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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

Preprint (BiorXiv)​

Intergenic polyA/T tracts explain the propensity of yeast de novo genes to encode transmembrane domains

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Nikolaos Vakirlis; Timothy Fuqua​​

Nature Communications

2025-05-21 | Journal article

DOI: 10.1038/s41467-025-60023-w

The latent cis-regulatory potential of mobile DNA in Escherichia coli

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Timothy Fuqua; Andreas Wagner

PLoS Comp. Bio.

2025-01-29 | Journal article

DOI: 10.1371/journal.pcbi.1012349

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

eLIFE

2024-12-20 | Journal article

DOI: 10.7554/eLife.98654.3​

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

DOI: 10.1098/rstb.2022.0054

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

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

Nature

2020-11-12 | Journal article

DOI: 10.1038/s41586-020-2816-5

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

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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

Email

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