Publications by Sangsoo Kim (Corresponding author in bold)

Back to Home

PubMed search of my publications

Google Scholar Citation Map

Click here for Google Scholar search for the articles published with Genomics & Informatics

Updated Jan. 15, 2017

Bioinformatics & Applications

ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining.

Park SH, Lee SM, Kim YJ, Kim S.

BMC Bioinformatics. 2016 Dec 13;17(Suppl 16):452. doi: 10.1186/s12859-016-1307-z. PMID: 28105934


An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes.

Cho YS, Kim H, Kim HM, Jho S, Jun J, Lee YJ, Chae KS, Kim CG, Kim S, Eriksson A, Edwards JS, Lee S, Kim BC, Manica A, Oh TK, Church GM, Bhak J.

Nat Commun. 2016 Nov 24;7:13637. doi: 10.1038/ncomms13637. PMID:27882922


Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.

Kim S, Cho YS, Kim HM, Chung O, Kim H, Jho S, Seomun H, Kim J, Bang WY, Kim C, An J, Bae CH, Bhak Y, Jeon S, Yoon H, Kim Y, Jun J, Lee H, Cho S, Uphyrkina O, Kostyria A, Goodrich J, Miquelle D, Roelke M, Lewis J, Yurchenko A, Bankevich A, Cho J, Lee S, Edwards JS, Weber JA, Cook J, Kim S, Lee H, Manica A, Lee I, O'Brien SJ, Bhak J, Yeo JH. 

Genome Biol. 2016 Oct 11;17(1):211. PMID:27802837


Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.

DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium; Asian Genetic Epidemiology Network Type 2 Diabetes (AGEN-T2D) Consortium; South Asian Type 2 Diabetes (SAT2D) Consortium; Mexican American Type 2 Diabetes (MAT2D) Consortium; Type 2 Diabetes Genetic Exploration by Nex-generation sequencing in muylti-Ethnic Samples (T2D-GENES) Consortium, Mahajan A, Go MJ, Zhang W, Below JE, Gaulton KJ, Ferreira T, Horikoshi M, Johnson AD, Ng MC, Prokopenko I, Saleheen D, Wang X, Zeggini E, Abecasis GR, Adair LS, Almgren P, Atalay M, Aung T, Baldassarre D, Balkau B, Bao Y, Barnett AH, Barroso I, Basit A, Been LF, Beilby J, Bell GI, Benediktsson R, Bergman RN, Boehm BO, Boerwinkle E, Bonnycastle LL, Burtt N, Cai Q, Campbell H, Carey J, Cauchi S, Caulfield M, Chan JC, Chang LC, Chang TJ, Chang YC, Charpentier G, Chen CH, Chen H, Chen YT, Chia KS, Chidambaram M, Chines PS, Cho NH, Cho YM, Chuang LM, Collins FS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Danesh J, Das D, de Faire U, Dedoussis G, Deloukas P, Dimas AS, Dina C, Doney AS, Donnelly PJ, Dorkhan M, van Duijn C, Dupuis J, Edkins S, Elliott P, Emilsson V, Erbel R, Eriksson JG, Escobedo J, Esko T, Eury E, Florez JC, Fontanillas P, Forouhi NG, Forsen T, Fox C, Fraser RM, Frayling TM, Froguel P, Frossard P, Gao Y, Gertow K, Gieger C, Gigante B, Grallert H, Grant GB, Grrop LC, Groves CJ, Grundberg E, Guiducci C, Hamsten A, Han BG, Hara K, Hassanali N, Hattersley AT, Hayward C, Hedman AK, Herder C, Hofman A, Holmen OL, Hovingh K, Hreidarsson AB, Hu C, Hu FB, Hui J, Humphries SE, Hunt SE, Hunter DJ, Hveem K, Hydrie ZI, Ikegami H, Illig T, Ingelsson E, Islam M, Isomaa B, Jackson AU, Jafar T, James A, Jia W, Jöckel KH, Jonsson A, Jowett JB, Kadowaki T, Kang HM, Kanoni S, Kao WH, Kathiresan S, Kato N, Katulanda P, Keinanen-Kiukaanniemi KM, Kelly AM, Khan H, Khaw KT, Khor CC, Kim HL, Kim S, Kim YJ, Kinnunen L, Klopp N, Kong A, Korpi-Hyövälti E, Kowlessur S, Kraft P, Kravic J, Kristensen MM, Krithika S, Kumar A, Kumate J, Kuusisto J, Kwak SH, Laakso M, Lagou V, Lakka TA, Langenberg C, Langford C, Lawrence R, Leander K, Lee JM, Lee NR, Li M, Li X, Li Y, Liang J, Liju S, Lim WY, Lind L, Lindgren CM, Lindholm E, Liu CT, Liu JJ, Lobbens S, Long J, Loos RJ, Lu W, Luan J, Lyssenko V, Ma RC, Maeda S, Mägi R, Männisto S, Matthews DR, Meigs JB, Melander O, Metspalu A, Meyer J, Mirza G, Mihailov E, Moebus S, Mohan V, Mohlke KL, Morris AD, Mühleisen TW, Müller-Nurasyid M, Musk B, Nakamura J, Nakashima E, Navarro P, Ng PK, Nica AC, Nilsson PM, Njølstad I, Nöthen MM, Ohnaka K, Ong TH, Owen KR, Palmer CN, Pankow JS, Park KS, Parkin M, Pechlivanis S, Pedersen NL, Peltonen L, Perry JR, Peters A, Pinidiyapathirage JM, Platou CG, Potter S, Price JF, Qi L, Radha V, Rallidis L, Rasheed A, Rathman W, Rauramaa R, Raychaudhuri S, Rayner NW, Rees SD, Rehnberg E, Ripatti S, Robertson N, Roden M, Rossin EJ, Rudan I, Rybin D, Saaristo TE, Salomaa V, Saltevo J, Samuel M, Sanghera DK, Saramies J, Scott J, Scott LJ, Scott RA, Segrè AV, Sehmi J, Sennblad B, Shah N, Shah S, Shera AS, Shu XO, Shuldiner AR, Sigurđsson G, Sijbrands E, Silveira A, Sim X, Sivapalaratnam S, Small KS, So WY, Stančáková A, Stefansson K, Steinbach G, Steinthorsdottir V, Stirrups K, Strawbridge RJ, Stringham HM, Sun Q, Suo C, Syvänen AC, Takayanagi R, Takeuchi F, Tay WT, Teslovich TM, Thorand B, Thorleifsson G, Thorsteinsdottir U, Tikkanen E, Trakalo J, Tremoli E, Trip MD, Tsai FJ, Tuomi T, Tuomilehto J, Uitterlinden AG, Valladares-Salgado A, Vedantam S, Veglia F, Voight BF, Wang C, Wareham NJ, Wennauer R, Wickremasinghe AR, Wilsgaard T, Wilson JF, Wiltshire S, Winckler W, Wong TY, Wood AR, Wu JY, Wu Y, Yamamoto K, Yamauchi T, Yang M, Yengo L, Yokota M, Young R, Zabaneh D, Zhang F, Zhang R, Zheng W, Zimmet PZ, Altshuler D, Bowden DW, Cho YS, Cox NJ, Cruz M, Hanis CL, Kooner J, Lee JY, Seielstad M, Teo YY, Boehnke M, Parra EJ, Chambers JC, Tai ES, McCarthy MI, Morris AP.

