CDK4 coexpression with Ras generates malignant human epidermal tumorigenesis
Lazarov, M., Kubo, Y., Cai, T., Dajee, M., Tarutani, M., Lin, Q., … Khavari, P. A. (2002). CDK4 coexpression with Ras generates malignant human epidermal tumorigenesis. NATURE MEDICINE, 8(10), 1105–14.

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), 1762–67.

Modeling Inducible Human Tissue Neoplasia Identifies an Extracellular Matrix Interaction Network Involved in Cancer Progression
Reuter, J. A., Ortiz-Urda, S., Kretz, M., Garcia, J., Scholl, F. A., Pasmooij, A. M. G., … Khavari, P. A. (2009). Modeling Inducible Human Tissue Neoplasia Identifies an Extracellular Matrix Interaction Network Involved in Cancer Progression. CANCER CELL, 15(6), 477–88.

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), 119–30.

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), 477–81.

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), 170–74.

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), 1263–67.

Gene therapy: Progress, problems, prospects.
Blau, H., & Khavari, P. (1997). Gene therapy: Progress, problems, prospects. NATURE MEDICINE, 3(6), 612–13.

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), 788–92.

Sustainable cutaneous gene delivery
Deng, H., Lin, Q., & Khavari, P. A. (1997). Sustainable cutaneous gene delivery. NATURE BIOTECHNOLOGY, 15(13), 1388–91.

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.

Towards development of an in vitro model of human BC formation.
Oro, A. E., Fan, H., Khavari, P. A., & Scott, M. P. (1998). Towards development of an in vitro model of human BC formation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 110(4), 500–500.

Towards development of an in vitro model of human BCC formation.
Oro, A. E., Fan, H., Khavari, P. A., & Scott, M. P. (1998). Towards development of an in vitro model of human BCC formation. DEVELOPMENTAL BIOLOGY, 198(1), 196–96.

Analysis of human basal cell carcinoma gene expression at a genomic scale via cDNA microarrays
Fan, H., Barry, C. T., Baek, S. C., Lin, Q., Brown, P. O., & Khavari, P. A. (1999). Analysis of human basal cell carcinoma gene expression at a genomic scale via cDNA microarrays. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 528–28.

cDNA microarray screening for genes differentially expressed in keratinocyte stem cell enriched populations
Freiberg, R., Barry, C., Fang, M., Alvarez-Saavedra, E., Robbins, P., BROWN, P., & Khavari, P. (1999). cDNA microarray screening for genes differentially expressed in keratinocyte stem cell enriched populations. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 560–60.

Genome-wide characterization of NF-01 kappa B target genes in human epithelial cells via high density cDNA microarrays
Hinata, K., Barry, C., BROWN, P., & Khavari, P. (1999). Genome-wide characterization of NF-01 kappa B target genes in human epithelial cells via high density cDNA microarrays. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 637–37.

Genomic analysis of human squamous cell carcinoma gene expression via cDNA microarrays
Fan, H., Barry, C., Lin, Q., Baek, S., BROWN, P., & Khavari, P. (1999). Genomic analysis of human squamous cell carcinoma gene expression via cDNA microarrays. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 558–58.

Identification of new keratinocyte differentiation candidates genes by a genome-wide screening approach
Freiberg, R., Barry, C., BROWN, P., & Khavari, P. (1999). Identification of new keratinocyte differentiation candidates genes by a genome-wide screening approach. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 624–24.

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.

Scaffold-Kinase interaction blockade selectively inhibits Ras-MAPK tumorigenesis
Jameson, K. L., Zehnder, A., & Khavari, P. A. (2012). Scaffold-Kinase interaction blockade selectively inhibits Ras-MAPK tumorigenesis. Presented at the 75th Annual Meeting of the Society-for-Investigative-Dermatology, RALEIGH,NC,NC,NC,NC,NC,NC,NC: NATURE PUBLISHING GROUP.

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.

Profiling genomic expression in disorders of epidermal proliferation identifies Egr-1 as a potent regulator of epidermal growth
Wee, S., Lin, Q., Tao, S., Fan, H., & Khavari, P. (2001). Profiling genomic expression in disorders of epidermal proliferation identifies Egr-1 as a potent regulator of epidermal growth. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 477–77.

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.

BAF53A enforces the epidermal progenitor state by re-targeting the SWI/SNF/BAF chromatin remodeling complex away from differentiation gene promoters
Bao, X., Tang, J., Tao, S., Qu, K., Crabtree, G. R., & Khavari, P. A. (2012). BAF53A enforces the epidermal progenitor state by re-targeting the SWI/SNF/BAF chromatin remodeling complex away from differentiation gene promoters. Presented at the 75th Annual Meeting of the Society-for-Investigative-Dermatology, RALEIGH,NC,NC,NC,NC,NC,NC,NC: NATURE PUBLISHING GROUP.

