SpiderNet identifies cell-cell communication programs from spatial transcriptomics data, revealing key interactions and their associations with phenotypes and therapeutic responses.

bioRxiv · Sep 27, 2026 · PreprintBioinformatics

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

Job Dekker, Betül Akgöl Oksuz, Yang Zhang, Ye Wang, Miriam K. Minsk, Shuzhen Kuang, Liyan Yang, Johan Harmen Gibcus, Nils Krietenstein, Oliver J. Rando, Jie Xu, Derek H. Janssens, Steven Henikoff, Alexander Kukalev, Andréa Willemin, , Feng Yue

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.

Nature · Dec 17, 2025Peer-reviewedGenomics

DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks

Wenduo Cheng, Zhenqiao Song, Yang Zhang, Shike Wang, Danqing Wang, Muyu Yang, Lei Li, Jian Ma

The paper introduces DNALO_SCPLOWONGC_SCPLOWBO_SCPLOWENCHC_SCPLOW, a benchmark suite for long-range DNA prediction tasks, and evaluates five methods on five genomics tasks.

Nature Communications · Nov 18, 2025Peer-reviewedBioinformatics

Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function

Omid Gholamalamdari, Tom van Schaik, Yuchuan Wang, Pradeep Kumar, Liguo Zhang, Yang Zhang, Gabriela Andrea Hernandez Gonzalez, Athanasios E Vouzas, Peiyao A Zhao, David M. Gilbert, Jian Ma, Bas van Steensel, Andrew S. Belmont

The paper examines genome organization in human cells relative to nuclear locales, finding that gene expression and replication timing correlate with different nuclear structures and that LADs and iLADs compete for lamina attachment.

eLife · Apr 25, 2025Peer-reviewedGenomics

Complete sequencing of ape genomes

DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar, Dmitry Antipov, Brandon D. Pickett, Yana Safonova, Francesco Montinaro, Yanting Luo, Joanna Malukiewicz, Jessica M. Storer, Jiadong Lin, Abigail N Sequeira, , Zhenmiao Zhang

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

Nature · Apr 9, 2025Peer-reviewedGenomics

Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome

Xiaopeng Zhu, Yang Zhang, Yuchuan Wang, Dechao Tian, Andrew S. Belmont, Jason R. Swedlow, Jian Ma

Nucleome Browser integrates heterogeneous 4D Nucleome data into an interactive platform for visualization and exploration across biological contexts.

Nature Methods · Jul 21, 2022Peer-reviewedBioinformatics

CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing

Yang Yang, Yuchuan Wang, Yang Zhang, Jian Ma

The paper introduces a machine learning method to predict DNA replication timing from sequence features and identifies genome-wide sequence elements that modulate replication timing.

bioRxiv · Apr 21, 2022 · PreprintBioinformatics

TSA-Seq reveals a largely hardwired genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

Liguo Zhang, Yang Zhang, Yu Chen, Omid Gholamalamdari, Yuchuan Wang, Jian Ma, Andrew S. Belmont

Genome Research · Feb 1, 2021Peer-reviewedGenomics

SPIN reveals genome-wide landscape of nuclear compartmentalization

Yuchuan Wang, Yang Zhang, Ruochi Zhang, Tom van Schaik, Liguo Zhang, Takayo Sasaki, Daniel Peric‐Hupkes, Yu Chen, David M. Gilbert, Bas van Steensel, Andrew S. Belmont, Jian Ma

The paper introduces SPIN, a method to identify genome-wide nuclear spatial localization patterns by integrating nuclear compartment mapping and chromatin interaction data.

Genome biology · Jan 14, 2021Peer-reviewedBioinformatics

MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome

Dechao Tian, Ruochi Zhang, Yang Zhang, Xiaopeng Zhu, Jian Ma

MOCHI identifies heterogeneous interactome modules in the nucleus by clustering gene loci with frequent spatial contacts and shared transcription factor regulation across five cell types.

Genome Research · Feb 1, 2020Peer-reviewedBioinformatics

Comparing 3D genome organization in multiple species using Phylo-HMRF

Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma

This paper introduces Phylo-HMRF, a probabilistic model to analyze 3D genome organization across species using Hi-C data, revealing evolutionary patterns in chromatin structure.

Cell Systems · Jun 1, 2019Peer-reviewedBioinformatics

TSA-Seq Mapping of Nuclear Genome Organization

Yu Chen, Yang Zhang, Yuchuan Wang, Liguo Zhang, Eva Karina Brinkman, Stephen A. Adam, Robert D. Goldman, Bas van Steensel, Jian Ma, Andrew S. Belmont

The paper introduces TSA-Seq, a method to measure chromosomal distances to nuclear structures and reveals a spatial gradient in genome activity correlated with nuclear compartments.

The Journal of Cell Biology · Aug 28, 2018Peer-reviewedGenomics

Continuous-trait probabilistic model for comparing multi-species functional genomic data

Yang Yang, Quanquan Gu, Yang Zhang, Takayo Sasaki, Julianna Crivello, Rachel J. Waugh O'Neill, David M. Gilbert, Jian Ma

This paper introduces a probabilistic model to compare multi-species functional genomic data, showing it can identify genomic regions with distinct evolutionary patterns of DNA replication timing across primates.

Cell Systems · Jun 21, 2018Peer-reviewedBioinformatics

Predicting CTCF-mediated chromatin loops using CTCF-MP

Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang, Jian Ma

This study identifies sequence-based features that predict CTCF-mediated chromatin loops using a machine learning model called CTCF-MP.

Bioinformatics · Apr 12, 2018Peer-reviewedBioinformatics