Nat Genet. 2014 Mar;46(3):234-44. doi: 10.1038/ng.2897. Epub 2014 Feb 9. PMID: 24509480


DNA methylation analysis of CD4+ T cells in patients with psoriasis.

Park GT, Han J, Park SG, Kim S, Kim TY. Arch Dermatol Res. 2014 Apr;306(3):259-68. doi: 10.1007/s00403-013-1432-8. Epub 2013 Dec 10. PMID: 24323136




Gene-set based genome-wide association analysis for the speed of sound in two skeletal sites of Korean women.

Kwon JS, Kim SBMB Rep. 2014 Jun;47(6):348-53 . PMID: 24286325


Minke whale genome and aquatic adaptation in cetaceans.

Yim HS, Cho YS, Guang X, Kang SG, Jeong JY, Cha SS, Oh HM, Lee JH, Yang EC, Kwon KK, Kim YJ, Kim TW, Kim W, Jeon JH, Kim SJ, Choi DH, Jho S, Kim HM, Ko J, Kim H, Shin YA, Jung HJ, Zheng Y, Wang Z, Chen Y, Chen M, Jiang A, Li E, Zhang S, Hou H, Kim TH, Yu L, Liu S, Ahn K, Cooper J, Park SG, Hong CP, Jin W, Kim HS, Park C, Lee K, Chun S, Morin PA, O'Brien SJ, Lee H, Kimura J, Moon DY, Manica A, Edwards J, Kim BC, Kim S, Wang J, Bhak J, Lee HS, Lee JH. Nat Genet. 2014 Jan;46(1):88-92. doi: 10.1038/ng.2835. Epub 2013 Nov 24. PMID:24270359

The tiger genome and comparative analysis with lion and snow leopard genomes. Cho YS, Hu L, Hou H, Lee H, Xu J, Kwon S, Oh S, Kim HM, Jho S, Kim S, Shin YA, Kim BC, Kim H, Kim CU, Luo SJ, Johnson WE, Koepfli KP, Schmidt-Küntzel A, Turner JA, Marker L, Harper C, Miller SM, Jacobs W, Bertola LD, Kim TH, Lee S, Zhou Q, Jung HJ, Xu X, Gadhvi P, Xu P, Xiong Y, Luo Y, Pan S, Gou C, Chu X, Zhang J, Liu S, He J, Chen Y, Yang L, Yang Y, He J, Liu S, Wang J, Kim CH, Kwak H, Kim JS, Hwang S, Ko J, Kim CB, Kim S, Bayarlkhagva D, Paek WK, Kim SJ, O'Brien SJ, Wang J, Bhak J. Nat Commun. 2013;4:2433. doi:10.1038/ncomms3433. PMID:24045858

Whole genome comparison of donor and cloned dogs.Kim HM, Cho YS, Kim H, Jho S, Son B, Choi JY, Kim S, Lee BC, Bhak J, Jang G. Sci Rep. 2013 Oct 21;3:2998. doi: 10.1038/srep02998. PMID:24141358

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 U S A. 2012 Mar 20;109(12):4574-9. doi: 10.1073/pnas.1118892109. Epub 2012 Mar 6. PMID:22396590

Common polymorphism near the MC4R gene is associated with type 2 diabetes: data from a meta-analysis of 123,373 individuals. Xi B, Takeuchi F, Chandak GR, Kato N, Pan HW; AGEN-T2D Consortium, Zhou DH, Pan HY, Mi J. Diabetologia. 2012 Oct;55(10):2660-6. doi: 10.1007/s00125-012-2655-5. Epub 2012 Aug 7. PMID:22869321

