Available to mentor
Engineers have developed methods to transmit information efficiently and reliably so that two people can carry out conversations using various communication technologies. Communication is also essential in music: an orchestra conductor and musicians make eye contacts to create rich, harmonious sound together. Similar mechanisms exist inside our cells to regulate gene expression and function. In cells, communication between a gene and sequences that regulate the gene occurs through physical contact. Our goal is to understand how this communication occurs within the nucleus. To do so, we leverage 3D genome mapping technologies to capture the dynamic chromatin interactions and study gene regulation in the context of developmental biology. Interpreting these high-throughput sequencing data probing the (3D) genome, epigenome, and transcriptome requires sophisticated algorithms and computational tools, which we develop by using ideas from signal processing, graph theory, information theory, and coding theory.
Minji Lab
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Del Blanco B, Niñerola S, Martín-González AM, Paraíso-Luna J, Kim M, Muñoz-Viana R, Racovac C, Sanchez-Mut JV, Ruan Y, Barco Á. Nat Commun, 2024 Mar 7; 15 (1): 1781Journal ArticleKdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons.
DOI:10.1038/s41467-024-45773-3 PMID: 38453932 -
Kim M, Wang P, Clow PA, Chien IE, Wang X, Peng J, Chai H, Liu X, Lee B, Ngan CY, Yue F, Milenkovic O, Chuang JH, Wei C-L, Casellas R, Cheng AW, Ruan Y. 2024 Mar 27;PreprintMultifaceted roles of cohesin in regulating transcriptional loops.
DOI:10.1101/2024.03.25.586715 PMID: 38585764 -
Rana V, Peng J, Pan C, Lyu H, Cheng A, Kim M, Milenkovic O. bioRxiv,PreprintInterpretable Online Network Dictionary Learning for Inferring Long-Range Chromatin Interactions
DOI:10.1101/2023.12.16.571999 -
Rana V, Peng J, Pan C, Lyu H, Cheng A, Kim M, Milenkovic O. 2023 Dec 16; arXiv,PreprintInterpretable Online Network Dictionary Learning for Inferring Long-Range Chromatin Interactions
DOI:10.48550/arxiv.2312.10519 -
Peng J, Pan C, Lyu H, Kim M, Cheng A, Milenkovic O. bioRxiv,PreprintInferring Single-Molecule Chromatin Interactions via Online Convex Network Dictionary Learning
DOI:10.1101/2022.07.28.501904 -
Wang P, Feng Y, Zhu K, Chai H, Chang Y-T, Yang X, Liu X, Shen C, Gega E, Lee B, Kim M, Ruan X, Ruan Y. Curr Protoc, 2021 Aug; 1 (8): e174Journal ArticleIn situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing.
DOI:10.1002/cpz1.174 PMID: 34351700 -
Lee B, Wang J, Cai L, Kim M, Namburi S, Tjong H, Feng Y, Wang P, Tang Z, Abbas A, Wei C-L, Ruan Y, Li S. Sci Adv, 2020 Jul; 6 (28): eaay2078Journal ArticleChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization.
DOI:10.1126/sciadv.aay2078 PMID: 32832596 -
Zhang HB, Kim M, Chuang JH, Ruan Y. Bioinformatics, 2020 May 1; 36 (10): 3234 - 3235.Journal ArticlepyBedGraph: a python package for fast operations on 1D genomic signal tracks.
DOI:10.1093/bioinformatics/btaa061 PMID: 32044918