Paul Khavari
Biography[1]
Paul A. Khavari, M.D., Ph.D.[2] is the Carl J. Herzog Professor at Stanford University and the Founding Co-Director of the Stanford Program in Epithelial Biology[3]. His laboratory uses multiomic and computational approaches to study stem cell differentiation, cancer, and the genomics of common polygenic human diseases.
Education and training
Khavari grew up in Whitefish Bay and Bayside, Wisconsin. He studied biology and history at Stanford University then earned an MD at Yale University School of Medicine. He did research at the Brigham and Women's Hospital and Harvard Medical School before undertaking Dermatology residency training at Yale. He completed PhD studies in the laboratory of Gerald Crabtree at the Stanford University School of Medicine.
Khavari Laboratory Website[4]
http://khavarilab.stanford.edu/
Selected awards and honors
Shannon Award, National Institutes of Health
U.S. Presidential Early Career Award for Scientists and Engineers
V.A. Young Investigator Award, V.A. Palo Alto Health Care System
HHMI Junior Faculty Scholar Award, Stanford University
American Society for Clinical Investigation
Marion B. Sulzberger Memorial Award, American Academy of Dermatology
William Montagna Award, Society for Investigative Dermatology
Tanioku Kihei Memorial Award, Japanese Society for Investigative Dermatology
American Association of Physicians
American Skin Association 25th Anniversary Lifetime Scientific Achievement Award
Lila & Murray Gruber Cancer Research Award, American Academy of Dermatology
Kligman-Frost Leadership Award, Society for Investigative Dermatology
Stephen Rothman Memorial Award, Society for Investigative Dermatology
Selected former students and postdoctoral fellows and their current academic affiliations[5]
Keith Choate, Yale
Min Fang, University of Washington
Yoshi Kubo, University of Tokushima
Jennifer Zhang, Duke
George Sen, University of California, San Diego
Carolyn Lee, Stanford
Susana Ortiz-Urda, University of California, San Francisco
Cornelia Seitz, Göttingen
Todd Ridky, University of Pennsylvania
Markus Kretz, University of Regensburg
Kavita Sarin, Stanford
Kun Qu, University of Science & Technology of China
Xiaomin Bao, Northwestern
Bryan Sun, University of California, San Diego
Eon Rios, Stanford
Aparna Bhaduri, University of California, Los Angeles
Lisa Boxer, Harvard
Adam Rubin, M.I.T.
Joanna Kovalski, University of California, San Francisco
Philip Dumesic, Harvard
Rahm Ramanathan, Stanford
Yonglu Che, Stanford
Abbie Groff, M.I.T.
Lara Elcavage, Harvard
Andrew Ji, Mount Sinai
References
- ↑ "Paul A. Khavari, MD, PhD's Profile | Stanford Profiles". profiles.stanford.edu. Retrieved 2021-03-15.
- ↑ "Paul A. Khavari, MD, PhD's Profile | Stanford Profiles". profiles.stanford.edu. Retrieved 2021-03-15.
- ↑ "Program in Epithelial Biology". Program in Epithelial Biology. Retrieved 2021-03-15.
- ↑ "The Khavari Laboratory". The Khavari Laboratory. Retrieved 2021-03-15.
- ↑ "Alumni". The Khavari Laboratory. Retrieved 2021-03-15.
