일시:　2015년　3월　19일 목요일 오전　11시

　 　 　 　연사:　남 덕 우 교수님　(UNIST　생명과학과/수리과학과)

　 　 　 　장소:　서울대학교 25-1동 103호 국제회의실

Title:　Biclustering-based classification of condition-specific regulatory networks

Abstract:

Molecular regulators perform their functions by selecting target genes that are specific to a given cell condition. Here, we devised a novel approach for identifying condition-specific microRNA and transcription factor (TF) targets from a large collection of mRNA fold-change datasets. By biclustering the microRNA (or TF)-specific mRNA fold-change profiles followed by a progressive extension (PBE algorithm), subtle but coordinated changes in the target genes were successfully identified along with the corresponding cell conditions. PBE clearly outperformed existing biclustering algorithms in this task. The predicted targets and conditions were validated using publicly available datasets. By overlapping the resulting biclusters,　condition-specific　co-regulatory networks were constructed using a novel probability distribution. Two cancer networks were analyzed, in which many of the hubs and co-regulatory pairs are known to have important roles in cancer progression. Using this approach, we are going to classify tissue (or disease)-specific co-regulatory subnetworks.

Education

　 　 　 　 　~ 2002. 8. Ph.D. in Probability (Stochastic processes) from Dept. of Mathematical Sciences, KAIST: South Korea　

　 　 　 　 　Thesis: Optimal estimation and numerical methods for conditional diffusion processes (Advisor: Prof. Chang Sun Choi)

~ 1996. 2. B.S. Seoul National University (Mathematics Education)

Professional Experience

~ Present. Assistant Professor, School of Life Sciences, UNIST

　 　 　 　 　~ 2010. 2. Senior Researcher (Principal Investigator), National Institute for 　 　 　 Mathematical Sciences

　 　 　 　 　~ 2007. 1. Post doc./ Senior Researcher, National Genome Information Center (Currently, KOBIC), Korea Research Institute of Bioscience and Biotechnology

Selected Publications

- Bioinformatics

Dougu Nam+, Jin Kim+,Seon-YoungKimandSangsooKim*,GSA-SNP: a general approach for gene set analysis of polymorphisms,　Nucleic Acids Research, 2010 web server issue (2010)　(IF 8.278, Citation: 45 times)

Dougu Nam*, De-correlating expression in gene-set analysis,　Bioinformatics,　26　ECCB 2010 issue, i511–i516　(2010)　(IF 5.323, Citation: 5 times)

Sang-Mun Chi, Jin Kim, Seon-Young Kim* and *,ADGO2.0:Interpretingmicroarraydataandlistofgenesusingcompositeannotations,,2011webserverissue,W302-W306(2011)(IF 8.278, Citation: 4 times)

Sang-Mun Chi* and *,WegoLoc:accuratepredictionofproteinsubcellularlocalizationsusingweightedGeneOntologyInformation,Bioinformatics,　28(7):1028-30　(2012)　(IF 5.323, Citation: 11 times)

Siseon Lee, ,JoonYoungJung,Min-KyuOh,Byoung-InSang*,RobertJ.Mitchell*,IdentificationofEscherichia colibiomarkers responsive to various lignin-hydrolysate compounds,　Bioresource Technology,　114:450-6　(2012) (IF 4.750, Citation: 4 times)

Ji-sun Kwon, Jihye Kim, ,andSangsooKim*,PerformanceComparisonofTwoGeneSetAnalysisMethodsforGenome-wideAssociationStudyResults:GSA-SNPvsi-GSEA4GWAS,,10:123-127(2012)(Domestic, Citation: 3 times)

Vinuselvi Parisutham, Sang-Kyu Jung, ,andSungKuKLee*,Transcriptome-drivensyntheticre-modelingofEscherichiacolitoenhancecellobioseutilization,,103:50-57(2013)(IF 2.386)

Mohammed Dwidar,　Dougu Nam*, Robert J. Mitchell*, Indole negatively impacts predation by and its release from the bdelloplast,　Environmental Microbiology,　published online: 28 APR (2014) (IF 5.756)

Sang-Mun Chi, Young-Kyo Seo, Young-Kyu Park,　Sora Yoon, Chan Young Park, Yong Sung Kim, Seon-Young Kim*,　Dougu Nam*, REGNET: Mining context-specific human transcription networks using composite genomic information,　BMC Genomics,　15:450-459 (2014).

YR Yang, H-J Jang,　S Yoon, YH Lee,　D Nam, IS Kim, H Lee, H Kim, JH Choi, BH Kang, SH Ryu and P-G Suh, OGA heterozygosity suppresses intestinal tumorigenesis in Apcmin/þ mice,　Oncogenesis, 3: e109 (2014)

Dougu Nam*, Effect of the absolute statistic on gene-sampling gene-set analysis methods,　Statistical Methods in Medical Research, accepted.　(IF 2.957, 4%, Statistics & Probability)

- Probability and Stochastic Processes

Hyung Geun Kim and　Dougu Nam*, Optimal estimation of diffusion processes hidden by general obstacles,　Journal of applied probability,　38, 1067-1073 (2001) (IF 0.553)

Changsun Choi and　Dougu Nam*,　Some boundary crossing results for linear diffusion processes,　Statistics and probability letters,　62, 281-291 (2003) (IF 0.531)

Changsun Choi and　Dougu Nam*,　Interpolation for partly hidden diffusion processes,　Stochastic processes and their applications,　113, 199-216 (2004) (IF 0.953)

Dougu Nam*,　On exact convergence rate of strong numerical schemes for stochastic differential equations,　Bull. Korean Mathematical Society　,　44. 125-130 (2007) (IF 0.388)