Publications
Selected preprints
*: equal contributions, +: (co-)correspondence, underlined: group members
2024
Multifaceted roles of cohesin in regulating transcriptional loops
Minji Kim*, Ping Wang*, Patricia A. Clow*, I (Eli) Chien, Xiaotao wang, Jianhao Peng, Haoxi Chai, Xiyuan Liu, Byoungkoo Lee, Chew Yee Ngan, Feng Yue, Olgica Milenkovic, Jeffrey H. Chuang, Chia-Lin Wei, Rafael Casellas, Albert W. Cheng+, Yijun Ruan+
bioRxiv. Link.
2023
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+
bioRxiv. Link.
Peer-reviewed Journal Articles
*: equal contributions, +: (co-)correspondence, underlined: group members
2024
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. PubMed.
2021
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. PubMed.
2020
pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks
Henry B. Zhang, Minji Kim+, Jeffrey H. Chuang, Yijun Ruan
Bioinformatics. 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. PubMed.
2019
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. 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. PubMed.
2018
ChIPWig: Random Access-Enabling Lossless and Lossy Compression Method for ChIP-seq Data
Vida Ravanmehr, Minji Kim, Zhiying Wang, Olgica Milenkovic+
Bioinformatics. PubMed.
2017
TeachEnG: a Teaching Engine for Genomics
Minji Kim, Yeonsung Kim, Lei Qian, Jun S. Song+
Bioinformatics. PubMed.
2016
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. 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. PubMed.
2015
HyDRA: Gene Prioritization via Hybrid Distance-Score Rank Aggregation
Minji Kim+, Farzad Farnoud, Olgica Milenkovic
Bioinformatics. PubMed.