Physician Scientist Incubator Track
Program Description
The Department of Pathology Physician Scientist Incubator Track (PSIT) is a formal career development program for those residents preparing for a career in which the majority of their professional time (generally, 70% or more) will be devoted to extramurally funded basic, translational or clinical research. Typical applicants have a strong research portfolio and have an MD, PhD.
Residency candidates interested in the PSIT are required to meet with department leadership (Chair or Vice Chair of Research) to discuss their candidacy during our interview season. If selected, a commitment will be made during residency recruitment season by the Chair, contingent upon matching.
Support
After completing their clinical residency training, these graduates of our training program are then eligible for up to three years of salary support for postdoctoral research as a faculty instructor with a minor clinical service component. During this three-year period, the Physician Scientist is expected to work closely with her or his mentor to launch a strong research program and apply for external support from the NIH, e.g., K08 award, and foundations. The clinical service component must be discussed with and approved by the appropriate service director and Chair. During the second year of clinical training, a meeting with the Chair should take place for planning.
Labs
The Department will assist residents in finding a suitable laboratory at Stanford for their mentored research training; the director of the laboratory may be a faculty member in the Department of Pathology or any other department in the University.
Indeed, Stanford University has an outstanding School of Engineering, which, together with the School of Medicine, has established a Bioengineering Department. Stanford University also has outstanding Departments of Biology, Chemistry and Statistics in the School of Humanities and Sciences.
In addition, Stanford CHEM-H is building bridges across the postdoctoral scholar community in chemistry, engineering, and medicine to encourage the execution of innovative research aimed at addressing challenges in human health from a multi-disciplinary perspective.
Physician Scientist Pathway Alumni
Natasha Weiser, MD, PhD
Instructor in Pathology, Stanford University
Research Focus and Awards
Education
Professional Education
MD, University of Michigan Medical School, 2019
PhD, University of Michigan, 2019
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2022
Publications
Danica Wiredja, MD, PhD
Molecular Genetic Pathology Fellow, Stanford University
Research Focus and Awards
The three-dimensional organization of the human genome and its effect on gene regulation
Education
Professional Education
MD, Case Western Reserve University School of Medicine, 2019
PhD, Case Western Reserve University, 2018
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2022
Publications
Fabian Grubert, MD, PhD
Instructor in Pathology, Stanford University
Research Focus and Awards
The three-dimensional organization of the human genome and its effect on gene regulation
Education
Professional Education
MD, Charité – Universitätsmedizin Berlin, 2005
PhD, Charité – Universitätsmedizin Berlin, 2010
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2021
Publications
Landscape of cohesin-mediated chromatin loops in the human genome. Grubert F, Srivas R, Spacek DV, Kasowski M, Ruiz-Velasco M, Sinnott-Armstrong N, Greenside P, Narasimha A, Liu Q, Geller B, Sanghi A, Kulik M, Sa S, Rabinovitch M, Kundaje A, Dalton S, Zaugg JB, Snyder M. Nature. 2020 Jul;583(7818):737-743. doi: 10.1038/s41586-020-2151-x. Epub 2020 Jul 29. PMID: 32728247; PMCID: PMC7410831.
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M. Cell. 2015 Aug 27;162(5):1051-65. doi: 10.1016/j.cell.2015.07.048. Epub 2015 Aug 20. PMID: 26300125; PMCID: PMC4556133.
Defining a personal, allele-specific, and single-molecule long-read transcriptome. Tilgner H, Grubert F, Sharon D, Snyder MP. Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9869-74. doi: 10.1073/pnas.1400447111. Epub 2014 Jun 24. PMID: 24961374; PMCID: PMC4103364.
Extensive variation in chromatin states across humans. Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Science. 2013 Nov 8;342(6159):750-2. doi: 10.1126/science.1242510. Epub 2013 Oct 17. PMID: 24136358; PMCID: PMC4075767.
Kevin Kolahi, MD, PhD
Pathologist - Director, Precision Medicine Pathology, AbbVie Inc., San Francisco, CA
Research Focus and Awards
Ovarian Cancer
Organoids
Education
Professional Education
MD, Oregon Health & Sciences University, 2018
PhD, Oregon Health & Sciences University, 2018
Residency
Anatomic Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2021
Publications
A CRISPR/Cas9-Engineered ARID1A-Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation. Lo YH, Kolahi KS, Du Y, Chang CY, Krokhotin A, Nair A, Sobba WD, Karlsson K, Jones SJ, Longacre TA, Mah AT, Tercan B, Sockell A, Xu H, Seoane JA, Chen J, Shmulevich I, Weissman JS, Curtis C, Califano A, Fu H, Crabtree GR, Kuo CJ. Cancer Discov. 2021 Jun;11(6):1562-1581. doi: 10.1158/2159-8290.CD-20-1109. Epub 2021 Jan 15. PMID: 33451982.
