Biography
Professional Summary
Education & Certifications
- Medical Education: Yale School Of Medicine (1988) CT
- Fellowship: Stanford University School of Medicine (1994) CA
- Residency: Stanford University School of Medicine (1991) CA
- Board Certification: American Board of Dermatology, Dermatology (1992)
- Internship: Yale-New Haven Hospital (1989) CT
- Residency: Yale - New Haven Hospital (1990) CT
Administrative Appointments
- Chair Department of Dermatology, Stanford University School of Medicine (2010 - Present)
- Co-Director, Stanford Program in Epithelial Biology (1999 - Present)
Publications
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Stable nonviral genetic correction of inherited human skin disease
Ortiz-Urda, S., Thyagarajan, B., Keene, D. R., Lin, Q., Fang, M., Calos, M. P., & Khavari, P. A. (2002). Stable nonviral genetic correction of inherited human skin disease. NATURE MEDICINE, 8(10), 1166–70. -
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NF-kappa B blockade and oncogenic Ras trigger invasive human epidermal neoplasia
Dajee, M., Lazarov, M., Zhang, J. Y., Cai, T., Green, C. L., Russell, A. J., … Khavari, P. A. (2003). NF-kappa B blockade and oncogenic Ras trigger invasive human epidermal neoplasia. NATURE, 421(6923), 639–43. -
Type VII collagen is required for Ras-driven human epidermal tumorigenesis
Ortiz-Urda, S., Garcia, J., Green, C. L., Chen, L., Lin, Q., Veitch, D. P., … Khavari, P. A. (2005). Type VII collagen is required for Ras-driven human epidermal tumorigenesis. SCIENCE, 307(5716), 1773–76. -
Use of human tissue to assess the oncogenic activity of melanoma-associated mutations
Chudnovsky, Y., Adams, A. E., Robbins, P. B., Lin, Q., & Khavari, P. A. (2005). Use of human tissue to assess the oncogenic activity of melanoma-associated mutations. NATURE GENETICS, 37(7), 745–49. -
CHARACTERIZATION OF A COFACTOR THAT REGULATES DIMERIZATION OF A MAMMALIAN HOMEODOMAIN PROTEIN
Mendel, D. B., Khavari, P. A., Conley, P. B., Graves, M. K., Hansen, L. P., Admon, A., & Crabtree, G. R. (1991). CHARACTERIZATION OF A COFACTOR THAT REGULATES DIMERIZATION OF A MAMMALIAN HOMEODOMAIN PROTEIN. SCIENCE, 254(5039), 1762–1767. -
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DNMT1 maintains progenitor function in self-renewing somatic tissue
Sen, G. L., Reuter, J. A., Webster, D. E., Zhu, L., & Khavari, P. A. (2010). DNMT1 maintains progenitor function in self-renewing somatic tissue. NATURE, 463(7280), 563–U189. -
ZNF750 Is a p63 Target Gene that Induces KLF4 to Drive Terminal Epidermal Differentiation
Sen, G. L., Boxer, L. D., Webster, D. E., Bussat, R. T., Qu, K., Zarnegar, B. J., … Khavari, P. A. (2012). ZNF750 Is a p63 Target Gene that Induces KLF4 to Drive Terminal Epidermal Differentiation. DEVELOPMENTAL CELL, 22(3), 669–77. -
Control of somatic tissue differentiation by the long non-coding RNA TINCR.
Kretz, M., Siprashvili, Z., Chu, C., Webster, D. E., Zehnder, A., Qu, K., … Khavari, P. A. (2013). Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature, 493(7431), 231–35. -
THE RETINOBLASTOMA PROTEIN AND BRG1 FORM A COMPLEX AND COOPERATE TO INDUCE CELL-CYCLE ARREST
Dunaief, J. L., Strober, B. E., Guha, S., Khavari, P. A., Alin, K., Luban, J., … Goff, S. P. (1994). THE RETINOBLASTOMA PROTEIN AND BRG1 FORM A COMPLEX AND COOPERATE TO INDUCE CELL-CYCLE ARREST. CELL, 79(1), 119–130. -
NUCLEOSOME DISRUPTION AND ENHANCEMENT OF ACTIVATOR BINDING BY A HUMAN SW1/SNF COMPLEX
Kwon, H., Imbalzano, A. N., Khavari, P. A., Kingston, R. E., & GREEN, M. R. (1994). NUCLEOSOME DISRUPTION AND ENHANCEMENT OF ACTIVATOR BINDING BY A HUMAN SW1/SNF COMPLEX. NATURE, 370(6489), 477–481. -
BRG1 CONTAINS A CONSERVED DOMAIN OF THE SWI2/SNF2 FAMILY NECESSARY FOR NORMAL MITOTIC GROWTH AND TRANSCRIPTION
Khavari, P. A., Peterson, C. L., Tamkun, J. W., Mendel, D. B., & Crabtree, G. R. (1993). BRG1 CONTAINS A CONSERVED DOMAIN OF THE SWI2/SNF2 FAMILY NECESSARY FOR NORMAL MITOTIC GROWTH AND TRANSCRIPTION. NATURE, 366(6451), 170–174. -
Corrective gene transfer in the human skin disorder lamellar ichthyosis
Choate, K. A., Medalie, D. A., Morgan, J. R., & Khavari, P. A. (1996). Corrective gene transfer in the human skin disorder lamellar ichthyosis. NATURE MEDICINE, 2(11), 1263–1267. -
Gene therapy: Progress, problems, prospects.
