Publications
Publications
*: equal contributions, +: (co-)correspondence, underlined: group members
3D chromatin compartment of round spermatids encodes the spatiotemporal program of histone-to-protamine exchange in spermiogenesis
Mashiat Rabbani, Zachary Apell, Timothy J. Parnell, Lindsay Moritz, Sion Kim, Sowmya Srinivasan, Ritvija Agrawal, Alexander Vargo, Peter Orchard, Wenxin Xie, Lydia Freddolino, Alan P. Boyle, Jun Z. Li, Bluma J. Lesch, Bradley Cairns, Minji Kim+, Thomas E. Wilson+, Saher Sue Hammoud+
bioRxiv (2026). Link.
HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets
Sion Kim, Joseph T. Jackson, Henry B. Zhang, Minji Kim+
bioRxiv (2026). Link.
MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets
Sion Kim and Minji Kim+
bioRxiv (2025). Link.
*: equal contributions, +: (co-)correspondence, underlined: group members
Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies
Jamin Wu, Shi-Chun A. Chu, Jang Cho, Misha Movahed-Ezazi, Kristyn Galbraith, ..., Marcin P. Cieslik, Minji Kim, Anthony D. Schmitt, Matija Snuderl+, Russell J. H. Ryan+
Cell Genomics (2026). PubMed.
Interplay between cohesin and RNA Polymerase II in regulating chromatin interactions and gene transcription
Minji Kim*, Ping Wang*, Patricia A. Clow*, Eli Chien, Xiaotao Wang, Jianhao Peng, Haoxi Chai, Xiyuan Liu, Byoungkoo Lee, Chew Yee Ngan, Olgica Milenkovic, Jeffrey H. Chuang, Chia-Lin Wei, Rafael Casellas, Albert W. Cheng+, Yijun Ruan+
Nature Structural and Molecular Biology (2026). PubMed.
An integrated view of the structure and function of the human 4D nucleome
4D Nucleome Consortium, Job Dekker+, ..., Ping Wang, Haoxi Chai, Minji Kim, Yijun Ruan, ..., Frank Alber+, Jian Ma+, William S. Noble+, Feng Yue+
Nature (2026). PubMed.
Chrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods
Nandita J. Gupta, Zachary Apell, Minji Kim+
Bioinformatics (2025). PubMed.
Multiscale Hybrid Surface Topographies Orchestrate Immune Regulation, Antibacterial Defense, and Tissue Regeneration
Mohammad Asadi Tokmedash, Jacob Robins, J. Scott VanEpps, Minji Kim, Jouha Min+
Advanced Healthcare Materials (2025). PubMed.
Evolutionary divergence in CTCF-mediated chromatin topology drives transcriptional innovation in humans
Xia Wu, Dan Xiong, Rong Liu, Xingqiang Lai, Yuhan Tian, ..., Minji Kim, Wenjun Xin, Tianyun Wang, Andy Peng Xiang, Zhonghui Tang+
Nature Communications (2025). PubMed.
Interpretable Online Network Dictionary Learning for Inferring Long-Range Chromatin Interactions
Vishal Rana, Jianhao Peng, Chao Pan, Hanbaek Lyu, Albert Cheng, Minji Kim, Olgica Milenkovic+
PLoS Computational Biology (2024). PubMed.
Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons
Beatriz del Blanco, Sergio Niñerola, Ana M. Martín-González, Juan Paraíso-Luna, Minji Kim, Rafael Muñoz-Viana, Carina Racovac, Jose V. Sánchez-Mut, Yijun Ruan, Ángel Barco+
Nature Communications (2024). PubMed.
In Situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing
Ping Wang, Yuliang Feng, Kun Zhu, Haoxi Chai, Ya-Ting Chang, Xiyuan Liu, Chen Shen, Eva Gega, Byoungkoo Lee, Minji Kim, Xiaoan Ruan, Yijun Ruan+
Current Protocols (2021). PubMed.
pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks
Henry B. Zhang, Minji Kim+, Jeffrey H. Chuang, Yijun Ruan
Bioinformatics (2020). PubMed.
ChIA-PIPE: a fully automated pipeline for comprehensive ChIA-PET data analysis and visualization
Byoungkoo Lee, Jiahui Wang, Liuyang Cai, Minji Kim, Sandeep Namburi, Harianto Tjong, Yuliang Feng, Ping Wang, Zhonghui Tang, Ahmed Abbas, Chia-Lin Wei+, Yijun Ruan+, Sheng Li+
Science Advances (2020). PubMed.
MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms
Minji Kim, Meizhen Zheng, Simon Tian, Byoungkoo Lee, Jeffrey H. Chuang, Yijun Ruan+
Genome Biology (2019). PubMed.
Multiplex Chromatin Interactions with Single-Molecule Precision
Meizhen Zheng, Simon Tian, Daniel Capurso, Minji Kim, Rahul Maurya, Byoungkoo Lee, Emaly Piecuch, Liang Gong, Jufen Zhu, Zhihui Li, Chee-Hong Wong, Chew-Yee Ngan, Ping Wang, Xiaoan Ruan, Chia-Lin Wei, Yijun Ruan+
Nature (2019). PubMed.
ChIPWig: Random Access-Enabling Lossless and Lossy Compression Method for ChIP-seq Data
Vida Ravanmehr, Minji Kim, Zhiying Wang, Olgica Milenkovic+
Bioinformatics (2018). PubMed.
TeachEnG: a Teaching Engine for Genomics
Minji Kim, Yeonsung Kim, Lei Qian, Jun S. Song+
Bioinformatics (2017). PubMed.
Quantitative analysis and prediction of G-quadruplex forming sequences in dsDNA
Minji Kim*, Alex Kreig*, Chun-Ying Lee, H. Tomas Rube, Jacob Calvert, Jun S. Song+, Sua Myong+
Nucleic Acids Research (2016). PubMed.
MetaCRAM: an Integrated Pipeline for Metagenomic Data Processing and Compression
Minji Kim+, Xiejia Zhang, Jonathan G. Ligo, Farzad Farnoud, Venugopal V. Veeravalli, Olgica Milenkovic
BMC Bioinformatics (2016). PubMed.
HyDRA: Gene Prioritization via Hybrid Distance-Score Rank Aggregation
Minji Kim+, Farzad Farnoud, Olgica Milenkovic
Bioinformatics (2015). PubMed.