Organoids as Oracles for Precision Medicine in Rectal Cancer. Kolahi KS, Nakano M, Kuo CJ. Cell Stem Cell. 2020 Jan 2;26(1):4-6. doi: 10.1016/j.stem.2019.12.003. PMID: 31951587.
For complete publication list, please visit:
Google Scholar
Alexander Gitlin, MD, PhD
Instructor in Pathology, Stanford University
Research Focus and Awards
Inflammation
K08
Education
Professional Education
MD, Weill Cornell Medicine, Cornell University, 2017
PhD, The Rockefeller University, Immunology, 2016
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2020
Publications
Integration of innate immune signalling by caspase-8 cleavage of N4BP1. Gitlin AD, Heger K, Schubert AF, Reja R, Yan D, Pham VC, Suto E, Zhang J, Kwon YC, Freund EC, Kang J, Pham A, Caothien R, Bacarro N, Hinkle T, Xu M, McKenzie BS, Haley B, Lee WP, Lill JR, Roose-Girma M, Dohse M, Webster JD, Newton K, Dixit VM. Nature. 2020 Nov;587(7833):275-280. Epub 2020 Sep 24. PMID: 32971525.
Squalene emulsion-based vaccine adjuvants stimulate CD8 T cell, but not antibody responses, through a RIPK3-dependent pathway. Kim EH, Woodruff MC, Grigoryan L, Maier B, Lee SH, Mandal P, Cortese M, Natrajan MS, Ravindran R, Ma H, Merad M, Gitlin AD, Mocarski ES, Jacob J, Pulendran B. Elife. 2020 Jun 9;9:e52687. PMID: 32515732.
For complete publication list, please visit:
Google Scholar
Chris Hsiung, MD, PhD
Instructor in Pathology, Stanford University
Research Focus and Awards
Genetic interaction mapping of cancer cell states
Education
Professional Education
MD, Perelman School of Medicine, University of Pennsylvania, 2017
PhD, Perelman School of Medicine, University of Pennsylvania, Cell and Molecular Biology, 2016
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2020
Publications
For more information, please visit:
CAP Profile
Rohan Joshi, MD, PhD
Senior Machine Learning Physician Scientist, Tempus Labs, Inc.
Research Focus and Awards
Cancer, molecular genetics, and machine learning
Education
Professional Education
MD, Perelman School of Medicine, University of Pennsylvania, 2016
PhD, Perelman School of Medicine, University of Pennsylvania, Immunology,2013
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2020
Fellowship
Molecular Genetic Pathology, Stanford University School of Medicine, 2019
Publications
Predictive tool for identification of SARS-CoV-2 PCR-negative emergency department patients using routine test results. Joshi RP, Pejaver V, Hammarlund NE, Sung H, Lee SK, Furmanchuk A, Lee HY, Scott G, Gombar S, Shah N, Shen S, Nassiri A, Schneider D, Ahmad FS, Liebovitz D, Kho A, Mooney S, Pinsky BA, Banaei N. A J Clin Virol. 2020 Aug;129:104502.Epub 2020 Jun 10. PMID: 32544861; PMCID: PMC7286235.
A Survey of Somatic Mutations in 41 Genes in a Cohort of T-Cell Lymphomas Identifies Frequent Mutations in Genes Involved in Epigenetic Modification. Fernandez-Pol S, Ma L, Joshi RP, Arber DA. Appl Immunohistochem Mol Morphol. 2019 Jul;27(6):416-422. PMID: 29629950.
The Brief Case: Confirmed Positive HIV-1 Serologic Screening but Undetectable RNA Virus Load in a Pregnant Woman. Joshi RP, Gomez CA, Steiner D, Aziz N, Pinsky BA. J Clin Microbiol. 2017 Dec;55(12):3316-3320. PMID: 29180504; PMCID: PMC5703796.
Closing the Brief Case: Confirmed Positive HIV-1 Serological Screening but Undetectable RNA Virus Load in a Pregnant Woman. Joshi RP, Gomez CA, Steiner D, Aziz N, Pinsky BA. J Clin Microbiol. 2017 Dec;55(12):3566-3567. PMID: 29180505; PMCID: PMC5703824.
