui Park, Sang Ho Oh, Long Shi, Seong Jin Park, Jong Bhak, Yong-Doo Park, Zhen-Long Ren and Fei Zou. Journal of Biomolecular Structure & Dynamics, 2008, 26(3):395-401.

63) Structural Bioinformatics Analysis of Disease-related Mutations. Seong-Jin Park, Sangho Oh, Daeui Park and Jong Bhak. Genomics & Informatics, 2008(September), 6(3):142-146.

62) Identification of gene-related Korean patents and construction of a database sever for Korean patent sequences. Byungwook Lee, Seon Kyu Kim, Tae Hyung Kim, Sangsoo Kim, Gee Chan Ryu and Jong Bhak. BIOTECHNOLOGY AND BIOPROCESS ENGINEERING, 2008, 13(2):248-251.

61) MassNet: a functional annotation service for protein mass spectrometry data. Daeui Park, Byoung-chul Kim, Seong-Woong Cho, Seong-Jin Park, Jong-Soon Choi, Seung Il Kim, Jong Bhak, and Sunghoon Lee. Nucleic Acids Research, 2008, 1-5.

60) Cyanobacterial hybrid kinase SLL0043 regulates phototaxis by suppressing pilin and twitching motility protein. Bong-Jeong Shin, Jeehyun Oh, Sungsoo Kang, Young-Ho Chung, Young Mok Park, Young Hwan Kim, Seungil Kim, Jong Bhak, and Jong-Soon Choi. JOURNAL OF MICROBIOLOGY, 2008, 46(3):300-308.

59) Automatic synthronization and distribution of biological databases and software over low-bandwidth networks among developing countries. Unitsa Sangket, Amornrat Phongdara, Wilaiwan Chotigeat, Darran Nathan, Woo-Yeon Kim, Jong Bhak, Chumpol Ngamphiw, Sissades Tongsima, Asif M. Khan, Honghuang Lin, and Tin Wee Tan. Bioinformatics, 2008, 24(2):299-301.

58) Pocket extraction on proteins via the Voronoi diagram of spheres. Donguk Kim, Cheol-Hyung Cho, Youngsong Cho, Joonghyun Ryu, Jonghwa Bhak, and Deok-Soo Kim. Journal of Molecular Graphics & Modelling, 2008, 26(7):1104-1112. (SCI)

57) Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. Jeong-Gu Kim, Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Yeong Tae Kim, Young-Jin Park, Hee Jung Cho, Hyunseok Park, Ki-Bong Kim, Kyong-Oh Yoon, Soo-Jun Park, Byoung-Moo Lee and Jong Bhak. BMC Bioinformatics, 2008, 9:41.

56) SNP@Promoter: A database of human SNPs (Single Nucleotide Polymorphisms) within putative promoter region. Byoung-Chul Kim, Woo-Yeon Kim, Daeui Park, Won-Hyong Chung, Kwang-sik Shin and Jong Bhak*. BMC Bioinformatics, 13 Feb. 2008, 9:S1-S2.

55) SynechoNET: integrated protein-protein interaction database of a model cyanobacterium /Synechocystis/ sp. PCC 6803. Woo-Yeon Kim*, Sungsoo Kang*, Byoung-Chul Kim, Jeehyun Oh, Seongwoong Cho, Jong Bhak§ , and Jong-Soon Choi§. BMC Bioinformatics, 13 Feb. 2008, 9:S1-S20.

54) Proteomic approaches to the analysis of atopic dermatitis and new insights from interactomics. Yong-Doo Park, Daeui Park, Jong Bhak and Jun-Mo Yang, PROTEOMICS - CLINICAL APPLICATIONS, 2008, 2(3):290-300 (2008 Annual Reviews issue).

53) Multi-resolution protein model. Deok-Soo Kim , Bohyung Lee , Chung-In Won , Donguk Kim, Joonghyun Ryu , Youngsong Cho, Chong-Min Kim, Sung-Hoon Lee, and Jonghwa Bhak. LECTURE NOTES IN COMPUTER SCIENCE, 2007, 4706(2):639-652.

52) GS2PATH: A web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data. Jin Ok Yang, Charny Park, Byungwook Lee, Sangsoo Kim, Jong Bhak*, and Hyun Goo Woo. Bioinformation, Dec. 30, 2007, 2(5):194-196.

51) Biological Object Downloader (BOD) Service for Easy Download and Management of Biological Databases. Daeui Park, Jungwoo Lee, Giseok Yoon, Sungsam Gong, and Jong Bhak. Genomics & Informatics, Dec. 2007, 5(4):196-199.

50) CONSORF: a consensus prediction system for prokaryotic coding sequences. Sungsoo Kang, Sung-Jin Yang, Sangsoo Kim*, and Jong Bhak*. Bioinformatics, 8 Oct. 2007, 23(22):3088-3090.