Blau, H., & Khavari, P. (1997). Gene therapy: Progress, problems, prospects. NATURE MEDICINE, 3(6), 612–613. -
Induction of basal cell carcinoma features in transgenic human skin expressing Sonic Hedgehog
Fan, H. R., Oro, A. E., Scott, M. P., & Khavari, P. A. (1997). Induction of basal cell carcinoma features in transgenic human skin expressing Sonic Hedgehog. NATURE MEDICINE, 3(7), 788–792. -
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Stable nonviral genetic correction of inherited human skin disease
Stable nonviral genetic correction of inherited human skin disease. (2002). Nature Medicine, 8. -
Invasive three-dimensional organotypic neoplasia from multiple normal human epithelia
Invasive three-dimensional organotypic neoplasia from multiple normal human epithelia. (2010). Nature Medicine, 16. -
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High throughput RNA sequencing of Sezary syndrome and cutaneous squamous cell carcinoma
Lee, C., Qu, K., Webster, D., Kretz, M., MAH, A., Ungewickell, A., … Khavari, P. (2011). High throughput RNA sequencing of Sezary syndrome and cutaneous squamous cell carcinoma. Presented at the 71st Annual Meeting of the Society-for-Investigative-Dermatology, PHOENIX,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ: NATURE PUBLISHING GROUP. -
Maintenance of the epidermal progenitor state requires the long non-coding RNA Linc8D
Lee, C., Kretz, M., Webster, D., Flockhart, R., Qu, K., MAH, A., … Khavari, P. (2011). Maintenance of the epidermal progenitor state requires the long non-coding RNA Linc8D. Presented at the 71st Annual Meeting of the Society-for-Investigative-Dermatology, PHOENIX,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ,AZ: NATURE PUBLISHING GROUP. -
Transcriptome sequencing in Sezary Syndrome identifies novel Sezary cell-associated transcripts
Lee, C., Ungewickell, A., Bhaduri, A., Qu, K., Webster, D., Armstrong, R., … Khavari, P. A. (2012). Transcriptome sequencing in Sezary Syndrome identifies novel Sezary cell-associated transcripts. Presented at the 75th Annual Meeting of the Society-for-Investigative-Dermatology, RALEIGH,NC,NC,NC,NC,NC,NC,NC,NC,NC: NATURE PUBLISHING GROUP. -
DNMT1 maintains epidermal progenitor function
Sen, G. L., Reuter, J. A., Webster, D. E., Zhu, L., & Khavari, P. (2010). DNMT1 maintains epidermal progenitor function. Presented at the Annual Meeting of the Society-for-Investigative-Dermatology, ATLANTA,GA,GA,GA,GA,GA,GA,GA: NATURE PUBLISHING GROUP. -
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ZNF750 is a p63 target that induces KLF4 to drive epidermal differentiation
Sen, G. L., Boxer, L., Webster, D., Bussat, R., Qu, K., Zarnegar, B., … Khavari, P. A. (2012). ZNF750 is a p63 target that induces KLF4 to drive epidermal differentiation. Presented at the 75th Annual Meeting of the Society-for-Investigative-Dermatology, RALEIGH,NC,NC,NC,NC,NC,NC,NC,NC: NATURE PUBLISHING GROUP. -
IDENTIFICATION OF A 205-KD KERATINOCYTE-EXPRESSED ACTIVATOR OF GLUCOCORTICOID RECEPTOR (GR)-DRIVEN GENE-TRANSCRIPTION
Khavari, P. A., & Petersen, C. L. (1993). IDENTIFICATION OF A 205-KD KERATINOCYTE-EXPRESSED ACTIVATOR OF GLUCOCORTICOID RECEPTOR (GR)-DRIVEN GENE-TRANSCRIPTION. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 100(4), 524–24. -
Functional characterization of class IIPI3-kinase in epidermal differentiation via targeted gene disruption and RNA interference
Harada, K., Cai, T., Truong, A., & Khavari, P. (2005). Functional characterization of class IIPI3-kinase in epidermal differentiation via targeted gene disruption and RNA interference. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 124(4), A98–A98. -
Type VII collagen is required for cellular invasiveness in epidermal carcinogenesis
Ortiz-Urda, S., Garcia, J., Marinkovich, M., & Khavari, P. (2005). Type VII collagen is required for cellular invasiveness in epidermal carcinogenesis. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 124(4), A25–A25. -
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Sustainable TGM1 gene delivery in human lamellar ichthyosis patient skin in vivo
Lin, Q., Deng, H., Fan, H., & Khavari, P. (1999). Sustainable TGM1 gene delivery in human lamellar ichthyosis patient skin in vivo. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 638–38. -
Invasive human melanocytic neoplasia generated using defined genetic elements
Chudnovsky, Y., Adams, A. E., Lin, Q., Robbins, P. B., & Khavari, P. (2004). Invasive human melanocytic neoplasia generated using defined genetic elements. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 122(3), A157–A157. -
Invasive human melanocytic neoplasia in a 3-dimensional model using defined genetic elements
Adams, A., Chudnovsky, Y., & Khavari, P. (2005). Invasive human melanocytic neoplasia in a 3-dimensional model using defined genetic elements. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 125(3), A58–A58. -
Two distinct roles for the laminin-5 beta 3 chain in epidermal carcinogenesis and adhesion
Waterman, E. A., Ortiz-Urda, S., Nguyen, N. T., Veitch, D. P., Horst, B. A., Dey, C. N., … Marinkovich, M. P. (2005). Two distinct roles for the laminin-5 beta 3 chain in epidermal carcinogenesis and adhesion. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 124(4), A22–A22. -
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Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition
Webster, D. E., Barajas, B., Bussat, R. T., Yan, K. J., Neela, P. H., Flockhart, R. J., … Khavari, P. A. (2014). Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition. GENOME RESEARCH, 24(5), 751–760. -
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Quantitative analysis of mammalian translation initiation sites by FACS-seq.
