The paper identifies autoimmune disease-associated variants that disrupt transcription factor-cofactor complex assembly and enhancer activity using the CASCADE method in Jurkat T cells.

bioRxiv · May 22, 2026 · PreprintGenomics

Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals

Berkay ENGİN, Mohamed Yousry ElSadec, Joseph Alexander Finkelberg, Tommy Henry Taslim, Daniel L. Bryant, Luis F. Soto-Ugaldi, Susan Kales, Ching‐Huang Ho, Maryam Dashtiahangar, George D. Muñoz-Esquivel, Elvis Morara, Jacob Purinton, Benedetta D’Elia, Rodrigo I. Castro, Harshpreet Chandok, , Juan I. Fuxman Bass

The paper creates a regulatory atlas of HIV-1 and HIV-2 by analyzing transcriptional variation across clades, isolates, and individuals using MPRAs and predictive models.

bioRxiv · Apr 6, 2026 · PreprintMicrobiology

Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in Synovial Sarcoma

Konstantinos V. Floros, Carter K. Fairchild, Jinxiu Li, Kun Zhang, Jane L. Roberts, Richard Kurupi, Durga Paudel, Yanli Xing, Bin Hu, Vita Kraskauskiene, Nayyerehalsadat Hosseini, Shanwei Shen, Melissa M. Inge, Kyllie Smith-Fry, Li Li, , Anthony C. Faber

This study shows that inhibiting SUMOylation with TAK-981 stabilizes cBAF complexes and disrupts the SS18::SSX-driven transcriptome in synovial sarcoma, leading to tumor inhibition.

Nature Communications · Nov 5, 2025Peer-reviewedCancer Biology

Single Nucleus MultiOmics Links Novel Transcription Factor Motifs to Murine Hepatic Sex Differences in Chromatin Accessibility and Metabolic Dysfunction-Associated Steatotic Liver Disease

Kritika Karri, Ting-Ya Chang, Maxim Pyatkov, Shashi Gandhi, Trevor Siggers, David J. Waxman

This study uses single-nucleus multi-omics to identify sex-specific transcription factor motifs linked to chromatin accessibility and MASLD in mouse liver.

bioRxiv · Oct 31, 2025 · PreprintGenomics

Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation

Melissa M. Inge, Rebekah Miller, Heather Hook, David Bray, Jessica L. Keenan, Rose W. Zhao, Thomas D. Gilmore, Trevor Siggers

The paper introduces CoRec, a method to profile TF-COF complexes, revealing KAT-TF interactions and their role in H3K27ac regulation.

Nucleic Acids Research · Aug 14, 2024Peer-reviewedMolecular Biology

A multi-tiered map of EMT defines major transition points and identifies vulnerabilities

Indranil Paul, Dante Bolzan, Ahmed Youssef, Keith A. Gagnon, Heather Hook, Gopal Karemore, Michael UJ Oliphant, Weiwei Lin, Qian Liu, Sadhna Phanse, Carl A. White, Dzmitry Padhorny, Sergei Kotelnikov, Guillaume P. Andrieu, Christopher S. Chen, , Andrew Emili

The paper maps EMT transitions through multi-omic profiling, identifies key regulatory factors, and reveals discordance between molecular layers in human mammary epithelial cells.

bioRxiv · Jun 1, 2021 · PreprintSystems Biology

Customizable high-throughput platform for profiling cofactor recruitment to DNA to characterize cis-regulatory elements and screen non-coding single-nucleotide polymorphisms

David Bray, Heather Hook, Rose W. Zhao, Jessica L. Keenan, Ashley R. Penvose, Yemi Osayame, Nima Mohaghegh, Trevor Siggers

The paper introduces CASCADE, a high-throughput platform to profile cofactor recruitment to DNA variants, identifying key regulators and ETS sites in macrophages.

bioRxiv · Apr 21, 2020 · PreprintGenomics

Varied effects of algal symbionts on transcription factor NF-κB in a sea anemone and a coral: possible roles in symbiosis and thermotolerance

Katelyn M. Mansfield, Phillip A. Cleves, Emily Van Vlack, Nicola G. Kriefall, Brooke E. Benson, Dimitrios J. Camacho, Olivia Hemond, Monique Pedroza, Trevor Siggers, John R. Pringle, Sarah W. Davies, Thomas D. Gilmore

The paper investigates the role of NF-κB in cnidarian-algal symbiosis and thermotolerance in Aiptasia and Pocillopora damicornis, showing differential expression and effects on survival and bleaching.

bioRxiv · May 17, 2019 · PreprintMolecular Biology

Biophysical Principles of Lineage Factor PU.1 Binding Revealed by NextPBMs

Nima Mohaghegh, David Bray, Jessica L. Keenan, Ashley R. Penvose, Kellen K Andrilenas, Vijendra Ramlall, Trevor Siggers

The paper introduces nextPBMs to study TF binding with PTMs and cofactors, revealing PU.1's binding modes and cofactor influences in monocytes.

Nucleic Acids Research · Jan 16, 2019Peer-reviewedMolecular Biology