Diego Calderon, PhD

Assistant Professor
Department of Bioengineering and Therapeutic Sciences
calderon
[email protected]
1550 Fourth Street, Rm 584E
UCSF Box 2911
San Francisco, CA 94158
United States

Links

UCSF Profiles

What I do

My lab studies how DNA is translated into life and how genetic mutations can lead to disease using cutting-edge computational and experimental techniques. Recently, I have been excited to apply deep learning and other machine learning approaches to interpret results from massively parallel reporter assays (MPRAs), single-cell assays, and CRISPR screens.

Departmental research area

pharmacogenomics and genomics
computational biology and chemistry

My research expertise

genomics, genetics, gene regulation, computational biology

Professional background

Degrees

PhD, Biomedical Informatics, Stanford University
BA, Computer Science and Biology, Wesleyan University

Biography

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.

Research keywords

  • 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
  • Single-Cell Analysis
  • Oligodendroglia
  • Gene Expression Regulation, Developmental
  • embryonic development
  • Microglia
  • Allelic Imbalance
  • Chromatin
  • software
  • B-Lymphocytes
  • Drosophila Proteins
  • Drosophila melanogaster
  • Response Elements
  • T-Lymphocytes
  • Gene Expression Regulation
  • Killer Cells, Natural
1. Career Awards at the Scientific Interface (CASI), Burroughs Wellcome Fund, 2022
2. K99/R00 Pathway to Independence Award (declined), NIH, 2022
3. NRSA Individual Postdoctoral Fellowship (F32), NIH, 2021-2022
4. Graduated with Honors, Wesleyan University, 2013

Publications

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.
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.
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.
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.
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 Aug 05; 377(6606):eabn5800.
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 Mar; 54(3):328-341.
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 Nov 08; 366(6466):708-714.
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.
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.
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.
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.