Non-invasive topical immunization by a peptide vaccine against hepatitis B and rubella virus
Tao, S., Dajee, M., Wee, S., & Khavari, P. (2001). Non-invasive topical immunization by a peptide vaccine against hepatitis B and rubella virus. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 435–35.

Generation of transgenic skin with regulated NF-kappa B function and epidermis deficient in the Re1A/p65 indicate that NF-kappa B subunits regulate epidermal growth but not differentiation
Zhang, Y., Kimmel, R., Tao, S., & Khavari, P. (2002). Generation of transgenic skin with regulated NF-kappa B function and epidermis deficient in the Re1A/p65 indicate that NF-kappa B subunits regulate epidermal growth but not differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 267–67.

TNFR1 signaling to JNK opposes NF-kB to promotes epidermal neoplasia
Zhang, J. Y., Tao, S., Ridky, T. W., & Khavari, P. (2006). TNFR1 signaling to JNK opposes NF-kB to promotes epidermal neoplasia. Presented at the 67th Annual Meeting of the Society-for-Investigative-Dermatology, PHILADELPHIA,PA,PA,PA,PA,PA,PA,PA: NATURE PUBLISHING GROUP.

Disrupting TNFR1-JNK-AP1 action inhibits Ras-driven human epidermal neoplasia
Zhang, J. Y., Tao, S., & Khavari, P. (2005). Disrupting TNFR1-JNK-AP1 action inhibits Ras-driven human epidermal neoplasia. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 124(4), A97–A97.

Spatially localized Ras action inhibits epidermal differentiation and promotes growth capacity via the Raf effector pathway
Dajee, M., Deng, H., Tao, S., & Khavari, P. (2001). Spatially localized Ras action inhibits epidermal differentiation and promotes growth capacity via the Raf effector pathway. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 403–.

Induction of invasive human epidermal neoplasia resembling squamous cell carcinoma (SCC) by defined genetic elements Ras and CDK4
Kubo, Y., Dajee, M., Lazarov, M., Tao, S., & Khavari, P. (2001). Induction of invasive human epidermal neoplasia resembling squamous cell carcinoma (SCC) by defined genetic elements Ras and CDK4. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 472–72.

Profiling genomic expression in disorders of epidermal proliferation identifies Egr1 as a potent regulator of epidermal growth.
Fang, M., Wee, S. A., Fan, H., Morrisey, G., Tao, S., Lin, Q., & Khavari, P. A. (2001). Profiling genomic expression in disorders of epidermal proliferation identifies Egr1 as a potent regulator of epidermal growth. AMERICAN JOURNAL OF HUMAN GENETICS, 69(4), 220–20.

Rv inhibition lends to epidermal proliferation in vivo
Deng, H., Seitz, C., & Khavari, P. (1999). Rv inhibition lends to epidermal proliferation in vivo. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 641–41.

NF-kappa B triggers cell cycle arrest in epidermis via specific induction of the cyclin-dependent kinase inhibitor p21(Cip1).
Seitz, C. S., Deng, H., & Khavari, P. A. (1998). NF-kappa B triggers cell cycle arrest in epidermis via specific induction of the cyclin-dependent kinase inhibitor p21(Cip1). JOURNAL OF INVESTIGATIVE DERMATOLOGY, 110(4), 475–75.

Durable gene delivery to human epidermis in vivo: Relative contributions of gene regulatory elements and stem cell targeting.
Khavari, P. A., Lin, Q., & Deng, H. (1998). Durable gene delivery to human epidermis in vivo: Relative contributions of gene regulatory elements and stem cell targeting. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 110(4), 503–.

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), 751–60.

Activating HRAS Mutation in Nevus Spilus.
Sarin, K. Y., McNiff, J. M., Kwok, S., Kim, J., & Khavari, P. A. (2014). Activating HRAS Mutation in Nevus Spilus. Journal of Investigative Dermatology, 134(6), 1766–68.

Activating HRAS Mutation in Agminated Spitz Nevi Arising in a Nevus Spilus.
Sarin, K. Y., Sun, B. K., Bangs, C. D., Cherry, A., Swetter, S. M., Kim, J., & Khavari, P. A. (2013). Activating HRAS Mutation in Agminated Spitz Nevi Arising in a Nevus Spilus. JAMA Dermatology , 149(9), 1077–81.

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), 2013–26.

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), 2013–26.

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.

