Physician Scientist Training Program (PSTP)

​UCSD Pediatric Physician Scientist Training Program 

The Department of Pediatrics at UC San Diego has a Physician Scientist Training Program (PSTP) developed to promote and encourage scientific investigation during physician training and to provide a pipeline for future fellows and faculty for our department. The program is open to residents with MD/PhD degrees and others with very strong research backgrounds who plan to pursue academic careers with a research emphasis.  The goal of the PSTP is for residents to successfully transition into the UCSD pediatric subspecialty fellowship of their choice after successfully completing residency. This allows for continuity of research projects and optimized integration with clinical training to prepare trainees for their first junior faculty positions. 
Our PSTP offers research-enhanced pediatric residency training through the American Board of Pediatrics Integrated Research Pathway and Accelerated Research Pathway. The program also has the flexibility to accommodate similarly enhanced training outside of the ABP pathways if a different training model better fits the resident’s academic goals.

Research Opportunities

Residents in the Pediatric PSTP have full access to the thriving research community both within UCSD and at other prominent research institutions throughout San Diego. UC San Diego and specifically the Department of Pediatrics have a very strong research portfolio allowing trainees to find mentors and collaborators in every area of medicine. Our Pediatric department has been ranked in the top-10 pediatric departments in the country in NIH research funding for the last 5 years. Residents and fellows training at UCSD can also choose mentors in other UC San Diego departments as well as at collaborating institutions in San Diego including the Scripps Research Institute, the Salk Institute for Biological Studies, the Sanford-Burnham Medical Research Institute, and the La Jolla Institute for Immunology.


We understand the importance of mentorship in paving the way for a successful academic research career. Physician-Scientist track residents are matched with both general pediatric mentors and research-specific mentors in their area(s) of interest. There is also a PSTP oversight committee that will meet regularly with residents for advice and to ensure that they are progressing as expected and receiving the support they need to succeed. 

Physician Scientist Training Program Oversight Committee Members

​Gabriel Haddad, MD
Chair, Department of Pediatrics
Research Focus: Cellular and Molecular Mechanisms Involved in Response to Oxygen Deprivation
Haddad Lab

Victor Nizet, MD
Vice-Chair for Basic Research
Research Focus: Bacterial Pathogenesis and Innate Immunity
Nizet Lab  

​Tariq Rana, PhD
Vice-Chair for Innovation in Therapeutics
Research Focus: RNA and Chemical Biology Approaches to Therapeutics
Rana Lab 

Hal Hoffman, MD
Division Chief of Allergy Immunology
Research Focus: Genetics of Rare Human Disorders
Hoffman Lab 

Peter Zage, MD, PhD
Division of Hematology-Oncology
Research Focus: Novel Targets and Treatment for Children with Solid Tumors
Zage Lab

Research Support

In agreement with the associated UCSD pediatric fellowship programs, funding will be made available for an extra year of fellowship to facilitate a successful transition to junior faculty roles.
The resources of the UC San Diego Altman Clinical and Translational Research Institute are available to trainees.


We work with each resident to develop a personalized schedule that works best for them and their goals.  
  • Accelerated Research Pathway: 2 years of residency followed by a 4-year subspecialty fellowship that includes an extra year for research
  • Integrated Research Pathway: 3 years of residency including up to 11 months of research integrated into your residency schedule
In the Integrated research pathway, a majority of intern year is spent doing pediatric rotations with opportunities to explore possible research labs and mentors. During the second and third years of residency, we offer research blocks (up to 11 months total) that can be personalized to focus on either intermixed research and clinical rotations or a few more extended blocks of research time. 

