publications

2025

1. Integrating genetic subtypes with PET scan monitoring to predict outcome in diffuse large B-cell lymphoma

   Matı́as S Mendeville, Jurriaan Janssen, G Tjitske Los-de Vries, Erik Dijk, Julia Richter, Marcel Nijland, Margaretha GM Roemer, Phylicia Stathi, Nathalie J Hijmering, Reno Bladergroen, and others

   Nature Communications, 2025
2. DNA methylation and copy number alterations in the progression of HPV-associated high-grade vulvar intraepithelial lesion

   Flavia Runello, Aude Jary, Sylvia Duin, Yongsoo Kim, Kahren Eer, Féline O Voss, Nikki B Thuijs, Maaike CG Bleeker, and Renske DM Steenbergen

   International Journal of Cancer, 2025
3. Epstein-Barr virus status drives morphological and molecular intra-tumour heterogeneity in gastric cancer: insights from a case report and literature review

   Irene Gullo, Maria Luı́sa Sacramento, Rui Morais, Yongsoo Kim, Paul P Eijk, Ana Mafalda Rocha, Diana Baptista, João Santos-Antunes, Bauke Ylstra, and Fátima Carneiro

   Virchows Archiv, 2025

2024

1. Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions

   Stacey EP Joosten, Sebastian Gregoricchio, Suzan Stelloo, Elif Yapıcı, Chia-Chi Flora Huang, Kerim Yavuz, Maria Donaldson Collier, Tunç Morova, Umut Berkay Altintaş, Yongsoo Kim, and others

   Genome Research, 2024
2. Hidden RNA profiles of cells in the tumor microenvironment accurately revealed by malignant cell fraction-informed deconvolution

   Yongsoo Kim, Jurriaan Janssen, Teodora Radonic, Mischa Steketee, Saskia Asten, Paul Eijk, Febe Maldegem, David Noske, Idris Bahce, Juan Garcia Vallejo, and others

   2024
3. Accurate detection of copy number aberrations in FFPE samples using the mFAST-SeqS approach

   Aude Jary, Yongsoo Kim, Kirsten Rozemeijer, Paul P Eijk, Ramon P Zee, Maaike CG Bleeker, Saskia M Wilting, and Renske DM Steenbergen

   Experimental and Molecular Pathology, 2024

2023

1. Multi-scale spatial modeling of immune cell distributions enables survival prediction in primary central nervous system lymphoma

   Margaretha GM Roemer, Tim Brug, Erik Bosch, Daniella Berry, Nathalie Hijmering, Phylicia Stathi, Karin Weijers, Jeannette Doorduijn, Jacoline Bromberg, Mark Wiel, and Yongsoo Kim

   Iscience, 2023
2. A comprehensive overview of RNA deconvolution methods and their application

   Yebin Im and Yongsoo Kim

   Molecules and cells, 2023
3. Enhancer profiling identifies epigenetic markers of endocrine resistance and reveals therapeutic options for metastatic castration-resistant prostate cancer patients

   Tesa M Severson, Yanyun Zhu, Stefan Prekovic, Karianne Schuurman, Holly M Nguyen, Lisha G Brown, Sini Hakkola, Yongsoo Kim, Jeroen Kneppers, Simon Linder, and others

   medRxiv, 2023
4. Prognostic value of T-cell density in the tumor center and outer margins in gastric cancer

   Tanya TD Soeratram, Hedde D Biesma, Jacqueline MP Egthuijsen, Elma Meershoek-Klein Kranenbarg, Henk H Hartgrink, Cornelis JH Velde, Aart Mookhoek, Erik Dijk, Yongsoo Kim, Bauke Ylstra, and others

   Modern Pathology, 2023
5. The Impact of Genetic Subtypes of Diffuse Large B-Cell Lymphoma for Outcome Prediction and Interpretation of FDG-PET treatment Response Monitoring

   Bauke Ylstra, Matias Mendeville, Jurriaan Janssen, G Tjitske Los-de Vries, Erik Dijk, Julia Richter, Marcel Nijland, Margaretha Roemer, Phylicia Stathi, Nathalie Hijmering, and others