Ethnic variability in the allelic distribution of pharmacogenes between Korean and other populations. Kim IW, Kim KI, Chang HJ, Yeon B, Bang SJ, Park T, Kwon JS, Kim S, Oh JM. Pharmacogenet Genomics. 2012 Dec;22(12):829-36. doi: 10.1097/FPC.0b013e328358dd70. PMID:22955668

A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans. Li H, Gan W, Lu L, Dong X, Han X, Hu C, Yang Z, Sun L, Bao W, Li P, He M, Sun L, Wang Y, Zhu J, Ning Q, Tang Y, Zhang R, Wen J, Wang D, Zhu X, Guo K, Zuo X, Guo X, Yang H, Zhou X; DIAGRAM Consortium; AGEN-T2D Consortium, Zhang X, Qi L, Loos RJ, Hu FB, Wu T, Liu Y, Liu L, Yang Z, Hu R, Jia W, Ji L, Li Y, Lin X. Diabetes. 2013 Jan;62(1):291-8. doi: 10.2337/db12-0454. Epub 2012 Sep 6. PMID:22961080

CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes. Choi J, Cheong K, Jung K, Jeon J, Lee GW, Kang S, Kim S, Lee YW, Lee YH. Nucleic Acids Res. 2013 Jan;41(Database issue):D714-9. doi: 10.1093/nar/gks1163. Epub 2012 Nov 27. PMID:23193288

Partial AUC maximization for essential gene prediction using genetic algorithms. Hwang KB, Ha BY, Ju S, Kim S. BMB Rep. 2013 Jan;46(1):41-6. PMID:23351383

Pattern discovery of multivariate phenotypes by association rule mining and its scheme for genome-wide association studies.Park SH, Kim S. Int J Data Min Bioinform. 2012;6(5):505-20. PMID:23155779

A methodology for multivariate phenotype-based genome-wide association studies to mine pleiotropic genes.

Park SH, Lee JY, Kim SBMC Syst Biol. 2011 Dec 14;5 Suppl 2:S13. Epub 2011 Dec 14.

PMID:
 
22784570
 
[PubMed - in process] 
Free PMC Article

The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis or atopic dermatitis. Han J, Park SG, Bae JB, Choi J, Lyu JM, Park SH, Kim HS, Kim YJ, Kim S, Kim TY. Biochem Biophys Res Commun. 2012 May 25;422(1):157-163. PMID:22564738 DOI

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. PMID:22242128 Free PMC Article

Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. Cho YS, Chen CH, Hu C, Long J, Ong RT, Sim X, Takeuchi F, Wu Y, Go MJ, Yamauchi T, Chang YC, Kwak SH, Ma RC, Yamamoto K, Adair LS, Aung T, Cai Q, Chang LC, Chen YT, Gao Y, Hu FB, Kim HL, Kim S, Kim YJ, Lee JJ, Lee NR, Li Y, Liu JJ, Lu W, Nakamura J, Nakashima E, Ng DP, Tay WT, Tsai FJ, Wong TY, Yokota M, Zheng W, Zhang R, Wang C, So WY, Ohnaka K, Ikegami H, Hara K, Cho YM, Cho NH, Chang TJ, Bao Y, Hedman ÅK, Morris AP, McCarthy MI; DIAGRAM Consortium; MuTHER Consortium, Takayanagi R, Park KS, Jia W, Chuang LM, Chan JC, Maeda S, Kadowaki T, Lee JY, Wu JY, Teo YY, Tai ES, Shu XO, Mohlke KL, Kato N, Han BG, Seielstad M. Nat Genet. 2011 Dec 11;44(1):67-72. doi: 10.1038/ng.1019. PMID:22158537

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.PMID:21483678[PubMed - indexed for MEDLINE] Free PMC Article

A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis. Kim J, Ahn Y, Lee K, Park SH, Kim SBMC Bioinformatics. 2010 Aug 21;11:434. PubMed PMID: 20727194. 

Recapitulation of two genomewide association studies on blood pressure and essential hypertension in the Korean population. Hong KW, Jin HS, Lim JE, Kim S, Go MJ, Oh B. J Hum Genet. 2010 30 Jun; 55(6):336-41. Epub 2010 Apr 23.PMID: 20414254

GSA-SNP: a general approach for gene set analysis of polymorphisms. Nam D, Kim J, Kim SY, Kim S. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W749-54. PMID: 20501604

Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble. Sung E, Kim S, Shin W. BMC Bioinformatics. 2010 May 18;11(1):256. PMID: 20478076. Full text

Genetic evidence supports linguistic affinity of Mlabri--a hunter-gatherer group in Thailand. Xu S, Kangwanpong D, Seielstad M, Srikummool M, Kampuansai J, Jin L; HUGO Pan-Asian SNP Consortium

BMC Genet. 2010 Mar 19;11:18. PubMed PMID: 20302622; PubMed Central PMCID: PMC2858090. 