Fellowship Opportunities 

  • The Department of Pediatrics has active fellowships in all areas of pediatrics. Physician-Scientist track residents are anticipated to enter a fellowship at UCSD as long as residency performance was excellent. 
  • T32 Training Grants 
  • AMSPDC PSDP: We have been very successful in securing Association of Medical School Pediatric Department Chairs (AMSPDC) fellowship training awards
  • Twice monthly research symposia
  • Access to the UCSD Clinical Research Enhancement through Supplemental Training (CREST) program

Transition to Faculty Positions

Current Research Pathway Residents

​Alexander Carlson, MD, PhD

Undergraduate: Point Loma Nazarene University (BS in Biochemistry)
Medical School: University of North Carolina at Chapel Hill
PhD Research Focus: The role of the gut microbiome in modulating early brain development and behavior through the gut-brain axis. This work detailed novel associations of the infant gut microbiome with cognitive development, fear behavior, and brain development. 
Current Projects: My research projects focus on the intersection of the human gut microbiome with the developmental origins of health and disease framework. These include 1. The Gut Microbiome in Prenatal Arsenic Exposure and Infant Neurodevelopment. 2. Prenatal Toxic Stress and Infant Microbiome Development. 3. Investigating a Diagnostic and Etiologic Role of the Gut Microbiome in Autism. 
What would I like to tell applicants: Researchers at UCSD are excited to meet you and want to work with you! We are building our PSTP to ensure participants leave the program as outstanding clinicians and with a firm foundation of postgraduate research to launch their careers as a physician-scientists.
Favorite Thing About San Diego: Beach volleyball days with my co-residents!

Carlson, A. L., Xia, K., Azcarate-Peril, M. A., Rosin, S. P., Fine, J. P., Mu, W., Zopp, J. B., Kimmel, M. C., Styner, M. A., Thompson, A. L., Propper, C. B. & Knickmeyer, R. C. Infant gut microbiome composition is associated with non-social fear behavior in a pilot study. Nat. Commun. 12, 1–16 (2021). doi: 

Rosin, S. P., Xia, K., Azcarate-Peril, M. A., Carlson, A. L., Propper, C. B., Thompson, A. L., Grewen, K. & Knickmeyer, R. C. A Preliminary Study of Gut Microbiome Variation and HPA Reactivity in Healthy Infants. Psychoneuroendocrinology (2021). doi: 

Gao, W., Salzwedel, A. P., Carlson, A. L., Xia, K., Azcarate-Peril, M. A., Styner, M. A., Thompson, A. L., Geng, X., Goldman, B. D., Gilmore, J. H. & Knickmeyer, R. C. Gut microbiome and brain functional connectivity in infants-a preliminary study focusing on the amygdala. Psychopharmacology (Berl). 81, S300 S301 (2019). doi:10.1007/s00213-018-5161-8  

Carlson, A. L., Xia, K., Azcarate-Peril, M. A., Goldman, B. D., Ahn, M., Styner, M. A., Thompson, A. L., Geng, X., Gilmore, J. H. & Knickmeyer, R. C. Infant Gut Microbiome Associated With Cognitive Development. Biological Psychiatry (2017). doi:10.1016/j.biopsych.2017.06.021 

Alex Ghaben, MD, PhD

Undergraduate: Massachusetts Institute of Technology in Boston, MA (Chemical Biological Engineering and Biology) 
Medical School: UT Southwestern Medical School 
PhD Research Focus: Adipocyte-specific molecular mechanisms that influence systemic metabolic health independent of weight - further defining the role of adipose tissue as an endocrine tissue. To this end, using physiologically relevant mouse models to understand how altered intracellular adipocyte signaling influences the endocrine/paracrine function of adipocytes with downstream effects on processes such as adipogenesis and energy homeostasis. 
Favorite Thing About San Diego: Having easy access to both the beach and the mountains!

