Minji Kim

Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells

The paper investigates cohesin-mediated chromatin loop extrusion in human cells, revealing two dynamic modes of extrusion and showing that CTCF depletion increases extrusion activity.

3D chromatin compartment of round spermatids encodes the spatiotemporal program of histone-to-protamine exchange in spermiogenesis

The paper defines a 3D chromatin compartment blueprint that programs histone-to-protamine exchange during spermiogenesis using ATAC-seq, CUT&Tag, and Hi-C.

Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies

This study uses FFPE-compatible Hi-C to detect enhancer-hijacking rearrangements in lymphoid cancers, identifying clinically relevant drivers missed by standard methods.

HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets

HiChIA-Rep quantifies similarity between chromatin interaction datasets by integrating 1D and 2D signals, distinguishing replicates and factors better than existing tools.

Multifaceted roles of cohesin in regulating transcriptional loops

This study investigates cohesin's role in transcriptional loops and DNA replication using human cells, finding that cohesin loss affects long-range chromatin interactions and up-regulates early initiation zone genes.

An integrated view of the structure and function of the human 4D nucleome

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

Chrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods

Chrom-Sig de-noises 1-dimensional genomic coverage tracks using signal processing to separate signal from noise, validated across multiple datasets.

MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets

MIA-Jet detects chromatin jets in 3D genome data, revealing their dependence on cohesin and CTCF, and outperforms existing methods across multiple species and datasets.

Structural Variants at Intronic CTCF Loop Anchors Drive Differential Exon Usage

The paper identifies structural variants at CTCF loop anchors that influence alternative splicing by disrupting chromatin looping in mouse ESCs.

Interpretable Online Network Dictionary Learning for Inferring Long-Range Chromatin Interactions

This paper introduces an interpretable online dictionary learning method for analyzing long-range chromatin interactions in Drosophila using ChIA-Drop data.

Inferring Single-Molecule Chromatin Interactions via Online Convex Network Dictionary Learning

The paper introduces an algorithm to infer chromatin interaction patterns from ChIA-Drop data and demonstrates its ability to reconstruct interaction networks and identify functional chromatin elements.

ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization

ChIA-PIPE is a fully automated pipeline for analyzing and visualizing ChIA-PET data, including quality assessment and visualization tools.

pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks

pyBedGraph is a Python package that rapidly computes summary statistics for genomic signal tracks, outperforming existing tools by up to 245 times.

Multiplex chromatin interaction analysis by signal processing and statistical algorithms

The paper introduces MIA-Sig, an algorithm to de-noise chromatin interaction data and identify topological domains and inter-domain contacts.

ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions

ChIA-DropBox is a computational pipeline for analyzing ChIA-Drop data, reconstructing chromatin complexes, and visualizing multiplex chromatin interactions.

Multiplex Chromatin Interaction Analysis with Single-Molecule Precision

This paper introduces a method to analyze multiplex chromatin interactions with single-molecule precision and shows they contribute to topologically associated domains and gene regulation.

ChIPWig: A Random Access-Enabling Lossless And Lossy Compression Method For ChIP-Seq Data

ChIPWig compresses ChIP-seq Wig data with lossless and lossy modes, achieving high compression rates while preserving peak calling and motif discovery accuracy.

TeachEnG: a Teaching Engine for Genomics

TeachEnG is an interactive online tool that helps students learn sequence alignment and phylogenetic tree reconstruction through instructional games.