Mapping human genetic diversity in Asia. HUGO Pan-Asian SNP Consortium, Abdulla MA, Ahmed I, Assawamakin A, Bhak J, Brahmachari SK, Calacal GC, Chaurasia A, Chen CH, Chen J, Chen YT, Chu J, Cutiongco-de la Paz EM, De Ungria MC, Delfin FC, Edo J, Fuchareon S, Ghang H, Gojobori T, Han J, Ho SF, Hoh BP, Huang W, Inoko H, Jha P, Jinam TA, Jin L, Jung J, Kangwanpong D, Kampuansai J, Kennedy GC, Khurana P, Kim HL, Kim K, Kim S, Kim WY, Kimm K, Kimura R, Koike T, Kulawonganunchai S, Kumar V, Lai PS, Lee JY, Lee S, Liu ET, Majumder PP, Mandapati KK, Marzuki S, Mitchell W, Mukerji M, Naritomi K, Ngamphiw C, Niikawa N, Nishida N, Oh B, Oh S, Ohashi J, Oka A, Ong R, Padilla CD, Palittapongarnpim P, Perdigon HB, Phipps ME, Png E, Sakaki Y, Salvador JM, Sandraling Y, Scaria V, Seielstad M, Sidek MR, Sinha A, Srikummool M, Sudoyo H, Sugano S, Suryadi H, Suzuki Y, Tabbada KA, Tan A, Tokunaga K, Tongsima S, Villamor LP, Wang E, Wang Y, Wang H, Wu JY, Xiao H, Xu S, Yang JO, Shugart YY, Yoo HS, Yuan W, Zhao G, Zilfalil BA; Indian Genome Variation Consortium. Science. 2009 Dec 11;326(5959):1541-5. PMID: 20007900


Remodeling of global transcription patterns of Cryptococcus neoformans genes mediated by the stress-activated HOG signaling pathways. Ko YJ, Yu YM, Kim GB, Lee GW, Maeng PJ, Kim S, Floyd A, Heitman J, Bahn YS. Eukaryot Cell. 2009 Aug;8(8):1197-217. Epub 2009 Jun 19. PMID: 19542307

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, Dae-Soo 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 Res. September 2009 19: 1622-1629; Published in Advance May 26, 2009, doi:10.1101/gr.092197.109

A Scheme for Filtering SNPs Imputed in 8,842 Korean Individuals Based on the International HapMap Project Data. Kichan Lee, Sangsoo Kim. Genomics & Informatics 2009 June 30; 7(2):136-140.
 
Prediction of protein-protein interaction types using association rule based classification.
Sung Hee Park, Jose A Reyes, David R Gilbert, Ji Woong Kim and Sangsoo Kim. BMC Bioinformatics 2009 Jan 28, 10:36.

Genome data mining for everyone. Gir Won Lee & Sangsoo Kim. BMB reports 2008 Nov. 30; 41(11):757-764.

Identification of SNP markers for common CNV regions and association analysis of risk of subarachnoid aneurysmal hemorrhage in Japanese population. Bae JS, Cheong HS, Kim JO, Lee SO, Kim EM, Lee HW, Kim S, Kim JW, Cui T, Inoue I, Shin HD. Biochem Biophys Res Commun. 2008 Sep 5;373(4):593-6. Epub 2008 Jul 2.

Haplotype Phylogeny of a 200kb Region in the Human Chromosome X Terminal Band (q28). Sangsoo Kim. Genomics & Informatics 2008 Sept.; 6(3):130-5.

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T. Nucleic Acids Res. 2008 Jan;36(Database issue):D793-9. Epub 2007 Dec 18.

GS2PATH: A web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data. Yang JO, Charny P, Lee B, Kim S, Bhak J, Woo HG. Bioinformation. 2007 Dec 30;2(5):194-6.

Identification of Gene-related Korean Patents and Construction of a Database Server for Korean Patent Sequences Byungwook Lee , Seon-Kyu Kim , Taehyung Kim , Sang Soo Kim , Gee Chan Ryu , and Jong Bhak.  Biotechnology and Bioprocess Engineering 2008 Apr. 30, 13(2): 248-251. DOI/10.1007/s12257-007-0183-9 (SCIE IF 1.694).

CONSORF: a consensus prediction system for prokaryotic coding sequences Kang S, Yang SJ, Kim S, Bhak J. Bioinformatics. 2007 Nov 15;23(22):3088-90. Epub 2007 Oct 31. PMID: 17977885

Identification of molecular markers for the oncogenic differentiation of hepatocellular carcinoma Yu GR, Kim SH, Park SH, Cui XD, Xu DY, Yu HC, Cho BH, Yeom YI, Kim SS, Kim SB, Chu IS, Kim DG. Exp Mol Med. 2007 Oct 31;39(5):641-52. PMID: 18059140

Meta- and gene set analysis of stomach cancer gene expression data Kim SY, Kim JH, Lee HS, Noh SM, Song KS, Cho JS, Jeong HY, Kim WH, Yeom YI, Kim NS, Kim S, Yoo HS, Kim YS. Mol Cells. 2007 Oct 31;24(2):200-9. PMID: 17978572

Conformational flexibility in mammalian 15S-lipoxygenase: Reinterpretation of the crystallographic data Choi J, Chon JK, Kim S, Shin W. Proteins 2007 Sep 10;70(3):1023-1032  PMID: 17847087

Impact of transcriptional properties on essentiality and evolutionary rate Choi JK, Kim SC, Seo J, Kim S, Bhak J. Genetics 2007 Jan;175(1):199-206. Epub 2006 Oct 22.  PMID: 17057246

An efficient top-down search algorithm for learning Boolean networks of gene expression Dougu NamContact Information, Seunghyun Seo Contact Information and Sangsoo Kim  Machine Learning (2006) Oct.; 65(1):229-245. DOI: 10.1007/s10994-006-9014-z.

Gene expression profiling of human HBV- and/or HCV-associated hepatocellular carcinoma cells using expressed sequence tags Yoon SY, Kim JM, Oh JH, Jeon YJ, Lee DS, Kim JH, Choi JY, Ahn BM, Kim S, Yoo HS, Kim YS, Kim NS.  Int. J. Oncol. 2006 Aug; 29(2):315-27.

Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information Lee S, Lee B, Jang I, Kim S, Bhak J. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W99-103.  PMID: 16845118

 

Molecular evolution of the periphilin gene in relation to human endogenous retrovirus m element Huh JW, Kim TH, Yi JM, Park ES, Kim WY, Sin HS, Kim DS, Min DS, Kim SS, Kim CB, Hyun BH, Kang SK, Jung JS, Lee WH, Takenaka O, Kim HS. J Mol Evol. 2006 Jun;62(6):730-7. Epub 2006 Apr 11. PMID: 16612547

 

Adenovirus-mediated transfer of siRNA against PTTG1 inhibits liver cancer cell growth in vitro and in vivo Cho-Rok J, Yoo J, Jang YJ, Kim S, Chu IS, Yeom YI, Choi JY, Im DS. Hepatology. 2006 May;43(5):1042-52. PMID: 16628636

 

Functional annotation and analysis of Korean patented biological sequences using bioinformatics Lee BW, Kim TH, Kim SK, Kim SS, Ryu GC, Bhak J. Mol Cells. 2006 Apr 30;21(2):269-75.  PMID: 16682823

 

Transcriptome analysis of human gastric cancer JH. Oh, J.O. Yang, Y. Hahn, M-R. Kim, S-S. Byun, Y-J. Jeon, J-M. Kim, K-S. Song, S-M. Noh, S. Kim, H-S. Yoo, Y.S. Kim, N-S. Kim Mammalian Genome (2005) 16(12):942-54.

 

Differential Coexpression Analysis Using Microarray Data and Its Application to Human Cancer J.K. Choi, U. Yu, O.J. Yoo, S. Kim Bioinformatics (2005) 21(24):4348-55.

 

Stage-dependent gene expression profiles during natural killer cell development Classification H-S. Kang, E-M. Kim, S. Lee, S-R. Yoon, T. Kawamura, Y-C. Lee, S. Kim, P-K. Myung, S.M. Wang, < xml="true" prefix="st1" namespace="">I. Choi Genomics (2005) 86(5):551-65.

 

Molecular Phylogeny and Geography of Korean Medaka Fish (Oryzias latipes) T-W. Kang, E-H. Lee, M-S. Kim, S-G. Paik, S. Kim, C-B. Kim Molecules and Cells (2005) 20(1):151-6.

 

Euclidean Voronoi Diagrams of 3D Spheres and Applications to Protein Structure Analysis D-S. Kim, Y. Cho, D. Kim, S. Kim, J. Bhak, S-H. Lee Japan J. Indust. Appl. Math (2005) 22:251-5.

 

Multifunctional Drug Delivery System Using Starch-Alginate Beads for Controlled Release Y.J. Kim, H.G. Park, Y.L. Yang, Y. Yoon, S. Kim, E. Oh Biol. Pharm. Bull. (2005) 28(2):394-7 

 

 

Classification of Peroxiredoxin Subfamilies Using Regular Expressions Jae Kyung Chon, Jongkeun Choi, Sang Soo Kim and Whanchul Shin Genomiocs & informatics (2005) 3(2):55-60.

 

TO-GO: a Java-based Gene Ontology navigation environment Ungsik Yu, Yoon Jeong Choi, Jung Kyoon Choi, and Sangsoo Kim Bioinformatics (2005) 21(17) 3580-1. doi:10.1093/bioinformatics/bti560

 

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) 21:2541-3. doi:10.1093/bioinformatics/bti366

 

FESD: a Functional Element SNPs Database in human Hyo Jin Kang, Kyoung Oak Choi, Byung-Dong Kim, Sangsoo Kim, Young Joo Kim Nucleic Acids Research (2005) 33 Database issue:D518-22. doi:10.1093/nar/gki082

 

TFExplorer: integrated analysis database for predicted transcription regulatory elements Jinsoo Kim, Jungmin Seo, Young Seek Lee, and Sangsoo Kim Bioinformatics (2005) 21:548-50. doi:10.1093/bioinformatics/bti048

        

Feature genes of hepatitis B virus-positive hepatocellular carcinoma, established by its molecular discrimination approach using prediction analysis of microarray Kim BY, Lee JG, Park S, Ahn JY, Ju YJ, Chung JH, Han CJ, Jeong SH, Yeom YI, Kim S, Lee YS, Kim CM, Eom EM, Lee DH, Choi KY, Cho MH, Suh KS, Choi DW, Lee KH Biochim Biophys Acta. 2004 Dec 24;1739(1):50-61. doi:10.1016/j.bbadis.2004.07.004

 

 Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, Roberto A. Barrero, Takuro Tamura, Yumi Yamaguchi-Kabata, Motohiko Tanino, Kei Yura, Satoru Miyazaki, Kazuho Ikeo, Keiichi Homma, Arek Kasprzyk, Tetsuo Nishikawa, Mika Hirakawa, Jean Thierry-Mieg, Danielle Thierry-Mieg, Jennifer Ashurst, Libin Jia, Mitsuteru Nakao, Michael A. Thomas, Nicola Mulder, Youla Karavidopoulou, Lihua Jin, Sangsoo Kim, Tomohiro Yasuda, Boris Lenhard, Eric Eveno, Yoshiyuki Suzuki, Chisato Yamasaki, Jun-ichi Takeda, Craig Gough, Phillip Hilton, Yasuyuki Fujii, Hiroaki Sakai,, Susumu Tanaka, Clara Amid, Matthew Bellgard, Maria de Fatima Bonaldo, Hidemasa Bono, Susan K. Bromberg, Anthony Brookes, Gopal Gopinathrao, Elspeth Bruford, Piero Carninci, Claude Chelala, Christine Couillault, SandroJ. de Souza, Marie- Anne Debily, Marie-Dominique Devignes, Inna Dubchak, Toshinori Endo, Anne Estreicher, Eduardo Eyras, Kaoru Fukami-Kobayashi, Esther Graudens, Yoonsoo Hahn, Michael Han, Ze-Guang Han, Kousuke Hanada, Katsuyuki Hashimoto, Ursula Hinz, Momoki Hirai, Teruyoshi Hishiki, Ian Hopkinson, Sandrine Imbeaud, Hidetoshi Inoko,, Alexander Kanapin, Takeya Kasukawa, Janet Kelso, Paul Kersey, Reiko Kikuno, Kouichi Kimura, Bernhard Korn, Vladimir Kuryshev, Izabela Makalowska, Takashi Makino, Shuhei Mano, Regine Mariage-Samson, Jun Mashima, Hideo Matsuda, Hans-Werner Mewes, Shinsei Minoshima, Keiichi Nagai, Hideki Nagasaki, Rajni Nigam, Osamu Ogasawara, Osamu Ohara, Masafumi Ohtsubo, Norihiro Okada, Toshihisa Okido, Satoshi Oota, Motonori Ota, Toshio Ota, Tetsuji Otsuki, Dominique Piatier-Tonneau, Annemarie Poustka , Shuang-Xi Ren, Naruya Saitou, Katsunaga Sakai, Shigetaka Sakamoto, Ryuichi Sakate, Ingo Schupp, Florence Servant, Stephen Sherry, Nobuyoshi Shimizu, Mary Shimoyama, Andrew J. Simpson, Bento Soares, Charles Steward, Makiko Suwa, Mami Suzuki, Aiko Takahashi, Gen Tamiya, Hiroshi Tanaka, Todd Taylor, Joseph D. Terwilliger, Per Unneberg, Vamsi Veeramachaneni, Shinya Watanabe, Laurens Wilming, Norikazu Yasuda, Hyang-Sook Yoo, Marvin Stodolsky, Wojciech Makalowski, Mitiko Go, Kenta Nakai, Toshihisa Takagi, Minoru Kanehisa, Yoshiyuki Sakaki, John Quackenbush, Yasushi Okazaki, Yoshihide Hayashizaki, Winston Hide, Ranajit Chakraborty, Ken Nishikawa, Hideaki Sugawara, Yoshio Tateno, Zhu Chen, Michio Oishi, Peter Tonellato, Rolf Apweiler, Kousaku Okubo, Lukas Wagner, Stefan Wiemann, Robert L Strausberg, Takao Isogai, Charles Auffray, Nobuo Nomura, Takashi Gojobori, Sumio Sugano Public Library of Science Biology (2004) 2:1-21. (coverdate June 2004) http://biology.plosjournals.org

 

 Integrative analysis of multiple gene expression profiles applied to liver cancer study Jung Kyoon Choi1, Jong Young Choi, Dae Ghon Kim, Dong Wook Choi, Bu Yeo Kim, Kee Ho Lee, Young Il Yeom, Hyang Sook Yoo, Ook Joon Yoo, Sangsoo Kim FEBS Lett. (2004) 565:93-100, (coverdate 7 May 2004). IF 3.91 (SCI)

 

WIGED: Web-based data integration system for the analysis of gene expression in disease J.O. Yang, U. Yu, S. Kim Key Engineering Materials (2005) 277:41 (SCI)

 

Gene cataloging and expression profiling in human gastric cancer by expressed sequence tags N-S. Kim, Y. Hahn, J-H. Oh, K-J. Oh, J-M. Kim, H-S. Park, S. Kim, S-M. Rho, H-S. Yoo, Y. S. Kim Genomics (2004) 83:1024-1045, IF 3.42 (SCI)

 

Bioinformatics in the post-genome era U. Yu, S.H. Lee, Y.J. Kim, S. Kim Journal of Biochemistry and Molecular Biology (2004) 37:75-82. IF 0.96 (SCIE)

 

Expression Profiling and Subtype-Specific Expression of Stomach cancer Byungsik Kim, Seunghyun Bang, Seungkoo Lee, Soonok Kim, Yusun Jung, Changhee Lee, Kyungho Choi, Seong-Gene Lee, Kiwhan Lee, Yongsung Lee, Sang-Soo Kim, Yeong-Il Yeom, Yong-Sung Kim, Hyang-Sook Yoo, Kyuyoung Song, and Inchul Lee Cancer Research (2003) 63:8248-8255. IF 8.32 (SCI)


Combining multiple microarray studies and modeling interstudy variation J.K. Choi, U. Yu, S. Kim, O.J. Yoo  Bioinformatics (2003) 19 Suppl. 1:i84-i90. IF 4.62 (SCI) 

 

 

X-ray Crystallography & Drug Design

Discovery of LB30057, A Benzamidrazone-based selective oral thrombin inhibitor.  Yeong Soo Oh, Mkyung Yun, Sang Yeul Hwang, Seongwon Hong, Youseung Shin, Koo Lee, Kyung Hee Yoon, Yung Joon Yoo, Dong Soo Kim, Sun Hwa Lee, Yong Hee Lee, Hee Dong Park, Chang Ho Lee, Sang Koo Lee and Sangsoo Kim  Bioorganic & Medicinal Chemistry Letters (1998) 8:631-634.

