Publications - Kim lab at McGill U

After starting the Kim lab in October 2021

Publications

Bold indicates Kim lab members; *, Co-first authors; #, Co-corresponding authors

1. Jo KB*, Alruwaili MM*, Kim DE*, Koh Y*, Kim H*, You K, Kim JS, Sane S, Guo Y, Wright JP, Naranjo MN, Coté AG, Roth FP, Hill DE, Choi JH, Lee H, Matreyek KA, Farh KKH, Park JE#, Kim H#, Bakin AV#, Kim DK#. BOGO: a proteome-wide gene overexpression platform for discovering rational cancer combination therapies. Nature Biotechnology. 2026. Under revision. BioRxiv. 2025 Sep 2;673780. (Direct link)

2. Yun S*, Kim S*, Kim S*, Kim DK, Lee EJ#, Lee H#. Parallel Genome-wide CRISPR Screens Reveal SORL1 and ZFYVE19 as Sequential Host Determinants of Salmonella Infection. Advanced Science. 2025 Nov 23:e15042. (PMID: 41276924)

3. Kim S, Woo Y, Um D, Chun I, Noh SJ, Ji HA, Jung N, Goo BS, Yoo JY, Mun DJ, Nghi TD, Nhung TTM, Han SH, Lee SB, Lee W, Yun J, So KH, Kim DK, Jang H, Suh Y, Rah JC, Baek ST, Yoon KJ, Kim MS, Kim TK, and Park SK. Perturbed cell fate decision by schizophrenia-associated AS3MTd2d3 isoform during corticogenesis. Science Advances. 2025 Mar 28;11(13):eadp8271. (PMID: 40153497, PMCID: PMC11952104)

4. Maseko SB, Puttemans J, Bramerloo Y, Blibek K, Blavier J, Ntombela T, Van Molle I, Joseph J, Olivet J, Saha D, Degey M, Hamaidia M, Jain PJ, Geraldine P, Zimmermann P, Kim DK, Baiwir D, Willems L, Njock MS, Dequiedt F, Salehi-Ashtiani K, Ballet S, Volkov AN, Twizere JC. Inhibitors of Tax1‐PDZ interactions block HTLV‐1 viral transmission by changing EV composition. Journal of Extracellular Vesicles. 2025 Aug;14(8):e70137 (PMID: 40767036). BioRxiv. 2021. 457680. (Direct link)

5. Billmann M*, Costanzo M*, Zhang X*, Hassan AZ*, Rahman M*, Brown KR*, Chan KS, Tong AHY, Pons C, Ward HN, Ross C, van Leeuwen J, Aregger M, Lawson KA, Mair B, Roth AF, Sen NE, Forster D, Tan G, Mero P, Masud SN, Lee Y, Aguilera-Uribe M, Usaj M, Almeida SMT, Aulakh K, Bhojoo U, Birkadze S, Budijono N, Cai X, Caumanns JJ, Chandrashekhar M, Chang D, Climie R, Dasgupta K, Drazic A, Echenique JIR, Gacesa R, Farias AG, Habsid A, Horecka I, Kantautas K, Ji F, Kim DK, Lee SY, Liang W, Lim J, Lin K, Lu X, Nami B, Nixon A, Mikolajewicz N, Nedyalkova L, Rohde T, Rodrigues MS, Soste M, Schultz E, Wang W, Seetharaman A, Shuteriqi E, Sizova O, Taylor DT, Tereshchenko M, Tieu D, Turowec J, Ubhi T, Varland S, Wang KE, Wang ZY, Wei J, Xiao YX, Brown GW, Cravatt BF, Dixon SJ, Wyatt HDM, Röst HL, Roth FP, Xia T, Bader GD, Loewith R, Davis NG, Andrews B#, Myers C#, Moffat J#, Boone C#. A global genetic interaction map of a human cell reveals conserved principles of genetic networks. Cell. 2025. Under revision. BioRxiv. 2025. 662193 (Direct link)

6. Sim J, Lim S, Lee C, Kim HJ, Lee W, Kim H, Lee H, Kim K, Teli MK, Jo KB, Wright J, Noh M, Kim DK, Kim MH, Choi DW, Choi TS, Lee H, Yoon H. Oxygen-dependent phase separation is associated with mitochondrial import of PHD3 and regulation of cancer metabolism via PC hydroxylation. Experimental & Molecular Medicine. 2025. Under revision.