1. Ji AL, Rubin AJ, Thrane K, Jian S, Reynolds DL, Meyers RM, Guo MG, Bhaduri A, Meyers JM, Hollmig SH, Aasi SZ, Nolan GP, Lundeberg J, Khavari PA. Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma. Cell 182:497-514, 2020. PMID: 32946785[1]
2. Rubin, Adam J et al. “Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.” Cell vol. 176,1-2 (2019): 361-376.e17. doi:10.1016/j.cell.2018.11.022 PMID: 30580963[2]
3. Kovalski JR, Bhaduri A, Zehnder AM, Neela PH, Che Y, Wozniak GG, Khavari PA. The functional proteome of oncogenic Ras includes mTORC2. Molecular Cell 73:830-844, 2019. PMID: 30639242[3]
4. Ramanathan M, Majzoub K, Carette JE, Khavari PA. Rapid RNA-protein interaction detection in living cells. Nature Methods 14:207-212, 2018. PMID: 29400715[4]
5. Rubin AJ, Barajas BC, Furlan-Magaril M, Mumbach MR, Lopez-Pajares V, Kim DS, Spivakov M, Wingett S, Greenleaf WJ, Kundaje A, Snyder MP, Chang HY, Fraser P, Khavari PA. Dynamic and pre-established enhancer-promoter contacts regulate terminal differentiation. Nature Genetics 49:1522-1528 2017. PMID: 28805829[5]
6. Bao X, Siprashvili Z, Zarnegar BJ, Shenoy RM, Rios EJ, Nady N, Qu K, Mah A, Webster DE, Rubin AJ, Wozniak GG, Tao S, Wysocka J, Khavari PA. CSNK1a1 regulates PRMT1 to maintain the progenitor state in self-renewing somatic tissue. Developmental Cell 43:227-239, 2017. PMID: 28943242[6]
7. Siprashvili Z, Webster DE, Ungewickell AJ, Bhaduri A, Flockhard R, Zarnegar BJ, Che Y, Meschi F, Puglisi JD, Khavari PA. SNORD50A/B non-coding RNAs bind K-Ras and are recurrently deleted in human cancer. Nature Genetics 48:53-58, 2016. PMID: 26595770[7]
8. Zarnegar BJ, Flynn RA, Shen Y, Do BT, Chang HY, Khavari PA. Ultraefficient irCLIP platform for characterization of protein-RNA interactions. Nature Methods 13:489-492, 2016. PMID: 27111506[8]
9. Ungewickell A, Bhaduri A, Synder MP, Kim Y, Khavari PA. Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2. Nature Genetics 47:1056-1060, 2015. PMID: 26258847[9]
10. Lopez-Pajares V, Qu K, Zhang J, Webster DE, Barajas B, Siprashvili Z, Zarnegar BJ, Boxer LD, Rios EJ, Tao S, Kretz M, and Khavari PA. A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. Developmental Cell 32:693-706, 2015. PMID: 25805135[10]
11. Bhaduri A, Ungewickell A, Boxer LD, Lopez-Pajares V, Khavari PA. Network analysis identifies regulation of epidermal differentiation by MPZL3 & FDXR. Developmental Cell 35:444-457, 2015. PMID: 26609959[11]
12. Lee CS, Rios EJ, Siprashvili Z, Straight A, Khavari PA. Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma. Nature Genetics 46:1060-1062, 2014. PMID: 25194279[12]
13. Boxer LD, Barajas B, Tao S, Zhang J, Khavari PA. ZNF750 interacts with KLF4, RCOR1, and CTBP1/2 chromatin regulators to repress progenitor genes. Genes & Development 28:2013-26, 2014. PMID: 25228645[13]
14. Jameson KL, Mazur PK, Zehnder AM, Zhang J, Zarnegar B, Sage J, Khavari PA. IQGAP1 selectively targets Ras-MAP kinase driven tumors. Nature Medicine 19:626-30 2013. PMID: 23603816[14]
15. Bao X, Lopez-Pajares V, Crabtree GR, Khavari PA. ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent KLF4 induction. Cell Stem Cell 12:193-203, 2013. PMID: 23395444[15]
16. Kretz M, Siprashvili Z, Chu C, Webster DE, Spitale RC, Flynn RA, Raj A, Rinn JL, Chang HY, Khavari PA. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493:231-5, 2013. PMID: 23201690[16]
17. Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GX, Chow J, Kim GE, Rinn JL, Chang HY, Siprashvili Z and Khavari PA. Suppression of progenitor differentiation requires the long non-coding RNA ANCR. Genes & Development 26:338-43, 2012. PMID: 22302877[17]
18. Sen GL, Boxer LD, Webster DE, Bussat RT, Qu K, Zarnegar BJ, Johnston D, Siprashvili Z and Khavari PA. ZNF750 is a p63 target gene that induces KLF4 to drive terminal epidermal differentiation. Developmental Cell 22:669–677, 2012. PMID: 22364861[18]