Structural modification of an orally active thrombin inhibitor, LB30057: replacement of the D-pocket-binding naphthyl moiety.  Koo Lee, Sang Yeul Hwang, Seongwon Hong, Chang Yong Hong, Chang-seok Lee, Youseung Shin, Sangsoo Kim, Mikyung Yun, Yung Joon Yoo, Myunggyun Kang and Yeong Soo Oh  Bioorganic & Medicinal Chemistry (1998) 6:869-876.

 

Rational design of selective thrombin inhibitors.  Sangsoo Kim, Sang Yeul Hwang, Young Kwan Kim, Mikyung Yun and Yeong Soo Oh Bioorganic & Medicinal Chemistry Letters (1997) 7:769-774.

 

Total synthesis of (+)-cladantholide and (-)-estafiatin: 5.exo,7-endo radical cyclization strategy for the construction of guaianolide skeleton.  Eun Lee, Jong Won Lim, Cheol Hwan Yoon, Yong-suk Sung, Young Kwon Kim, Mikyung Yun and Sangsoo Kim  Journal of the American Chemical Society (1997) 119:8391-8392.

 

Design, synthesis, and characterization of dipeptide isostere containing cis-epoxide for the irreversible inactivation of HIV protease.  Chang Sun Lee, Nakyen Choy, Chihyo Park, Hoil Choi, Young Chan Son, Sangsoo Kim, Jong Hoa Ok, Heungsik Yoon and Sung Chun Kim Bioorganic & Medicinal Chemistry Letters (1996) 6:589-594.

 

Fused Oxacycle synthesis via radical cyclization of β-alkoxyacrylates.  Eun Lee, Jin Sung Tae, You Hoon Chong, Yong Cheol Park, Mikyung Yun and Sangsoo Kim  Tetrahedron Letters (1994) 35:129-132.

 

Orthocyclophanes. 3.  Ketonands, novel ketonic crowns of polyoxo[1n]orthocyclophane constitution.  Woo Young Lee, Chang Hee Park, Hyo-Jung Kim and Sangsoo Kim  The Journal of Organic Chemistry (1994) 59:878-884.

 

Crystallization and preliminary X-ray crystallographic analysis of phospholipid transfer protein from maize seedings.  Dong Hae Shin, Kwang Yeon Hwang, Kyeong Kyu Kim, Sangsoo Kim, Robert M. Sweet and Se Won Suh  Proteins (1994) 19:80-83.

 

Solid-state reactions of iridium(I)-1,5-cyclooctadiene compounds with CO: synthesis of cationic (1,5-cyclooctadiene)carbonyliridium(I) complexes.  Chong Shik Chin, Byeongno Lee and Sangsoo Kim  Organometallics (1993) 12:1462-1466.

 

A novel star-shaped crown ether: spontaneous isomerization of a macrocyclic polyketone to a spirobicyclic polyketal.  Woo Young Lee, Chang Hee Park and Sangsoo Kim  Journal of the American Chemical Society (1993) 115:1184-1185.

 

Preparation of a cyclopropane-containing analogue of artemisinin.  Soo-Un Kim, Jin-Hyuk Choi and Sangsoo Kim  Journal of Natural Products (1993) 56:857-863.

 

Solution dynamics and crystal structure of CpMoOs3(CO)10(μ-H)2[μ 3-η2-C(O)CH2Tol].  Joon T. Park, Jeong-Ju Cho, Kang-Moon Chun, Sock-Sung Yun and Sangsoo Kim  Bull. Korean Chem. Soc. (1993) 14:137.

 

A novel (Tricobaltiomethoxy)silatrane: Synthesis and structure of [Co3(CO)9{μ2-COSi(O CH2CH2)3N}].  Myong W. Kim, Dong Seon Uh, Sangsoo Kim and Youngkyu Do Inorganic Chemistry (1993) 32:5883.

 

Novel exo-nido-cupracarborane wih an unusual solution fluxionality. Synthesis and structure of [9,10-exo-{Cu(PPh3)2}-9,10-(μ-H)2-7,8-nido-C2B9H10].  Young-Whan Park, Jinkwon Kim, Sangsoo Kim and Youngkyu Do Chemistry Letters (1993) 121-124.

 

X-ray crystallographic study of covalently modified carboxypeptidase A by 2-benzyl-3,4-epoxybutanoic acid, a pseudomechanism-based inactivator.  Mikyung Yun, Chihyo Park, Sangsoo Kim, Doohyun Nam, Sung Chun Kim and Dong H. Kim  Journal of the American Chemical Society (1992) 114:2281-2282.

 

Crystallization and preliminary X-ray crystallographic analysis of lipase from Pseudomonas cepacia.  Kyeong Kyu Kim, Kwang Yeon Hwang, Hye Sung Jeon, Sangsoo Kim, Robert M. Sweet, Chul Hak Yang and Se Won Suh  Journal of Molecular Biology  (1992) 227:1258-1262.

 

Synthesis, reactivity, and molecular structure of [(phenylsilatrane)Mn(CO)2P(OMe)3]ClO4.  Ae-Soon Oh, Young Keun Chung and Sangsoo Kim Organometallics (1992) 11:1394-1398.

 

Endo-σ-bonded group 14 heterodicarboranes: Syntheis of [Ph3MC2B9H11]- [M=Germanium(IV), Tin(IV) and structure of [10-endo-(SnPh3)-10-μ-H-7,8-nido-C2B9H10][trans-Ir(CO)(PPh3)2(MeCN)].  Jinkwon Kim, Sangsoo Kim and YoungKyu Do J. Chem. Soc., Chem. Commun. (1992) 938.