For complete publication list, please visit:
Google Scholar
Maya Kasowski, MD, PhD, MMP
Assistant Professor of Pathology, Stanford University
Research Focus and Awards
Links between genetic variation, gene regulation, and disease
KL2 Award
Education
Professional Education
MD, Yale University School of Medicine, 2016
PhD, Yale University School of Medicine, 2011
MMP, University of Pennsylvania, the Graduate School of Arts and Sciences, 2004
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2019
Publications
Landscape of cohesin-mediated chromatin loops in the human genome. Grubert F, Srivas R, Spacek DV, Kasowski M, Ruiz-Velasco M, Sinnott-Armstrong N, Greenside P, Narasimha A, Liu Q, Geller B, Sanghi A, Kulik M, Sa S, Rabinovitch M, Kundaje A, Dalton S, Zaugg JB, Snyder M. Nature. 2020 Jul;583(7818):737-743. Epub 2020 Jul 29. PMID: 32728247; PMCID: PMC7410831.
Extensive variation in chromatin states across humans. Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. 2013 Nov 8;342(6159):750-2. Epub 2013 Oct 17. PMID: 24136358; PMCID: PMC4075767.
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M. Cell. 2015 Aug 27;162(5):1051-65. Epub 2015 Aug 20. PMID: 26300125; PMCID: PMC4556133.
Variation in transcription factor binding among humans. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M. Science. 2010 Apr 9;328(5975):232-5. Epub 2010 Mar 18. PMID: 20299548; PMCID: PMC2938768.
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Eric Gars, MD
Clinical Instructor in Pathology, Stanford University
Research Focus and Awards
Acute Myeloid Leukemia
Education
Professional Education
MD, University of Florida College of Medicine, 2015
Residency
Anatomic Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2018
Fellowship
Hematopathology Fellowship, Stanford University School of Medicine, 2022
Publications
Upregulation of CD47 Is a Host Checkpoint Response to Pathogen Recognition. Tal MC, Torrez Dulgeroff LB, Myers L, Cham LB, Mayer-Barber KD, Bohrer AC, Castro E, Yiu YY, Lopez Angel C, Pham E, Carmody AB, Messer RJ, Gars E, Kortmann J, Markovic M, Hasenkrug M, Peterson KE, Winkler CW, Woods TA, Hansen P, Galloway S, Wagh D, Fram BJ, Nguyen T, Corey D, Kalluru RS, Banaei N, Rajadas J, Monack DM, Ahmed A, Sahoo D, Davis MM, Glenn JS, Adomati T, Lang KS, Weissman IL, Hasenkrug KJ. mBio. 2020 Jun 23;11(3):e01293-20. PMID: 32576678; PMCID: PMC7315125.
Enasidenib drives human erythroid differentiation independently of isocitrate dehydrogenase 2. Dutta R, Zhang TY, Köhnke T, Thomas D, Linde M, Gars E, Stafford M, Kaur S, Nakauchi Y, Yin R, Azizi A, Narla A, Majeti R. J Clin Invest. 2020 Apr 1;130(4):1843-1849. PMID: 31895700; PMCID: PMC7108889.
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Granja JM, Klemm S, McGinnis LM, Kathiria AS, Mezger A, Corces MR, Parks B, Gars E, Liedtke M, Zheng GXY, Chang HY, Majeti R, Greenleaf WJ. Nat Biotechnol. 2019 Dec;37(12):1458-1465. Epub 2019 Dec 2. PMID: 31792411; PMCID: PMC7258684.
The life and death of the germinal center. Gars E, Butzmann A, Ohgami R, Balakrishna JP, O'Malley DP. Ann Diagn Pathol. 2020 Feb;44:151421. Epub 2019 Nov 13. PMID: 31751845.
Bone marrow histomorphological criteria can accurately diagnose hemophagocytic lymphohistiocytosis. Gars E, Purington N, Scott G, Chisholm K, Gratzinger D, Martin BA, Ohgami RS. Haematologica. 2018 Oct;103(10):1635-1641. Epub 2018 Jun 14. PMID: 29903767; PMCID: PMC6165820.
A replicable CD271+ mesenchymal stromal cell density score: bringing the dysfunctional myelodysplastic syndrome niche to the diagnostic laboratory. Gars E, Yousry SM, Babu D, Kurzer JH, George TI, Gratzinger D. Leuk Lymphoma. 2017 Jul;58(7):1730-1732. Epub 2016 Nov 3. PMID: 27808583.
Endothelial cell derived angiocrine support of acute myeloid leukemia targeted by receptor tyrosine kinase inhibition. Drusbosky L, Gars E, Trujillo A, McGee C, Meacham A, Wise E, Scott EW, Cogle CR. Leuk Res. 2015 Sep;39(9):984-9. Epub 2015 Jul 2. PMID: 26189107.
