Research Summary

I am a developmental biologist as well as a pediatrician and clinical geneticist, and I am interested in translating an understanding of developmental mechanisms into advances for regenerative medicine. After completing the MD/PhD degrees and a pediatric residency, I trained in Medical Genetics. As a physician scientist, I treat patients with various syndromes, including those that predispose patients to cancer. As the Chief of the Division of Genetics at UCSF and Chair of the Division of Craniofacial Anomalies at UCSF, I take a strong interest in integrating clinical and research activities. Work in my research group centers on organ development and regeneration, with a major focus on understanding the processes underlying stem cell-based renewal and on integrating evolutionary and developmental approaches.

Research Funding

  • September 15, 2020 - June 30, 2025 - The physical and molecular mechanisms of intestinal villus morphogenesis and repair , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01DK126376
  • September 5, 2014 - August 31, 2024 - The roles of regional specialization, mechanical forces and epigenetic memory after perturbation and injury of the intestinal stem cell microenvironment , Principal Investigator . Sponsor: NIH, Sponsor Award ID: U01DK103147
  • August 1, 2021 - July 31, 2024 - Enamel atlas: systems-level amelogenesis tools at multiple scales , Principal Investigator . Sponsor: NIH, Sponsor Award ID: UH3DE028872
  • September 22, 2016 - June 30, 2024 - Harnessing natural stem cell-based strategies for mammalian dental renewal , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R35DE026602


University of California, Berkeley, B.A., 1993, Spanish
Yale University, New Haven, CT, Ph.D., 1999, Genetics
Yale University, New Haven, CT, M.D., 2000
Yale-New Haven Hospital, New Haven, CT, 2000-2003, Pediatrics
University of California, San Francisco, 2003-2007, Clinical Genetics

Honors & Awards

  • 2010
    New Innovator Award, National Institutes of Health
  • 2013
    Physician Scientist Award, California Institute of Regenerative Medicine
  • 2013
    Elected Member, American Society for Clinical Investigation
  • 2013
    Outstanding Faculty Mentorship Award, UCSF Graduate Students' Association
  • 2014
    Larry L. Hillblom Distinguished Professor in Craniofacial Anomalies, UCSF
  • 2014
    Elected Fellow, American Association for the Advancement of Science (AAAS)
  • 2015
    E. Mead Johnson Award, Society for Pediatric Research
  • 2015
    Faculty Research Lecturer Award, UCSF School of Dentistry
  • 2016
    Charles J. Epstein Professor of Human Genetics, UCSF
  • 2016
    Inaugural Sustaining Outstanding Achievement in Research (SOAR) R35 Award, National Institute of Dental and Craniofacial Research
  • 2017
    Craniofacial Biology Distinguished Scientist Award, International Association for Dental Research
  • 2017
    Lawrence A. Tabak Lecturer, University of Rochester
  • 2018
    Elected Member, National Academy of Medicine (NAM)