   2023
6. Molecular subtyping significantly improves outcome prediction in diffuse large B-cell lymphoma

   Matias Mendeville, G Tjitske Los-de Vries, Jurriaan Janssen, Julia Richter, Erik Dijk, Marcel Nijland, Margaretha GM Roemer, Phylicia Stathi, Nathalie J Hijmering, Reno Bladergroen, and others

   Computational solutions in genomic pathology of non-Hodgkin lymphomas, 2023

2022

1. A bioinformatics perspective on molecular classification of diffuse large B-cell lymphoma

   Matias Mendeville, Jurriaan Janssen, Yongsoo Kim, Erik Dijk, Daphne Jong, and Bauke Ylstra

   Leukemia, 2022
2. Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer toward androgen independence

   Simon Linder, Marlous Hoogstraat, Suzan Stelloo, Nils Eickhoff, Karianne Schuurman, Hilda Barros, Maartje Alkemade, Elise M Bekers, Tesa M Severson, Joyce Sanders, and others

   Cancer discovery, 2022
3. Impact of classical and basal-like molecular subtypes on overall survival in resected pancreatic cancer in the SPACIOUS-2 multicentre study

   J Annelie Suurmeijer, Eline C Soer, Mark PG Dings, Yongsoo Kim, Marin Strijker, Bert A Bonsing, Lodewijk AA Brosens, Olivier R Busch, Jesse V Groen, Johannes B Halfwerk, and others

   British Journal of Surgery, 2022
4. Double-strand break toxicity is chromatin context independent

   Anoek Friskes, Lisa Koob, Lenno Krenning, Tesa M Severson, Emma S Koeleman, Xabier Vergara, Michael Schubert, Jeroen Berg, Bastiaan Evers, Anna G Manjón, and others

   Nucleic acids research, 2022
5. A robust copy number based clonality classification for multiple pulmonary tumors in routine pathology practice by shallow next generation sequencing of formalin fixed clinical specimens

   Bárbara Andrade Barbosa, Teodora Radonic, Yongsoo Kim, and Bauke Ylstra

   Cancer Research, 2022

2021

1. Bayesian log-normal deconvolution for enhanced in silico microdissection of bulk gene expression data

   Bárbara Andrade Barbosa, Saskia D Asten, Ji Won Oh, Arantza Farina-Sarasqueta, Joanne Verheij, Frederike Dijk, Hanneke WM Laarhoven, Bauke Ylstra, Juan J Garcia Vallejo, Mark A Wiel, and Yongsoo Kim

   Nature communications, 2021

2020

1. Epigenetic profiling demarcates molecular subtypes of muscle-invasive bladder cancer

   KE Vos, DJ Vis, E Nevedomskaya, Y Kim, Woonyoung Choi, D McConkey, LFA Wessels, BWG Rhijn, W Zwart, and MS Heijden

   Scientific Reports, 2020

2019

1. Optimized ChIP-seq method facilitates transcription factor profiling in human tumors

   Abhishek A Singh, Karianne Schuurman, Ekaterina Nevedomskaya, Suzan Stelloo, Simon Linder, Marjolein Droog, Yongsoo Kim, Joyce Sanders, Henk Van Der Poel, Andries M Bergman, and others

   Life science alliance, 2019
2. GATA3 truncating mutations promote cistromic re-programming in vitro, but not mammary tumor formation in mice

   Lisette M Cornelissen, Roebi Bruijn, Linda Henneman, Yongsoo Kim, Wilbert Zwart, and Jos Jonkers

   Journal of Mammary Gland Biology and Neoplasia, 2019
3. DNA end-resection in highly accessible chromatin produces a toxic break

   Jeroen Berg, Stacey EP Joosten, YongSoo Kim, Anna G Manjón, Lenno Krenning, Lisa Koob, Femke M Feringa, Rob Klompmaker, Bram Broek, Kees Jalink, and others

