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Julia Zeitlinger

B.Sc., Human Biology, King’s College
Ph.D., Molecular Biology, University of London and European Molecular Biology Laboratory

Portrait of Julia Zeitlinger, Ph.D.

"We’re not pressured to develop a drug or cure disease and so this allows us to focus on fundamental problems. We share this love of foundational science."

Research Areas

Development and Regeneration, Genetics and Genomics, Molecular and Cell Biology, Systems Biology

Courses Taught

Gene Expression: Transcription to Translation; Genomic and Computational Approaches to Understanding Gene Expression; Laboratory Rotation; Thesis Laboratory



Neaves Award


Hudson Prize


Pew Scholar


National Institutes of Health New Innovator Award

Julia Zeitlinger, Ph.D., is a developmental and computational biologist where she serves as an Investigator at the Stowers Institute.

The Zeitlinger Lab focuses on gene regulation using the fruit fly, Drosophila, with the goal of uncovering principles that can be applied to human development and disease. Her team also studies both the coding and non-coding portions of DNA that impact gene expression and regulation.

Growing up in Germany, Zeitlinger loved math, science and the arts. The time she spent in school theater productions inspired dreams of becoming an actress. But ultimately, she fell in love with developmental biology during her anatomy classes in Germany and her first stint at laboratory research at King’s College London. Zeitlinger went on to earn a Ph.D. in developmental genetics from the European Molecular Biology Laboratory in Heidelberg and pursued a postdoctoral fellowship at the Massachusetts Institute of Technology, intrigued by the up-and-coming field of genomics and an opportunity to reconnect with her love for math.

In 2007, she joined the Stowers Institute, where she found a perfect alignment with the Institute’s scientific research focus on genomics, transcription, and developmental biology. Since then she has combined her analytical skills and creativity to develop the latest genomics technologies and to understand the complexities of gene regulation during development.

Featured Publications

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.

Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA Polymerase pausing

Shao W, Alcantara SG, Zeitlinger J. eLife. 2019;8:e41461. doi: 41410.47554/eLife.41461.

Paused RNA polymerase II inhibits new transcriptional initiation

Shao W, Zeitlinger J. Nat Genet. 2017;49:1045-1051.


Drosophila poised enhancers are generated during tissue patterning with the help of repression

Koenecke N, Johnston J, He Q, Meier S, Zeitlinger J. Genome Res. 2017;27:64-74.

Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation.

Sun Y, Nien CY, Chen K, Liu HY, Johnston J, Zeitlinger J, Rushlow C. Genome Res. 2015;25:1703-14.

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.

He Q, Johnston J, Zeitlinger J. Nat Biotechnol. 2015;33:395-401.

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