Dissecting noncoding and pathogen RNA-protein interactomes
Flynn, R. A., Martin, L., Spitale, R. C., Do, B. T., Sagan, S. M., Zarnegar, B., … Chang, H. Y. (2015). Dissecting noncoding and pathogen RNA-protein interactomes. RNA-A PUBLICATION OF THE RNA SOCIETY, 21(1), 135–43.

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.

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.

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.

Genomic Profiling of a Human Organotypic Model of AEC Syndrome Reveals ZNF750 as an Essential Downstream Target of Mutant TP63
Zarnegar, B. J., Webster, D. E., Lopez-Pajares, V., Hunt, B. V. S., Qu, K., Yan, K. J., … Khavari, P. A. (2012). Genomic Profiling of a Human Organotypic Model of AEC Syndrome Reveals ZNF750 as an Essential Downstream Target of Mutant TP63. AMERICAN JOURNAL OF HUMAN GENETICS, 91(3), 435–43.

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.

Research Techniques Made Simple: Emerging Methods to Elucidate Protein Interactions through Spatial Proximity
Che, Y., & Khavari, P. A. (2017). Research Techniques Made Simple: Emerging Methods to Elucidate Protein Interactions through Spatial Proximity. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 137(12), E197–E203.

Metabolomic analysis reveals an essential role for glucose in epidermal differentiation
Lopez-Pajares, V., Bhaduri, A., Garcia, O., Guerrero, A., Gowrishankar, G., Che, Y., … Khavari, P. (2018). Metabolomic analysis reveals an essential role for glucose in epidermal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 138(5), S123.

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.

KRAS regulation by small non-coding RNAs and SNARE proteins
Che, Y., & Khavari, P. (2018). KRAS regulation by small non-coding RNAs and SNARE proteins. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 138(5), S27.

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.

Profiling of rotavirus 3'UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication.
Ren, L., Ding, S., Song, Y., Li, B., Ramanathan, M., Co, J., … Greenberg, H. B. (2019). Profiling of rotavirus 3'UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication. The Journal of Biological Chemistry.

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.

Author Correction: Methods to study RNA-protein interactions.
Ramanathan, M., Porter, D. F., & Khavari, P. A. (2019). Author Correction: Methods to study RNA-protein interactions. Nature Methods.

Mammalian epithelial development, homeostasis and Raf-induced hyperplasia rely on Mek1/2 MAPK kinases
Scholl, F. A., Dumesic, P. A., Barragan, D. I., Harada, K., Bissonauth, V., Charron, J., & Khavari, P. A. (2007). Mammalian epithelial development, homeostasis and Raf-induced hyperplasia rely on Mek1/2 MAPK kinases. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 127, S76.

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.

Effects of altered calcium ATPase function on epidermal carcinogenesis
Kimmel, R. A., Ridky, T. W., & Khavari, P. (2006). Effects of altered calcium ATPase function on epidermal carcinogenesis. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 126, 19.

Genetic immunization by topical application of naked DNA to normal skin
Fan, H., Lin, Q., Morrissey, G., & Khavari, P. (1999). Genetic immunization by topical application of naked DNA to normal skin. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 638.

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.

The structural integrity of individual keratin filament networks is dispensable for epidermal tumorigenesis
Ridky, T. W., Yang, E., Leachman, S., & Khavari, P. (2005). The structural integrity of individual keratin filament networks is dispensable for epidermal tumorigenesis. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 124(4), A72.

The Society's casework in 2004: Review of selected cases (Ancient Monuments Society)
Lazarov, M., Green, C. L., Zhang, J. Y., Kubo, Y., Dajee, M., & Khavari, P. A. (2005). The Society's casework in 2004: Review of selected cases (Ancient Monuments Society). TRANSACTIONS OF THE ANCIENT MONUMENTS SOCIETY, 49, 87–128.

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.

Discovery of differential RNA binding and regulation by the APOL4 protein to disease-linked psoriasis CDSN gene variants using RaPID
Ransohoff, J. D., Ramanathan, M., & Khavari, P. A. (2017). Discovery of differential RNA binding and regulation by the APOL4 protein to disease-linked psoriasis CDSN gene variants using RaPID. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 137(5), S71.

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.

RNA-protein interaction detection (RaPID) in living cells uncovers post-transcriptional regulation in carcinogenesis
Ramanathan, M., Majzoub, K., Roth, J., Gai, H., Palmer, T., Carette, J., & Khavari, P. A. (2017). RNA-protein interaction detection (RaPID) in living cells uncovers post-transcriptional regulation in carcinogenesis. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 137(5), S21.

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.

Regulation of epidermal differentiation by MAF and MAFB
Lopez-Pajares, V., Barajas, B. C., Rubin, A., & