Publication

Structural proteomics reveals a coagulation–complement accessibility signature of macrovascular invasion in hepatocellular carcinoma

Ahrum Son#, Moon Haeng Hur#, Eun Ju Cho, Jaeho Ji, Eunjeong Han, Yunho Choi, Jumin Park, Heejin Lee, Sujin Park, Su Jong Yu*, Hyunsoo Kim*

bioRxiv, In Submitted

Keywords: Hepatocellular carcinoma; Macrovascular invasion; Structural proteomics; Complement and coagulation; Serum biomarkers

A targeted plasma-proteomic axis separates autoimmune thyroid disease from growth-hormone deficiency

Eunjeong Han#, Jaeho Ji#, Yunho Choi, Jumin Park, Heejin Lee, Sujin Park, Ahrum Son, Sukdong Yoo, Chong Kun Cheon*, Hyunsoo Kim*

bioRxiv, In Submitted

Keywords: Aging; Targeted proteomics; Plasma biomarkers; Autoimmune thyroid disease; Growth-hormone deficiency; Machine-learning classification

Age-dependent Structural Reorganization of the Human Plasma Proteome

Jaeho Ji#, Yeonhee Kim#, Eunjeong Han, Yunho Choi, Jumin Park, Heejin Lee, Sujin Park, Ahrum Son*, Hyunsoo Kim*

bioRxiv, In Submitted

Keywords: Aging; Plasma Proteome; Structural Proteomics; Covalent Protein Painting; Protein–Protein Interaction

Sex and race shape serum protein biomarkers and bias diagnostic reference intervals

Ahrum Son#,*, Jaeho Ji, Eunjeong Han, Yunho Choi, Jumin Park, Heejin Lee, Sujin Park, Hyunsoo Kim*

bioRxiv, In Submitted

Keywords: Targeted mass spectrometry; Reference intervals; Sex differences; Genetic ancestry; Protein biomarkers

A targeted mass-spectrometry plasma proteome for simultaneous multi-disease screening

Ahrum Son#,*, Jaeho Ji, Eunjeong Han, Yunho Choi, Jumin Park, Heejin Lee, Sujin Park, Hyunsoo Kim*

bioRxiv, In Submitted

Keywords: Plasma proteomics, Targeted mass spectrometry, Multi-disease screening, Protein biomarkers, Machine-learning classification

Proteomic Signatures of Hepatitis B Virus Mutations Reveal Genotype-Specific Host Responses and Biomarker Candidates

Ahrum Son#, Eun Ju Cho#, Jaeho Ji, Ziyun Kim, Su Jong Yu*, Bum-Joon Kim*, Hyunsoo Kim*

bioRxiv, In Submitted

Keywords: Hepatitis B Virus, Serum proteome, Machine learning, Genotype

Biomarker Discovery via Integrative Multi-omics for Children exposed to Humidifier Disinfectant

Jaeho ji#, Ahrum Son, Mi-Jin Kang, Jeonghun Yeom, Hyun Ju Yoo, Kwoneel Kim, Jeong-Hyun Kim, Hea Young Oh, Shin Ah Kim, So-Yeon Lee, Seung-Hwa Lee, Soo-Jong Hong*, Hyunsoo Kim*

bioRxiv, In Submitted

Keywords: Humidifier disinfectant; Multi-omics; Multi-marker panel; Integrin-related signaling; Chronic respiratory conditions

Integrated NanoLC and UPLC-MS Platforms for Single Cell and Complex Mixture Analysis

Jaeho ji#, Eunjeong Han, Kyuhan Kwon, Woojin Kim, Ahrum Son*, Hyunsoo Kim*

ChemRxiv, In Submitted

Keywords: Targeted mass spectrometry; Multiple reaction monitoring; Integrated nanoLC-UPLC platform; Multiple heart-cutting 2D-LC

In Silico Design of APOE ɛ4 Interaction Inhibitor Peptides for Alzheimer's Disease

Jaeho ji#, Eunjeong Han, Jongham Park, Ahrum Son*, Hyunsoo Kim*

bioRxiv, In Submitted

Keywords: Alzheimer's Disease, APOE ε4, Protein-Protein Interaction, Peptide Design

