Diego Calderon, PhD

Diego Calderon, PhD

Assistant Professor, Bioengineering and Therapeutic Sciences, UCSF Investigator, CZ Biohub – San Francisco

Cancer Center Program Membership

Molecular Oncology

1550 Fourth Street, #584E
San Francisco, CA 94158

UCSF Profiles

Lab Website

Research Summary

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.

Education

  • 2019 – 2024 Postdoctoral Scholar Fellow, University of Washington
  • 2013 – 2019 Ph.D. graduate student, Biomedical Informatics, Stanford University
  • 2012 University of Utah Summer Research Program participant

Honors & Awards

  • 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

Selected Publications

  1. Suiter CC, Calderon D, Lee DS, Chiu M, Jain S, Chardon FM, Lee C, Daza RM, Trapnell C, Zheng N, Shendure J. Combinatorial mapping of E3 ubiquitin ligases to their target substrates. Mol Cell. 2025 Feb 20; 85(4):829-842.e6.  View on PubMed
  2. 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, single-cell CRISPRa screening for cell type specific regulatory elements. Nat Commun. 2024 Sep 18; 15(1):8209.  View on PubMed
  3. Lalanne JB, Regalado SG, Domcke S, Calderon D, Martin BK, Li X, Li T, Suiter CC, Lee C, Trapnell C, Shendure J. Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nat Methods. 2024 Jun; 21(6):983-993.  View on PubMed
  4. 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. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. bioRxiv. 2024 Apr 30.  View on PubMed
  5. 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. Cell. 2024 May 09; 187(10):2411-2427.e25.  View on PubMed
  6. Li X, Chen W, Martin BK, Calderon D, Lee C, Choi J, Chardon FM, McDiarmid T, Kim H, Lalanne JB, Nathans JF, Shendure J. Chromatin context-dependent regulation and epigenetic manipulation of prime editing. bioRxiv. 2023 Apr 12.  View on PubMed
  7. 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. The continuum of Drosophila embryonic development at single-cell resolution. Science. 2022 08 05; 377(6606):eabn5800.  View on PubMed
  8. 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. Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nat Genet. 2022 03; 54(3):328-341.  View on PubMed
  9. 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. Ancient Rome: A genetic crossroads of Europe and the Mediterranean. Science. 2019 11 08; 366(6466):708-714.  View on PubMed
  10. 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. Landscape of stimulation-responsive chromatin across diverse human immune cells. Nat Genet. 2019 10; 51(10):1494-1505.  View on PubMed
  11. 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. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Res. 2018 01; 28(1):122-131.  View on PubMed
  12. Calderon D, Bhaskar A, Knowles DA, Golan D, Raj T, Fu AQ, Pritchard JK. Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression. Am J Hum Genet. 2017 Nov 02; 101(5):686-699.  View on PubMed
  13. 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. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proc Natl Acad Sci U S A. 2013 Dec 17; 110(51):20651-6.  View on PubMed

Go to UCSF Profiles, powered by CTSI