Author

Deborah A. Chasman

University of Wisconsin–MadisonORCID 0000-0002-7324-0131Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Bioinformatics· 2 Systems Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:gene regulatory network inference· 3 Approach:statistical model· 3 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Assay:Hi-C· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Sara KnaackiD· 2 shared Sushmita RoyiD· 2 shared Alireza Fotuhi SiahpiraniiD· 1 shared Anthony GitteriD· 1 shared Audrey P. GaschiD· 1 shared Evgenia ShishkovaiD· 1 shared James Livingston Thomson· 1 shared Joshua J. CooniD· 1 shared

Activity by Year

2018-2020 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 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 papersBioinformatics

Sara KnaackORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

BioinformaticsbioRxivPreprintJul 18, 2020

Dynamic regulatory module networks for inference of cell type-specific transcriptional networks

Alireza Fotuhi Siahpirani, Sara Knaack, Deborah A. Chasman…·Sushmita Roy

This paper introduces DRMN, a method to infer cell type-specific transcriptional networks from multi-omic data, showing it accurately predicts cis-regulators and models network dynamics.

6 citations

bulk RNA-seqATAC-seq

𝕏 PostBluesky

BioinformaticsNature CommunicationsPeer-reviewedDec 6, 2019

In silico prediction of high-resolution Hi-C interaction matrices

Shilu Zhang, Deborah A. Chasman, Sara Knaack, Sushmita Roy

HiC-Reg predicts high-resolution Hi-C interaction matrices from regulatory signals, identifying topologically associated domains and CTCF motifs.

120 citations

Hi-Cstatistical model

𝕏 PostBluesky

Systems BiologyPLoS Computational BiologyPeer-reviewedMay 8, 2018

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

Matthew E. MacGilvray, Evgenia Shishkova, Deborah A. Chasman…·Audrey P. Gasch

The paper infers a signaling network regulating phosphorylation changes in yeast during salt stress, revealing novel interactions between stress and growth pathways.

23 citations

yeastproteomics

𝕏 PostBluesky