Integrative Analysis of Proteomics and Metabolomics Reveals Impacts of Sam2 Knockout on Autism Spectrum Disorders

Jaeho Ji#, Cheol Soo Choi, Cheol-Hee Kim, Ahrum Son*, Hyunsoo Kim*

bioRxiv, In Submitted

Essential Resources for Curated Immune Markers and Antibody Panels in Cytometry Analysis

Seongyun Choi#, Jaeho Ji#, Eunjeong Han, Ahrum Son*, Hyunsoo Kim*

Scientific Reports (ISSN: 2045-2322) (IF=4.9, Rank=15.0%) (07/27/2026)

bioRxiv: https://www.biorxiv.org/content/10.1101/2025.10.13.682059v1

Keywords: Immune cell markers, Antibody panels, Flow cytometry, Mass cytometry, Single-cell analysis, Immunophenotyping 

Biobank innovation consortium for mental, intellectual and neurodevelopmental disorders study: BICMINDS

Sungjin Kim#, Cheol-Hee Kim, Kyung‑Seok Han, Nam-Shik Kim, Hyunsoo Kim, Kyu-Sun Lee, Han Hyuk Lim, Eunhee Kim, Jon Soo Kim, Hyewon Woo, Jay Chol Choi, Hoon-Chul Kang, Chong Kun Cheon, and Yoo-Mi Kim*

Journal of Genetic Medicine (ISSN 2383-8442 ) (06/30/2026)

Structural Signature of Plasma Proteins Classifies the Status of Alzheimer’s Disease

Ahrum Son#, Hyunsoo Kim, Jolene K. Diedrich, Casimir Bamberger, Heather M. Wilkins, Jeffrey M. Burns, Jill K. Morris, Robert A. Rissman, Russell H. Swerdlow, John R. Yates III*

Nature Aging (EISSN: 2662-8465) (IF=25.0, Rank=0.61%) (02/26/2026)

Featured by NIH News:

https://www.nih.gov/news-events/news-releases/study-measuring-changes-protein-structure-establishes-new-class-alzheimers-biomarkers

Featured by Scripps Research News and Events:

https://www.scripps.edu/news-and-events/press-room/2026/20260309-yates-alzheimers.html

BRIC 한빛사:

https://www.ibric.org/bric/hanbitsa/han-interview.do?mode=view&id=100680&authorId=33852#!/list

Expert Perspectives on Enhancing Analytical Methods for Multi-Ingredient Dietary Supplements (MIDS): A Qualitative Study

Ingyeong Ko#, Hae Jin Park, Hyunsoo Kim, Kwang Suk Ko, Jieun Oh*

Foods (EISSN: 2304-8158) (IF=5.1, Rank=23.2%) (10/22/2025)

Elucidating Interactome Dynamics of the A2A Adenosine Receptor

Wonseok Lee#, Ahrum Son#, Jaeho Ji, Eunjeong Han, Ja-Young Cho, Ju-Won Kim, Young-Ok Kim, Hee Jeong Kong*, Hyunsoo Kim*

Journal of Proteome Research (ISSN: 1535-3893) (IF=3.8, Rank=17.6%) (07/09/2025)

bioRxiv: https://www.biorxiv.org/content/10.1101/2024.07.08.601789v1

The sV184A variant in HBsAg specific to HBV subgenotype C2 leads to enhanced viral replication and apoptotic cell death induced by PERK-eIF2α-CHOP-mediated ER stress

Yu-Min Choi#, Dong Hyun Kim#, Eun Ju Cho#, Ziyun Kim, Junghwa Jang, Hyunsoo Kim, Su Jong Yu*, Bum-Joon Kim*

Journal of Medical Virology (ISSN: 0146-9071) (IF=6.8, Rank=9.8%) (02/20/2025)

Dual-Cys Bacteriophytochromes: Intermediates in Cyanobacterial Phytochrome Evolution?