Activation of the vascular niche supports leukemic progression and resistance to chemotherapy. Poulos MG, Gars EJ, Gutkin MC, Kloss CC, Ginsberg M, Scandura JM, Rafii S, Butler JM. Exp Hematol. 2014 Nov;42(11):976-986.e3.Epub 2014 Aug 29. PMID: 25179751; PMCID: PMC4254082.
Human ESC-derived hemogenic endothelial cells undergo distinct waves of endothelial to hematopoietic transition. Rafii S, Kloss CC, Butler JM, Ginsberg M, Gars E, Lis R, Zhan Q, Josipovic P, Ding BS, Xiang J, Elemento O, Zaninovic N, Rosenwaks Z, Sadelain M, Rafii JA, James D. Blood. 2013 Jan 31;121(5):770-80. Epub 2012 Nov 20. PMID: 23169780.
Development of a vascular niche platform for expansion of repopulating human cord blood stem and progenitor cells. Butler JM, Gars EJ, James DJ, Nolan DJ, Scandura JM, Rafii S. Blood. 2012 Aug 9;120(6):1344-7. Epub 2012 Jun 18. PMID: 22709690; PMCID: PMC3418723.
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Steven Baker, MD, PhD
Assistant Professor, University of Utah
Research Focus and Awards
Transfusion Medicine and Coagulation
Education
Professional Education
MD, Baylor College of Medicine, 2014
PhD, Baylor College of Medicine, Developmental Biology, 2012
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2017
Fellowship
Transfusion Medicine, Stanford University School of Medicine, 2021
Publications
Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiring mechanical ventilation. Baker SA, Kwok S, Berry GJ, Montine TJ. PLoS One. 2021 Feb 16;16(2):e0247060. PMID: 33592054; PMCID: PMC7886150.
Creatine transport and pathological changes in creatine transporter deficient mice. Wawro AM, Gajera CR, Baker SA, Nirschl JJ, Vogel H, Montine TJ. J Inherit Metab Dis. 2021 Jan 2. Epub ahead of print. PMID: 33389772.
Implementation of Whole-Blood Impedance Aggregometry for Heparin-Induced Thrombocytopenia Functional Assay and Case Discussion. Jin J, Baker SA, Hall ET, Gombar S, Bao A, Zehnder JL. Am J Clin Pathol. 2019 Jun 5;152(1):50-58. PMID: 31165165.
Real-Time Clinical Decision Support Decreases Inappropriate Plasma Transfusion. Shah N, Baker SA, Spain D, Shieh L, Shepard J, Hadhazy E, Maggio P, Goodnough LT. Am J Clin Pathol. 2017 Aug 1;148(2):154-160. PMID: 28898990.
An RNA interference screen identifies druggable regulators of MeCP2 stability. Lombardi LM, Zaghlula M, Sztainberg Y, Baker SA, Klisch TJ, Tang AA, Huang EJ, Zoghbi HY. Sci Transl Med. 2017 Aug 23;9(404):eaaf7588. PMID: 28835516; PMCID: PMC5736385.
Transportation Cooler Interventions Reduce Plasma and RBC Product Wastage. Metcalf RA, Baker SA, Goodnough LT, Shah N. Am J Clin Pathol. 2016 Jul;146(1):18-24. Epub 2016 Jun 29. PMID: 27357292.
A study of the mutational landscape of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma. Ozawa MG, Bhaduri A, Chisholm KM, Baker SA, Ma L, Zehnder JL, Luna-Fineman S, Link MP, Merker JD, Arber DA, Ohgami RS. Mod Pathol. 2016 Oct;29(10):1212-20. Epub 2016 Jun 24. PMID: 27338637; PMCID: PMC5047957.
For complete publication list, please visit:
PubMed
Saurabh Gombar, MD, PhD
Adjunct Clinical Assistant Professor of Pathology, Stanford University
Chief Medical Officer, Atropos Health, Palo Alto, CA
Research Focus and Awards
Clinical Informatics
Education
Professional Education
MD, Albert Einstein College of Medicine, 2014
PhD, Albert Einstein College of Medicine, Systems & Computational Biology, 2014
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2017
Publications
Persistent detection of SARS-CoV-2 RNA in patients and healthcare workers with COVID-19. Gombar S, Chang M, Hogan CA, Zehnder J, Boyd S, Pinsky BA, Shah NH. J Clin Virol. 2020 Aug;129:104477. Epub 2020 May 30. PMID: 32505778; PMCID: PMC7260561.