   BioRxiv, 2019
4. A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation

   Gozde Korkmaz, Zohar Manber, Rui Lopes, Stefan Prekovic, Karianne Schuurman, Yongsoo Kim, Hans Teunissen, Koen Flach, Elzo de Wit, Giorgio G Galli, and others

   Nucleic acids research, 2019
5. A CRISPR-Cas9 screen identifies essential CTCF anchor sites for the mitogenic function of ER-alpha in breast cancer

   Gozde Korkmaz, Zohar Manber, Rui Marques Lopes, Stefan Prekovic, Karianne Schuurman, Yongsoo Kim, Hans Teunissen, Koen Flach, Elzo Wit, Giorgio Galli, and others

   Nucleic Acids Research, 2019
6. Genomic data integration by WON-PARAFAC identifies interpretable factors for predicting drug-sensitivity in vivo

   Yongsoo Kim, Tycho Bismeijer, Wilbert Zwart, Lodewyk FA Wessels, and Daniel J Vis

   Nature communications, 2019
7. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

   Michael P Menden, Dennis Wang, Mike J Mason, Bence Szalai, Krishna C Bulusu, Yuanfang Guan, Thomas Yu, Jaewoo Kang, Minji Jeon, Russ Wolfinger, and others

   Nature communications, 2019

2018

1. Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer

   Tesa M Severson, Yongsoo Kim, Stacey EP Joosten, Karianne Schuurman, Petra Van Der Groep, Cathy B Moelans, Natalie D Ter Hoeve, Quirine F Manson, John W Martens, Carolien HM Van Deurzen, and others

   Nature communications, 2018
2. Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis

   Suzan Stelloo, Ekaterina Nevedomskaya, Y Kim, Liesbeth Hoekman, OB Bleijerveld, T Mirza, LFA Wessels, Wytske M Weerden, AFM Altelaar, AM Bergman, and others

   Oncogene, 2018
3. Chemical profiling of primary mesothelioma cultures defines subtypes with different expression profiles and clinical responses

   Laurel M Schunselaar, Josine MMF Quispel-Janssen, Yongsoo Kim, Constantine Alifrangis, Wilbert Zwart, Paul Baas, and Jacques Neefjes

   Clinical Cancer Research, 2018
4. CUEDC1 is a primary target of ERαessential for the growth of breast cancer cells

   Rui Lopes, Gozde Korkmaz, Sonia Aristin Revilla, Romy Vliet, Remco Nagel, Lars Custers, Yongsoo Kim, Pieter C Van Breugel, Wilbert Zwart, Behzad Moumbeini, and others

   Cancer Letters, 2018
5. Identifying biomarkers of anti-cancer drug synergy using multi-task learning

   Nanne Aben, Julian R Ruiter, Evert Bosdriesz, Yongsoo Kim, Gergana Bounova, Daniel J Vis, Lodewyk FA Wessels, and Magali Michaut

   bioRxiv, 2018
6. Nuclear receptor Nur77 limits the macrophage inflammatory response through transcriptional reprogramming of mitochondrial metabolism

   Duco Steven Koenis, Lejla Medzikovic, Pieter Bas Loenen, Michel Weeghel, Stephan Huveneers, Mariska Vos, Ingrid Johanna Evers-van Gogh, Jan Bossche, Dave Speijer, Yongsoo Kim, and others

   Cell reports, 2018
7. The Estrogen Receptor chromatin binding landscape in human tumors

   Stacey Joosten, Tesa Severson, Yongsoo Kim, Karianne Schuurman, Lodewyk Wessels, Wilbert Zwart, and others

   In Endocrine Abstracts, 2018
8. Integrative epigenetic taxonomy of primary prostate cancer

   Suzan Stelloo, Ekaterina Nevedomskaya, Yongsoo Kim, Karianne Schuurman, Eider Valle-Encinas, João Lobo, Oscar Krijgsman, Daniel Simon Peeper, Seiwon Laura Chang, Felix Yi-Chung Feng, and others

