プロフィール詳細

プロジェクトを作成

★★★★★

☆☆☆☆☆

★★★★★

☆☆☆☆☆

Dr. Ryangguk K.に依頼

United States

Bioinformatics consultant with +15 years of experience with genomic variant annotation pipelines

プロフィール概要

Creator of OakVar and OpenCRAVAT. Expert in Python and high performance programming in Rust, cloud computing, and web server development.

専門分野

• ☆ Computational Biology
• ☆ Biochemistry
• ☆ Structural Biology
• ☆ Molecular Biology
• ☆ Omics
• ☆ Genomics
• ☆ Next Generation Sequencing (NGS)
• ☆ Data Analysis
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Structural Bioinformatics
• ☆ Python
• ☆ SQL
• ☆ R
• ☆ Scikit-learn
• ☆ Software Development
• ☆ Web Application Development
• ☆ Cloud Application Development

サービス

• Consulting
• Data & AI

Consulting Scientific and Technical Consulting

Data & AI Data Visualization, Big Data Analytics

職務経験

CEO/Founder

Oak Bioinformatics, LLC

12月 2020 - 現在

Bioinformatics Scientist

Kiromic BioPharma, Inc

7月 2021 - 12月 2021

Bioinformatics specialist

In Silico Solutions, LLC

1月 2011 - 6月 2021

Postdoctoral Researcher

University of North Carolina at Charlotte

1月 2008 - 12月 2010

Postdoctoral Researcher

Georgia Institute of Technology

1月 2006 - 12月 2007

学歴

PhD in Biotechnology

Seoul National University

3月 1998 - 8月 2004

MS in Biotechnology

Seoul National University

3月 1996 - 2月 1998

認定資格

• 認定資格の詳細は未入力です。

出版物

JOURNAL ARTICLE

Ryangguk Kim, Efstathios-Iason Vlachavas, Konstantinos Voutetakis, Vivian Kosmidou, Spyridon Tsikalakis, Spyridon Roditis, Konstantinos Pateas, Kymberleigh Pagel, Stephan Wolf, Gregor Warsow, et al. (2025). Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer . Molecular Oncology.

Pagel KA, Kim R, Moad K, Busby B, Lily Zheng, Collin Tokheim, Ryan M, Karchin R (2020). Integrated Informatics Analysis of Cancer-Related Variants . JCO clinical cancer informatics.

Masica DL, Douville C, Collin Tokheim, Bhattacharya R, Kim R, Moad K, Ryan MC, Karchin R (2017). CRAVAT 4: Cancer-Related Analysis of Variants Toolkit . Cancer research.

Zhang Y, Liang Huang, Haiqing Fu, Smith OK, Lin CM, Koichi Utani, Mishal Rao, William Reinhold, Redon CE, Ryan M, et al. (2016). A replicator-specific binding protein essential for site-specific initiation of DNA replication in mammalian cells . Nature communications.

Smith OK, Kim R, Haiqing Fu, Martin MM, Lin CM, Koichi Utani, Zhang Y, Marks AB, Lalande M, Chamberlain S, et al. (2016). Distinct epigenetic features of differentiation-regulated replication origins . Epigenetics & chromatin.

Collin Tokheim, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R (2016). Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure . Cancer research.

Douville C, Masica DL, Stenson PD, David N. Cooper, Gygax DM, Kim R, Ryan M, Karchin R (2015). Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel) . Human mutation.

Haiqing Fu, Martin MM, Regairaz M, Liang Huang, You Y, Lin CM, Ryan M, Kim R, Shimura T, Pommier Y, et al. (2015). The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage . Nature communications.

Kim R, Smith OK, Wong WC, Ryan AM, Ryan MC, Aladjem MI (2015). ColoWeb: a resource for analysis of colocalization of genomic features . BMC genomics.

Niknafs N, Kim D, Kim R, Mark Diekhans, Ryan M, Stenson PD, David N. Cooper, Karchin R (2013). MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures . Human genetics.

Haiqing Fu, Maunakea AK, Martin MM, Liang Huang, Zhang Y, Ryan M, Kim R, Lin CM, Zhao K, Aladjem MI (2013). Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle . PLoS genetics.

Douville C, Carter H, Kim R, Niknafs N, Mark Diekhans, Stenson PD, David N. Cooper, Ryan M, Karchin R (2013). CRAVAT: cancer-related analysis of variants toolkit . Bioinformatics (Oxford, England).

Turner D, Kim R, Guo JT (2012). TFinDit: transcription factor-DNA interaction data depository . BMC bioinformatics.

Ryan MC, Cleland J, Kim R, Wong WC, John Weinstein (2012). SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts . Bioinformatics (Oxford, England).

Ryan MC, Cleland J, Kim R, Wong WC, John Weinstein (2012). SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts . Bioinformatics (Oxford, England).

Kim R, Corona RI, Hong B, Guo JT (2011). Benchmarks for flexible and rigid transcription factor-DNA docking . BMC structural biology.

Martin MM, Ryan M, Kim R, Anna Zakas, Haiqing Fu, Lin CM, William Reinhold, Sean Davis, Bilke S, Liu H, et al. (2011). Genome-wide depletion of replication initiation events in highly transcribed regions . Genome research.

Kim R, Guo JT (2010). Systematic analysis of short internal indels and their impact on protein folding . BMC structural biology.

Kim R, Guo JT (2009). PDA: an automatic and comprehensive analysis program for protein-DNA complex structures . BMC genomics.

Kim R, Skolnick J (2008). Assessment of programs for ligand binding affinity prediction . Journal of computational chemistry.

PREPRINT

Ryangguk Kim, Kulaga Anton, Borysova Olga, Karmazin Alexey, Koval Maria, Usanov Nikolay, Fedorova Alina, Evfratov Sergey, Pushkareva Malvina, Tacutu Robi(2024). Just-DNA-Seq, open-source personal genomics platform: longevity science for everyone . arXiv

Kymberleigh A Pagel, Rick Kim, Kyle Moad, Ben Busby, Lily Zheng, Matthew Hynes-Grace, Collin Tokheim, Michael Ryan, Rachel Karchin (2019). OpenCRAVAT, an open source collaborative platform for the annotation of human genetic variation .

CONFERENCE PAPER

Ryangguk Kim, J. McCafferty, Jun-tao Guo (2009). A systematic study of homologous protein structures with insertions/deletions. Comput Syst Bioinformatics Conf.