7. Ng D, Kazazian K, Lee K, Lu Y, Ali A, Pacholczyk K, Brar S, Connor J, Jurisica I, McCulloch C, Kim DK, Swallow C, and Magalhaes M. Transcriptomic profiling of a novel gastric implantation model identifies mechanisms and pathways that drive implantation into explanted human peritoneum. Cancer Gene Therapy. 2025. Under revision. BioRxiv. 2025. 648628 (Direct link)

8. Lambourne L*, Yadav A*, Wang Y*, Desbuleux A*, Kim DK, Cafarelli T, Pons C, Kovács IA, Jailkhani N, Schlabach S, Ridder DD, Luck K, Bian W, Shen Y, Mee M, Jacob Y, Lemmens I, Rolland T, Tavernier J, Spirohn K, Zhong Q, Aloy P, Hao T, Charloteaux B, Roth FP#, Hill DE#, Calderwood MA#, Twizere JC#, Vidal M#. Experimental assessment of AI-based interactome mapping. Nature Communications. 2025. Under revision. BioRxiv. 2021. 435663. (Direct link)

9. Mount HO, Urbanus ML, Sheykhkarimli D, Cote AG, Laval F, Coppin G, Kishore N, Li R, Spirohn-Fitzgerald K, Petersen MO, Knapp JJ, Kim DK, Twizere JC, Calderwood MA, Vidal M, Roth FP, Ensminger AW. A comprehensive two-hybrid analysis to explore the L. pneumophila effector-effector interactome. mSystems. 2024 Nov 11:e0100424 (PMID: 39526800). BioRxiv. 2024.587239. (Direct link)

10. Yu J*, Sane S*, Kim JE*, Yun S*, Kim HJ, Jo KB, Wright JP, Khoshdoozmasouleh N, Lee K, Oh HT, Thiel K, Parvin A, Williams X, Hannon C, Lee H#, Kim DK#. Biogenesis and delivery of extracellular vesicles: harnessing the power of EVs for diagnostics and therapeutics. Frontiers in Molecular Biosciences. 2024 Jan 3:10:1330400. (Cited 63 times; PMID: 38234582; PMCID: PMC10791869)

11. Brière R, … , Kim DK, …, Emilie Joos. 2023 Canadian Surgery Forum: Sept. 20-23, 2023. Canadian Journal of Surgery. 2023 Dec 13;66(6 Suppl 1):S54-S136. (PMID: 38173057; PMCID: PMC10718225)

12. Kim Y, Kim Y, Lim HJ, Kim DK, Park JH, Oh CM. Integrative single-cell transcriptome analysis provides new insights into post-COVID-19 pulmonary fibrosis and potential therapeutic targets. Journal of Medical Virology. 2023 Nov;95(11):e29201. (PMID: 37966390)

13. Weller B, Lin CW, Pogoutse O, Sauer M, Rosa NM, Strobel A, Young V, Knapp J, Rayhan A, Falter C, Kim DK, Roth FR, Falter-Braun P. A resource of human coronavirus protein-coding sequences in a flexible, multi-purpose Gateway Entry clone collection. G3: Genes, Genomes, Genetics. 2023 Jun 2;13(7):jkad105. (PMID: 37267226)

