¡¡
Tae-Min Kim. M.D.,Ph.D.
Postdoctoral fellow/Research associate
Current affiliation: Center for Biomedical
Informatics, Harvard Medical School, Shattuck St. 10, Boston, MA 02115
¡¡
¡¤
rSW-seq: algorithm
for detection of copy number alterations in deep sequencing data
rSW-seq
is designed to identify copy number alterations between tumor-vs-matched normal genomes (or between normal-vs-normal genomes for CNV detection) from deep sequencing
data generated by next-generation sequencing. Compared to other algorithms (BreakDancer or MoDIL) using PEM
(paired-end mapping) signatures, rSW-seq uses
¡®read-depth¡¯ as primary measure, which can be applied to single-end sequencing
read set.
BMC Bioinformatics. 2010;11:432. Pubmed
The source code of rSW-seq is available on request.
¡¤
PathCluster: a framework for gene set-based hierarchical clustering
Gene clustering is a powerful technique in the analysis
of large-scaled gene expression data.
In PathCluster, genes belonging to the gene
sets are measured for the expression similarity or distance in a pairwise manner and the distance between gene sets can be
visualized in conventional 'tree-like' dendrogram
using PathCluster. In the dendrogram,
the possible relationship between distinct molecular functions (e.g., GO terms)
or between transcription/small RNA regulators (e.g., motif synergy between two
corresponding transcriptional regulators) can be visually investigated.
Bioinformatics. 2008; 24:1957 PubMed - PathCluster installation
package with online manual is available here.
¡¤
GEAR: Genomic Enrichment Analysis for Regional DNA
copy number changes
GEAR algorithm has been
developed to functionally analyze the genome-wide alterations detected by
array-CGH platform. Two kinds of genomic signatures (i.e., the coordinated
genomic dosage changes of functionally related genes), primary and clinical
signatures can be identified from highly recurrent or class-specific genomic
alterations linking such alterations with respective biological functions by
using GEAR algorithm. GEAR also
measures the enrichment of gene sets for user-defined custom alterations
facilitating the functional analysis of various types of genomic variants.
Bioinformatics. 2008; 24:420 PubMed - GEAR
installation package with online manual is available here.
¡¤
GSECA: Inferring biological functions and
associated transcriptional regulators using Gene Set Expression Coherence
Analysis
GSECA is an analytical
framework that identifies functional categories and associated transcriptional
regulatory logics by using expression coherence of predefined functional and
regulatory motif gene sets. As an integrative and comprehensive method
exploiting the biological information in terms of functional and regulatory
motif gene sets, the proposed algorithm generates a number of testable
hypotheses: X1 and X2 transcriptional regulators synergistically regulate
function Y under cellular condition Z. With extended versatility coping with
various kinds of expression datasets, GSECA would help to elucidate the interactions
between molecular functions and related transcriptional regulators.
BMC Bioinformatics. 2007; 8:453 PubMed
- GSECA
install package with supplementary files are available here.
¡¤
BSEA: Identification of transcriptional regulators
using Binding Site Enrichment Analysis
The method of BSEA (binding site enrichment analysis)
adopts the algorithm of gene set enrichment analysis (GSEA; more specifically
PAGE, parametrical version of GSEA) and takes the entire array platforms into
accounts identifying key transcriptional cis-sequences and corresponding trans-acting factors (transcriptional
factors). BSEA can identify key regulators for global microarray data in which
transcriptional regulation plays a major role. As a generalized method, BSEA
would help to elucidate the transcriptional regulatory networks, the primary
challenges in functional genomics.
In Silico Biol. 2006. 6:0049. PubMed
– Perl script and associated datasets are available on request.
Biblography (Leading author)
Kim
TM, Xi R, Luquette LJ, Park R,
Johnson MD, Park PJ
Functional genomic
analysis of chromosomal aberrations in a compendium of cancer genomes.
Submitted.
Kim
TM, Ramires V, Barrera-Chimal J, Bobadilla NA, Park PJ, Vaidya
VS.
Gene expression analysis reveals the
cell cycle and kinetochore genes participating in
renal ischemia reperfusion injury and early development in kidney.
PLoS
One. 2011;6(9):e25679. Epub
2011 Sep 28. Pubmed
Kim TM, Ha SA, Kim HK, Yoo J, Kim S, Yim SH, Jung SH,
Kim DW, Chung YJ, Kim JW.
Gene expression signatures associated
with the in vitro resistance to two tyrosine kinase
inhibitors, nilotinib and imatinib.
Blood Cancer Journal (2011) 1, e32; doi:10.1038/bcj.2011.32
Kim TM, Huang W, Park R,
Park PJ, Johnson MD
A developmental taxonomy of glioblastoma
defined and maintained by microRNAs.
