Author

Scott Ronquist

University of MichiganORCID 0000-0002-6514-9194Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Bioinformatics· 2 Cell Biology· 1 Genomics· 1 Immunology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:statistical model· 5 Assay:Hi-C· 4 Assay:bulk RNA-seq· 3 Assay:ChIP-seq· 3 Research Focus:gene regulatory network inference· 3 Organism:human· 3 Research Focus:cancer & tumor microenvironment· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

Indika RajapakseiD· 5 shared Lindsey A. MuiriD· 4 shared Sijia LiuiD· 3 shared Stephen LindslyiD· 3 shared Can CheniD· 2 shared Gabrielle A. DotsoniD· 2 shared Max S. WichaiD· 2 shared Walter MeixneriD· 2 shared

Activity by Year

2017-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 36 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

5 shared papersBioinformatics

Indika RajapakseORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Rearrangement of T Cell Genome ArchitectureRegulates GVHD

Yaping Sun, Gabrielle A. Dotson, Lindsey A. Muir, Scott Ronquist, Katherine I. Oravecz-Wilson, Daniel Peltier, Keisuke Seike, Lu Li, Walter Meixner, Indika Rajapakse, Pavan R. Reddy

This study shows that WAPL regulates T cell 3D genome structure, affecting activation, proliferation, and GVHD severity.

iScience · Aug 6, 2022Peer-reviewedImmunology

Functional Organization of the Maternal and Paternal Human 4D Nucleome

Stephen Lindsly, Wenlong Jia, Haiming Chen, Sijia Liu, Scott Ronquist, Can Chen, Xingzhao Wen, Cooper M. Stansbury, Gabrielle A. Dotson, Charles Ryan, Alnawaz Rehemtulla, Gilbert S. Omenn, Max S. Wicha, Shuai Cheng Li, Lindsey A. Muir, Indika Rajapakse

The paper investigates allele-specific relationships between gene expression and genome structure in human cells using integrated haplotype-resolved data.

iScience · Nov 16, 2021Peer-reviewedGenomics

4DNvestigator: Time Series Genomic Data Analysis Toolbox

Stephen Lindsly, Can Chen, Sijia Liu, Scott Ronquist, Samuel Dilworth, Michael D. Perlman, Indika Rajapakse

The paper introduces 4DNvestigator, a toolbox for analyzing time series Hi-C and RNA-seq data, with methods to quantify network and tensor entropy and detect significant changes over time.

Nucleus · Jan 1, 2021Peer-reviewedBioinformatics

Genome Architecture Leads a Bifurcation in Cell Identity

Sijia Liu, Haiming Chen, Scott Ronquist, Laura Seaman, Nicholas Ceglia, Lindsey A. Muir, Walter Meixner, Pin-Yu Chen, Gerald Higgins, Pierre Baldi, Steve Smale, Alfred Hero, Indika Rajapakse

This study shows that MYOD1-mediated reprogramming of human fibroblasts into muscle cells involves a genome architecture bifurcation point preceding transcriptional changes.

bioRxiv · Dec 21, 2017 · PreprintCell Biology

An Algorithm for Cellular Reprogramming

Scott Ronquist, Geoff Patterson, Lindsey A. Muir, Stephen Lindsly, Haiming Chen, Markus A. Brown, Max S. Wicha, Anthony M. Bloch, Roger W. Brockett, Indika Rajapakse

The paper introduces a data-guided algorithm for cellular reprogramming using transcription factors, validated on human fibroblasts and showing potential for tissue regeneration and cancer cell reprogramming.

Proceedings of the National Academy of Sciences · Oct 24, 2017Peer-reviewedBioinformatics