14. Tang HW*, Spirohn K*, Hu Y, Hao T, Kovács IA, Gao Y, Binari R, Yang-Zhou D, Wan K, Bader JS, Balcha D, Bian W, Booth BW, Cote AG, de Rouck S, Desbuleux A, Kim DK, Knapp JJ, Lee WX, Lemmens I, Li C, Li M, Li R, Lim HJ, Luck K, Markey D, Pollis C, Rangarajan S, Rodiger J, Schlabach S, Shen Y, TeeKing B, Roth FP, Tavernier J, Calderwood MA, Celniker SE#, Vidal M#, Perrimon N#, Hill DE, Mohr SE#. Next-generation large-scale binary protein interaction network for Drosophila melanogaster. Nature Communications. 2023 Apr 15;14(1):2162. (PMID: 37061542; PMCID: PMC10105736). BioRxiv. 2022. 502359 (Direct link)

15. 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. 2023 Jan;41(1):140-149. Cover Story. (Cited 76 times; PMID: 36217029). BioRxiv. 2021. 433877. (Direct link)

16. Kim JE, Li B, Fei L, Miyake H, Ayar E, Kim DK, Sherman P, Rossant J, Guo G, Pierro A, Kim TH. Gut microbiota promotes stem cell differentiation through stromal niches in early postnatal development. Immunity. 2022 Dec 13;55(12):2300-2317.e6. (PMID: 36473468)

17. Choi D, Khan N, Montermini L, Tawil N, Meehan B, Kim DK, Roth FR, Divangahi M, Rak J. Quantitative proteomics and biological activity of extracellular vesicles engineered to express SARS-CoV-2 spike protein. Journal of Extracellular Biology. 2022 Oct;1(10):e58. (PMID: 36710959, PMCID: PMC9874654)

18. Kim KH, Oh Y, Liu J, Dababneh S, Xia Y, Kim RY, Kim DK, Ban K, Husain M, Hui CC, Backx P. Irx5 and transient outward K+ current (Ito) contribute to transmural contractile heterogeneities in the mouse ventricle. American Journal of Physiology: Heart and Circulatory Physiology. 2022 May 1;322(5):H725-H741. (PMID: 35245131)

19. 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. (Cited 26 times, PMID: 34660591, PMCID: PMC8517337)

Patents

1. Lee H, Kim H, Yu J, Kim DK, Kim JS, Jo KB, Sane S

Amplification method of the spacer region of sgRNA

l Application (Link): Republic of Korea (Aug 2025, 10-2025-0120971)

2. Bakin A, Kim DK, Lim HJ, Alruwaili M.

Methods for sequentially administering TAS-102 and BCL-2 inhibitor for cancer treatment.

l Invention disclosure: USA (2023, 63/501,310)

l Application (Link): PCT and USA (Nov 2024, PCT/US2024/028755)

In Preparation

1. Kim JS*, Jeong C*, Kim S*, Kim H*, Lee S, Jo KB, Ha SH, Sane S, Kim S, Wright JP, Jin B, Cote AG, Seo JH, Park G, Choi JH, Park JH, Roth FP, Hill D, Lee H, Matreyek KA, Kairs SN, Tsu BL, Kim S, Barnes CA, Shin JH, Durcan TM, Yoon KJ#, Kim DK#, Kim HJ#. Integrative Plasma Proteomics and Functional Genomics Reveal Key Biomarkers and Mechanisms in Parkinson's Disease.

2. Sane S*, Song C*, Kim H, Kim JS, Yun S, Jo KB, Yu J, Kim HJ, Tawil N, Cote AG, Choi JH, Park JH, Roth FP, Hill DE, Matreyek KA, Rak J, Lee H#, Kim DK#. Deciphering the biogenesis and uptake mechanisms of extracellular vesicles.

3. Kim SH*, Kim J*, …, Kim DK#, Yoon KJ#. Proteome-scale discovery of post-transplantation survival inducers for dopamine-positive neurons.

4. Park SA*, Park IG*, Kim JS*, Lee E*, Jeong SH, Yeo SY, Song JW, Ko J, Lee J, Park EJ, Kim EY, Kim DK#, Lee JM#. Targeting PRRX1 via UCH-L1/3 Inhibition Reprograms CAFs and Suppresses Tumor Growth.