Hee Wook Yang#, Ji-Young Song, Ji-Joon Song, Young Won Kim, Nathan C Rockwell, Woojin Kim, Hyunsoo Kim, J Clark Lagarias, Youn-Il Park*

FEBS Journal (ISSN: 1742-464X) (IF=5.5, Rank=18.5%) (01/13/2025)

Recent Advances in Omics, Computational Models, and Advanced Screening Methods for Drug Safety and Efficacy

Ahrum Son#, Jongham Park, Woojin Kim, Yoonki Yoon, Sangwoon Lee, Jaeho Ji, Hyunsoo Kim*

Toxins (EISSN: 2072-6651), 12 (11), 822 (IF=3.9, Rank=21.7%) (11/14/2024)

Using In Vivo Intact Structure for System-wide Quantitative Analysis of Changes in Proteins

Ahrum Son#, Hyunsoo Kim, Jolene K. Diedrich, Casimir Bamberger, Daniel B. McClatchy, Stuart A. Lipton, John R. Yates III*

Nature Communications (EISSN: 2041-1723), 15, 9310 (IF=14.7, Rank=6.0%) (10/29/2024)

BRIC 한빛사:

https://www.ibric.org/bric/hanbitsa/treatise.do?mode=treatise-view&id=95091&authorId=33852#!/list

Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence

Ahrum Son#, Jongham Park, Woojin Kim, Yoonki Yoon, Sangwoon Lee, Yongho Park, Hyunsoo Kim*

Molecules (EISSN: 1420-3049), 29(19), 4626 (IF=4.2, Rank=28.1%) (09/29/2024)

Mass Spectrometry Advancements and Applications for Biomarker Discovery, Diagnostic Innovations, and Personalized Medicine

Ahrum Son#, Woojin Kim, Jongham Park, Yongho Park, Wonseok Lee, Sangwoon Lee, Hyunsoo Kim*

International Journal of Molecular Sciences (ISSN: 1661-6596), 25(18), 9880 (IF=4.9, Rank=21.1%) (09/12/2024)

Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics

Ahrum Son#, Woojin Kim, Jongham Park, Wonseok Lee, Yerim Lee, Seongyun Choi, Hyunsoo Kim*

International Journal of Molecular Sciences (ISSN: 1661-6596), 25(17), 9725 (IF=4.9, Rank=21.1%) (09/08/2024)

Social Media Channels:  X, LinkedIn, Facebook

Integrating Computational Design and Experimental Approaches for Next-Generation Biologics

Ahrum Son#, Jongham Park, Woojin Kim, Wonseok Lee, Yoonki Yoon, Jaeho Ji, Hyunsoo Kim*

Biomolecules (EISSN: 2218-273X), 14(9), 1073 (IF=4.8, Rank=21.4%) (08/27/2024)

Applicability of Selected Reaction Monitoring for Precise Screening Tests

Ahrum Son#, Woojin Kim, Wonseok Lee, Jongham Park, Hyunsoo Kim*

Expert Review of Proteomics (ISSN: 1478-9450), 21, 237-246 (IF=3.4, Rank=36.4%) (05/08/2024)

A protein–protein interaction analysis tool for targeted cross-linking mass spectrometry

Jongham Park#, Ahrum Son#, Hyunsoo Kim*

Scientific Reports (ISSN: 2045-2322), 13 (1), 22103 (IF=3.8, Rank=18.7%) (12/13/2023)

bioRxiv: https://www.biorxiv.org/content/10.1101/2023.04.04.535369v1

A circulating cell-free DNA methylation signature for the detection of hepatocellular carcinoma

Si-Cho Kim#, Da-Won Kim#, Eun Ju Cho#, Jin-Young Lee, Jiwon Kim, Chaesun Kwon, Jeongsil Kim-Ha, Suk Kyun Hong, YoungRok Choi, Nam-Joon Yi, Kwang-Woong Lee, Kyung-Suk Suh, Won Kim, Woojin Kim, Hyunsoo Kim, Yoon Jun Kim, Jung-Hwan Yoon, Su Jong Yu*, Young-Joon Kim*

Molecular Cancer (EISSN: 1476-4598), 22 (1), 164 (IF=27.7, Rank=1.4%) (10/06/2023)

Clinical application of multiple reaction monitoring-mass spectrometry to human epidermal growth factor receptor 2 measurements as a potential diagnostic tool for breast cancer therapy

Misol Do#, Hyunsoo Kim#, Injoon Yeo, Jihyeon Lee, In Ae Park, Han Suk Ryu, Youngsoo Kim*

Clinical Chemistry (ISSN: 0009-9147). 66 (10), 1339-1348 (IF=7.3, Rank=3.4%) (10/01/2020)