Noderer, W. L., Flockhart, R. J., Bhaduri, A., Diaz de Arce, A. J., Zhang, J., Khavari, P. A., & Wang, C. L. (2014). Quantitative analysis of mammalian translation initiation sites by FACS-seq. Molecular Systems Biology, 10, 748-? -
ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes.
Boxer, L. D., Barajas, B., Tao, S., Zhang, J., & Khavari, P. A. (2014). 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. -
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Advances in skin grafting and treatment of cutaneous wounds
Sun, B. K., Siprashvili, Z., & Khavari, P. A. (2014). Advances in skin grafting and treatment of cutaneous wounds. SCIENCE, 346(6212), 941–45. -
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A LncRNA-MAF:MAFB Transcription Factor Network Regulates Epidermal Differentiation
Lopez-Pajares, V., Qu, K., Zhang, J., Webster, D. E., Barajas, B. C., Siprashvili, Z., … Khavari, P. A. (2015). A LncRNA-MAF:MAFB Transcription Factor Network Regulates Epidermal Differentiation. DEVELOPMENTAL CELL, 32(6), 693–706. -
Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma.
Lee, C. S., Bhaduri, A., Mah, A., Johnson, W. L., Ungewickell, A., Aros, C. J., … Khavari, P. A. (2014). Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma. Nature Genetics, 46(10), 1060–62. -
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Network Analysis Identifies Mitochondria! Regulation of Epidermal Differentiation by MPZL3 and FDXR
Bhaduri, A., Ungewickell, A., Boxer, L. D., Lopez-Pajares, V., Zarnegar, B. J., & Khavari, P. A. (2015). Network Analysis Identifies Mitochondria! Regulation of Epidermal Differentiation by MPZL3 and FDXR. DEVELOPMENTAL CELL, 35(4), 444–57. -
CALML5 is a ZNF750-and TINCR-induced protein that binds stratifin to regulate epidermal differentiation
Sun, B. K., Boxer, L. D., Ransohoff, J. D., Siprashvili, Z., Qu, K., Lopez-Pajares, V., … Khavari, P. A. (2015). CALML5 is a ZNF750-and TINCR-induced protein that binds stratifin to regulate epidermal differentiation. GENES & DEVELOPMENT, 29(21), 2225–30. -
The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer.
Siprashvili, Z., Webster, D. E., Johnston, D., Shenoy, R. M., Ungewickell, A. J., Bhaduri, A., … Khavari, P. A. (2016). The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer. Nature Genetics, 48(1), 53–58. -
A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63.
Bao, X., Rubin, A. J., Qu, K., Zhang, J., Giresi, P. G., Chang, H. Y., & Khavari, P. A. (2015). A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome Biology, 16(1), 284-? -
7SK-BAF axis controls pervasive transcription at enhancers.
Flynn, R. A., Do, B. T., Rubin, A. J., Calo, E., Lee, B., Kuchelmeister, H., … Chang, H. Y. (2016). 7SK-BAF axis controls pervasive transcription at enhancers. Nature Structural & Molecular Biology, 23(3), 231–38. -
RAC1 activation drives pathologic interactions between the epidermis and immune cells
Winge, M. C. C., Ohyama, B., Dey, C. N., Boxer, L. M., Li, W., Ehsani-Chimeh, N., … Marinkovich, M. P. (2016). RAC1 activation drives pathologic interactions between the epidermis and immune cells. JOURNAL OF CLINICAL INVESTIGATION, 126(7), 2661–77. -
irCLIP platform for efficient characterization of protein-RNA interactions
Zarnegar, B. J., Flynn, R. A., Shen, Y., Do, B. T., Chang, H. Y., & Khavari, P. A. (2016). irCLIP platform for efficient characterization of protein-RNA interactions. NATURE METHODS, 13(6), 489-? -
Safety and Wound Outcomes Following Genetically Corrected Autologous Epidermal Grafts in Patients With Recessive Dystrophic Epidermolysis Bullosa.
Siprashvili, Z., Nguyen, N. T., Gorell, E. S., Loutit, K., Khuu, P., Furukawa, L. K., … Marinkovich, M. P. (2016). Safety and Wound Outcomes Following Genetically Corrected Autologous Epidermal Grafts in Patients With Recessive Dystrophic Epidermolysis Bullosa. JAMA, 316(17), 1808–17. -
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HiChIP: efficient and sensitive analysis of protein-directed genome architecture.
Mumbach, M. R., Rubin, A. J., Flynn, R. A., Dai, C., Khavari, P. A., Greenleaf, W. J., & Chang, H. Y. (2016). HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nature Methods, 13(11), 919–22. -
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.
Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., … Chang, H. Y. (2017). An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature Methods. -
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.
Mumbach, M. R., Satpathy, A. T., Boyle, E. A., Dai, C., Gowen, B. G., Cho, S. W., … Chang, H. Y. (2017). Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nature Genetics. -
CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue.
Bao, X., Siprashvili, Z., Zarnegar, B. J., Shenoy, R. M., Rios, E. J., Nady, N., … Khavari, P. A. (2017). CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue. Developmental Cell, 43(2), 227–39.e5. -
Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.
Rubin, A. J., Barajas, B. C., Furlan-Magaril, M., Lopez-Pajares, V., Mumbach, M. R., Howard, I., … Khavari, P. A. (2017). Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nature Genetics, 49(10), 1522–28. -
RNA-protein interaction detection in living cells.
Ramanathan, M., Majzoub, K., Rao, D. S., Neela, P. H., Zarnegar, B. J., Mondal, S., … Khavari, P. A. (2018). RNA-protein interaction detection in living cells. Nature Methods. -
Phase I clinical trial for recessive dystrophic epidermolysis bullosa using genetically corrected autologous keratinocytes
Siprashvili, Z., Nguyen, N. T., Gorell, E., Loutit, K., Khuu, P., Furukawa, L. K., … Marinkovich, M. (2015). Phase I clinical trial for recessive dystrophic epidermolysis bullosa using genetically corrected autologous keratinocytes. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Factors That May Promote an Effective Local Research Environment
Wang, K., Lee, C. S., Marinkovich, M. P., Chang, H. Y., Oro, A. E., & Khavari, P. A. (2016). Factors That May Promote an Effective Local Research Environment. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 136(8), 1529–31. -
Laminin-5 Beta 3 chain promotes epidermal carcinogenesis through type VII collagen binding and pi3k activation
Sakai, N., Waterman, E. A., Nguyen, N. E., Horst, B. A., Veitch, D. P., Dey, C. N., … Marinkovich, M. (2006). Laminin-5 Beta 3 chain promotes epidermal carcinogenesis through type VII collagen binding and pi3k activation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 126, 24. -
Phase I/IIa clinical trial for recessive dystrophic epidermolysis bullosa using genetically corrected autologous keratinocytes
Siprashvili, Z., Nguyen, N., Gorell, E., Loutit, K., Dutt-Singkh, Y., Nazaroff, J., … Marinkovich, M. (2017). Phase I/IIa clinical trial for recessive dystrophic epidermolysis bullosa using genetically corrected autologous keratinocytes. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Phase I/IIa clinical trial for recessive dystrophic epidermolysis bullosa using EB-101 (COL7A1 gene-corrected autologous keratinocytes)
Siprashvili, Z., Nguyen, N. T., Gorell, E. S., Loutit, K., Dutt-Singkh, Y., Nazaroff, J., … Marinkovich, M. P. (2017). Phase I/IIa clinical trial for recessive dystrophic epidermolysis bullosa using EB-101 (COL7A1 gene-corrected autologous keratinocytes). HUMAN GENE THERAPY. MARY ANN LIEBERT, INC. -
Phase 1 clinical trial of genetically corrected autologous epidermal keratinocytes for recessive dystrophic epidermolysis bullosa
Siprashvili, Z., Nguyen, N. T., Gorell, E., Khuu, P., Furukawa, L., Lorenz, H. P., … Lane, A. T. (2014). Phase 1 clinical trial of genetically corrected autologous epidermal keratinocytes for recessive dystrophic epidermolysis bullosa. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
A novel therapeutic inhibits Rac1 mediated invasion and metastasis in a newly described in vivo model of human melanoma
Winge, M. C., Kovalski, J., Nguyen, N. T., Wu, D., Zehnder, A., Khavari, P., & Marinkovich, M. (2015). A novel therapeutic inhibits Rac1 mediated invasion and metastasis in a newly described in vivo model of human melanoma. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 135, S71. -
Attenuated netrin-1 receptor mediated regulation of tiam1 is required for rac1 mutant melanoma progression
Winge, M. C. G., Kovalski, J., Nguyen, N. T., Wu, D., Zehnder, A., Khavari, P. A., & Marinkovich, M. (2017). Attenuated netrin-1 receptor mediated regulation of tiam1 is required for rac1 mutant melanoma progression. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 137(5), S139. -
Identification of the KNSTRN proteome by APEX2 targeting
Lee, C., Mah, A., Nguyen, C., & Khavari, P. (2015). Identification of the KNSTRN proteome by APEX2 targeting. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 135, S25. -
Recurrent point mutations in KNSTRN and disruption of multiple notch signaling genes in cutaneous squamous cell carcinoma
Lee, C., Bhaduri, A., Mah, A., Ungewickell, A., Aros, C., Nguyen, C., … Khavari, P. (2014). Recurrent point mutations in KNSTRN and disruption of multiple notch signaling genes in cutaneous squamous cell carcinoma. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Phase I clinical trial for Recessive Dystrophic Epidermolysis Bullosa using genetically corrected autologous keratinocytes
Siprashvili, Z., Nguyen, N. T., Gorell, E. S., Loutit, K., Khuu, P., Furukawa, L. K., … Marinkovich, P. (2016). Phase I clinical trial for Recessive Dystrophic Epidermolysis Bullosa using genetically corrected autologous keratinocytes. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Transcript-indexed ATAC-seq for precision immune profiling.