5. Sheykhkarimli D, Kuang D, Zagari F, Haddad G, Rahan A, Kishore N, Cote AG, Knapp J, Li R, Skalic M, Mee M, Colabella C, Strobel A, Gebbia M, Kitaygorodsky J, Yachi N, Petsalaki E, Li S, Ho B, Torres N, Bader G, Petrovic U, Vidal M, Hill D, Kim DK#, Roth FR#. Environment-dependent binary protein interactome of a cell.

During the entire career of Dae-Kyum

Publications

Published (*, Co-first authors; #, Co-corresponding authors; bold, Kim lab members

A total of 66 publications, including 3 last/co-last and 11 first/co-first author papers)

– Kim lab homepage (https://kimlab.us)

– Google Scholar (Citations, 10165; h-index, 37; i10-index, 50) / NCBI BioSketch / Twitter / LinkedIn / Facebook

11. Brière R, … , Kim DK, …, Emilie Joos. 2023 Canadian Surgery Forum: Sept. 20-23, 2023. Canadian Journal of Surgery. 2023 Dec 13;66(6 Suppl 1):S54-S136. (PMID: 38173057; PMCID: PMC10718225)

------------------------------------- After I started my first independent position ------------------------------------------

20. Kerselidou D, Dohai BS, Nelson DR, Daakour S, De Cock N, Kim DK, Olivet J, El Assal DC, Jaiswal A, Saha D, Pain C, Matthijssens F, Lemaitre P, Herfs M, Chapuis J, Ghesquière B, Vertommen D, Kriechbaumer V, Knoops K, Lopez-Iglesias C, van Zandvoort M, Lambert JC, Hanson J, Desmet C, Thiry M, Lauersen KJ, Vidal M, Van Vlierberghe P, Dequiedt F, Salehi-Ashtiani K, Twizere JC. Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells. Science Advances. 2021 May 7;7(19):eabe8349. (PMID: 33962942, PMCID: PMC8104865) BioRxiv. 2020. 275925. (Direct link)

21. Kim NE, Kim DK, Song Y. SARS-CoV-2 nonstructural proteins 1 and 13 suppress caspase-1 and activation of the NLRP3 inflammasome. Microorganisms. 2021 Feb 26;9(3):494. (PMID: 33652815)

22. Oh Y, Yang S, Lu X, Jana S, Izaddoustdar F, Gao X, Debi R, Kim DK, Kim KH, Yang P, Kassiri X, Lakin R, Backx PH. Transcriptomic bioinformatic analyses of atria uncover involvement of pathways related to strain and post-translational modification of collagen in increased atrial fibrillation vulnerability in intensely exercised mice. Frontiers in Physiology. 2020 Dec 23:11:605671. (PMID: 33424629, PMCID: PMC7793719)

23. 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 69 times; PMID: 32763951) >5K clones were distributed so far. PrePrints. 2020 2020040009. (Direct link)

24. Luck K*, 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 1265 times; PMID: 32296183, PMCID: PMC7169983). BioRxiv. 2019 605451. (Direct link)

25. Choi DS*#, Go G*, Kim DK, Lee J, Park SM, Di Vizio D, Gho YS#. Quantitative proteomic analysis of trypsin-treated extracellular vesicles to identify the real-vesicular proteins. Journal of Extracellular Vesicles. 2020 Apr 30;9(1):1757209. (PMID: 32489530, PMCID: PMC7241501)

26. Laurent EMN, Sofianatos Y, Komarova A, Gimeno JP, Samavarchi-Tehrani P, Kim DK, Abdouni H, Duhamel M, Cassonnet P, Knapp JJ, Kuang D, Chawla A, Sheykhkarimli D, Rayhan A, Li R, Pogoutse O, Hill DE, Calderwood MA, Falter-Braun P, Aloy P, Stelzl U, Vidal M, Gingras AC, Pavlopoulos GA, Van Der Werf S, Fournier I, Roth FP, Salzet M, Demeret C, Jacob Y, Coyaud E. Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms. BioRxiv. 2020 272955. (Direct link)