Occurrence and Timing of Subsequent SARS-CoV-2 RT-PCR Positivity Among Initially Negative Patients. Long DR, Gombar S, Hogan CA, Greninger AL, OReilly Shah V, Bryson-Cahn C, Stevens B, Rustagi A, Jerome KR, Kong CS, Zehnder J, Shah NH, Weiss NS, Pinsky BA, Sunshine J. medRxiv [Preprint]. 2020 May 8:2020.05.03.20089151.Update in: Clin Infect Dis. 2020 Jun 07;: PMID: 32511542; PMCID: PMC7274223.
Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome. Röltgen K, Powell AE, Wirz OF, Stevens BA, Hogan CA, Najeeb J, Hunter M, Wang H, Sahoo MK, Huang C, Yamamoto F, Manohar M, Manalac J, Otrelo-Cardoso AR, Pham TD, Rustagi A, Rogers AJ, Shah NH, Blish CA, Cochran JR, Jardetzky TS, Zehnder JL, Wang TT, Narasimhan B, Gombar S, Tibshirani R, Nadeau KC, Kim PS, Pinsky BA, Boyd SD. Sci Immunol. 2020 Dec 7;5(54):eabe0240. PMID: 33288645; PMCID: PMC7857392.
It is time to learn from patients like mine. Gombar S, Callahan A, Califf R, Harrington R, Shah NH. NPJ Digit Med. 2019 Mar 19;2:16. PMID: 31304364; PMCID: PMC6550176.
Estimating the efficacy of symptom-based screening for COVID-19. Callahan A, Steinberg E, Fries JA, Gombar S, Patel B, Corbin CK, Shah NH. NPJ Digit Med. 2020 Jul 13;3:95. PMID: 32695885; PMCID: PMC7359358.
High Frequency of SARS-CoV-2 RNAemia and Association With Severe Disease. Hogan CA, Stevens BA, Sahoo MK, Huang C, Garamani N, Gombar S, Yamamoto F, Murugesan K, Kurzer J, Zehnder J, Pinsky BA. Clin Infect Dis. 2020 Sep 23:ciaa1054. Epub ahead of print. PMID: 32965474; PMCID: PMC7543277.
Large-Scale Testing of Asymptomatic Healthcare Personnel for Severe Acute Respiratory Syndrome Coronavirus 2. Hogan CA, Gombar S, Wang H, Röltgen K, Shi RZ, Holubar M, Chang SI, Lee GM, Boyd SD, Zehnder J, Pinsky BA. Emerg Infect Dis. 2021 Jan;27(1):250–4. Epub 2020 Nov 30. PMID: 33256889; PMCID: PMC7774535.
Implementation of Whole-Blood Impedance Aggregometry for Heparin-Induced Thrombocytopenia Functional Assay and Case Discussion. Jin J, Baker SA, Hall ET, Gombar S, Bao A, Zehnder JL. Am J Clin Pathol. 2019 Jun 5;152(1):50-58. PMID: 31165165.
A predictive tool for identification of SARS-CoV-2 PCR-negative emergency department patients using routine test results. Joshi RP, Pejaver V, Hammarlund NE, Sung H, Lee SK, Furmanchuk A, Lee HY, Scott G, Gombar S, Shah N, Shen S, Nassiri A, Schneider D, Ahmad FS, Liebovitz D, Kho A, Mooney S, Pinsky BA, Banaei N. J Clin Virol. 2020 Aug;129:104502. Epub 2020 Jun 10. PMID: 32544861; PMCID: PMC7286235.
Measure what matters: Counts of hospitalized patients are a better metric for health system capacity planning for a reopening. Kashyap S, Gombar S, Yadlowsky S, Callahan A, Fries J, Pinsky BA, Shah NH. J Am Med Inform Assoc. 2020 Jul 1;27(7):1026-1131. PMID: 32548636; PMCID: PMC7337779.
Clostridium difficile PCR Cycle Threshold Predicts Free Toxin. Senchyna F, Gaur RL, Gombar S, Truong CY, Schroeder LF, Banaei N. J Clin Microbiol. 2017 Sep;55(9):2651-2660. Epub 2017 Jun 14. PMID: 28615471; PMCID: PMC5648702.
SMiRK: an Automated Pipeline for miRNA Analysis. Milholland B, Gombar S, Suh Y. Source J Genom. 2015 Jun;1(1):http://www.researchsource.org/journals/getarchivedata/5/36/SMiRK:-an-Automated-Pipeline-for-miRNA-Analysis. PMID: 26613105; PMCID: PMC4657868.
Big data modeling to predict platelet usage and minimize wastage in a tertiary care system. Guan L, Tian X, Gombar S, Zemek AJ, Krishnan G, Scott R, Narasimhan B, Tibshirani RJ, Pham TD. Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11368-11373. Epub 2017 Oct 9. PMID: 29073058; PMCID: PMC5664553.
