Multiplex chromatin interactions with single-molecule precision M Zheng, SZ Tian, D Capurso, M Kim, R Maurya, B Lee, E Piecuch, ... Nature 566 (7745), 558-562, 2019 | 231 | 2019 |
HyDRA: gene prioritization via hybrid distance-score rank aggregation M Kim, F Farnoud, O Milenkovic Bioinformatics 31 (7), 1034-1043, 2015 | 36 | 2015 |
ChIA-PIPE: a fully automated pipeline for comprehensive ChIA-PET data analysis and visualization B Lee, J Wang, L Cai, M Kim, S Namburi, H Tjong, Y Feng, P Wang, ... Science advances 6 (28), eaay2078, 2020 | 31 | 2020 |
Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA M Kim, A Kreig, CY Lee, HT Rube, J Calvert, JS Song, S Myong Nucleic Acids Research 272, 2016 | 23 | 2016 |
MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression M Kim, X Zhang, JG Ligo, F Farnoud, VV Veeravalli, O Milenkovic BMC bioinformatics 17 (1), 94, 2016 | 19 | 2016 |
In situ Chromatin Interaction Analysis Using Paired‐End Tag Sequencing P Wang, Y Feng, K Zhu, H Chai, Y Chang, X Yang, X Liu, C Shen, E Gega, ... Current protocols 1 (8), e174, 2021 | 18 | 2021 |
MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms M Kim, M Zheng, SZ Tian, B Lee, JH Chuang, Y Ruan Genome biology 20, 1-13, 2019 | 11 | 2019 |
ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions SZ Tian, D Capurso, M Kim, B Lee, M Zheng, Y Ruan bioRxiv, 613034, 2019 | 7 | 2019 |
ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data V Ravanmehr, M Kim, Z Wang, O Milenković Bioinformatics 34 (6), 911-919, 2018 | 6 | 2018 |
pyBedGraph: a python package for fast operations on 1D genomic signal tracks HB Zhang, M Kim, JH Chuang, Y Ruan Bioinformatics 36 (10), 3234-3235, 2020 | 4 | 2020 |
TeachEnG: a Teaching Engine for Genomics M Kim, Y Kim, L Qian, J Song Bioinformatics 33 (20), 3296-3298, 2017 | 4 | 2017 |
Gene prioritization via weighted Kendall rank aggregation M Kim, F Raisali, F Farnoud, O Milenkovic 2013 5th IEEE International Workshop on Computational Advances in Multi …, 2013 | 4 | 2013 |
MetaPar: metagenomic sequence assembly via iterative reclassification M Kim, JG Ligo, A Emad, F Farnoud, O Milenkovic, VV Veeravalli 2013 IEEE Global Conference on Signal and Information Processing, 43-46, 2013 | 4 | 2013 |
An integrated view of the structure and function of the human 4D nucleome J Dekker, BA Oksuz, Y Zhang, Y Wang, MK Minsk, S Kuang, L Yang, ... bioRxiv, 2024 | 3 | 2024 |
Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons B Del Blanco, S Niñerola, AM Martín-González, J Paraíso-Luna, M Kim, ... Nature Communications 15 (1), 1781, 2024 | 3 | 2024 |
MCUIUC—A new framework for metagenomic read compression JG Ligo, M Kim, A Emad, O Milenkovic, VV Veeravalli 2013 IEEE Information Theory Workshop (ITW), 1-5, 2013 | 3 | 2013 |
Multifaceted roles of cohesin in regulating transcriptional loops M Kim, P Wang, PA Clow, IE Chien, X Wang, J Peng, H Chai, X Liu, B Lee, ... bioRxiv, 2024 | 1 | 2024 |
Interpretable online network dictionary learning for inferring long-range chromatin interactions V Rana, J Peng, C Pan, H Lyu, A Cheng, M Kim, O Milenkovic PLoS computational biology 20 (5), e1012095, 2024 | | 2024 |