Ghaben AL, Scherer PE. Adipogenesis and Metabolic Disease. Nature Review Molecular and Cellular Biology 2019. PMID 30610207

Kusminski CM, Ghaben AL, Morely TS, Samms RJ, Adams AC, An Y, Johnson JA, Joffin N, Crewe C, Holland WL, Gordillo R, Schere PE. A novel model of diabetic complications: Adipocyte Mitochondrial Dysfunction Triggers Massive β-cell Hyperplasia. Diabetes, 2020. PMID: 31882562

Hepler C, Shao M, Ghaben AL, Pearson MJ, Vishvanath L, Sharma AX, Morely TS, Holland WL, Gupta RK. Directing visceral white adipocyte precursors to a thermogenic adipocyte fate improves insulin sensitivity in obese mice. Elife, 2017. PMID: 28722653

Crewe C, Funcke JB, Li S, Joffin N, Gliniak CM, Ghaben AL, An YA, Sadek HA, Akgul Y, Chen S, Samovski D, Fischer-Posovsky P, Kusminski CM, Klein S, Scherer PE. Extracellular vesicle-based interorgan transport of mitochondria from energetically stressed adipocytes. Cell Metabolism, 2021. PMID: 34418352.

Ben Hills, MD, PhD 

Undergraduate: Northeastern University in Boston, MA (Behavioral Neuroscience) 
Medical School: Dartmouth Geisel School of Medicine 
PhD: Microbiology and Immunology, Dartmouth College 
PhD Research Focus: Determining how post-translational modification of the transcription factor Foxo1 impacts CD8 T cell differentiation, survival, and formation of long-lived immunologic memory.
Current Projects: I am currently applying for an IRB to study immune system development from birth to early adulthood with a specific focus on B cell and T cell maturation using parallel single-cell transcriptomic and proteomic methods.
What would I like to tell applicants: I couldn't imagine a better place to embark on my physician-scientist career. Between UCSD and other local institutes such as Salk, Scripps, and LJI, we have the opportunity to work with world-class investigators across the spectrum of biological and biomedical sciences. We have incredible support from UCSD/Rady to tailor our training to best suit our individual needs and career goals. Finally, we get to train in a beautiful setting that allows us to recharge and develop interesting ideas about science and medicine in our free time.
Favorite Thing About San Diego: The confluence of the ocean, desert, and mountains is uniquely beautiful. Also, this is the first place I’ve lived where I can drive 10 minutes and see seals/sea lions. 

Abdullah L, Hills LB, Winter EB, Huang YH. Diverse Roles of Akt in T cells. Immunometabolism. 2021;3(1):e210007. doi: 10.20900/immunometab20210007. PMID: 33604081 

Hills LB, Abdullah L, Lust HE, Degefu H, Huang YH. Foxo1 Serine 209 Is a Critical Regulatory Site of CD8 T Cell Differentiation and Survival. J Immunol. 2021 206(1):89-100. doi: 10.4049/jimmunol.2000216. PMID: 33229443 

Wang X, Hills LB, Huang YH. Lipid and protein co-regulation of PI3K effectors Akt and Itk in lymphocytes. Frontiers in Immunology 2015 6:117. 

Howe JR 6th, Li ES, Streeter SE, Rahme GJ, Chipumuro E, Russo GB, Litzky JF, Hills LB, Rodgers KR, Skelton PD, Luikart BW. MiR-338-3p regulates neuronal maturation and suppresses glioblastoma proliferation. PLoS One. 2017 May 11;12(5):e0177661. doi: 10.1371/journal.pone.0177661. PMID: 28493990; PMCID: PMC5426787. 

Hills LB, Masri A, Konno K, Kakegawa W, Lam A-TN, Lim-Melia E, Chandy N, Hill RS, Partlow JN, Al-Saffar M, Nasir R, Stoler JM, Barkovich AJ, Watanabe M, Yuzaki M, Mochida GH. Deletions in GRID2 lead to a recessive syndrome of cerebellar ataxia and tonic upgaze in humans. Neurology – 2013 (Vol. 81, Issue 16, pp. 1378-1386) 

Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A, Park PJ, Walsh CA. Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain. Cell – 2012 (Vol. 151, Issue 3, pp. 483-496) 