Implementation of Automated Calculation of Free and Bioavailable Testosterone in Epic Beaker Laboratory Information System. Chung MC, Gombar S, Shi RZ. J Pathol Inform. 2017 Jul 25;8:28. PMID: 28828199; PMCID: PMC5545775.
Epigenetics decouples mutational from environmental robustness. Did it also facilitate multicellularity? Gombar S, MacCarthy T, Bergman A. PLoS Comput Biol. 2014 Mar 6;10(3):e1003450. PMID: 24604070; PMCID: PMC3945085.
Real-Time Electronic Tracking of Diarrheal Episodes and Laxative Therapy Enables Verification of Clostridium difficile Clinical Testing Criteria and Reduction of Clostridium difficile Infection Rates. Truong CY, Gombar S, Wilson R, Sundararajan G, Tekic N, Holubar M, Shepard J, Madison A, Tompkins L, Shah N, Deresinski S, Schroeder LF, Banaei N.J Clin Microbiol. 2017 May;55(5):1276-1284. Epub 2017 Mar 1. PMID: 28250001; PMCID: PMC5405247.
Association of Systemic Diseases With Surgical Treatment for Obstructive Sleep Apnea Compared With Continuous Positive Airway Pressure. Ibrahim B, de Freitas Mendonca MI, Gombar S, Callahan A, Jung K, Capasso R.JAMA Otolaryngol Head Neck Surg. 2021 Jan 21:e205179.Epub ahead of print. PMID: 33475682; PMCID: PMC7821084.
Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing. Gombar S, Jung HJ, Dong F, Calder B, Atzmon G, Barzilai N, Tian XL, Pothof J, Hoeijmakers JH, Campisi J, Vijg J, Suh Y. BMC Genomics. 2012 Jul 31;13:353. PMID: 22846614; PMCID: PMC3563618.
MicroRNA transcriptome analysis identifies miR-365 as a novel negative regulator of cell proliferation in Zmpste24-deficient mouse embryonic fibroblasts. Xiong XD, Jung HJ, Gombar S, Park JY, Zhang CL, Zheng H, Ruan J, Li JB, Kaeberlein M, Kennedy BK, Zhou Z, Liu X, Suh Y. Mutat Res. 2015 Jul;777:69-78. Epub 2015 Apr 24. PMID: 25983189; PMCID: PMC4654172.
A high-throughput, near-saturating screen for type III effector genes from Pseudomonas syringae. Chang JH, Urbach JM, Law TF, Arnold LW, Hu A, Gombar S, Grant SR, Ausubel FM, Dangl JL. Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2549-54.Epub 2005 Feb 8. PMID: 15701698; PMCID: PMC549004.
Plasmacytic posttransplant lymphoproliferative disorder with hyperviscosity syndrome in a child after liver transplant. Yang CH, Gombar S, Twist CJ, Gratzinger D, Esquivel CO, Lau AH. Hepatology. 2016 Dec;64(6):2250-2252. Epub 2016 Jul 5. PMID: 27227484; PMCID: PMC5115971.
Clinical Accuracy and Impact of Plasma Cell-Free DNA Fungal PCR Panel for Non-Invasive Diagnosis of Fungal Infection. Senchyna F, Hogan CA, Murugesan K, Moreno A, Ho DY, Subramanian A, Schwenk HT, Budvytiene I, Costa HA, Gombar S, Banaei N. Clin Infect Dis. 2021 Feb 19:ciab158. Epub ahead of print. PMID: 33606010.
SARS-CoV-2 infection and COVID-19 severity in individuals with prior seasonal coronavirus infection. Gombar S, Bergquist T, Pejaver V, Hammarlund NE, Murugesan K, Mooney S, Shah N, Pinsky BA, Banaei N. Diagn Microbiol Infect Dis. 2021 Feb 9;100(2):115338. Epub ahead of print. PMID: 33610036; PMCID: PMC7871798.
Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients. Long DR, Gombar S, Hogan CA, Greninger AL, O'Reilly-Shah V, Bryson-Cahn C, Stevens B, Rustagi A, Jerome KR, Kong CS, Zehnder J, Shah NH, Weiss NS, Pinsky BA, Sunshine JE. Clin Infect Dis. 2021 Jan 27;72(2):323-326. PMID: 33501950; PMCID: PMC7314163.
