
Timothy Fuqua, Ph.D.
I am a molecular biologist working as a postdoc at the University of Zurich, Switzerland. My research focuses on the evolution of gene expression, and where new gene expression comes from, which is oftentimes called regulatory emergence. We research these questions in both prokaryotes (E. coli ) and eukayotes (D. melanogaster ), using a combination of high-throughput experimental techniques such as massively parallel reporter assays (MPRAs) and computational methods including machine learning. Check out the Publications and About Me sections below to see more.
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For editors, see the Contact section for peer-review requests!
Publications
2025-01-29 | PLoS Comp. Bio.
Spherical harmonics texture extraction for versatile analysis of biological objects
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Oane Gros; Josiah B Passmore; Noa Borst; Dominik Kutra; Wilco Nijenhuis; Timothy Fuqua; Lukas C Kapitein; Justin M Crocker; Anna Kreshuk; Simone Koehler
2024-12-20 | eLife
The emergence and evolution of gene expression in genome regions replete with regulatory motifs
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Timothy Fuqua; Yiqiao Sun; Andreas Wagner
Philosophical Transactions of the Royal Society B: Biological Sciences
2023-05-22 | Journal article
Mutational scans reveal differential evolvability of Drosophila promoters and enhancers
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Xueying C. Li; Timothy Fuqua; Maria Elize van Breugel; Justin Crocker
2023-10-25 | Preprint
Mobile DNA is replete with hotspots for the de novo emergence of gene regulation
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Timothy Fuqua; Andreas Wagner
Developmental Cell
2023-01 | Journal article
DOI: 10.1016/j.devcel.2022.12.003
Part of ISSN: 1534-5807
Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development
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Rafael Galupa; Gilberto Alvarez-Canales; Noa Ottilie Borst; Timothy Fuqua; Lautaro Gandara; Natalia Misunou; Kerstin Richter; Mariana R.P. Alves; Esther Karumbi; Melinda Liu Perkins et al.er
Scientific Reports
2021-12 | Journal article
DOI: 10.1038/s41598-021-89676-5
Part of ISSN: 2045-2322
An open-source semi-automated robotics pipeline for embryo immunohistochemistry
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Timothy Fuqua; Jeff Jordan, Aliaksandr Halavatyi, Christian Tischer, Kerstin Richter, Justin Crocker
Dense and pleiotropic regulatory information in a developmental enhancer
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Timothy Fuqua; Jeff Jordan; Maria Elize van Breugel; Aliaksandr Halavatyi; Christian Tischer; Peter Polidoro; Namiko Abe; Albert Tsai; Richard S. Mann; David L. Stern et al.
About me
My academic journey (so far):
Position
4. Postdoc
Nov 2021 – Present
Zurich, Switzerland
The University of Zurich (UZH)
Prof. Dr. Andreas Wagner
3. PhD Degree
Jul 2017 – Sep 2021 Heidelberg, Germany
European Molecular Biology Laboratory (EMBL)
The Evolutionary Landscape of a Developmental Enhancer
Dr. Justin Crocker

2. Visiting Scientist
Jul 2017 – Oct 2017
Ashburn, USA
HHMI Janelia Research Campus
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Dr. David L. Stern​
1. Bachelor’s Degree
Aug 2013 – May 2017 Iowa City, USA
The University of Iowa – Genetics and Biotechnology
Characterizing DNA Regulatory Elements in D. melanogaster
Dr. Albert Erives