Diego Calderon, PhD | Biomedical Sciences Graduate Program

Assistant Professor

Primary Thematic Area

P_Bioengineering

Secondary Thematic Area

Research Summary

Our lab’s research focus is on developing and applying impactful genomic technologies toward understanding gene regulation underlying development and human diseases.

[email protected]

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. 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.

Publications

Combinatorial mapping of E3 ubiquitin ligases to their target substrates.

Molecular cell

Suiter CC, Calderon D, Lee DS, Chiu M, Jain S, Chardon FM, Lee C, Daza RM, Trapnell C, Zheng N, Shendure J

Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements.

Nature communications

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

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

Chardon FM, McDiarmid TA, Page NF, Martin B, Domcke S, Regalado SG, Lalanne J?, Calderon D, Starita LM, Sanders SJ, Ahituv N, Shendure J

Chromatin context-dependent regulation and epigenetic manipulation of prime editing.

Cell

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

Li X, Chen W, Martin BK, Calderon D, Lee C, Choi J, Chardon FM, McDiarmid T, Kim H, Lalanne JB, Nathans JF, Shendure J

The continuum of Drosophila embryonic development at single-cell resolution.

Science (New York, N.Y.)

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

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.)

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, Grifoni R, Guidi A, La Pastina F, Loreti E, Manacorda D, Matullo G, Morretta S, Nava A, Fiocchi Nicolai V, Nomi F, Pavolini C, Pentiricci M, Pergola P, Piranomonte M, Schmidt R, Spinola G, Sperduti A, Rubini M, Bondioli L, Coppa A, Pinhasi R, Pritchard JK

Landscape of stimulation-responsive chromatin across diverse human immune cells.

Nature genetics

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, Marson A, Pritchard JK

Impact of regulatory variation across human iPSCs and differentiated cells.

Genome research

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

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

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, Yandell M, Calderon D, Renjifo C, Currier RB, Salgado D, Pla D, Sanz L, Hyder AS, Ribeiro JM, Arntzen JW, van den Thillart GE, Boetzer M, Pirovano W, Dirks RP, Spaink HP, Duboule D, McGlinn E, Kini RM, Richardson MK