Satpathy, A. T., Saligrama, N., Buenrostro, J. D., Wei, Y., Wu, B., Rubin, A. J., … Chang, H. Y. (2018). Transcript-indexed ATAC-seq for precision immune profiling. Nature Medicine. -
The functions and unique features of long intergenic non-coding RNA.
Ransohoff, J. D., Wei, Y., & Khavari, P. A. (2018). The functions and unique features of long intergenic non-coding RNA. Nature Reviews. Molecular Cell Biology, 19(3), 143–57. -
Targeting pathogenic interactions between Rac1 and NCK1 in psoriasis
Winge, M. C. G., Nasrallah, M., Fuhriman, J. M., Ramanathan, M., Azameera, A., Nguyen, N., … Marinkovich, M. (2018). Targeting pathogenic interactions between Rac1 and NCK1 in psoriasis. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Single-cell RNA-sequencing reveals SCC intratumoral heterogeneity
Ji, A., Rubin, A., Hollmig, S., Aasi, S., & Khavari, P. (2018). Single-cell RNA-sequencing reveals SCC intratumoral heterogeneity. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 138(5), S31. -
Cancer-Associated Long Noncoding RNA SMRT-2 Controls Epidermal Differentiation
Lee, C. S., Mah, A., Aros, C. J., Lopez-Pajares, V., Bhaduri, A., Webster, D. E., … Khavari, P. A. (2018). Cancer-Associated Long Noncoding RNA SMRT-2 Controls Epidermal Differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 138(6), 1445–49. -
Decoding regulatory sequence across skin differentiation with deep learning
Kim, D., Risca, V., Chappell, J., Shi, M., Zhao, Z., Jung, N., … Khavari, P. (2018). Decoding regulatory sequence across skin differentiation with deep learning. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Small non-coding RNAs control the MAPK/ERK pathway
Siprashvili, Z., Shenoy, R. M., Elcavage, L., & Khavari, P. (2018). Small non-coding RNAs control the MAPK/ERK pathway. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
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Dynamic morphogen-p63 chromatin interactions that guide epigenetic changes and p63 activity in surface ectoderm commitment
Pattison, J., Melo, S., Piekos, S., Torkelson, J., Mumbach, M. R., Rubin, A., … Oro, A. E. (2018). Dynamic morphogen-p63 chromatin interactions that guide epigenetic changes and p63 activity in surface ectoderm commitment. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
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Phase I / II Clinical Trial for Recessive Dystrophic Epidermolysis Bullosa Using EB-101 (COL7A1 Gene-Corrected Autologous Keratinocytes)
Tang, J. Y., Marinkovich, M. P., Siprashvili, Z., Nguyen, N. T., Gorell, E. S., Loutit, K., … Lane, A. T. (2018). Phase I / II Clinical Trial for Recessive Dystrophic Epidermolysis Bullosa Using EB-101 (COL7A1 Gene-Corrected Autologous Keratinocytes). MOLECULAR THERAPY. CELL PRESS. -
IQGAP1, an ERK1/2 MAPK scaffold, is an oncogenic target in canine melanoma
Zehnder, A., Lee, B., Neela, P., & Khavari, P. (2015). IQGAP1, an ERK1/2 MAPK scaffold, is an oncogenic target in canine melanoma. CANCER RESEARCH, 75. -
Transcriptome sequencing in squamous cell carcinoma identifies novel skin malignancy regulated transcripts
Lee, C., Ungewickell, A., Bhaduri, A., Qu, K., Webster, D., Aros, C., … Khavari, P. A. (2012). Transcriptome sequencing in squamous cell carcinoma identifies novel skin malignancy regulated transcripts. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 132, S29. -
Epidermal tissue differentiation and lipid barrier function requires the long non-coding RNA Linc19A
Kretz, M., Webster, D., Siprashvili, Z., Zehnder, A., Lee, C., Flockhart, R., … Khavari, P. (2011). Epidermal tissue differentiation and lipid barrier function requires the long non-coding RNA Linc19A. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment.
Pattison, J. M., Melo, S. P., Piekos, S. N., Torkelson, J. L., Bashkirova, E., Mumbach, M. R., … Oro, A. E. (2018). Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment. Nature Genetics. -
Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.
Rubin, A. J., Parker, K. R., Satpathy, A. T., Qi, Y., Wu, B., Ong, A. J., … Khavari, P. A. (2018). Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks. Cell. -
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Methods to study RNA-protein interactions.
