Diego Calderon, PhD

Title(s)Assistant Professor, Bioengineering
SchoolSchool of Pharmacy
PronounsHe/Him/His
ORCID ORCID Icon0000-0002-6990-9066 Additional info
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    Collapse Biography 
    Collapse education and training
    Stanford UniversityPhDBiomedical Informatics
    Wesleyan UniversityBAComputer Science and Biology
    Collapse awards and honors
    Burroughs Wellcome Fund2022Career Awards at the Scientific Interface (CASI)
    NIH2022K99/R00 Pathway to Independence Award (declined)
    NIH2021  - 2022NRSA Individual Postdoctoral Fellowship (F32)

    Collapse Overview 
    Collapse overview
    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.

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Combinatorial mapping of E3 ubiquitin ligases to their target substrates. Mol Cell. 2025 Feb 20; 85(4):829-842.e6. Suiter CC, Calderon D, Lee DS, Chiu M, Jain S, Chardon FM, Lee C, Daza RM, Trapnell C, Zheng N, Shendure J. PMID: 39919746; PMCID: PMC11845296.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. Nat Commun. 2024 Sep 18; 15(1):8209. 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. PMID: 39294132; PMCID: PMC11411074.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    3. Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nat Methods. 2024 Jun; 21(6):983-993. Lalanne JB, Regalado SG, Domcke S, Calderon D, Martin BK, Li X, Li T, Suiter CC, Lee C, Trapnell C, Shendure J. PMID: 38724692; PMCID: PMC11166576.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    4. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. bioRxiv. 2024 Apr 30. 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. PMID: 37034704; PMCID: PMC10081248.
      View in: PubMed   Mentions:
    5. Chromatin context-dependent regulation and epigenetic manipulation of prime editing. Cell. 2024 May 09; 187(10):2411-2427.e25. 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. PMID: 38608704; PMCID: PMC11088515.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    6. Chromatin context-dependent regulation and epigenetic manipulation of prime editing. bioRxiv. 2023 Apr 12. Li X, Chen W, Martin BK, Calderon D, Lee C, Choi J, Chardon FM, McDiarmid T, Kim H, Lalanne JB, Nathans JF, Shendure J. PMID: 37090511; PMCID: PMC10120711.
      View in: PubMed   Mentions:
    7. The continuum of Drosophila embryonic development at single-cell resolution. Science. 2022 08 05; 377(6606):eabn5800. 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. PMID: 35926038; PMCID: PMC9371440.
      View in: PubMed   Mentions: 32     Fields:    
    8. Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nat Genet. 2022 03; 54(3):328-341. 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. PMID: 35288709; PMCID: PMC8920898.
      View in: PubMed   Mentions: 62     Fields:    
    9. Ancient Rome: A genetic crossroads of Europe and the Mediterranean. Science. 2019 11 08; 366(6466):708-714. 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. PMID: 31699931; PMCID: PMC7093155.
      View in: PubMed   Mentions: 82     Fields:    Translation:Humans
    10. Landscape of stimulation-responsive chromatin across diverse human immune cells. Nat Genet. 2019 10; 51(10):1494-1505. 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. PMID: 31570894; PMCID: PMC6858557.
      View in: PubMed   Mentions: 127     Fields:    Translation:HumansCells
    11. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Res. 2018 01; 28(1):122-131. 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. PMID: 29208628; PMCID: PMC5749177.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansCells
    12. Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression. Am J Hum Genet. 2017 Nov 02; 101(5):686-699. Calderon D, Bhaskar A, Knowles DA, Golan D, Raj T, Fu AQ, Pritchard JK. PMID: 29106824; PMCID: PMC5673624.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansCells
    13. 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. 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. PMID: 24297900; PMCID: PMC3870661.
      View in: PubMed   Mentions: 188     Fields:    Translation:AnimalsCells
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