 

μ3-η2-acyl and μ-alkylidene complexes of a molybdenum-triosmium cluster. Crystal structure of CpMoOs3(CO)9(μ-O)( μ-CHCH2Tol). Park JT, Chung MK, Chun KM, Yun SS, Kim S Organomet. (1992) 11:3313-3319.

 

Internal hydride assisted C-O bond scission of a μ3-η2-coordinated acyl and an apparent rotation of μ-alkylidene carbon in molybdenum-triosmium cluster compounds.  Joon T. Park, Kang M. Chun, Sock S. Yun and Sangsoo Kim  Bulletin of the Korean Chemical Society (1991) 12:249-251.

 

Crystallization and preliminary structure analysis of an insect virus with T=4 quasi-symmetry: Nudurelia capensis ω virus. Jean Cavaralli, Wu Bomu, Lars Liljas, Sangsoo Kim, Wladek Minor, Sanjeev Munshi, Steve Muchmore, Tim Schmidt and John E. Johnson Acta. Cryst. (1991) B47:23-29.

 

Crystallization and a preliminary X-ray crystallographic study of α-amylase from Bacillus licheniformis. Suk Yeong Lee, Sangsoo Kim, Robert M. Sweet and Se Won Suh Archiv. Biochem. Biophys. (1991) 291:255-257.

 

Conformational variability of a picornavirus capsid: pH-dependent structural changes of Mengo virus related to its host receptor attachment site and disassembly. Kim S, Boege U, Krishnaswamy S, Minor I, Smith TJ, Luo M, Scraba DG, Rossmann MG  Virology. (1990) Mar;175(1):176-90.

 

Crystal structure of human rhinovirus serotype 1A (HRV1A). Kim S, Smith TJ, Chapman MS, Rossmann MC, Pevear DC, Dutko FJ, Felock PJ, Diana GD, McKinlay MA  J Mol Biol. 1989 Nov 5;210(1):91-111.

 

Auto-indexing oscillation photographs. Sangsoo Kim J. Appl. Cryst. (1989) 22:53-60.

 

Electrocatalysis of anodic oxygen transfer reactions: comparison of structural data with electrocatalytic phenomena for bismuth-doped lead dioxide. Yeo I-H, Kim S, Jacobson RA, Johnson DC J. Electrochem. Soc. (1989) 136:1395-1401.

 

Structure of (R,S)-hesperetin monohydrate. Shin W, Kim S, Chun KS Acta Cryst. (1987) C43:1946-1949.

 

Synthesis, stereochemistry, mechanisms of formation, and X-ray crystal structures of enantiomerically pure π-allylpalladium compounds formed via palladium-promoted ring opening of bicycled alkenes. Larock RC, Song H. Kim S, Jacobson RA J. Chem. Soc., Chem. Commun (1987) 834-836.

 

Synthesis, reactions, and structures of dioxycarbene complexes of rhenium. Miessler GL, Kim S, Jacobson RA, Angelici RJ Inorg. Chem. (1987) 26:1690-1695.

 

Synthesis and structure of the “linear” tetranuclear cluster [(MoO2S2)2Fe2S2]4-: Implications for aqueous Mo-Fe-S chemistry. Anglin RJ, Kurtz Jr DM, Kim S, Jacobson RA Inorg. Chem. (1987) 26:1470-1472.

 

Reactions of the Thiocarbyne [HB(pz)3](CO)2W(CSMe) and Thiocarbene [HB(pz)3](CO)2W[2-CH(SMe)]+ Complexes with Phosphines. H.P. Kim, S.Kim, R.A. Jacobson, and R.J. Angelici, Organometallics (1986) 5:2481

 

Synthesis and structure of ternary molybdenum oxides MMo8O10 (M = Li or Zn) having orthogonal nonintersecting octahedral cluster chains. Lii K-H, McCarley RE, Kim S, Jacobson RA J. Solid St. Chem. (1986) 64:347-358.

 

Syntheses and Structures of [HB(pz)3](CO)2(CS)W-Au(PR)3 Complexes. First Examples of a Semibridging CS Ligand. H.P. Kim, S. Kim, R.A. Jacobson, and R.J. Angelici,  J. Am. Chem. Soc. (1986) 108:5154

 

Characterization, structure, and conformation of a dinuclear platinum(I) complex with mixed halide-phosphine ligands trans to the metal-metal bond. Blau RJ, Espenson JH, Kim S, Jacobson RA Inorg. Chem. (1986) 25:757-763.

 

Synthesis from diamine of mono- and dinuclear cyclopentadienyliron dicarbonyl carbamoyl compounds. Crystal and molecular structure of (-CONH(CH2)2NHCO)[CpFe(CO)2]2. Lindsay AJ, Kim S, Jacobson RA, Angelici RJ Organomet. (1984) 3:1523-1530.

 

Synthesis of an η2-CH(SMe) Carbene Ligand by Protonation of the Carbyne in [HB(pz)3](CO)2W(CSMe).  A Possible Model Step in CO Hydrogenation. H.P. Kim, S. Kim, R.A. Jacobson, and R.J. Angelici,  Organometallics (1984) 3:1124.

 

Preparation and molecular structure of the Nickel(II) perchlorate complex of a hexaadentate macrobicyclic ligand, 1,3,6,8,10,13,16,19-octaazabicyclo[6.6.6]eicosane. Suh MP, Shin W, Kim D, Kim S Inorg. Chem. (1984) 23:618-620.

 

The crystal and molecular structure of Thiamphenicol. Shin W and Kim S Bull. Kor. Chem. Soc. (1983) 4:79-83.