Ramanathan, M., Porter, D. F., & Khavari, P. A. (2019). Methods to study RNA-protein interactions. Nature Methods, 16(3), 225–34. -
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Sustained survival and production of recombinant protein by genetically engineered human fibroblasts after intradermal injection
Siprashvili, Z., Ridky, T. W., & Khavari, P. (2006). Sustained survival and production of recombinant protein by genetically engineered human fibroblasts after intradermal injection. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
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Direct cutaneous plasmid DNA delivery via single intradermal injection of the cis-acting Sleeping Beauty transposon system
Siprashvili, Z., Mikkelsen, J. G., Yant, S., Kay, M., & Khavari, P. (2005). Direct cutaneous plasmid DNA delivery via single intradermal injection of the cis-acting Sleeping Beauty transposon system. JOURNAL OF INVESTIGATIVE DERMATOLOGY. BLACKWELL PUBLISHING INC. -
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Dynamic and stable enhancer-promoter contacts regulate epidermal terminal differentiation
Lopez-Pajares, V., Rubin, A., Barajas, B., Furlan-Magaril, M., Mumbach, M., Greenleaf, W., … Khavari, P. A. (2017). Dynamic and stable enhancer-promoter contacts regulate epidermal terminal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
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The SNORD86 small non-coding RNA binds and regulates Rac1
Rios, E., Bhaduri, A., Siprashvili, Z., Zarnegar, B., & Khavari, P. A. (2017). The SNORD86 small non-coding RNA binds and regulates Rac1. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
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K-RAS oncogene activation is regulated by a snoRNA/SNARE protein axis that controls its subcellular transport
Che, Y., Siprashvili, Z., Kovalski, J., & Khavari, P. A. (2017). K-RAS oncogene activation is regulated by a snoRNA/SNARE protein axis that controls its subcellular transport. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
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Small non-coding snoRNAs control Ras superfamily GTPases in stem cell differentiation and cancer
Zarnegar, B., Rios, E., Siprashvili, Z., & Khavari, P. A. (2016). Small non-coding snoRNAs control Ras superfamily GTPases in stem cell differentiation and cancer. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
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The BAF/SWI/SNF complex controls genome accessibility to p63 during epidermal differentiation
Bao, X., Rubin, A., Qu, K., Zhang, J., Giresi, P., Chang, H., & Khavari, P. (2015). The BAF/SWI/SNF complex controls genome accessibility to p63 during epidermal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
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Regulated lentivectors for controlled and reversible cutaneous gene delivery
Siprashvili, Z., & Khavari, P. (2002). Regulated lentivectors for controlled and reversible cutaneous gene delivery. JOURNAL OF INVESTIGATIVE DERMATOLOGY. BLACKWELL PUBLISHING INC. -
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Transposase-based stable nonviral laminin 5 gene delivery in junctional epidermolysis bullosa
Ortiz-Urda, S., Yant, S., Scholl, F., Siprashvili, Z., Chen, P., Kay, M., & Khavari, P. (2002). Transposase-based stable nonviral laminin 5 gene delivery in junctional epidermolysis bullosa. JOURNAL OF INVESTIGATIVE DERMATOLOGY. BLACKWELL PUBLISHING INC. -
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Impact of a patient-derived hepatitis C viral RNA genome with a mutated microRNA binding site.
Mata, M., Neben, S., Majzoub, K., Carette, J., Ramanathan, M., Khavari, P. A., & Sarnow, P. (2019). Impact of a patient-derived hepatitis C viral RNA genome with a mutated microRNA binding site. PLoS Pathogens, 15(5), e1007467. -
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Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment
Pattison, J. M., Melo, S. P., Piekos, S. N., Torkelson, J. L., Bashkirova, E., Mumbach, M. R., … Oro, A. E. (2018). Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment. NATURE GENETICS, 50(12), 1658-+. -
Methods to study RNA-protein interactions
Ramanathan, M., Porter, D. F., & Khavari, P. A. (2019). Methods to study RNA-protein interactions. NATURE METHODS, 16(3), 225–34. -
The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2
Kovalski, J. R., Bhaduri, A., Zehnder, A. M., Neela, P. H., Che, Y., Wozniak, G. G., & Khavari, P. A. (2019). The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2. MOLECULAR CELL, 73(4), 830-+. -
Unraveling keratinocyte gene regulatory networks with single-cell cripsr screening and epigenomic profiling
Ramanathan, M., Rubin, A., Parker, K., Satpathy, A., Greenleaf, W., Chang, H., & Khavari, P. (2019). Unraveling keratinocyte gene regulatory networks with single-cell cripsr screening and epigenomic profiling. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Small non-coding RNA SNORA12 effects MAPK1 signaling
Siprashvili, Z., Shenoy, R. M., Elcavage, L., & Khavari, P. A. (2019). Small non-coding RNA SNORA12 effects MAPK1 signaling. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Dissecting intratumoral heterogeneity and microenvironment interactions in SCC through single-cell RNA-sequencing
Ji, A., Rubin, A., Reynolds, D., Guo, M., Bhaduri, A., George, B., … Khavari, P. (2019). Dissecting intratumoral heterogeneity and microenvironment interactions in SCC through single-cell RNA-sequencing. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 139(5), S24. -
Uncovering causative, noncoding genetic variants in cutaneous diseases
Wozniak, G., Shen, Y., Rubin, A., Neela, P., & Khavari, P. (2019). Uncovering causative, noncoding genetic variants in cutaneous diseases. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 139(5), S68. -
Characterization of novel MAPK interactor with potential in therapeutic development
Jiang, T. E., Che, Y., Seelman, A., Guenin, C., & Khavari, P. (2019). Characterization of novel MAPK interactor with potential in therapeutic development. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 139(5), S69. -
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Ras functional proximity proteomics establishes mTORC2 as new direct ras effector.
Kovalski, J. R., Shanderson, R. L., & Khavari, P. A. (2019). Ras functional proximity proteomics establishes mTORC2 as new direct ras effector. Oncotarget, 10(50), 5126–35. -
Genetic and genomic studies of pathogenic EXOSC2 mutations in the newly described disease SHRF implicate the autophagy pathway in disease pathogenesis.