19. Flockhart RJ, Webster DE, Qu K, Mascarenhas N, Kovalski J, Kretz M and Khavari PA. BRAFV600E remodels the melanocyte transcriptome and induces the long non-coding RNA BANCR to regulate melanoma cell migration. Genome Research 22:1006-1014, 2012. PMID: 22581800[19]
20. Sen GL, Reuter JA, Webster DE, Zhu L, Khavari PA. DNMT1 maintains progenitor function in self-renewing somatic tissue. Nature 463:563-567, 2010. PMID: 20081831[20]
21. Ridky TW, Chow JM, Wong DJ and Khavari PA. Invasive 3-dimensional organotypic neoplasia from multiple normal human epithelia. Nature Medicine 16: 1450-1455, 2010. PMID: 21102459[21]
22. Reuter JA, Ortiz-Urda S, Chang HY & Khavari PA. Inducible human tissue tumorigenesis identifies an extracellular matrix interaction network involved in cancer progression. Cancer Cell 15:477-488, 2009. PMID: 19477427[22]
23. Chudnovsky Y, Adams AE, Robbins PB, Lin Q and Khavari PA. Use of human tissue to assess the oncogenic activity of melanoma-associated mutations. Nature Genetics 37:745-749, 2005. PMID: 15951821[23]
24. Ortiz-Urda S, Garcia J, Chen L, Lin Q, Veitch DP, Sakai LY, Lee H, Marinkovich MP and Khavari PA. Type VII collagen is required for human epidermal tumorigenesis. Science 307:1773-1776, 2005. PMID: 15774758[24]
25. Dajee M, Lazarov M, Zhang JY, Cai T, Marinkovich MP, Lin Q and Khavari PA. NF-kB blockade and oncogenic Ras trigger invasive human epidermal neoplasia. Nature 421: 639-643, 2003. PMID: 12571598[25]
26. Lazarov M, Kubo Y, Cai T, Dajee M, Tarutani M, Lin Q, Fang M, Tao S and Khavari PA. CDK4 co-expression with Ras generates malignant human epidermal tumorigenesis. Nature Medicine 8:1105-1114, 2002. PMID: 12357246[26]
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- ↑ Ji, Andrew L.; Rubin, Adam J.; Thrane, Kim; Jiang, Sizun; Reynolds, David L.; Meyers, Robin M.; Guo, Margaret G.; George, Benson M.; Mollbrink, Annelie; Bergenstråhle, Joseph; Larsson, Ludvig (2020-09-17). "Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma". Cell. 182 (6): 1661–1662. doi:10.1016/j.cell.2020.08.043. ISSN 1097-4172. PMC 7505493 Check
|pmc=value (help). PMID 32946785 Check|pmid=value (help). - ↑ Rubin, Adam J.; Parker, Kevin R.; Satpathy, Ansuman T.; Qi, Yanyan; Wu, Beijing; Ong, Alvin J.; Mumbach, Maxwell R.; Ji, Andrew L.; Kim, Daniel S.; Cho, Seung Woo; Zarnegar, Brian J. (10 January 2019). "Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks". Cell. 176 (1–2): 361–376.e17. doi:10.1016/j.cell.2018.11.022. ISSN 1097-4172. PMC 6329648. PMID 30580963.
- ↑ Kovalski, Joanna R.; Bhaduri, Aparna; Zehnder, Ashley M.; Neela, Poornima H.; Che, Yonglu; Wozniak, Glenn G.; Khavari, Paul A. (21 February 2019). "The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2". Molecular Cell. 73 (4): 830–844.e12. doi:10.1016/j.molcel.2018.12.001. ISSN 1097-4164. PMC 6386588. PMID 30639242.
- ↑ Ramanathan, Muthukumar; Majzoub, Karim; Rao, Deepti S.; Neela, Poornima H.; Zarnegar, Brian J.; Mondal, Smarajit; Roth, Julien G.; Gai, Hui; Kovalski, Joanna R.; Siprashvili, Zurab; Palmer, Theo D. (March 2018). "RNA-protein interaction detection in living cells". Nature Methods. 15 (3): 207–212. doi:10.1038/nmeth.4601. ISSN 1548-7105. PMC 5886736. PMID 29400715.
- ↑ Rubin, Adam J.; Barajas, Brook C.; Furlan-Magaril, Mayra; Lopez-Pajares, Vanessa; Mumbach, Maxwell R.; Howard, Imani; Kim, Daniel S.; Boxer, Lisa D.; Cairns, Jonathan; Spivakov, Mikhail; Wingett, Steven W. (October 2017). "Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation". Nature Genetics. 49 (10): 1522–1528. doi:10.1038/ng.3935. ISSN 1546-1718. PMC 5715812. PMID 28805829.
- ↑ Bao, Xiaomin; Siprashvili, Zurab; Zarnegar, Brian J.; Shenoy, Rajani M.; Rios, Eon J.; Nady, Natalie; Qu, Kun; Mah, Angela; Webster, Daniel E.; Rubin, Adam J.; Wozniak, Glenn G. (23 October 2017). "CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue". Developmental Cell. 43 (2): 227–239.e5. doi:10.1016/j.devcel.2017.08.021. ISSN 1878-1551. PMC 5659279. PMID 28943242.