   Nature communications, 2018

2017

1. Estrogen receptor αwields treatment-specific enhancers between morphologically similar endometrial tumors

   Marjolein Droog, Ekaterina Nevedomskaya, Gwen M Dackus, Renske Fles, Yongsoo Kim, Harry Hollema, Marian J Mourits, Petra M Nederlof, Hester H Van Boven, Sabine C Linn, and others

   Proceedings of the National Academy of Sciences, 2017
2. DNase-active TREX1 frame-shift mutants induce serologic autoimmunity in mice

   Tomomi Sakai, Takuya Miyazaki, Dong-Mi Shin, Yong-Soo Kim, Chen-Feng Qi, Robert Fariss, Jeeva Munasinghe, Hongsheng Wang, Alexander L Kovalchuk, Parul H Kothari, and others

   Journal of autoimmunity, 2017

2016

1. Comparative cistromics reveals genomic cross-talk between FOXA1 and ERαin tamoxifen-associated endometrial carcinomas

   Marjolein Droog, Ekaterina Nevedomskaya, Yongsoo Kim, Tesa Severson, Koen D Flach, Mark Opdam, Karianne Schuurman, Patrycja Gradowska, Michael Hauptmann, Gwen Dackus, and others

   Cancer Research, 2016
2. Neoadjuvant tamoxifen synchronizes ERαbinding and gene expression profiles related to outcome and proliferation

   Tesa M Severson, Ekaterina Nevedomskaya, Justine Peeters, Thomas Kuilman, Oscar Krijgsman, Annelot Van Rossum, Marjolein Droog, Yongsoo Kim, Rutger Koornstra, Inès Beumer, and others

   Oncotarget, 2016
3. A guide to studying human hair follicle cycling in vivo

   Ji Won Oh, Jennifer Kloepper, Ewan A Langan, Yongsoo Kim, Joongyeub Yeo, Min Ji Kim, Tsai-Ching Hsi, Christian Rose, Ghil Suk Yoon, Seok-Jong Lee, and others

   Journal of Investigative Dermatology, 2016

2014

1. Inference of dynamic networks using time-course data

   Yongsoo Kim, Seungmin Han, Seungjin Choi, and Daehee Hwang

   Briefings in bioinformatics, 2014
2. TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information

   Yongsoo Kim, Jin-Hyeok Jang, Seungjin Choi, and Daehee Hwang

   Bioinformatics, 2014

2012

1. Integration analysis of quantitative proteomics and transcriptomics data identifies potential targets of frizzled-8 protein-related antiproliferative factor in vivo

   Wei Yang, Yongsoo Kim, Taek-Kyun Kim, Susan K Keay, Kwang Pyo Kim, Hanno Steen, Michael R Freeman, Daehee Hwang, and Jayoung Kim

   BJU international, 2012
2. Characterization of ARF-BP1/HUWE1 interactions with CTCF, MYC, ARF and p53 in MYC-driven B cell neoplasms

   Chen-Feng Qi, Yong-Soo Kim, Shao Xiang, Ziedulla Abdullaev, Ted A Torrey, Siegfried Janz, Alexander L Kovalchuk, Jiafang Sun, Delin Chen, William C Cho, and others

   International journal of molecular sciences, 2012

2011

1. Principal network analysis: identification of subnetworks representing major dynamics using gene expression data

   Yongsoo Kim, Taek-Kyun Kim, Yungu Kim, Jiho Yoo, Sungyong You, Inyoul Lee, George Carlson, Leroy Hood, Seungjin Choi, and Daehee Hwang

   Bioinformatics, 2011
2. Quantitative proteomics identifies a β-catenin network as an element of the signaling response to frizzled-8 protein-related antiproliferative factor

   Wei Yang, Yeun Goo Chung, Yongsoo Kim, Taek-Kyun Kim, Susan K Keay, Chen-Ou Zhang, Mihee Ji, Daehee Hwang, Kwang Pyo Kim, Hanno Steen, and others

   Molecular & Cellular Proteomics, 2011

2008

1. From proteomics toward systems biology: integration of different types of proteomics data into network models

   Sang-Chul Rho, Sung-Yong You, Yong-Soo Kim, and Dae-Hee Hwang

   BMB reports, 2008