Yang, X., Bayat, V., DiDonato, N., Zhao, Y., Zarnegar, B., Siprashvili, Z., … Lu, B. (2019). Genetic and genomic studies of pathogenic EXOSC2 mutations in the newly described disease SHRF implicate the autophagy pathway in disease pathogenesis. Human Molecular Genetics. -
KRAS regulation by small non-coding RNAs and SNARE proteins.
Che, Y., Siprashvili, Z., Kovalski, J. R., Jiang, T., Wozniak, G., Elcavage, L., & Khavari, P. A. (2019). KRAS regulation by small non-coding RNAs and SNARE proteins. Nature Communications, 10(1), 5118. -
Genome-wide meta-analysis identifies eight new susceptibility loci for cutaneous squamous cell carcinoma.
Sarin, K. Y., Lin, Y., Daneshjou, R., Ziyatdinov, A., Thorleifsson, G., Rubin, A., … Han, J. (2020). Genome-wide meta-analysis identifies eight new susceptibility loci for cutaneous squamous cell carcinoma. Nature Communications, 11(1), 820. -
Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation.
Carter, A. C., Xu, J., Nakamoto, M. Y., Wei, Y., Zarnegar, B. J., Shi, Q., … Chang, H. Y. (2020). Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation. ELife, 9. -
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.
Ji, A. L., Rubin, A. J., Thrane, K., Jiang, S., Reynolds, D. L., Meyers, R. M., … Khavari, P. A. (2020). Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. Cell. -
Structural modularity of the XIST ribonucleoprotein complex.
Lu, Z., Guo, J. K., Wei, Y., Dou, D. R., Zarnegar, B., Ma, Q., … Chang, H. Y. (2020). Structural modularity of the XIST ribonucleoprotein complex. Nature Communications, 11(1), 6163. -
easyCLIP analysis of RNA-protein interactions incorporating absolute quantification.
Porter, D. F., Miao, W., Yang, X., Goda, G. A., Ji, A. L., Donohue, L. K., … Khavari, P. A. (2021). easyCLIP analysis of RNA-protein interactions incorporating absolute quantification. Nature Communications, 12(1), 1569. -
SARS-CoV-2 B.1.1.7 and B.1.351 spike variants bind human ACE2 with increased affinity.
Ramanathan, M., Ferguson, I. D., Miao, W., & Khavari, P. A. (2021). SARS-CoV-2 B.1.1.7 and B.1.351 spike variants bind human ACE2 with increased affinity. The Lancet. Infectious Diseases. -
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.
Ji, A. L., Rubin, A. J., Thrane, K., Jiang, S., Reynolds, D. L., Meyers, R. M., … Khavari, P. A. (2020). Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. Cell, 182(6), 1661–1662. -
Dissecting intercellular communication in adult human skin with single-cell and spatial transcriptomics
Ji, A., Thrane, K., Guo, M., Rubin, A., Kim, D., Hollmig, T., … Khavari, P. (2021). Dissecting intercellular communication in adult human skin with single-cell and spatial transcriptomics. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 141(5), S17. -
Metabolomic identification of an essential glucose-IRF6 axis in differentiation
Lopez-Pajares, V., Bhaduri, A., Guerrero, A., Zhao, Y., Donohue, L., Guo, M., … Khavari, P. (2021). Metabolomic identification of an essential glucose-IRF6 axis in differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 141(5), S24. -
SARS-CoV-2 B.1.1.7 and B.1.351 Spike variants bind human ACE2 with increased affinity.
Ramanathan, M., Ferguson, I. D., Miao, W., & Khavari, P. A. (2021). SARS-CoV-2 B.1.1.7 and B.1.351 Spike variants bind human ACE2 with increased affinity. BioRxiv : the Preprint Server for Biology. -
Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics.
Longo, S. K., Guo, M. G., Ji, A. L., & Khavari, P. A. (2021). Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. Nature Reviews. Genetics. -
Mutant collagen COL11A1 enhances cancerous invasion.
Lee, C. S., Siprashvili, Z., Mah, A., Bencomo, T., Elcavage, L. E., Che, Y., … Khavari, P. A. (2021). Mutant collagen COL11A1 enhances cancerous invasion. Oncogene. -
The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation.
Meyers, J. M., Ramanathan, M., Shanderson, R. L., Beck, A., Donohue, L., Ferguson, I., … Khavari, P. A. (2021). The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation. PLoS Pathogens, 17(10), e1009412. -
The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation.
Meyers, J. M., Ramanathan, M., Shanderson, R. L., Donohue, L., Ferguson, I., Guo, M. G., … Khavari, P. A. (2021). The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation. BioRxiv : the Preprint Server for Biology. -
The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation.
Kim, D. S., Risca, V. I., Reynolds, D. L., Chappell, J., Rubin, A. J., Jung, N., … Khavari, P. A. (2021). The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. Nature Genetics. -
Super-resolved spatial transcriptomics by deep data fusion.
Bergenstrahle, L., He, B., Bergenstrahle, J., Abalo, X., Mirzazadeh, R., Thrane, K., … Maaskola, J. (2021). Super-resolved spatial transcriptomics by deep data fusion. Nature Biotechnology. -
Targeted Proteomic Approaches for Proteome-Wide Characterizations of the AMP-Binding Capacities of Kinases.
Miao, W., Yin, J., Porter, D. F., Jiang, X., Khavari, P. A., & Wang, Y. (2022). Targeted Proteomic Approaches for Proteome-Wide Characterizations of the AMP-Binding Capacities of Kinases. Journal of Proteome Research. -
PROBER identifies proteins associated with programmable sequence-specific DNA in living cells.
Mondal, S., Ramanathan, M., Miao, W., Meyers, R. M., Rao, D., Lopez-Pajares, V., … Khavari, P. A. (2022). PROBER identifies proteins associated with programmable sequence-specific DNA in living cells. Nature Methods, 19(8), 959–968. -
Spatially resolved clonal copy number alterations in benign and malignant tissue.
Erickson, A., He, M., Berglund, E., Marklund, M., Mirzazadeh, R., Schultz, N., … Lundeberg, J. (2022). Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature, 608(7922), 360–367. -
Glucose controls protein-protein interactions and epidermal differentiation
Lopez-Pajares, V., Bhaduri, A., Zhao, Y., Gowrishankar, G., Donohue, L., Guo, M., … Khavari, P. (2022). Glucose controls protein-protein interactions and epidermal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
An essential role for CRL complex signaling in epidermal differentiation
Winge, M. C., Reynolds, D. L., Ducoli, L., Meyers, R. M., & Khavari, P. (2022). An essential role for CRL complex signaling in epidermal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
PROBER: overcoming the high noise of DNA-protein interactions studies
Mondal, S., & Khavari, P. (2022). PROBER: overcoming the high noise of DNA-protein interactions studies. NATURE METHODS, 19(9), 1044. -
Glucose dissociates DDX21 dimers to regulate mRNA splicing and tissue differentiation.
Miao, W., Porter, D. F., Lopez-Pajares, V., Siprashvili, Z., Meyers, R. M., Bai, Y., … Khavari, P. A. (2023). Glucose dissociates DDX21 dimers to regulate mRNA splicing and tissue differentiation. Cell, 186(1), 80. -
Analyzing RNA-Protein Interactions by Cross-Link Rates and CLIP-seq Libraries.
Porter, D. F., Garg, R. M., Meyers, R. M., Miao, W., Ducoli, L., Zarnegar, B. J., & Khavari, P. A. (2023). Analyzing RNA-Protein Interactions by Cross-Link Rates and CLIP-seq Libraries. Current Protocols, 3(1), e659. -
A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation.
Donohue, L. K., Guo, M. G., Zhao, Y., Jung, N., Bussat, R. T., Kim, D. S., … Khavari, P. A. (2022). A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation. Cell Genomics, 2(11). -
Functional characterization of human genomic variation linked to polygenic diseases.
Fabo, T., & Khavari, P. (2023). Functional characterization of human genomic variation linked to polygenic diseases. Trends in Genetics : TIG. -
The spatial landscape of clonal somatic mutations in benign and malignant tissue
Erickson, A., Berglund, E., He, M., Marklund, M., Mirzazadeh, R., Schultz, N., … Lundenberg, J. (2022). The spatial landscape of clonal somatic mutations in benign and malignant tissue. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Advances in cutaneous squamous cell carcinoma.
Winge, M. C., Kellman, L. N., Guo, K., Tang, J. Y., Swetter, S. M., Aasi, S. Z., … Khavari, P. A. (2023). Advances in cutaneous squamous cell carcinoma. Nature Reviews. Cancer. -
A single nucleotide activity map of skin disease variants and transcription factors that modulate them
Porter, D., Reynolds, D. L., Meyers, R., Miao, W., Hong, A. W., Yang, X., … Khavari, P. A. (2023). A single nucleotide activity map of skin disease variants and transcription factors that modulate them. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseases.
Guo, M. G., Reynolds, D. L., Ang, C. E., Liu, Y., Zhao, Y., Donohue, L. K., … Khavari, P. A. (2023). Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseases. Nature Genetics. -
Mitochondrial Raf1 Regulates Glutamine Catabolism.
Shanderson, R. L., Ferguson, I. D., Siprashvili, Z., Ducoli, L., Li, A. M., Miao, W., … Khavari, P. A. (2024). Mitochondrial Raf1 Regulates Glutamine Catabolism. BioRxiv : the Preprint Server for Biology.
Clinical Trials
Clinical trials are research studies that evaluate a new medical approach, device, drug, or other treatment. As a Stanford Health Care patient, you may have access to the latest, advanced clinical trials.
Open trials refer to studies currently accepting participants. Closed trials are not currently enrolling, but may open in the future.
- Pilot Trial to Evaluate the Effect of Vitamin D on Melanocyte Biomarkers »
- Analysis of Cutaneous and Hematologic Disorders by High-Throughput Nucleic Acid Sequencing »
- Gene Transfer for Recessive Dystrophic Epidermolysis Bullosa »
- Characteristics of Adult Patients With Recessive Dystrophic Epidermolysis Bullosa »
Practice Locations
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Stanford Health Care provides comprehensive services to refer and track patients, as well as the latest information and news for physicians and office staff. For help with all referral needs and questions, visit Referral Information.
You may also submit a web referral or complete a referral form and fax it to 650-320-9443 or email the Referral Center at ReferralCenter@stanfordhealthcare.org.
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