Dae-Kyum Kim

PhD

Specializing In:

Functional genomics and proteomics Drug resistance Protein-protein interaction Extracellular vesicle Stem cell differentiation

About Dae-Kyum Kim

Biography:

Visit my lab page to learn more about my research at Roswell Park: https://kimlab.us/

Throughout Dae-Kyum's career, Dae-Kyum has focused on the generation and integration of functional genomics data to propose novel hypotheses for experimental validation or new clinical biomarkers. During his undergraduate training, he developed an efficient sequence comparison method to classify proteins with respect to their structures (Interdisciplinary Bio Central. 2011 Oct 19;3(14):1-9.). During his Ph.D. training, he began to explore experimental research. He used well-established high-throughput screening methods such as mass spectrometry and RNA-seq to investigate the proteomic and transcriptomic components of extracellular vesicles (Proteomics. 2011 Aug;11(16):3424-9.) and further built a web-based database called EVpedia (Bioinformatics. 2015 Mar 15;31(6):933-9.). During his postdoctoral training, he explored protein-protein interactions systematically to understand various molecular mechanisms underlying human disease. He and his collaborators applied our next-generation sequencing-based yeast-two hybrid techniques to build the Human Reference Interactome (HuRI) that includes ~90% of all human protein-coding genes (Nature. 2020 Apr;580(7803):402-408.). Furthermore, they applied their new barcode sequencing-based yeast two-hybrid to find conditional interactions among yeast proteins in four different conditions to find the novel gain of interactions and further identified protein-protein interactions between SARS-CoV-2 and host proteins (Nature Biotechnology (2022). https://doi.org/10.1038/s41587-022-01475-z / G3: Genes, Genomes, Genetics. 2020 Sep 2;10(9):3399-3402).

Going through these transitions between various fields, Dae-Kyum gained strong expertise for both experimental and computational backgrounds, which enabled him to design a novel functional genomics pipeline to identify new biomarkers. Now, as a new principal investigator at Roswell Park since October 2021, he and his team would like to further pursue the translation of functional genomics tools to precision medicine, by exploring novel approaches to evaluate proteome-scale gene overexpression effects under various conditions to find novel drug combinations to combat chemotherapeutic resistance (https://kimlab.us/?page_id=278). The functional genomics approach always needs extensive teamwork spirit, for example, leading large teams as shown in EVpedia and HuRI projects, which included ~100 authors each. In addition, he also has efficient administrative skills to ensure tasks are completed in a timely fashion, as proven in SARS-CoV-2 projects conducted during the pandemic, which is an important virtue for the starting PI. Further, displaying his aptitude as a principal investigator, his first lab member (Hyobin Julianne Lim) and he have already published their first paper from Kim lab about an approach to integrate hundreds of extracellular vesicles proteomics data (Frontiers in Cell and Developmental Biology. 2021 Oct 1;9:734950.). Dae-Kyum strongly believes this expertise and qualification will lead this project successfully at Roswell Park, and find novel targets for proactive therapy and diagnosis of cancer via a new functional genomics approach.

Positions

Roswell Park Comprehensive Cancer Center

  • Assistant Professor of Oncology
  • Department of Cancer Genetics and Genomics

Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo

  • Assistant Professor

Background

Education and Training:

  • 2009-2015 - PhD - Systems biology, Pohang University of Science and Technology, Pohang, South Korea
  • 2006-2009 - BSc - Pohang University of Science and Technology, Pohang, South Korea

Fellowship:

  • 2015-2021 - Post-doctoral Fellow - Systems biology, Donnelly Centre at the University of Toronto, Canada

Honors & Awards:

  • 2017-2019 - Banting Postdoctoral Fellowship
  • 2018-2019 - Next-generation NET Grant
  • 2017-2018 - Korean Postdoctoral Fellowship for Training Abroad
  • 2010-2015 - National Junior Research Fellowship
  • 2009-2011 - Cheong-am Graduate Fellowship
  • 2006-2009 - Samsung SDI Scholarship for Undergraduate Students
  • 2006-2009 - National Research Foundation Fellowship for Young Scientists

Research

Research Overview:

We have a broad research interest in developing and utilizing novel functional genomics platforms to generate large-scale data to solve clinical problems, such as drug resistance in cancer chemotherapy. Our lab adapts three state-of-the-art tools to perform high-throughput overexpression perturbation screens to look for novel players in human disease: i) the ORFeome library (a proteome-wide collection of barcoded human genes), ii) Bxb1-landing pad system (genetic engineering system to express a single gene per cell) and iii) Barcode Fusion Genetics-Yeast Two-Hybrid (proteomics method that can screen millions of interactions at once). Our perturbation datasets will allow us to proactively find markers leading to malignancy, which will serve to help interpret patient genomes and transcriptomes.
Please check our lab website for more information (https://kimlab.us).

