Diego Calderon, PhD
Assistant Professor
Bioengineering
School of Pharmacy
Dr. Diego Calderon was raised in nearby Fresno, California. He received his B.A. from Wesleyan University and subsequently conducted his Ph.D. research on the genetics underlying complex traits at Stanford University.
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Intrigued by massively parallel molecular biology, he then went on to become a postdoctoral fellow at the University of Washington, where he led projects involving the computational analysis of large-scale single-cell data and developed new massively parallel reporter assays to investigate gene regulation. In 2024, Diego joined UCSF as an Assistant Professor in the Department of Bioengineering and Therapeutic Sciences. The Calderon Lab broadly aims to understand all aspects of how DNA is translated into life using cutting-edge computational and experimental techniques. Our projects typically focus on using these techniques to study how DNA mutations can lead to disease or to characterize the cellular control of gene expression, but our interests encompass many topics generally related to DNA.
Awards
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- Career Awards at the Scientific Interface (CASI), Burroughs Wellcome Fund, 2022
- K99/R00 Pathway to Independence Award (declined), NIH, 2022
- NRSA Individual Postdoctoral Fellowship (F32), NIH, 2021-2022
- Graduated with Honors, Wesleyan University, 2013
Education & Training
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- PhD Biomedical Informatics Stanford University
- BA Computer Science and Biology Wesleyan University
Interests
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- biology
- GWAS
- massively parallel reporter assays
- bioinformatics
- genomics
- genome-wide association studies
- evolution
- genome editing
- MPRA
- single-cell assays
- gene regulation
- human disease
- computational biology
- CRISPR
- genetics
Websites
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- LinkedIn (linkedin.com)
- Google Scholar (scholar.google.com)
- SoP profile (pharmacy.ucsf.edu)
- Twitter (twitter.com)
Publications (12)
Top publication keywords:
Single-Cell AnalysisOligodendrogliaGene Expression Regulation, DevelopmentalEmbryonic DevelopmentMicrogliaCRISPR-Cas SystemsEnhancer Elements, GeneticChromatinSoftwareB-LymphocytesDrosophila melanogasterDrosophila ProteinsResponse ElementsT-LymphocytesKiller Cells, Natural
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Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements.
Nature communications 2024 Chardon FM, McDiarmid TA, Page NF, Daza RM, Martin BK, Domcke S, Regalado SG, Lalanne JB, Calderon D, Li X, Starita LM, Sanders SJ, Ahituv N, Shendure J -
Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters.
Nature methods 2024 Lalanne JB, Regalado SG, Domcke S, Calderon D, Martin BK, Li X, Li T, Suiter CC, Lee C, Trapnell C, Shendure J -
Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements.
bioRxiv : the preprint server for biology 2024 Chardon FM, McDiarmid TA, Page NF, Daza RM, Martin B, Domcke S, Regalado SG, Lalanne JB, Calderon D, Li X, Starita LM, Sanders SJ, Ahituv N, Shendure J -
Chromatin context-dependent regulation and epigenetic manipulation of prime editing.
Cell 2024 Li X, Chen W, Martin BK, Calderon D, Lee C, Choi J, Chardon FM, McDiarmid TA, Daza RM, Kim H, Lalanne JB, Nathans JF, Lee DS, Shendure J -
Chromatin context-dependent regulation and epigenetic manipulation of prime editing.
bioRxiv : the preprint server for biology 2023 Li X, Chen W, Martin BK, Calderon D, Lee C, Choi J, Chardon FM, McDiarmid T, Kim H, Lalanne JB, Nathans JF, Shendure J
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The continuum of Drosophila embryonic development at single-cell resolution.
Science (New York, N.Y.) 2022 Calderon D, Blecher-Gonen R, Huang X, Secchia S, Kentro J, Daza RM, Martin B, Dulja A, Schaub C, Trapnell C, Larschan E, O'Connor-Giles KM, Furlong EEM, Shendure J -
Systematic reconstruction of cellular trajectories across mouse embryogenesis.
Nature genetics 2022 Qiu C, Cao J, Martin BK, Li T, Welsh IC, Srivatsan S, Huang X, Calderon D, Noble WS, Disteche CM, Murray SA, Spielmann M, Moens CB, Trapnell C, Shendure J -
Ancient Rome: A genetic crossroads of Europe and the Mediterranean.
Science (New York, N.Y.) 2019 Antonio ML, Gao Z, Moots HM, Lucci M, Candilio F, Sawyer S, Oberreiter V, Calderon D, Devitofranceschi K, Aikens RC, Aneli S, Bartoli F, Bedini A, Cheronet O, Cotter DJ, Fernandes DM, Gasperetti G, … -
Landscape of stimulation-responsive chromatin across diverse human immune cells.
Nature genetics 2019 Calderon D, Nguyen MLT, Mezger A, Kathiria A, Müller F, Nguyen V, Lescano N, Wu B, Trombetta J, Ribado JV, Knowles DA, Gao Z, Blaeschke F, Parent AV, Burt TD, Anderson MS, Criswell LA, Greenleaf WJ, … -
Impact of regulatory variation across human iPSCs and differentiated cells.
Genome research 2017 Banovich NE, Li YI, Raj A, Ward MC, Greenside P, Calderon D, Tung PY, Burnett JE, Myrthil M, Thomas SM, Burrows CK, Romero IG, Pavlovic BJ, Kundaje A, Pritchard JK, Gilad Y -
Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression.
American journal of human genetics 2017 Calderon D, Bhaskar A, Knowles DA, Golan D, Raj T, Fu AQ, Pritchard JK -
The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.
Proceedings of the National Academy of Sciences of the United States of America 2013 Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wüster W, Woods AE, Logan JM, Harrison RA, Castoe TA, de Koning AP, Pollock DD, …