Pre-prints

High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo

Sergio Garcia-Moreno Alcantara, Simon Bourdareau, Melanie Weilert, Julia Zeitlinger (2025) BioRxiv

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

Melanie Weilert, Kaelan J. Brennan, Khyati Dalal, Sabrina Krueger, Haining Jiang, Rosa Martinez-Corral, Julia Zeitlinger (2025) BioRxiv

PISA: a versatile interpretation tool for visualizing cis-regulatory rules in genomic data

Charles E. McAnany, Melanie Weilert, Grishma Mehta,  Fahad Kamulegeya, Jennifer M. Gardner, Anshul Kundaje, Julia Zeitlinger (2025) BioRxiv

Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model

Khyati Dalal, Charles McAnany, Melanie Weilert, Mary Cathleen McKinney, Sabrina Krueger, Julia Zeitlinger (2025) Cell Genomics

Featured Publications

Perspective on recent developments and challenges in regulatory and systems genomics

Zeitlinger J, Roy S, Ay F, Mathelier A, Medina-Rivera A, Mahony S, Sinha S, Ernst J. Bioinform Adv. 2025;5:vbaf106.

Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model

Dalal K, McAnany C, Weilert M, McKinney MC, Krueger S, Zeitlinger J. Cell Genom. 2025:100821.

Co-option of the trichome-forming network initiated the evolution of a morphological novelty in Drosophila eugracilis

Rice G, Gaitan-Escudero T, Charles-Obi K, Zeitlinger J, Rebeiz M. Curr Biol. 2024;34:5284-5294 e5283.

The multi-lineage transcription factor ISLI controls cardiomyocyte cell fate through interaction with NKX2.5

Maven BEJ, Gifford CA, Weilert M, Gonzalez-Teran B, Huttenhain R, Pelonero A, Ivey KN, Samse-Knapp K, Kwong W, Gordon D, McGregor M, Nishino T, Okorie E, Rossman S, Costa MW, Krogan NJ, Zeitlinger J, Srivastava D. Stem Cell Rep. [published ahead of print October 21 2023]. 2023.

Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation

Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. [published ahead of print August 8 2023]. Dev Cell 2023;58:1-19.

Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development.

Ramalingam V, Yu X, Slaughter BD, Unruh JR, Brennan KJ, Onyshchenko A, Lange JJ, Natarajan M, Buck M, Zeitlinger J. Nat Commun. 2023;14:5862 doi: 10.1038/s41467-023-41408-1.

Short tandem repeats bind transcription factorsto tune eukaryotic gene expression

Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordan R, Zeitlinger J, Kundaje A, Fordyce PM.  Science. 2023;381:eadd1250.

Emerging questions in transcriptional regulation : What are the sequence rules driving gene regulation?

Nora EP, Aerts S, Wittkopp PJ, Bussemaker HJ, Bulyk M, Sinha S, Zeitlinger J, Crocker J, Fuxman Bass JI. Cell Syst. 2023;14:247-251.

Off the deep end: What can deep learning do for the gene expression field?

Raicu AM, Fay JC, Rohner N, Zeitlinger J, Arnosti DN. J Biol Chem. 2023;299:102760.

The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters

Soffers JHM, Alcantara SG, Li X, Shao W, Seidel CW, Li H, Zeitlinger J, Abmayr SM, Workman JL. PLoS Genet. 2021;17:e1009668. doi: 10.1371/journal.pgen.1009668.

Base-resolution models of transcription-factor binding reveal soft motif syntax

Avsec Z, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Nat Genet. 2021;53:354-366.