- ↑ Siprashvili, Zurab; Webster, Dan E.; Johnston, Danielle; Shenoy, Rajani M.; Ungewickell, Alexander J.; Bhaduri, Aparna; Flockhart, Ross; Zarnegar, Brian J.; Che, Yonglu; Meschi, Francesca; Puglisi, Joseph D. (January 2016). "The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer". Nature Genetics. 48 (1): 53–58. doi:10.1038/ng.3452. ISSN 1546-1718. PMC 5324971. PMID 26595770.
- ↑ Zarnegar, Brian J.; Flynn, Ryan A.; Shen, Ying; Do, Brian T.; Chang, Howard Y.; Khavari, Paul A. (June 2016). "irCLIP platform for efficient characterization of protein-RNA interactions". Nature Methods. 13 (6): 489–492. doi:10.1038/nmeth.3840. ISSN 1548-7105. PMC 5477425. PMID 27111506.
- ↑ Ungewickell, Alexander; Bhaduri, Aparna; Rios, Eon; Reuter, Jason; Lee, Carolyn S.; Mah, Angela; Zehnder, Ashley; Ohgami, Robert; Kulkarni, Shashikant; Armstrong, Randall; Weng, Wen-Kai (September 2015). "Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2". Nature Genetics. 47 (9): 1056–1060. doi:10.1038/ng.3370. ISSN 1546-1718. PMC 6091217. PMID 26258847.
- ↑ Lopez-Pajares, Vanessa; Qu, Kun; Zhang, Jiajing; Webster, Dan E.; Barajas, Brook C.; Siprashvili, Zurab; Zarnegar, Brian J.; Boxer, Lisa D.; Rios, Eon J.; Tao, Shiying; Kretz, Markus (2015-03-23). "A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation". Developmental Cell. 32 (6): 693–706. doi:10.1016/j.devcel.2015.01.028. ISSN 1878-1551. PMC 4456036. PMID 25805135.
- ↑ Bhaduri, Aparna; Ungewickell, Alexander; Boxer, Lisa D.; Lopez-Pajares, Vanessa; Zarnegar, Brian J.; Khavari, Paul A. (2015-11-23). "Network Analysis Identifies Mitochondrial Regulation of Epidermal Differentiation by MPZL3 and FDXR". Developmental Cell. 35 (4): 444–457. doi:10.1016/j.devcel.2015.10.023. ISSN 1878-1551. PMC 4845910. PMID 26609959.
- ↑ Lee, Carolyn S.; Bhaduri, Aparna; Mah, Angela; Johnson, Whitney L.; Ungewickell, Alexander; Aros, Cody J.; Nguyen, Christie B.; Rios, Eon J.; Siprashvili, Zurab; Straight, Aaron; Kim, Jinah (October 2014). "Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma". Nature Genetics. 46 (10): 1060–1062. doi:10.1038/ng.3091. ISSN 1546-1718. PMC 4324615. PMID 25194279.
- ↑ Boxer, Lisa D.; Barajas, Brook; Tao, Shiying; Zhang, Jiajing; Khavari, Paul A. (2014-09-15). "ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes". Genes & Development. 28 (18): 2013–2026. doi:10.1101/gad.246579.114. ISSN 1549-5477. PMC 4173152. PMID 25228645.
- ↑ Jameson, Katherine L.; Mazur, Pawel K.; Zehnder, Ashley M.; Zhang, Jiajing; Zarnegar, Brian; Sage, Julien; Khavari, Paul A. (May 2013). "IQGAP1 scaffold-kinase interaction blockade selectively targets RAS-MAP kinase-driven tumors". Nature Medicine. 19 (5): 626–630. doi:10.1038/nm.3165. ISSN 1546-170X. PMC 4190012. PMID 23603816.
- ↑ Bao, Xiaomin; Tang, Jiong; Lopez-Pajares, Vanessa; Tao, Shiying; Qu, Kun; Crabtree, Gerald R.; Khavari, Paul A. (2013-02-07). "ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent induction of KLF4". Cell Stem Cell. 12 (2): 193–203. doi:10.1016/j.stem.2012.12.014. ISSN 1875-9777. PMC 3661004. PMID 23395444.
- ↑ Kretz, Markus; Siprashvili, Zurab; Chu, Ci; Webster, Dan E.; Zehnder, Ashley; Qu, Kun; Lee, Carolyn S.; Flockhart, Ross J.; Groff, Abigail F.; Chow, Jennifer; Johnston, Danielle (2013-01-10). "Control of somatic tissue differentiation by the long non-coding RNA TINCR". Nature. 493 (7431): 231–235. doi:10.1038/nature11661. ISSN 1476-4687. PMC 3674581. PMID 23201690.