Selected Publications

  1. Devine J, Vidal-García M, Liu W, Neves A, Lo Vercio LD, Green RM, Richbourg HA, Marchini M, Unger CM, Nickle AC, Radford B, Young NM, Gonzalez PN, Schuler RE, Bugacov A, Rolian C, Percival CJ, Williams T, Niswander L, Calof AL, Lander AD, Visel A, Jirik FR, Cheverud JM, Klein OD, Birnbaum RY, Merrill AE, Ackermann RR, Graf D, Hemberger M, Dean W, Forkert ND, Murray SA, Westerberg H, Marcucio RS, Hallgrímsson B. MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. Sci Data. 2022 05 25; 9(1):230.  View on PubMed
  2. Lo M, Sharir A, Paul MD, Torosyan H, Agnew C, Li A, Neben C, Marangoni P, Xu L, Raleigh DR, Jura N, Klein OD. CNPY4 inhibits the Hedgehog pathway by modulating membrane sterol lipids. Nat Commun. 2022 May 03; 13(1):2407.  View on PubMed
  3. Bannister J, Wilms M, Aponte D, Katz D, Klein OD, Bernier FP, Spritz R, Hallgrimsson B, Forkert ND. A Deep Invertible 3D Facial Shape Model For Interpretable Genetic Syndrome Diagnosis. IEEE J Biomed Health Inform. 2022 Apr 05; PP.  View on PubMed
  4. Pincha N, Marangoni P, Haque A, Klein OD. Parallels in signaling between development and regeneration in ectodermal organs. Curr Top Dev Biol. 2022; 149:373-419.  View on PubMed
  5. Rusu I, Mennillo E, Bain JL, Li Z, Sun X, Ly KM, Rosli YY, Naser M, Wang Z, Advincula R, Achacoso P, Shao L, Razani B, Klein OD, Marson A, Turnbaugh JA, Turnbaugh PJ, Malynn BA, Ma A, Kattah MG. Microbial signals, MyD88, and lymphotoxin drive TNF-independent intestinal epithelial tissue damage. J Clin Invest. 2022 Mar 01; 132(5).  View on PubMed
  6. Yu T, Cazares O, Tang AD, Kim HY, Wald T, Verma A, Liu Q, Barcellos-Hoff MH, Floor SN, Jung HS, Brooks AN, Klein OD. SRSF1 governs progenitor-specific alternative splicing to maintain adult epithelial tissue homeostasis and renewal. Dev Cell. 2022 03 14; 57(5):624-637.e4.  View on PubMed
  7. Ma R, Gong D, You H, Xu C, Lu Y, Bergers G, Werb Z, Klein OD, Petritsch CK, Lu P. LGL1 binds to Integrin β1 and inhibits downstream signaling to promote epithelial branching in the mammary gland. Cell Rep. 2022 02 15; 38(7):110375.  View on PubMed
  8. Tidyman WE, Goodwin AF, Maeda Y, Klein OD, Rauen KA. MEK-inhibitor-mediated rescue of skeletal myopathy caused by activating Hras mutation in a Costello syndrome mouse model. Dis Model Mech. 2022 02 01; 15(2).  View on PubMed
  9. Shieh JT, Penon-Portmann M, Wong KHY, Levy-Sakin M, Verghese M, Slavotinek A, Gallagher RC, Mendelsohn BA, Tenney J, Beleford D, Perry H, Chow SK, Sharo AG, Brenner SE, Qi Z, Yu J, Klein OD, Martin D, Kwok PY, Boffelli D. Publisher Correction: Application of full-genome analysis to diagnose rare monogenic disorders. NPJ Genom Med. 2021 Oct 12; 6(1):88.  View on PubMed
  10. Palikuqi B, Rispal J, Klein O. Good Neighbors: The Niche that Fine Tunes Mammalian Intestinal Regeneration. Cold Spring Harb Perspect Biol. 2021 Sep 27.  View on PubMed
  11. Shieh JT, Penon-Portmann M, Wong KHY, Levy-Sakin M, Verghese M, Slavotinek A, Gallagher RC, Mendelsohn BA, Tenney J, Beleford D, Perry H, Chow SK, Sharo AG, Brenner SE, Qi Z, Yu J, Klein OD, Martin D, Kwok PY, Boffelli D. Application of full-genome analysis to diagnose rare monogenic disorders. NPJ Genom Med. 2021 Sep 23; 6(1):77.  View on PubMed
  12. Cazares O, Haque AS, Klein OD. Salivary gland: A budding genius. Dev Cell. 2021 08 23; 56(16):2271-2272.  View on PubMed
  13. Kim R, Yu T, Li J, Prochazka J, Sharir A, Green JBA, Klein OD. Early perturbation of Wnt signaling reveals patterning and invagination-evagination control points in molar tooth development. Development. 2021 07 15; 148(14).  View on PubMed
  14. Matthews HS, Palmer RL, Baynam GS, Quarrell OW, Klein OD, Spritz RA, Hennekam RC, Walsh S, Shriver M, Weinberg SM, Hallgrimsson B, Hammond P, Penington AJ, Peeters H, Claes PD. Large-scale open-source three-dimensional growth curves for clinical facial assessment and objective description of facial dysmorphism. Sci Rep. 2021 06 09; 11(1):12175.  View on PubMed
  15. Tallapragada NP, Cambra HM, Wald T, Keough Jalbert S, Abraham DM, Klein OD, Klein AM. Inflation-collapse dynamics drive patterning and morphogenesis in intestinal organoids. Cell Stem Cell. 2021 09 02; 28(9):1516-1532.e14.  View on PubMed
  16. Sanman LE, Chen IW, Bieber JM, Steri V, Trentesaux C, Hann B, Klein OD, Wu LF, Altschuler SJ. Transit-Amplifying Cells Coordinate Changes in Intestinal Epithelial Cell-Type Composition. Dev Cell. 2021 02 08; 56(3):356-365.e9.  View on PubMed
  17. Stella I, Helleringer M, Joud A, Chastagner P, Thomas R, Klein O. Optic pathway tumor in children: Toward a new classification for neurosurgical use. Neurochirurgie. 2021 Jul; 67(4):336-345.  View on PubMed
  18. Wong JC, Perez-Mancera PA, Huang TQ, Kim J, Grego-Bessa J, Del Pilar Alzamora M, Kogan SC, Sharir A, Keefe SH, Morales CE, Schanze D, Castel P, Hirose K, Huang GN, Zenker M, Sheppard D, Klein OD, Tuveson DA, Braun BS, Shannon K. KrasP34R and KrasT58I mutations induce distinct RASopathy phenotypes in mice. JCI Insight. 2020 11 05; 5(21).  View on PubMed
  19. Toda S, McKeithan WL, Hakkinen TJ, Lopez P, Klein OD, Lim WA. Engineering synthetic morphogen systems that can program multicellular patterning. Science. 2020 10 16; 370(6514):327-331.  View on PubMed
  20. Lu Y, Deng R, You H, Xu Y, Antos C, Sun J, Klein OD, Lu P. Asymmetric Stratification-Induced Polarity Loss and Coordinated Individual Cell Movements Drive Directional Migration of Vertebrate Epithelium. Cell Rep. 2020 10 13; 33(2):108246.  View on PubMed

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