Author

Alec R. Chapman

Broad InstituteORCID 0000-0002-6580-4005Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:human· 4 Approach:statistical model· 4 Research Focus:gene regulatory network inference· 3 Research Focus:database / resource· 2 Research Focus:differential expression· 2 Assay:DNA methylation· 2 Assay:scRNA-seq· 2 Assay:ATAC-seq· 1

Frequent Co-Authors

David F. LeeiD· 2 shared Déborah GérardiD· 2 shared Dennis HeckeriD· 2 shared Lasse SinkkoneniD· 2 shared Maria Pires PachecoiD· 2 shared Riley J. ManganiD· 2 shared Wenjie Sun· 2 shared Wenping MaiD· 2 shared

Activity by Year

2019-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersGenomics

David F. LeeORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

EpiATLAS - a reference for human epigenomic research

Quirin Manz, Misha Bilenky, Dennis Hecker, Nihit Aggarwal, Juliana Estefania Arcila-Galvis, Shamim Ashrafiyan, Nina Baumgarten, Fatemeh Behjati Ardakani, Paulo R. Branco Lins, Charles E. Breeze, David Brownlee, David Bujold, Alec R. Chapman, Savio Ho-Chit Chow, Tevfik Umut Dincer, , Samuel A. J. R. Aparicio

EpiATLAS provides a comprehensive collection of human reference epigenomes to advance epigenomic research and understanding of cellular function and disease.

bioRxiv · Jun 26, 2026 · PreprintGenomics

Epigenetic control of metabolic identity across cell types

Maria Pires Pacheco, Déborah Gérard, Riley J. Mangan, Alec R. Chapman, Dennis Hecker, M Kellis, Marcel H. Schulz, Lasse Sinkkonen, Thomas Sauter

The paper reconstructs metabolic networks across 58 human tissues and cell types using RNA-seq and epigenomic data, identifying core and cell-type-specific metabolic functions and their regulatory elements.

BMC Genomics · Dec 10, 2025Peer-reviewedSystems Biology

Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation Fetus

Feng Tian, Fan Zhou, Xiang Li, Wenping Ma, Honggui Wu, Ming Yang, Alec R. Chapman, David F. Lee, Longzhi Tan, Dong Xing, Guangjun Yin, Ayjan Semayel, Jing Wang, Jia Wang, Wenjie Sun, , Xiaoliang Sunney Xie

The paper introduces GeACT, a genomic database for human mid-gestation fetus cells, linking gene expression to chromatin states and identifying key transcription factors.

bioRxiv · Apr 12, 2020 · PreprintGenomics

Correlated Gene Modules Uncovered by Single-Cell Transcriptomics with High Detectability and Accuracy

Alec R. Chapman, David F. Lee, Wenting Cai, Wenping Ma, Xiang Li, Wenjie Sun, Xiaoliang Sunney Xie

The paper identifies correlated gene modules using single-cell RNA-seq, revealing biological functions and regulatory relationships through covariance analysis.

bioRxiv · Dec 31, 2019 · PreprintGenomics