- ↑ Kretz, Markus; Webster, Dan E.; Flockhart, Ross J.; Lee, Carolyn S.; Zehnder, Ashley; Lopez-Pajares, Vanessa; Qu, Kun; Zheng, Grace X. Y.; Chow, Jennifer; Kim, Grace E.; Rinn, John L. (2012-02-15). "Suppression of progenitor differentiation requires the long noncoding RNA ANCR". Genes & Development. 26 (4): 338–343. doi:10.1101/gad.182121.111. ISSN 1549-5477. PMC 3289881. PMID 22302877.
- ↑ Sen, George L.; Boxer, Lisa D.; Webster, Dan E.; Bussat, Rose T.; Qu, Kun; Zarnegar, Brian J.; Johnston, Danielle; Siprashvili, Zurab; Khavari, Paul A. (2012-03-13). "ZNF750 is a p63 target gene that induces KLF4 to drive terminal epidermal differentiation". Developmental Cell. 22 (3): 669–677. doi:10.1016/j.devcel.2011.12.001. ISSN 1878-1551. PMC 3306457. PMID 22364861.
- ↑ Flockhart, Ross J.; Webster, Dan E.; Qu, Kun; Mascarenhas, Nicholas; Kovalski, Joanna; Kretz, Markus; Khavari, Paul A. (June 2012). "BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration". Genome Research. 22 (6): 1006–1014. doi:10.1101/gr.140061.112. ISSN 1549-5469. PMC 3371703. PMID 22581800.
- ↑ Sen, George L.; Reuter, Jason A.; Webster, Daniel E.; Zhu, Lilly; Khavari, Paul A. (2010-01-28). "DNMT1 maintains progenitor function in self-renewing somatic tissue". Nature. 463 (7280): 563–567. doi:10.1038/nature08683. ISSN 1476-4687. PMC 3050546. PMID 20081831.
- ↑ Ridky, Todd W.; Chow, Jennifer M.; Wong, David J.; Khavari, Paul A. (December 2010). "Invasive three-dimensional organotypic neoplasia from multiple normal human epithelia". Nature Medicine. 16 (12): 1450–1455. doi:10.1038/nm.2265. ISSN 1546-170X. PMC 3586217. PMID 21102459.
- ↑ Reuter, Jason A.; Ortiz-Urda, Susana; Kretz, Markus; Garcia, John; Scholl, Florence A.; Pasmooij, Anna M. G.; Cassarino, David; Chang, Howard Y.; Khavari, Paul A. (2009-06-02). "Modeling inducible human tissue neoplasia identifies an extracellular matrix interaction network involved in cancer progression". Cancer Cell. 15 (6): 477–488. doi:10.1016/j.ccr.2009.04.002. ISSN 1878-3686. PMC 3050547. PMID 19477427.
- ↑ Chudnovsky, Yakov; Adams, Amy E.; Robbins, Paul B.; Lin, Qun; Khavari, Paul A. (July 2005). "Use of human tissue to assess the oncogenic activity of melanoma-associated mutations". Nature Genetics. 37 (7): 745–749. doi:10.1038/ng1586. ISSN 1061-4036. PMC 3063773. PMID 15951821.
- ↑ Ortiz-Urda, Susana; Garcia, John; Green, Cheryl L.; Chen, Lei; Lin, Qun; Veitch, Dallas P.; Sakai, Lynn Y.; Lee, Hyangkyu; Marinkovich, M. Peter; Khavari, Paul A. (2005-03-18). "Type VII collagen is required for Ras-driven human epidermal tumorigenesis". Science. 307 (5716): 1773–1776. doi:10.1126/science.1106209. ISSN 1095-9203. PMID 15774758.
- ↑ Dajee, Maya; Lazarov, Mirella; Zhang, Jennifer Y.; Cai, Ti; Green, Cheryl L.; Russell, Alan J.; Marinkovich, M. Peter; Tao, Shiying; Lin, Qun; Kubo, Yoshiaki; Khavari, Paul A. (2003-02-06). "NF-kappaB blockade and oncogenic Ras trigger invasive human epidermal neoplasia". Nature. 421 (6923): 639–643. doi:10.1038/nature01283. ISSN 0028-0836. PMID 12571598.
- ↑ Lazarov, Mirella; Kubo, Yoshiaki; Cai, Ti; Dajee, Maya; Tarutani, Masahito; Lin, Qun; Fang, Min; Tao, Shiying; Green, Cheryl L.; Khavari, Paul A. (October 2002). "CDK4 coexpression with Ras generates malignant human epidermal tumorigenesis". Nature Medicine. 8 (10): 1105–1114. doi:10.1038/nm779. ISSN 1078-8956. PMID 12357246.