27. Samavarchi-Tehrani P, Abdouni H, Knight JDR, Astori A, Samson R, Lin ZY, Kim DK, Knapp JJ, St-Germain J, Go CD, Larsen B, Cassonnet P, Demeret C, Jacob Y, Roth FP, Raught B and Gingras AC. A SARS-CoV-2 – host proximity interactome. BioRxiv. 2020 282103. (Direct link)

28. St-Germain JR, Astori A, Samavarchi-Tehrani P, Abdouni H, Macwan V, Kim DK, Knapp JJ, Roth FP, Gingras AC, Raught B. A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research. BioRxiv. 2020. 269175. (Direct link).

29. Yang F, Kim DK, Nakagawa H, Hayashi S, Imoto S, Stein L, Roth FP. Quantifying immune-based counterselection of somatic mutations. PLoS Genetics. 2019 Jul 25;15(7):e1008227. (PMID: 31344031, PMCID: PMC6657826)

30. Kovács IA, Luck K, Spirohn K, Wang Y, Pollis C, Schlabach S, Bian W, Kim DK, Kishore N, Hao T, Calderwood MA, Vidal M, Barabási AL. Network-based prediction of protein interactions. Nature Communications. 2019 Mar 18;10(1):1240. (PMID: 30886144, PMCID: PMC6423278)

31. Choi D, Montermini L, Kim DK, Meehan B, Roth FP, Rak J. The impact of oncogenic EGFRvIII on the proteome of extracellular vesicles released from glioblastoma cells. Molecular and Cellular Proteomics. 2018 Oct;17(10):1948-1964. (PMID: 30006486, PMCID: PMC6166673)

32. Chelakkot C*, Choi Y*, Kim DK, Park HT, Ghim J, Kwon Y, Jeon J, Kim MS, Jee YK, Gho YS, Kim YK#, Ryu SH#. Akkermansia muciniphila-derived extracellular vesicles influence gut permeability through regulation of tight junctions. Experimental & Molecular Medicine. 2018 Feb 23;50(2):e450. (PMID: 29472701, PMCID: PMC5903829)

33. Shelke GV*, Jagtap JC*, Kim DK, Shah RD, Das G, Shivayogi M, Pujari R, Shastry P. TNF-α and IFN-γ together up-regulates Par-4 expression and induce apoptosis in human neuroblastomas. Biomedicines. 2017 Dec 26;6(1). pii: E4. (PMID: 29278364, PMCID: PMC5874661)

34. Lee N, Kim DK, Han SH, Ryu HG, Park SJ, Kim KT#, Choi KY#. Comparative interactomes of VRK1 and VRK3 with their distinct roles in the cell cycle of liver cancer. Molecules and Cells. 2017 Sep 30;40(9):621-631. (PMID: 28927264, PMCID: PMC5638770)

35. Bin BH, Bhin J, Kim NH, Lee SH, Jung HS, Seo J, Kim DK, Hwang D, Fukada T, Lee AY, Lee TR#, Cho EG#. An Acrodermatitis enteropathica-associated Zn transporter, ZIP4, regulates human epidermal homeostasis. Journal of Investigative Dermatology. 2017 Apr;137(4):874-883. (PMID: 27940220)

36. Lässer C, Shelke GV, Yeri A, Kim DK, Crescitelli R, Raimondo S, Sjöstrand M, Gho YS, Jensen, KVK, Lötvall J. Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing. RNA Biology. 2017 Jan 2;14(1):58-72. (PMID: 27791479, PMCID: PMC5270547)

37. Lee N*, Park SJ*, Haddad G, Kim DK, Park SM, Park SK, Choi KY. Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation. Scientific Reports. 2016 Dec 15;6:39049. (PMID: 27976729, PMCID: PMC5157023)

