Author

Kaelan Brennan

Stowers Institute for Medical ResearchORCID 0000-0002-4237-4874Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 3 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Assay:ChIP-seq· 3 Research Focus:gene regulatory network inference· 3 Organism:Drosophila· 2 Approach:experimental assay· 2 Research Focus:cell type annotation· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Organism:human· 1

Frequent Co-Authors

Julia ZeitlingeriD· 3 shared Melanie WeilertiD· 2 shared Sabrina KruegeriD· 2 shared Ally W. H. YangiD· 1 shared Anastasiia OnyshchenkoiD· 1 shared Andrew B. StergachisiD· 1 shared Anshul Bharat KundajeiD· 1 shared Anusri PampariiD· 1 shared

Activity by Year

2022-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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3 shared papersGenomics

Julia ZeitlingerORCID

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Author profile →

4 papers

Recent·Most cited

Enhancer Tuning by Sequence-Specific Repressors

Lucia Ichino, Kaelan Brennan, Benjamin J. Mallory, Tomek Swigut, Stephanie C. Bohaczuk, Jaaved Mohammed, Devaraja Gouda Mudeppa, Saman Tabatabaee, Chunyang Ni, Andrew B. Stergachis, Joanna Wysocka

This study shows that SNAI1 and SNAI2 repressors tune enhancer activity by shifting chromatin states, affecting enhancer function and evolution.

bioRxiv · Sep 14, 2026 · PreprintMolecular Biology

Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs

Melanie Weilert, Kaelan Brennan, Khyati Dalal, Sabrina Krueger, Haining Jiang, Rosa Martinez-Corral, Julia Zeitlinger

The paper maps and interprets low-affinity transcription factor motifs in mESCs, showing they enhance chromatin accessibility and regulatory potential through cooperative interactions.

Cell Genomics · Aug 25, 2026Peer-reviewedGenomics

Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation

Kaelan Brennan, Melanie Weilert, Sabrina Krueger, Anusri Pampari, Hsiao‐Yun Liu, Ally W. H. Yang, Jason A. Morrison, Timothy R. Hughes, Christine A. Rushlow, Anshul Bharat Kundaje, Julia Zeitlinger

The paper uses deep learning to analyze chromatin accessibility in Drosophila embryos, revealing a two-phase process driven by pioneer TFs and enhancer-activating TFs.

Developmental Cell · Aug 8, 2023Peer-reviewedGenomics

Lola-I is a developmentally regulated promoter pioneer factor

Vivekanandan Ramalingam, Xinyang Yu, Brian D. Slaughter, Jay R. Unruh, Kaelan Brennan, Anastasiia Onyshchenko, Jeffrey J. Lange, Malini Natarajan, Michael Joseph Buck, Julia Zeitlinger

The paper shows that Lola-I, a Drosophila zinc finger transcription factor, regulates promoter accessibility and paused Pol II during development, similar to enhancer regulation by pioneer factors.

bioRxiv · Apr 25, 2022 · PreprintGenomics