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Junho Kim, Ph.D.

  RESEARCH AREAS  

Genome analysis, Bioinformatics, NGS analysis method development

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  CONTACT INFORMATION  

Postdoctoral Researcher

Translational Genome Informatics Laboratory

Severance Biomedical Science Institute

Yonsei University College of Medicine

ABMRC #511, 50-1 Yonsei-ro, Seodaemun-gu,

Seoul 03722, South Korea.

Office: +82-2-2228-0914

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  EDUCATION  

  • Ph.D. in Bio and Brain Engineering, KAIST, Daejeon, August 2014 

Dissertation: "Identification of Somatic Deletions in Neuropsychiatric Diseases using Massively Parallel Sequence Data"

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  • M.S. in Bio and Brain Engineering, KAIST, Daejeon, August 2009

Thesis: “Pathway-based Genome-wide Association Study using functional SNP Effects”

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  • B.S. in Bio and Brain Engineering, KAIST, Daejeon, Korea, January 2008 

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  PUBLICATIONS  

JOURNAL (Peer Reviewed)

  1. Junho Kim, Ju Heon Maeng, Jae Seok Lim, Hyeonju Son, Junehawk Lee, Jeong Ho Lee and Sangwoo Kim, Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination, Bioinformatics 2016 (under revision)

  2. Junho Kim, Sanghyeon Kim, Hojung Nam, Sangwoo Kim and Doheon Lee, SoloDel: A probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data, Bioinformatics 2015, 31(19): 3105-3113

  3. Jae Seok Lim, Woo-il Kim, Hoon-Chul Kang, Se Hoon Kim, Ah Hyung Park, Eun Kyung 
    Park, Young-Wook Cho, Sangwoo Kim, Ho Min Kim, Jeong A Kim, Junho Kim, Hwanseok Rhee, Seok-Gu Kang, Heung Dong Kim, Daesoo Kim, Dong-Seok Kim & Jeong Ho Lee, Brain somatic mutations in MTOR cause focal cortical dysplasia type II leading to intractable epilepsy, Nature Medicine 2015, 21 395-400

  4. Junho Kim, Jong-Yeon Shin, Jong-Il Kim, Jeong-Sun Seo, Maree J. Webster, Doheon Lee and Sanghyeon Kim, Somatic deletions implicated in functional diversity of brain cells of individuals with schizophrenia and unaffected controls, Scientific reports 2014, 4:3807

  5. Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, 
    Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ,    Shen Y, NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A, A Community computational challenge to predict the activity of pairs of compounds, Nature Biotechnology 32, 1213–1222

  6. Yongdeuk Hwang, Junho Kim, Jong-Yeon Shin, Jong-Il Kim, Jeong-Sun Seo, Maree J. Webster, Doheon Lee and Sanghyeon Kim, Gene expression profiling by mRNA sequencing reveals increased expression of immune/inflammation-related genes in the hippocampus of individuals with schizophrenia, Translational psychiatry 2013, 3:e321

  7. Hyojung Paik, Junho Kim, Sunjae Lee, Hyoung-Sam Heo, Cheol-Goo Hur and Doheon Lee, Prioritization of SNPs for genome-wide association studies using an interaction model of genetic variation, gene expression, and trait variation, Molecules and cells 2012, 33(4):351-361

  8. Hyojung Paik, Eunjung Lee, Inho Park, Junho Kim, Doheon Lee, Prediction of cancer prognosis with the genetic basis of transcriptional variations, Genomics 2011, 97(6):350357

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International Conferences

  1. Junho Kim, Ju Heon Maeng, Jae Seok Lim, Hyeonju Son, Junehawk Lee, Jeong Ho Lee and Sangwoo Kim, Systematic identification of false somatic variants caused by vector contamination, Annual international conference on research in computational molecular biology (RECOMB 2016), Santa Monica, CA, USA, Apr. 17-21, 2016

  2. Junho Kim, Ju Heon Maeng, Jae Seok Lim, Hyeonju Son, Junehawk Lee, Jeong Ho Lee and Sangwoo Kim, Identification and filtration of false somatic variants caused by vector contamination, Cold Spring Harbor Genome Informatics workshop (CSHL Genome Informatics 2015), NY, USA, Oct. 28-31, 2015

  3. Junho Kim, Sanghyeon Kim, Hojung Nam, Sangwoo Kim and Doheon Lee, SoloDel: A probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data, International Conference on Genome Informatics (GIW/ISCB-Asia 2014), Tokyo, Japan, Dec. 15-17, 2014

  4. Junho Kim, Sanghyeon Kim and Doheon Lee, Discovering potential etiology for schizophrenia with somatic deletions, the 6th Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB 2012), Shenzhen, China, Dec. 20-21, 2012

  5. Junho Kim and Doheon Lee, A new perspective of integrative genome-wide association analysis considering trans-eSNP effect, IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010), Hong Kong, China, Dec. 18-21, 2010

  6. Junho Kim and Doheon Lee, Pathway-based genome-wide association study using functional SNP effects, CBI-KSBSB joint conference (BIOINFO 2009), Busan, Korea, Nov. 4-6, 2009

 

 

  PATENTS  

Doheon Lee, Sangwoo Kim and Junho Kim, Methods for identifying and filtering of false somatic variants caused by laboratory vector contamination, Application No.1020160020841 (Korea) (2016.02.22)

 

Doheon Lee and Junho Kim, Detecting method for low-frequent somatic deletions with unmatched samples, Application No.1020140162533 (Korea) (2014.11.20) 

 

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  ACADEMIC ACTIVITIES  

Committee Chair, 2012 6th Asian Young Researchers Conference on Computational and Omics Biology, Beijing Genomics Institute, Shenzhen, China 


Committee Member, 2011 5th Asian Young Researchers Conference on Computational and Omics Biology, University of Science and Technology, Daejeon, Korea 

 

 

  SKILLS  

Next Generation Sequencing (NGS) data analysis and method development 

  • Algorithmic development for NGS analysis 

- Structural variation detection algorithms 
- Computational modeling for probabilistic analysis 

 

  • Conventional analysis for NGS data

- Mapping tools (bwa, tophat, etc.), and read processing tools (GATK, samtools, picard, etc.) 
- CNV and SV analysis tools (CNVNator, BreakDancer, Pindel) 

 

  • Building standalone tools with novel algorithms 

- Building command-line interface using JOptSimple (Java) 
- Software packaging and distribution via open-source repositories (GitHub and SourceForge) 
- Java, Python and other programming languages 

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Last Update: June 2, 2016

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