38. Lee N, Ryu HG, Kwon JH, Kim DK, Kim SR, Wang HJ, Kim KT, Choi KY. SIRT6 depletion suppresses tumor growth by promoting cellular senescence induced by DNA damage in HCC. PLoS One. 2016 Nov 8;11(11):e0165835. (PMID: 27824900, PMCID: PMC5100879)

39. Bin BH, Kim DK, Kim NH, Choi EJ, Bhin J, Kim ST, Gho YS, Lee AY, Lee TR#, Cho EG#. Fibronectin-containing extracellular vesicles protect melanocytes against ultraviolet radiation-induced cytotoxicity. Journal of Investigative Dermatology. 2016 May;136(5);957-66. (PMID: 26854492)

40. Kim DK. Next-generation mediator of intercellular communication – extracellular vesicles. Convergence Research Review. 2015 Dec;1(9):4-31. (Direct link)

41. Oh K*, Kim SR*, Kim DK, Seo MW, Lee C, Lee HM, Oh JE, Choi EY, Lee DS#, Gho YS#, Park KS#. In vivo differentiation of therapeutic insulin-producing cells from bone marrow cells via extracellular vesicle-mimetic nanovesicles. ACS Nano. 2015 Dec 22;9(12):11718-27. (PMID: 26513554)

42. Choi Y, Kwon Y, Kim DK, Jeon J, Jang SC, Wang T, Ban M, Kim MH, Jeon SG, Kim MS, Choi CS, Jee YK, Gho YS, Ryu SH, Kim YK. Gut microbe-derived extracellular vesicles induce insulin resistance and thereby impair glucose metabolism in skeletal muscles. Scientific Reports. 2015 Oct 29;5:15878. (PMID: 26510393, PMCID: PMC4625370)

43. Lee J*, Kim SH*, Choi DS*, Lee JS, Kim DK, Go G, Park SM, Kim SH, Shin JH, Chang CL#, Gho YS#. Proteomic analysis of extracellular vesicles derived from Mycobacterium tuberculosis. Proteomics. 2015 Oct;15(19):3331-7. (PMID: 26201501)

44. Lunavat TR*, Cheng L*, Kim DK, Bhadury J, Lässer C, Sharples RA, López MD, Nilsson J, Gho YS, Hill AF, Lötvall J. Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells - evidence of unique microRNA cargos. RNA Biology. 2015 Aug 3;12(8):810-23. (PMID: 26176991, PMCID: PMC4615768)

45. Minciacchi VR*, You S*, Spinelli C, Morley S, Zandian M, Aspuria PJ, Cavallini L, Ciadiello C, Sobreiro MR, Morello M, Kharmate G, Jang SC, Kim DK, Hosseini-Beheshti E, Guns E, Gleave M, Gho YS, Mathivanan S, Yang W, Freeman MR, Di Vizio D. Large oncosomes contain distinct protein cargo and represent a separate functional class of tumor-derived extracellular vesicles. Oncotarget. 2015 May 10;6(13):11327-41. (PMID: 25857301, PMCID: PMC4484459)

46. Kim DK, Lee J, Simpson R, Lötvall J, Gho YS. EVpedia: A community web resource for prokaryotic and eukaryotic extracellular vesicles research. Seminars in Cellular and Developmental Biology. 2015 Apr;40:4-7. (Cited 131 times; PMID: 25704310)

47. 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 423 times; PMID: 25388151, PMCID: PMC4375401)

48. Jang SC*, Kim SR*, Yoon YJ, Park KS, Kim JH, Lee J, Kim OY, Choi EJ, Kim DK, Choi DS, Kim YK, Park J, Di Vizio D#, Gho YS#. In vivo kinetic biodistribution of nano-sized outer membrane vesicles derived from bacteria. Small. 2015 Jan;11(4):456-61. Inside cover. (PMID: 25196673)