49) Genomic Distribution of Simple Sequence Repeats in Brassica rapa. Chang Pyo Hong, Zhong Yun Piao, Tae Wook Kang, Jacqueline Batley, Tae-Jin Yang, Yoon-Kang Hur, Jong Bhak, Beom-Seok Park, David Edwards, and Yong Pyo Lim. Mol. Cells, 6 March 2007, 23(3):349-356.

48) Impact of Transcriptional Properties on Essentiaity and Evolutionary Rate. Jung Kyoon Choi, Sang Cheol Kim, Jungmin Seo, Sangsoo Kim and Jong Bhak, Genetics, January 2007, 175:199-206.

47) 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, Park BS. Plant Cell, 2006, 18(6):1339-1347.

46) Parameter selection of pocket extraction algorithm using interaction interface. Kim Chong-Min, Won Chung-In, Ryu Joonghyun, Cho Cheol-Hyung, Bhak Jonghwa, and Kim Deok-Soo. September 2006, Journal of Zhejiang University - Science A, 7(9):1492-1499.

45) BioCC: An Openfree Hypertext Bio Community Cluster for Biology. Sungsam Gong, TaeHyung Kim, Jungsu Oh, Jekeun Kwon, SuAn Cho, Dan Bolser and Jong Bhak. Genomics & Informatics, September 2006, 4(3):125-128.

44) Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. Sunghoon Lee, Byungwook Lee, Insoo Jang, Sangsoo Kim and Jong Bhak. Nucleic Acids Research, April 19, 2006, 34:W99-W103. (ISSN:0305-1048)

43) Functional Annotation and Analysis of Korean Patented Biological Sequences Using Bioinformatics. Byung Wook Lee, Tae Hyung Kim, Seon Kyu Kim, Sang Soo Kim, Gee Chan Ryu, and Jong Bhak. Mol. Cells, March 2006, 21(2):269-275.

42) HExDB: Human EXon DataBase for Alternative Splicing Pattern Analysis and predicted human gene number. Junghwan Park, Minho Lee, Tae Hyung Kim, Jong Bhak, Genomics &Informatics, September 2005, 3(3):112-117.

41) 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. (ISSN:1471-2105)

40) Euclidean Voronoi diagrams of 3D sphereds and applications to protein structure analysis. Deok-Soo KIM, Youngsong CHO, Donguk KIM, Sangsoo KIM, Jonghwa BHAK and Sung-Hoon LEE. Japan Journal of Industrial and Applied Mathematics, June 2005, 22(2):251-265. (ISSN:0916-7005)

39) BioCovi: A visualization service for comparative genomics analysis, Jungsul Lee, Daeui Park and Jong Bhak. Genomics & Informatics, 2005, 3(2):52-54.

38) Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map). Daeui Park, Semin Lee, Dan Bolser, Michael Schroeder, Michael Lappe, Donghoon Oh and Jong Bhak. Bioinformatics, May 2005, 21(15):3234-3240. (ISSN:1367-4803)

37) PSIbase: a database of protein structural interactome map (PSIMAP). Sungsam Gong, Giseok Yoon Insoo Jang, Dan Bolser, Panos Dafas, Michael Schroeder, Hansol Choi, Yoobok Cho, Kyungsook Han, Sunghoon Lee, Hwanho Choi, Michael Lappe, Liisa Holm, Sangsoo Kim, Donghoon Oh, and Jonghwa Bhak. Bioinformatics, 2005, 21(10):2541-2543. (ISSN:1367-4803)

36) BioSubroutine: an open web server for bioinformatics algorithms and subroutines. Joowon Lee, Hana Kim, Wonhye Lee, Dongil Chung, and Jong Bhak. Genomics & Informatics, March 2005, 3(1):35-38.

35) Architecture of Basic Building Blocks in Protein and Domain Structural Interaction Networks. Hyun S. Moon, Jonghwa Bhak, Kwang H. Lee and Doheon Lee, Bioinformatics, 2005, 21(8):1479-1486. (ISSN:1367-4803)

34) 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 Jonghwa Bhak. BMC Genomics, 21 Dec. 2004, 5:97 p.1-5. (ISSN : 1471-2164)

33) The Atom of Evolution. Jonghwa Bhak, Dan Bolser, Daeui Park, Yoobok Cho, Kiesuk Yoon, Semin Lee, SungSam Gong, Insoo Jang, Changbum park, Maryana Huston, and Hwanho Choi. Genomics & Informatics, December 2004, 2(4):167-173.

32) Using convex hulls to extract interaction interfaces from known structures. Panos Dafas, Dan Bolser, Jacek Gomoluch, Jong Park, and Michael Schroeder. Bioinformatics, 2004, 20(10):1486-1490. (ISSN:1367-4803)

31) 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.

30) HPID: The Human Protein Interaction Database. Kyungsook Han, Byungkyu Park, Hyongguen Kim, Jinsun Hong and Jong Park. Bioinformatics, Apr. 29th, 2004, Vol. 20(15):2466-2470. (ISSN:1367-4803)

29) Large scale co-evolution analysis of Protein Structural Interlogues using the global Protein Structural Interactome Map(PSIMAP).Wankyu Kim, Dan M. Bolser, and Jong Park. Bioinformatics, 2004 Feb. 5th, 20(7):1138-1150. (ISSN : 1367-4803, Impact Factor : 5.742)

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

27) Challenges and New Approaches in Genomics and Bioinformatics. Jong Park and Kyungsook Han. Genomics & Informatics, September 2003, Vol. 1(1) 1-6.