BRIC 한빛사:

https://www.ibric.org/bric/hanbitsa/treatise.do?mode=treatise-view&id=68179&authorId=33847#!/list

Preparation of Tissue Samples for Large-scale Quantitative Mass Spectrometric Analysis 

Yoseop Kim#, Injoon Yeo#, Hyunsoo Kim, Minsoo Son, Youngsoo Kim*

Biotechnology and Bioprocess Engineering (ISSN: 1226-8372). 25 (4), 551-561 (IF=2.2, Rank=59.6%) (07/22/2020)

Web portal for analytical validation of MRM-MS assay abided with integrative multinational guidelines

JaeNyeon Kim#, Injoon Yeo#, Hyunsoo Kim#, Areum Sohn, Yosub Kim, Youngsoo Kim*

Scientific Reports (ISSN: 2045-2322). 10 (1), 1-9 (IF=4.0, Rank=23.9%) (07/02/2020)

Proteome Multimarker Panel with Multiple Reaction Monitoring-Mass Spectrometry for Early Detection of Hepatocellular Carcinoma

Injoon Yeo#, Gi-Ae Kim#, Hyunsoo Kim#, Ji Hyeon Lee, Areum Sohn, Geum-Youn Gwak, Jeong-Hoon Lee, Young-Suk Lim*, Youngsoo Kim*

Hepatology Communications (ISSN: 2471-254X). 4 (5), 753-768 (03/13/2020)

Clinically Applicable Deep Learning Algorithm Using Quantitative Proteomics Data

Hyunsoo Kim#, Yoseop Kim#, Buhm Han, Jin-Young Jang, Youngsoo Kim*

Journal of Proteome Research (ISSN: 1535-3893). 18 (8), 3195-3202 (IF=4.1, Rank=15.6%) (07/17/2019)

Cost-Effective Automated Preparation of Serum Samples for Reproducible Quantitative Clinical Proteomics

Jihyeon Lee#, Hyunsoo Kim#, Areum Sohn, Injoon Yeo, Youngsoo Kim*

Journal of Proteome Research (ISSN: 1535-3893). 18 (5), 2337-2345 (IF=4.1, Rank=15.6%) (04/15/2019)

Method validation by CPTAC guidelines for multi-protein marker assays using multiple reaction monitoring-mass spectrometry

Minsoo Son#, Hyunsoo Kim#, Injoon Yeo, Yosub Kim, Areum Sohn, Youngsoo Kim*

Biotechnology and Bioprocess Engineering (ISSN: 1226-8372). 24 (2), 343-358 (IF=2.2, Rank=59.6%) (03/01/2019)

Analysis of significant protein abundance from multiple reaction-monitoring data

Jong su Jun#, Jungsoo Gim, Yongkang Kim, Hyunsoo Kim, Su Jong Yu, Injun Yeo, Jiyoung Park, Jeong-Ju Yoo, Young Youn Cho, Dong Hyeon Lee, Eun Ju Cho, Jeong-Hoon Lee, Yoon Jun Kim, Seungyeoun Lee, Jung-Hwan Yoon, Youngsoo Kim, Taesung Park*

BMC Systems Biology (ISSN: 1752-0509). 12 (9), 123 (IF=2.0, Rank=37.3%) (12/31/2018)

Clinical Assay for AFP-L3 by Using Multiple Reaction Monitoring-Mass Spectrometry for Diagnosing Hepatocellular Carcinoma

Hyunsoo Kim#, Areum Sohn#, Injun Yeo, Su Jong Yu, Jung-Hwan Yoon, Youngsoo Kim*

Clinical Chemistry (ISSN: 0009-9147). 64 (8), 1230-1238 (IF=6.9, Rank=3.4%) (08/01/2018)

BRIC 한빛사:

https://www.ibric.org/bric/hanbitsa/treatise.do?mode=treatise-view&id=68197&authorId=33847#!/list

Fully validated SRM-MS-based method for absolute quantification of PIVKA-II in human serum: Clinical applications for patients with HCC

Areum Sohn#, Hyunsoo Kim#, Injun Yeo, Yoseop Kim, Minsoo Son, Su Jong Yu, Jung-Hwan Yoon, Youngsoo Kim*

