Featured Publications
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.
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.
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.