Dae-Kyum Kim
Hyobin Julianne Lim


Publications

Full Publications list on PubMed

Lim HJ*, Yoon H*, Kim H*, Kang YW, Kim JE, Kim OY, Lee EY, Twizere JC, Rak J#, Kim DK#. Extracellular vesicle proteomes shed light on the evolutionary, interactive, and functional divergence of their biogenesis mechanisms. Frontiers in Cell and Developmental Biology. 2021 Oct 1;9:734950. (PMID: 34660591, PMCID: PMC8517337)

Kim DK*, Weller B*, Lin CW*, Sheykhkarimli D*, Knapp JJ*, Kishore N, Sauer M, Rayhan A, Young V, Marin-de la Rosa N, Pogoutse O, Spirohn K, Strobel A, Laval F, Schwehn P, Li R, Rothballer S, Altmann M, Cassonnet P, Dugied G, Cote AG, Vergara LE, Hazelwood I, Liu BB, Nguyen M, Pandiarajan R, Coloma PAR, Willems L, Twizere JC, Demeret C, Jacob Y, Hao T, Hill DE, Falter C, Vidal M#, Calderwood MA#, Roth FP#, Falter-Braun P#. A proteome-scale map of the SARS-CoV-2–human contactome. Nature Biotechnology (2022). https://doi.org/10.1038/s41587-022-01475-z

Katja L*, Kim DK*, Lambourne L*, Spirohn K*, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie F, Charloteaux B, Choi D, Cote AG, Daley M, Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp J, Kovacs IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C, Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Chin SF, Choi SG, Colabella C, Coppin G, D'Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Gopal A, Haddad G, Helmy M, Jacob Y, Kassa Y, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson JN, Rangarajan S, Rasla J, Rayhan A, Rolland T, San Miguel A, Shen Y, Sheykhkarimli D, Sheynkman GM, Simonovsky E, Taşan M, Tejeda A, Twizere JC, Wang Y, Weatheritt R, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Tropepe V, Hill DE#, Vidal M#, Roth FP#, Calderwood MA#. A reference map of the human binary protein interactome. Nature. 2020 Apr;580(7803):402-408. (Cited 141 times; PMID: 32296183, PMCID: PMC7169983).

Kim DK*, Knapp JJ*, Kuang D*, Chawla A, Cassonnet P, Lee H, Sheykhkarimli D, Samavarchi-Tehrani P, Abdouni H, Rayhan A, Roujia Li, Pogoutse O, Coyaud É, van der Werf S, Demeret C, Gingras AC, Raught B, Jacob Y#, Roth FP#. A comprehensive, flexible collection of SARS-CoV-2 coding regions. G3: Genes, Genomes, Genetics. 2020 Sep 2;10(9):3399-3402. (Cited 18 times; PMID: 32763951)

Kim DK*, Lee J*, Kim SR, Choi DS, Yoon YJ, Kim JH, Go G, Nhung D, Hong K, Jang SC, Kim SH, Park KS, Kim OY, Park HT, Seo JH, Aikawa E, Baj-Krzyworzeka M, van Balkom BW, Belting M, Blanc L, Bond V, Bongiovanni A, Borràs FE, Buée L, Buzás EI, Cheng L, Clayton A, Cocucci E, Dela Cruz CS, Desiderio DM, Di Vizio D, Ekström K, Falcon-Perez JM, Gardiner C, Giebel B, Greening DW, Gross JC, Gupta D, Hendrix A, Hill AF, Hill MM, Nolte-'t Hoen E, Hwang DW, Inal J, Jagannadham MV, Jayachandran M, Jee YK, Jørgensen M, Kim KP, Kim YK, Kislinger T, Lässer C, Lee DS, Lee H, van Leeuwen J, Lener T, Liu ML, Lötvall J, Marcilla A, Mathivanan S, Möller A, Morhayim J, Mullier F, Nazarenko I, Nieuwland R, Nunes DN, Pang K, Park J, Patel T, Pocsfalvi G, Del Portillo H, Putz U, Ramirez MI, Rodrigues ML, Roh TY, Royo F, Sahoo S, Schiffelers R, Sharma S, Siljander P, Simpson RJ, Soekmadji C, Stahl P, Stensballe A, Stępień E, Tahara H, Trummer A, Valadi H, Vella LJ, Wai SN, Witwer K, Yáñez-Mó M, Youn H, Zeidler R, Gho YS. EVpedia: A community web portal for extracellular vesicles research. Bioinformatics. 2015 Mar 15;31(6):933-9. (Cited 274 times; PMID: 25388151, PMCID: PMC4375401)