Journal of Pharmaceutical and Biomedical Analysis (ISSN: 0731-7085). 156, 142-146 (IF=3.0, Rank=28.6%) (07/15/2018)

Quantitative Proteomic Analysis of Pancreatic Cyst Fluid Proteins Associated with Malignancy in Intraductal Papillary Mucinous Neoplasms

Misol Do#, Dohyun Han#, Joseph Injae Wang, Hyunsoo Kim, Wooil Kwon, SungHyo Park, Youngmin Han, Jin-Young Jang*, Youngsoo Kim*

Clinical proteomics (ISSN: 1542-6416). 15 (1), 17 (IF=2.9, Rank=35.4%) (04/18/2018)

Diagnostic performance enhancement of pancreatic cancer using proteomic multimarker panel

Jiyoung Park#, Yonghwan Choi#, Junghyun Namkung, Sung Gon Yi, Hyunsoo Kim, Jiyoung Yu, Yongkang Kim, Min-Seok Kwon, Wooil Kwon, Do-Youn Oh, Sun-Whe Kim, Seung-Yong Jeong, Wonshik Han, Kyu Eun Lee, Jin Seok Heo, Joon Oh Park, Joo Kyung Park, Song Cheol Kim, Chang Moo Kang, Woo Jin Lee, Seungyeoun Lee, Sangjo Han, Taesung Park, Jin-Young Jang*, Youngsoo Kim*

Oncotarget (ISSN: 1949-2553). 8 (54), 93117-93130 (01/12/2018)

Recent advances in proteomic profiling of pancreatic ductal adenocarcinoma (PDAC) and the road ahead

Hyunsoo Kim#, Joonho Park#, Joseph I. Wang, Youngsoo Kim*

Expert Review of Proteomics (ISSN: 1478-9450). 14 (11), 963-971 (IF=3.5, Rank=30.8%) (11/02/2017)

Quantitative proteomics reveals temporal proteomic changes in signaling pathways during BV2 microglial cell activation

Jongmin Woo#, Dohyun Han#, Joseph Wang, Joonho Park, Hyunsoo Kim, Youngsoo Kim*

Journal of Proteome Research (ISSN: 1535-3893). 16 (9), 3419-3432 (IF=4.0, Rank=17.9%) (09/01/2017)

Serum fibronectin distinguishes the early stages of hepatocellular carcinoma

Hyunsoo Kim#, JiYoung Park#, Yongkang Kim#, A-Reum Sohn, Injun Yeo, Su Jong Yu, Jung-Hwan Yoon, Taesung Park*, Youngsoo Kim*

Scientific Reports (ISSN: 2045-2322). 7 (1), 9449 (IF=4.1, Rank=18.8%) (08/25/2017)

Prediction of Response to Sorafenib in Hepatocellular Carcinoma: A Marker Panel by Multiple Reaction Monitoring-Mass Spectrometry

Hyunsoo Kim#, Su Jong Yu#, Injun Yeo, Young Youn Cho, Dong Hyeon Lee, Yuri Cho, Eun Ju Cho, Jeong-Hoon Lee, Yoon Jun Kim, Sungyoung Lee, Jongsoo Jun, Taesung Park, Jung-Hwan Yoon*, Youngsoo Kim*

Molecular & Cellular Proteomics (ISSN: 1535-9476). 16 (7), 1312-1323 (IF=5.2, Rank=11.5%) (07/01/2017)

A quantitative analytical method for PIVKA-II using multiple reaction monitoring-mass spectrometry for early diagnosis of hepatocellular carcinoma

Areum Sohn#, Hyunsoo Kim# Su Jong Yu, Jung-Hwan Yoon, Youngsoo Kim*

Analytical and Bioanalytical Chemistry (ISSN: 1618-264). 409 (11), 2829-2838 (IF=3.3, Rank=19.8%) (04/01/2017)

Targeted proteomics predict a sustained complete-response after transarterial chemoembolization and clinical outcomes in patients with hepatocellular carcinoma: a prospective cohort study

Su Jong Yu#, Hyunsoo Kim#, Hophil Min, Areum Sohn, Young Youn Cho, Jeong-Ju Yoo, Dong Hyeon Lee, Eun Ju Cho, Jeong-Hoon Lee, Jungsoo Gim, Taesung Park, Yoon Jun Kim, Chung Yong Kim, Jung-Hwan Yoon, Youngsoo Kim*