Cancer Res. 2011 May 1;71(9):3387-99. Epub 2011 Mar 8. Pubmed
Kim
TM, Park PJ
Advances in analysis of transcriptional
regulatory networks.
Wiley Interdiscip Rev Syst Biol Med. 2011 Jan-Feb;3(1):21-35.
Pubmed
Kim
TM, Luquette LJ, Xi R, Park PJ
rSW-seq: algorithm for detection of copy number
alterations in deep sequencing data.
BMC Bioinformatics. 2010; 11:432.
Pubmed
Yim SH, Kim TM*,
Hu HJ, Kim JH, Kim BJ, Lee JY, Han BG, Shin SH, Jung
SH, Chung YJ (* equally contributed)
Copy number variations in East-Asian
population and their evolutionary and functional implications.
Hum Mol Genet. 2010; 19(6):1001-8. Pubmed
Kim TM, Yim SH, Jeoung YB, Jung YC, Chung
YJ
PathCluster: a framework for gene set-based
hierarchical clustering.
Bioinformatics.
2008; 24:1957-8 PubMed
Kim TM, Yim SH, Jung YC, Park CK, Choi
JY, Park WS, Kwon MS, Fiegler H, Carter NP, Rhyu MG, Chung YJ.
Clinical implication of recurrent copy number alterations
in hepatocellular carcinoma and putative oncogenes in recurrent gains on 1q
Int J Cancer. 2008;
123(12):2808-15 PubMed
Kim TM, Yim
SH, Chung YJ.
Copy number variations in the human genome: potential
source for the individual diversity and disease association studies (Review).
Genomics
and Informatics. 2008;
6(1):1-7 Journal
Link
Kim TM, Jung YC, Rhyu MG, Jung MH, Chung YJ.
GEAR: Genomic Enrichment Analysis of Regional DNA copy number changes.
Bioinformatics. 2008; 24:420 PubMed
Kim TM, Chung YJ, Rhyu MG, Jung MH.
Inferring biological functions and associated
transcriptional regulators using Gene Set Expression Coherence Analysis
(GSECA).
BMC Bioinformatics. 2007; 8:453 PubMed
Kim TM, Chung YJ, Rhyu MG, Jung MH.
Genome-wide germline methylation
patterns inferred from local nucleotide frequency of repetitive sequences in
human genome.
Mamm Genome. 2007 Apr;18(4):277-85.
PubMed [Supplementary
files]
Kim TM, Jung MH.
Identification of transcriptional regulators using Binding
Site Enrichment Analysis (BSEA).
In Silico Biol. 2006. 6:0049. PubMed
Chung YJ*, Kim TM*, Kim
DW, Namkoong H, Kim HK, Ha SA, Kim S, Shin SM, Kim
JH, Lee YJ, Kang HM, Kim JW. (*equally contributed)
Gene expression signatures associated with the resistance to imatinib.
Leukemia.
2006 Sep;20(9):1542-50. PubMed
Kim TM, Yim SH, Lee JS, Kwon MS, Ryu JW,
Kang HM, Fiegler H, Carter NP, Chung YJ.
Genome-wide screening of genomic alterations and their clinicopathologic
implications in non-small cell lung cancers.
Clin Cancer Res. 2005 Dec 1;11(23):8235-42. PubMed
Kim TM, Jung YC, Rhyu MG.
Alu and L1 retroelements
are correlated with the tissue extent and peak rate of gene expression,
respectively.
J Korean Med Sci. 2004 Dec;19(6):783-92. PubMed
Kim TM, Hong SJ, Rhyu MG.
Periodic explosive expansion of human retroelements
associated with the evolution of the hominoid primate.
J Korean Med Sci. 2004 Apr;19(2):177-85. PubMed
Biblography (Co-author)
Kim
YJ, Lee HJ, Eisinger-Mathason TSK, Kim TM, Zhang A, Karl D, Nakazawa M, Ryeom S, Park PJ,
Simon MC, Yoon S.
Metronomic doxorubicin blocks
HIF-1¥á-mediated responses in sarcomas and augments the effects of anti-VEGF-A
therapy (collaboration with Dr. Sam Yoon).
Hodge JC, Kim TM, Dreyfuss JM, Somasundaram
P, Christacos NC, Quade BJ,
Park PJ, Stewart EA, Morton CC
Expression Profiling of Uterine Leiomyomata Cytogenetic Subgroups Reveals Distinct
Signatures in Matched Myometrium: Transcriptional Profiling
of the t(12;14) and Evidence in Support of Predisposing Genetic Heterogeneity.
Hum Mol Genet 2012 Feb 17. [Epub ahead of print] Pubmed
Yang
HW, Kim TM, Song SS, Shrinath N, Park R, Kalamarides
M, Park PJ, Black PM, Carroll RS, Johnson MD
Alternative Splicing of CHEK2 and
Co-Deletion With NF2 Promote Chromosomal Instability in Meningioma.