49. Choi DS, Kim DK, Kim YK, Gho YS. Proteomics of extracellular vesicles: Exosomes and ectosomes. Mass Spectrometry Reviews. 2015 Jul;34(4):474-90. Cover story. (PMID: 24421117)

50. Yoon YJ, Kim DK, Yoon CM, Park J, Kim YK, Roh TY#, Gho YS#. Egr-1 activation by cancer-derived extracellular vesicles promotes endothelial cell migration via ERK1/2 and JNK signaling pathways. PLoS One. 2014 Dec 12;9(12):e115170. (PMID: 25502753, PMCID: PMC4264882)

51. Lee N*, Kim DK*, Kim ES, Park SJ, Kwon JH, Shin J, Park SM, Moon YH, Wang HJ, Gho YS, Choi KY. Comparative interactomes of SIRT6 and SIRT7: implication of functional links to aging. Proteomics. 2014 Jul;14(13-14):1610-22. Featured article (Cited 105 times; PMID: 24782448)

52. Choi EB, Hong SW, Kim DK, Jeon SG, Kim KR, Cho SH#, Gho YS, Jee YK, Kim YK#. Decreased diversity of nasal microbiota and their secreted extracellular vesicles in patients with chronic rhinosinusitis based on a metagenomic analysis. Allergy. 2014 Apr;69(4):517-26. (PMID: 24611950)

53. Jeong J, Park YU, Kim DK, Lee S, Kwak Y, Lee SA, Lee H, Suh YH, Gho YS, Hwang D, Park SK. Cdk5 phosphorylates dopamine D2 receptor and attenuates downstream signaling. PLoS One. 2013 Dec 31;8(12):e84482. (PMID: 24391960, PMCID: PMC3877277)

54. Kang CS, Ban M, Choi EJ, Moon HG, Jeon JS, Kim DK, Park SK, Jeon SG, Roh TY, Myung SJ, Gho YS#, Kim JG#, Kim YK#. Extracellular vesicles derived from gut microbiota, especially Akkermansia muciniphila, protect the progression of dextran sulfate sodium-induced colitis. PLoS One. 2013 Oct 24;8(10):e76520. (PMID: 24204633, PMCID: PMC3811976)

55. Lee J*, Lee EY*, Kim SH, Kim DK, Park KS, Kim KP, Kim YK, Roh TY#, Gho YS#. Staphylococcus aureus extracellular vesicles carry biologically active beta-lactamase. Antimicrobial Agents and Chemotherapy. 2013 Jun;57(6):2589-95. F1000 Prime Recommendations, Introduced on MDLinx.com (PMID: 23529736, PMCID: PMC3716153)

56. Choi DS, Kim DK, Kim YK, Gho YS. Proteomics, transcriptomics, and lipidomics of exosomes and ectosomes. Proteomics. 2013 May;13(10-11):1554-71. (PMID: 23401200)

57. Kim DK*, Kang B*, Kim OY, Choi DS, Lee J, Kim SR, Go G, Yoon YJ, Kim JH, Jang SC, Park KS, Choi EJ, Kim KP, Desiderio DM, Kim YK, Lötvall J, Hwang D#, Gho YS#. EVpedia: an integrated database of high-throughput data for systemic analyses of extracellular vesicles. Journal of Extracellular Vesicles. 2013 Mar 19;2:20384. (Cited 614 times; PMID: 24009897, PMCID: PMC3760654)

58. Choi DS, Choi DY, Hong BS, Jang SC, Kim DK, Lee J, Kim YK, Kim KP#, Gho YS#. Quantitative proteomics of extracellular vesicles derived from human primary and metastatic colorectal cancer cells. Journal of Extracellular Vesicles. 2012 Sep 11;1:18704. (PMID: 24009881, PMCID: PMC3760640)