26) Visualisation and Graph-theoretic Analysis of a Large-scale Protein Structural Interactome. Dan M Bolser, Panos Dafas, Richard Harrington, Jong Park, and Michael Schroeder. BMC Bioinformatics, 8 October 2003, 4;45 p.1-22. (ISSN:1471-2105)

25) Visualization and Analysis of Protein Interactions. Byonghyon Ju, Byungkyu Park, Jong Park, and Kyungsook Han. Bioinformatics, 2003, 19(2):317-318. (ISSN:1367-4803)

24) Predicting Protein Interactions in Human by Homologous Interactions in Yeast. Hyongguen Kim, Jong Park and Kyungsook Han. Lecture Notes in Computer Science, 2003, Vol.2637, 159-165. (ISSN:0302-9743)

23) Large Scale Statistical Prediction of Protein-Protein Interaction by Potentially Interacting Domain (PID) Pair. Wankyu Kim, Jong Park, and Jungkeun Suh. Genome Informatics, 2002, 13: 42-50.

22) InterViewer: Dynamic Visualization of Protein-Protein Interactions. Kyungsook Han, Byonghyon Ju, and Jong Park. Lecture Notes in Computer Science, 2002, Vol.2528, 364-365. (ISSN:0302-9743)

21) Sequence similarity between stereocilin and otoancorin points to a unified mechanism for mechanotransduction in the mammalian inner ear. Luca Jovine, Jong Park, and Paul M Wassarman. BMC Cell Biology, 2002, 3:28 (ISSN-NO:1471-2121)

20) Protein Interactions in the Whole Human Genome. Kyungsook Han, Byunggyu Park, Hyongguen Kim, Hongjin Kim, and Jong Park. Genome Informatics, 2002, Vol.13, 318-319 (Poster presentation).

19) An Integrated Bioinformatic Search Server: Sequences, Structure, Interaction, and Function of Proteins (SSIF) Server. Jaehyung Lee, Insong Koh, Jong Park. Genome Informatics, 2001, 12: 480-481.

18) Protein Classification Comparison Server. Junhyung Park, Sungryong Ryu, Cheolmin Kim, Insong Koh, and Jong Park. Genome Informatics, 2001, 12: 350-351.

17) Conservation of Protein Interaction Network in Evolution. Jong Park and 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, Vol.17 Suppl.1, S149-S156. (ISMB 2001 paper printed in Bioinformatics) (ISSN:1367-4803)

15) Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. Park J, Lappe M. and Teichmann SA. Journal of Molecular Biology, 2001 Mar, 30;307(3):929-938. (ISSN : 0022-2836, Impact Factor : 5.542)

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., and Gerstein M. Nucleic Acids Res., 2001, 29(8):1750-1764. (ISSN:0305-1048)

13) A fully automatic evolutionary classification of protein folds: Dali domain dictionary version 3. Dietmann S., Park J., Notredame C., Heger A., Lappe M., and Holm L. Nucleic Acids Res., 2001 Jan, 29(1):55-57. (ISSN:0305-1048)

12) Estimating the significance of sequence order in protein secondary structure prediction. Jong Park, Sabine Dietmann, Andreas Heger, and Liisa Holm. Bioinformatics, 2000, 16(11):978-987. (for Issue 9) (ISSN:1307-4803)

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, 2000, 16(2), 117-124. (ISSN:1367-4803)

10) DaliLite workbench for protein structure comparison. Liisa Holm and Jong Park. Bioinformatics, 2000, Vol 16. Issue 6, p566-567. (ISSN:1367-4803)

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. (ISSN:1367-4803)

8) Sequence Search Algorithm Assessment and Testing Toolkit (SAT). Jong Park, Liisa Holm, and Cyrus Chothia. Bioinformatics, 2000, Vol 16. No.2, 104-110. (ISSN:1367-4803)

7) Sequence Comparisons Using Multiple Sequences Detect Three Times as Many Remote Homologues as Pairwise Methods. Park J., Karplus K., Barrett C., Hughey R., Haussler D., Hubbard T. and Chothia C., Journal of Molecular Biology, 11, Dec, 1998, 284(4):1201-1210. (ISSN:0022-2836)

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, and Cyrus Chothia, PNAS, 8, Dec, 1998, 95(25):14658-14663.

5) DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Jong Park and Sarah Teichmann. Bioinformatics, 1998, 14(2):144-50. (ISSN:1367-4803)

4) Intermediate sequences find distant sequence homologues. Jong Park, Sarah A. Teichmann, Tim Hubbard and Cyrus Chothia. Journal of Molecular Biology, 17, Oct, 1997, 273(1):349-354. (ISSN:0022-2836)



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