Neoplasia 2012 Jan; 14(1):20-8 Pubmed
Xi
R, Hadjipanayis A, Luquette
LJ, Kim TM, Lee E, Zhang J, Johnson
MD, Muzny D, Wheeler D, Gibbs R, Kucherlapati
R, Park PJ
Copy number variation detection in
whole-genome sequencing data using the Bayesian information criterion.
Proc Natl Acad Sci U S A. 2011 Nov 7. Pubmed
Zacharek SJ, Fillmore
CM, Lau AN, Gludish DW, Chou A, Ho JW, Zamponi R, Gazit R, Bock C, Jäger N, Smith ZD, Kim
TM, Saunders AH, Wong J, Lee JH, Roach RR, Rossi DJ, Meissner
A, Gimelbrant AA, Park PJ, Kim CF
Lung stem cell self-renewal relies on
BMI1-dependent control of expression at imprinted loci.
Cell stem cell. 2011 Sep 2;9:272-281
Pubmed
Cancer
Genome Atlas Research Network
Integrated genomic analysis of ovarian
carcinoma.
Nature. 2011 Jun 29;474:609-615
Pubmed
Krishnamoorthy
A, Ajay AK, Hoffmann D, Kim TM,
Ramirez V, Campanholle G, Bobadilla NA, Waikar SS, Vaidya VS
Fibrinogen is upregulated
following kidney damage and protects it against ischemia-reperfusion injury.
Blood. 2011 Aug 18;118(7):1934-42.
Epub 2011 Jun 17. Pubmed
Xi R, Kim TM, Park PJ
Detecting structural variation using
next generation sequencing.
Brief Funct Genomics. 2010 Dec;9(5-6):405-15. Epub 2011 Jan 6. Pubmed
Yoon
SS, Duda DG, Karl DL, Kim TM, Kambadakone AR, Chen YL, Rothrock C, Rosenberg AE, Nielsen GP, Kirsch DG, Choy E,
Harmon DC, Hornicek FJ, Dreyfuss
J, Ancukiewicz M, Sahani
DV, Park PJ, Jain RK, DeLaney TF.
Phase II Study of Neoadjuvant
Bevacizumab and Radiation Therapy for Resectable Soft Tissue Sarcomas.
Int J Radiat Oncol Biol Phys. 2010 Oct 5. Pubmed
Lim SH, Kim HS, Kim YK, Kim TM, Im S, Chung ME, Hong BY, Ko YJ, Kim HW, Lee JI
The functional effect of epigallocatechin gallate on
ischemic stroke in rats.
Acta
Neurobiol Exp (Wars). 2010; 70(1):40-6. Pubmed
Chung
YS, Kim HJ, Kim TM, Hong SH, Kwon
KR, An S, Park JH, Lee S, Oh IH
Undifferentiated hematopoietic cells are
characterized by a genome-wide undermethylation dip
around the transcription start site and a hierarchical epigenetic plasticity.
Blood. 2009; 114(24):4968-78. Pubmed
Jeong YB, Kim
TM, Chung YJ
CGHscape: a software framework for the
detection and visualization of copy number alterations.
Genomics and Informatics. 2008; 6:126-9 Journal
Link
Cho
SC, Yim SH, Yoo HI, Kim MY,
Jung GY, Shin GW, Kim BN, Hwang JW, Kang JJ, Kim TM, Chung YJ.
Copy number variations associated with idiopathic autism identified by
whole-genome array-CGH.
Psychiatr Genet. 2009;19(4):177-85 PubMed
Kwon
MS, Shin SH, Yim SH, Lee KY, Kang HM, Kim TM,
Chung YJ.
CD63 as a biomarker for predicting the clinical outcomes in adenocarcinoma of lung.
Lung Cancer. 2007 Jul;57(1):46-53.
PubMed
Kim
MY, Yim SH, Kwon MS, Kim TM, Shin SH, Kang HM,
Lee C, Chung YJ.
Recurrent genomic alterations with impact on survival in
colorectal cancer identified by genome-wide array CGH.
Gastroenterology. 2006 Dec;131(6):1913-24.
PubMed
Kim HB, Kong M, Kim TM, Suh YH, Kim WH, Lim
JH, Song JH, Jung MH.
NFATc4 and ATF3 negatively regulate adiponectin
gene expression in 3T3-L1 adipocytes.
Diabetes. 2006 May;55(5):1342-52.
PubMed
Chung YJ, Park BB, Kang YJ, Kim TM, Eaves CJ, Oh IH.
Unique effects of STAT3 on the early phase of
hematopoietic stem cell regeneration.
Blood. 2006 Apr 15;108(4):1208-15.
PubMed