Author

Jessica M. Halow

Altius Institute for Biomedical Sciences

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 4 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Assay:ChIP-seq· 4 Research Focus:gene regulatory network inference· 3 Approach:statistical model· 3 Organism:human· 2 Organism:mouse· 2 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1 Research Focus:database / resource· 1

Frequent Co-Authors

John A. StamatoyannopoulosiD· 4 shared Kristen LeeiD· 4 shared Richard S. SandstromiD· 4 shared Alex P. ReynoldsiD· 3 shared Daniel BatesiD· 3 shared Douglas Dunn· 3 shared Eric HaugeniD· 3 shared Eric RynesiD· 3 shared

Activity by Year

2020-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersGenomics

John A. StamatoyannopoulosORCID

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Author profile →

5 papers

Recent·Most cited

The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles

Jacob Matthew Schreiber, Carles A. Boix, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins‐Hooker, Bernhard Schölkopf, Gabriele Schweikert, Mateo Rojas-Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, , ENCODE Imputation Challenge Participants

The paper evaluates 23 imputation models for cross-cell type epigenomic data, finding quality assessment challenging due to distributional shifts, data availability, and redundant metrics.

Genome biology · Apr 18, 2023Peer-reviewedBioinformatics

Tissue context determines the penetrance of regulatory DNA variation

Jessica M. Halow, Rachel Byron, Megan S. Hogan, Raquel Ordóñez, Mark T. Groudine, M. A. Bender, John A. Stamatoyannopoulos, Matthew T. Maurano

The paper quantifies how tissue context influences the effect of regulatory DNA variants on transcription factor activity using allelic accessibility maps in mice.

Nature Communications · May 14, 2021Peer-reviewedGenomics

Index and biological spectrum of accessible DNA elements in the human genome

Wouter R. A. Meuleman, Alexander Muratov, Eric Rynes, Jessica M. Halow, Kristen Lee, Daniel Bates, Morgan Diegel, Douglas Dunn, Fidencio Jun Neri, Athanasios Teodosiadis, Alex P. Reynolds, Eric Haugen, Jemma S. Nelson, Audra Johnson, Mark Frerker, , John A. Stamatoyannopoulos

The paper creates high-precision maps of DNase I hypersensitive sites across 733 human biosamples and develops a regulatory vocabulary to annotate regulatory DNA, concentrating disease-associated signals.

Nature · Jul 29, 2020Peer-reviewedGenomics

Global reference mapping and dynamics of human transcription factor footprints

Jeff D. Vierstra, John E. Lazar, Richard S. Sandstrom, Jessica M. Halow, Kristen Lee, Daniel Bates, Morgan Diegel, Douglas Dunn, Fidencio Jun Neri, Eric Haugen, Eric Rynes, Alex P. Reynolds, Jemma S. Nelson, Audra Johnson, Mark Frerker, , John A. Stamatoyannopoulos

The paper maps transcription factor footprints across 243 human cell and tissue types, revealing their structure, function, and relationship to genetic variation and disease.

Nature · Jul 29, 2020Peer-reviewedGenomics

Atlas and developmental dynamics of mouse DNase I hypersensitive sites

Charles E. Breeze, John E. Lazar, Tim R. Mercer, Jessica M. Halow, Ida W. Smoak, Kristen Lee, Sean Ibarrientos, Andrés Castillo, Fidencio Jun Neri, Eric Haugen, Eric Rynes, Alex P. Reynolds, Daniel Bates, Morgan Diegel, Douglas Dunn, , John A. Stamatoyannopoulos

The paper creates a mouse regulatory DNA atlas by mapping DNase I hypersensitive sites across development and shows dynamic changes in regulatory elements and transcription factor activity.

bioRxiv · Jun 26, 2020 · PreprintGenomics