For complete list of publications and more information, please visit:
PubMed
CAP Profile
Ansuman Satpathy, MD, PhD
Associate Professor of Pathology, Stanford University
Co-founder of Immunai and Cartography Biosciences
Research Focus and Awards
Immunology, Genomics, Cancer Immunotherapy
National Cancer Institute K08 Award
Burroughs Welcome Fund Career Award for Medical Scientists
Parker Institute for Cancer Immunotherapy Bridge Scholar Award
Cancer Research Institute Irvington Fellowship
Bill and Melinda Gates Foundation Technology Award
Michelson Prize for Human Immunology
Education
Professional Education
MD, Washington University School of Medicine in St. Louis, 2014
PhD, Washington University School of Medicine in St. Louis, Immunology, 2014
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2017
Publications
Embryonic and adult-derived resident cardiac macrophages are maintained through distinct mechanisms at steady state and during inflammation. Epelman S, Lavine KJ, Beaudin AE, Sojka DK, Carrero JA, Calderon B, Brija T, Gautier EL, Ivanov S, Satpathy AT, Schilling JD, Schwendener R, Sergin I, Razani B, Forsberg EC, Yokoyama WM, Unanue ER, Colonna M, Randolph GJ, Mann DL. Immunity. 2014 Jan 16;40(1):91-104. PMID: 24439267; PMCID: PMC3923301.
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Lisa McGinnis, MD, PhD
Scientist, Genentech Inc., South San Francisco, CA
Education
Professional Education
MD, Stanford University School of Medicine, 2013
PhD, Stanford University School of Medicine, Immunology, 2011
Residency
Anatomic Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2016
Fellowship
Hematopathology, Stanford University School of Medicine, 2017
Publications
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Granja JM, Klemm S, McGinnis LM, Kathiria AS, Mezger A, Corces MR, Parks B, Gars E, Liedtke M, Zheng GXY, Chang HY, Majeti R, Greenleaf WJ. Nat Biotechnol. 2019 Dec;37(12):1458-1465. Epub 2019 Dec 2. PMID: 31792411; PMCID: PMC7258684.
PDGF-B exploits stromal EPO. McGinnis LM, Kuo CJ. Nat Med. 2012 Jan 6;18(1):22-4. PMID: 22227660.
Frequency of MAP2K1, TP53, and U2AF1 Mutations in BRAF-mutated Langerhans Cell Histiocytosis: Further Characterizing the Genomic Landscape of LCH. McGinnis LM, Nybakken G, Ma L, Arber DA. Am J Surg Pathol. 2018 Jul;42(7):885-890. PMID: 29649018.
A liver Hif-2α-Irs2 pathway sensitizes hepatic insulin signaling and is modulated by Vegf inhibition. Wei K, Piecewicz SM, McGinnis LM, Taniguchi CM, Wiegand SJ, Anderson K, Chan CW, Mulligan KX, Kuo D, Yuan J, Vallon M, Morton L, Lefai E, Simon MC, Maher JJ, Mithieux G, Rajas F, Annes J, McGuinness OP, Thurston G, Giaccia AJ, Kuo CJ. Nat Med. 2013 Oct;19(10):1331-1337.Epub 2013 Sep 15. PMID: 24037094; PMCID: PMC3795838.
Cross-talk between hypoxia and insulin signaling through Phd3 regulates hepatic glucose and lipid metabolism and ameliorates diabetes. Taniguchi CM, Finger EC, Krieg AJ, Wu C, Diep AN, LaGory EL, Wei K, McGinnis LM, Yuan J, Kuo CJ, Giaccia AJ. Nat Med. 2013 Oct;19(10):1325-30. Epub 2013 Sep 15. PMID: 24037093; PMCID: PMC4089950.
DNA double-strand breaks activate a multi-functional genetic program in developing lymphocytes. Bredemeyer AL, Helmink BA, Innes CL, Calderon B, McGinnis LM, Mahowald GK, Gapud EJ, Walker LM, Collins JB, Weaver BK, Mandik-Nayak L, Schreiber RD, Allen PM, May MJ, Paules RS, Bassing CH, Sleckman BP. Nature. 2008 Dec 11;456(7223):819-23. Epub 2008 Oct 12. PMID: 18849970; PMCID: PMC2605662.
Alanine-scanning mutations in domain 4 of anthrax toxin protective antigen reveal residues important for binding to the cellular receptor and to a neutralizing monoclonal antibody. Rosovitz MJ, Schuck P, Varughese M, Chopra AP, Mehra V, Singh Y, McGinnis LM, Leppla SH. J Biol Chem. 2003 Aug 15;278(33):30936-44. Epub 2003 May 27. PMID: 12771151.