Poduri A, Evrony GD, Cai X, Elhosary PC, Beroukhim R, Lehtinen MK, Hills LB, Heinzen EL, Hill A, Hill RS, Barry BJ, Bourgeois BFD, Riviello JJ, Barkovich AJ, Black PM, Ligon KL, Walsh CA. Somatic Activation of AKT3 Causes Hemispheric Developmental Brain Malformations. Neuron – 2012 (Vol. 74, Issue 1, pp. 41-48)

Mark Fang, MD, PhD

Undergraduate: Stanford University in Palo Alto, CA (BS in Biology and Mathematical & Computational Sciences) 
Medical School: UCSD School of Medicine 
PhD Research Focus: Designing a high throughput genetic and small molecule screen to study the mechanisms underlying Amyotrophic Lateral Sclerosis and to identify potential therapeutics. Also with focus on developing new tools for single cell sequencing and studying the RNA interactome.
Favorite things about San Diego: The people, the weather, UCSD/Rady, and the proximity to beaches, the Sierra Nevada, Disneyland, Vegas, Julian Pie, music festivals, Tucson (my fiancee's hometown)

Fang, M.Y., Markmiller, S., Vu, A.Q., Javaherian, A., Dowdle, W.E., Jolivet, P., Bushway, P.J., Castello, N.A., Baral, A., Chan, M.Y., Linsley, J.W., Linsley, D., Mercola, M., Finkbeiner, S., Lecuyer, E., Lewcock, J.W., Yeo, G.W.. Small-molecule modulation of TDP-43 recruitment to stress granules prevents persistent TDP-43 accumulation in ALS/FTD. Neuron. 2019, Sep; 103(5): 802-819. Cited in PubMed; PMID: 31272829

*Dhamdhere, G.R., *Fang, M.Y., Jiang, J., Lee, K., Cheng, D., Olveda, R.C., Liu, B., Mulligan, K.A., Carlson, J.C., Ransom, R.C., Weis, W.I., Helms, J.A.. Drugging a stem cell compartment using Wnt3a protein as a therapeutic. PLOS One. 2014, Jan; 9(1): e83650. Cited in PubMed; PMID: 24400074, *Equal contribution

Whyte, J.L., Smith, A.A., Liu, B., Manzano, W.R., Evans, N.D., Dhamdhere, G.R., Fang, M.Y., Chang, H.Y., Oro, A.E., Helms, J.A.. Augmenting endogenous Wnt signaling improves skin wound healing. PLOS One. 2013, Dec; 8(10): e76883. Cited in PubMed; PMID: 24204695

Leucht, P., Jiang, J., Du C., Bo L., Dhamdhere, G., Fang, M.Y., Monica, S.D., Urena, J.J., Cole, W., Smith, L.R., Castillo, A.B., Longaker, M.T., Helms, J.A.. Wnt3a reestablishes osteogenic capacity to bone grafts from aged animals. The Journal of Bone and Joint Surgery. 2013, Jul; 95(14): 1278. Cited in PubMed; PMID: 23864176

Markmiller S, Soltanieh S, Server KL, Mak R, Jin W, Fang M.Y., Luo E-C, Krach F, Yang D, Sen A, Fulzele A, Wozniak J, Gonzalez DJ, Kankel MW, Gao F-B, Bennet EJ, Lecuyer E, Yeo GW. Context-dependent and disease-specific diversity in protein interactions within Stress Granules. Cell, 2018 

Nelles DA, Fang M.Y., O’Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW. Programmable RNA Tracking in Live Cells with CRISPR/Cas9. 2016. Cell, S0092-8674(16)30204-5. 

Nelles DA, Fang M.Y., Aigner S, Yeo GW. Applications of Cas9 as an RNA-programmed RNA binding protein. 2015. Bioessays., Jul;37(7):732-9. 

Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang M.Y., Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW. 2016. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods.

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