The paper compares transcriptomes and chromatin accessibility in MEP, ERY, and MEG cells to reveal divergence in gene regulation during differentiation.

bioRxiv · Jun 30, 2025 · PreprintGenomics

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Guanjue Xiang, Xi He, Belinda M. Giardine, Kathryn J. Isaac, Dylan J. Taylor, Rajiv C. McCoy, Camden S. Jansen, Cheryl A. Keller, Alexander Q. Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, , Ross C. Hardison

This study identifies conserved and species-specific cis-regulatory elements in human and mouse blood cells using integrative epigenomic analysis and clustering.

Genome Research · Jul 1, 2024Peer-reviewedGenomics

Developmental stage- and site-specific transitions in lineage specification and gene regulatory networks in human hematopoietic stem and progenitor cells

Anindita Roy, Guanlin Wang, Deena Iskander, Sorcha O’Byrne, Natalina Elliott, Jennifer O’Sullivan, Gemma Buck, Elisabeth F. Heuston, Wei Xiong Wen, Alba Rodríguez-Meira, Peng Hua, Anastasios Karadimitiris, Adam J. Mead, David M. Bodine, Irene A.G. Roberts, , Supat Thongjuea

This study identifies site- and stage-specific transitions in gene regulatory networks and lineage specification in human hematopoietic stem and progenitor cells across developmental stages.

bioRxiv · Apr 20, 2021 · PreprintDevelopmental Biology

Effects of sheared chromatin length on ChIP-seq quality and sensitivity

Cheryl A. Keller, Alexander Q. Wixom, Elisabeth F. Heuston, Belinda M. Giardine, Chris C.‐S. Hsiung, Maria Long, Amber Miller, Stacie M. Anderson, April Cockburn, Gerd A. Blobel, David M. Bodine, Ross C. Hardison

This study investigates how chromatin shearing affects ChIP-seq quality and shows that sonication levels significantly impact signal quality and specificity for different transcription factors.

G3 Genes Genomes Genetics · Mar 31, 2021Peer-reviewedGenomics

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

Guanjue Xiang, Cheryl A. Keller, Elisabeth F. Heuston, Belinda M. Giardine, Lin An, Alexander Q. Wixom, Amber Miller, April Cockburn, Michael E.G. Sauria, Kathryn J. Isaac, Jens Lichtenberg, Berthold Göttgens, Qunhua Li, David M. Bodine, Shaun Mahony, , Ross C. Hardison

The paper integrates epigenomic and transcriptomic data from mouse hematopoiesis to identify regulatory elements and their dynamics across cell types.

Genome Research · Mar 1, 2020Peer-reviewedGenomics

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells

Ross C. Hardison, Yu Zhang, Cheryl A. Keller, Guanjue Xiang, Elisabeth F. Heuston, Lin An, Jens Lichtenberg, Belinda M. Giardine, David M. Bodine, Shaun Mahony, Qunhua Li, Feng Yue, Mitchell J. Weiss, Gerd A. Blobel, James Taylor, , Berthold Göttgens

The paper integrates GATA transcription factors and epigenomes in mouse hematopoietic cells using IDEAS to map regulatory landscapes and identify candidate cis-regulatory elements.

IUBMB Life · Nov 25, 2019Peer-reviewedGenomics

Snapshot: clustering and visualizing epigenetic history during cell differentiation

Guanjue Xiang, Belinda M. Giardine, Lin An, Chen Sun, Cheryl A. Keller, Elisabeth F. Heuston, David M. Bodine, Ross C. Hardison, Yu Zhang

Snapshot generates hierarchical visualizations of epigenetic features along cell differentiation hierarchies using epigenomic data from the VISION project.

bioRxiv · Dec 19, 2018 · PreprintBioinformatics