Calcineurin sets the bandwidth for discrimination of signals during thymocyte development. Gallo EM, Winslow MM, Canté-Barrett K, Radermacher AN, Ho L, McGinnis L, Iritani B, Neilson JR, Crabtree GR. Nature. 2007 Nov 29;450(7170):731-5. PMID: 18046413; PMCID: PMC5336393.
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Dylan Dodd, MD, PhD
Assistant Professor of Pathology, Stanford University
Research Focus and Awards
Harnessing metabolism within the gut microbiome to treat human disease
K08
Education
Professional Education
MD, University of Illinois at Urbana-Champaign, 2013
PhD, University of Illinois at Urbana-Champaign, Microbiology, 2010
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2016
Publications
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Albert Tsai, MD, PhD
Assistant Professor of Pathology, Stanford University
Research Focus and Awards
Hematopathology
Damon Runyon Cancer Research Foundation Fellowship
Education
Professional Education
MD, University of Southern California Keck School of Medicine, 2010
PhD, University of Southern California Keck School of Medicine, Biochemistry, 2008
Residency
Anatomic and Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2014
Fellowship
Hematopathology, Stanford University School of Medicine, 2015
Publications
Multiplexed single-cell morphometry for hematopathology diagnostics. Tsai AG, Glass DR, Juntilla M, Hartmann FJ, Oak JS, Fernandez-Pol S, Ohgami RS, Bendall SC. Nat Med. 2020 Mar;26(3):408-417. Epub 2020 Mar 11. PMID: 32161403; PMCID: PMC7301910.
An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. Glass DR, Tsai AG, Oliveria JP, Hartmann FJ, Kimmey SC, Calderon AA, Borges L, Glass MC, Wagar LE, Davis MM, Bendall SC. Immunity. 2020 Jul 14;53(1):217-232.e5. PMID: 32668225; PMCID: PMC7369630.
Mass Cytometry Phenotyping of Human Granulocytes Reveals Novel Basophil Functional Heterogeneity. Vivanco Gonzalez N, Oliveria JP, Tebaykin D, Ivison GT, Mukai K, Tsai MM, Borges L, Nadeau KC, Galli SJ, Tsai AG, Bendall SC. iScience. 2020 Oct 22;23(11):101724. PMID: 33205028; PMCID: PMC7653073.
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Kitchener Wilson, MD, PhD
Founder and CEO, Rosebud Biosciences Inc.
Research Focus and Awards
Drug discovery
NIH K08
Education
Professional Education
MD, Duke University School of Medicine, 2006
PhD, Stanford University, Bioengineering, 2010
Residency
Clinical Pathology, Physician Scientist Incubator Track, Stanford University School of Medicine, 2014
Fellowship
Molecular Genetic Pathology, Stanford University School of Medicine, 2013
Publications
Endogenous Retrovirus-Derived lncRNA BANCR Promotes Cardiomyocyte Migration in Humans and Non-human Primates. Wilson KD, Ameen M, Guo H, Abilez OJ, Tian L, Mumbach MR, Diecke S, Qin X, Liu Y, Yang H, Ma N, Gaddam S, Cunningham NJ, Gu M, Neofytou E, Prado M, Hildebrandt TB, Karakikes I, Chang HY, Wu JC. Dev Cell. 2020 Sep 28;54(6):694-709.e9. Epub 2020 Aug 6. PMID: 32763147; PMCID: PMC7529962.
A Rapid, High-Quality, Cost-Effective, Comprehensive and Expandable Targeted Next-Generation Sequencing Assay for Inherited Heart Diseases. Wilson KD, Shen P, Fung E, Karakikes I, Zhang A, InanlooRahatloo K, Odegaard J, Sallam K, Davis RW, Lui GK, Ashley EA, Scharfe C, Wu JC. Circ Res. 2015 Sep 11;117(7):603-11. Epub 2015 Aug 11. PMID: 26265630; PMCID: PMC4568077.
Induced pluripotent stem cells. Wilson KD, Wu JC. JAMA. 2015 Apr 28;313(16):1613-4. PMID: 25919522.
MicroRNA profiling of human-induced pluripotent stem cells. Wilson KD, Venkatasubrahmanyam S, Jia F, Sun N, Butte AJ, Wu JC. Stem Cells Dev. 2009 Jun;18(5):749-58. PMID: 19284351; PMCID: PMC3135181.
Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499. Wilson KD, Hu S, Venkatasubrahmanyam S, Fu JD, Sun N, Abilez OJ, Baugh JJ, Jia F, Ghosh Z, Li RA, Butte AJ, Wu JC. Circ Cardiovasc Genet. 2010 Oct;3(5):426-35. Epub 2010 Aug 23. PMID: 20733065; PMCID: PMC3057038.
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