Journal of Proteome Research (ISSN: 1535-3893). 16 (3), 1239-1248 (IF=4.0, Rank=17.7%) (03/03/2017)

Carboxymethyl-Lysine-Modified Plasma Proteins in Age-related Macular Degeneration

Joo Young Shin#, Areum Sohn, Hyunsoo Kim, Youngsoo Kim, Hyeong Gon Yu*

Biotechnology and Bioprocess Engineering (ISSN: 1226-8372). 22 (1), 52-59 (IF=1.2, Rank=85.1%) (02/01/2017)

Comparative studies for developing protein based cancer prediction model to maximize the ROC-AUC with various variable selection methods

Yongkang Kim#, Min-Seok Kwon, Yonghwan Choi, Sung Gon Yi, Junghyun Namkung, Sangjo Han, Wooil Kwon, Hyunsoo Kim, Sun Whe Kim, Jin-Young Jang, Youngsoo Kim, Seungyeoun Lee, Taesung Park*

International Journal of Data Mining and Bioinformatics (ISSN: 1748-5673). 16 (1), 64-76 (IF=0.6, Rank=89.5%) (07/01/2016)

Biomarker Development for Intraductal Papillary Mucinous Neoplasms Using Multiple Reaction Monitoring Mass Spectrometry

Yikwon Kim#, MeeJoo Kang#, Dohyun Han, Hyunsoo Kim, KyoungBun Lee, Sun-Whe Kim, Yongkang Kim, Taesung Park, Jin-Young Jang*, Youngsoo Kim*

Journal of Proteome Research (ISSN: 1535-3893). 15 (1), 100-113 (IF=4.3, Rank=17.9%) (01/04/2016)

Measurement of Glycosylated Alpha-Fetoprotein Improves Diagnostic Power over the Native Form in Hepatocellular Carcinoma

Hyunsoo Kim#, Kyunggon Kim#, Jonghwa Jin, Jiyoung Park, Su Jong Yu, Jung-Hwan Yoon*, Youngsoo Kim*

PLoS ONE (ISSN: 1932-6203). 9 (10), e110366 (IF=3.2, Rank=15.8%) (10/13/2014)

Development of Candidate Biomarkers for Pancreatic Ductal Adenocarcinoma Using Multiple Reaction Monitoring

Jiyoung Yu#, Kyunggon Kim#, MeeJoo Kang, Hyunsoo Kim, Sun Whe Kim, Jin-Young Jang#, Youngsoo Kim*

Biotechnology and Bioprocess Engineering (ISSN: 1226-8372). 18 (5), 1038-1047 (IF=1.2, Rank=75.9%) (09/01/2013)

Development of Biomarkers for Screening Hepatocellular Carcinoma Using Global Data Mining and Multiple Reaction Monitoring

Hyunsoo Kim#, Kyunggon Kim*, Su Jong Yu, Eun Sun Jang, Jiyoung Yu, Geunhee Cho, Jung-Hwan Yoon*, Youngsoo Kim*

PLoS ONE (ISSN: 1932-6203). 8 (5), e63468 (IF=3.5, Rank=14.5%) (05/22/2013)

Detection of Differential Proteomes Associated with the Development of Type 2 Diabetes in the Zucker Rat Model Using the iTRAQ Technique

Dohyun Han#, Sungyoon Moon, Hyunsoo Kim, Sung-E Choi, Soo-Jin Lee, Kyong Soo Park, Heesook Jun, Yup Kang, Youngsoo Kim*

Journal of Proteome Research (ISSN: 1535-3893). 10 (2), 564-577 (IF=5.1, Rank=13.9%) (02/04/2011)

Online monitoring of immunoaffinity-based depletion of high-abundance blood proteins by UV spectrophotometry using enhanced green fluorescence protein and FITC-labeled human serum albumin

Kyunggon Kim#, Jiyoung Yu, Hophil Min, Hyunsoo Kim, Byungwook Kim, Hyeong Gon Yu, Youngsoo Kim*

Proteome Science (ISSN: 1477-5956). 8 (1), 62 (IF=2.5, Rank=49.3%) (12/01/2010)