59. Yoon JH, Song P, Jang JH, Kim DK, Choi S, Kim J, Ghim J, Kim D, Park S, Lee H, Kwak D, Yea K, Hwang D, Suh PG, Ryu SH. Proteomic analysis of TNF-α-induced L6 myotube secretome reveals novel TNF-α-dependent myokines in diabetic skeletal muscle. Journal of Proteome Research. 2011 Dec 2;10(12):5315-25. (PMID: 22023146)

60. Yang JS*, Kim DK*, Kim J, Kim S. Global sequence homology detection using word conservation probability. Interdisciplinary Bio Central. 2011 Oct 19;3(14):1-9. (Direct link)

61. Lim S, Kim KR, Choi YS, Kim DK, Hwang D, Cha HJ. In vivo post-translational modifications of recombinant mussel adhesive protein in insect cells. Biotechnology Progress. 2011 Sep-Oct;27(5):1390-6. (PMID: 21732552)

62. Choi DS*, Kim DK*, Choi SJ*, Lee J, Choi JP, Rho S, Park SH, Kim YK, Hwang D#, Gho YS#. Proteomic analysis of outer membrane vesicles derived from Pseudomonas aeruginosa. Proteomics. 2011 Aug;11(16):3424-9. (Cited 283 times; PMID: 21751344)

63. Kim DK, Gho YS, Hwang D. Proteomic analysis of bacteria-derived extracellular vesicles. KOGO News. 2010 Jun;10(2):15-16. (Direct link)

64. Lee EY*, Choi DY*, Kim DK, Kim JW, Park JO, Kim S, Kim SH, Desiderio DM, Kim YK, Kim KP#, Gho YS#. Gram-positive bacteria produce membrane vesicles: proteomics-based characterization of Staphylococcus aureus-derived membrane vesicles. Proteomics. 2009 Dec;9(24):5425-36. (PMID: 19834908)

65. Jeon YB, Nam KH, Kim SL, Park YH, Kim KH, Kim JY, Kim DK, Jin KI, Kim SH. A new field δ scuti star: HD 235428. Publications of the Korean Astronomical Society, 2004;19:27-31. (Direct link)

66. Jeon YB, Nam KH, Kim SL, Park YH, Kim KH, Kim JY, Kim DK, Jin KI, Kim SH. A new field δ scuti star: GSC 03665-00576. Publications of the Korean Astronomical Society, 2004;19(1):33-37. (Direct link)

In Preparation

3. Kim SH*, Kim J*, …, Kim DK#, Yoon KJ#. Proteome-scale discovery of post-transplantation survival inducers for dopamine-positive neurons.

4. Park SA*, Park IG*, Kim JS*, Lee E*, Jeong SH, Yeo SY, Song JW, Ko J, Lee J, Park EJ, Kim EY, Kim DK#, Lee JM#. Targeting PRRX1 via UCH-L1/3 Inhibition Reprograms CAFs and Suppresses Tumor Growth.

Patents

1. Lee H, Kim H, Yu J, Kim DK, Kim JS, Jo KB, Sane S

Amplification method of the spacer region of sgRNA

l Application (Link): Republic of Korea (Aug 2025, 10-2025-0120971)

2. Bakin A, Kim DK, Lim HJ, Alruwaili M.

Methods for sequentially administering TAS-102 and BCL-2 inhibitor for cancer treatment.

l Invention disclosure: USA (2023, 63/501,310)

l Application (Link): PCT and USA (Nov 2024, PCT/US2024/028755)

--------------------------------------- After I started my first independent position ------------------------------------------------

3. Kim YK, Gho YS, Park KS, Hong BS, Kim JH, Kim YS, Lee WH, Kim JW, Kim DK.

Gut flora-derived extracellular vesicles, and method for searching for a disease model, vaccine, and candidate drug and for diagnosis using the same.

l Registration (Link): USA (2015, 9201072 / 2016, 9274109), Japan (2015, 102480932),

China (2014, 10-1350652), South Korea (2014, 10-1430283)

l Application: EU (2010, 2010-813880) / PCT (2010, PCT/KR2010/004747)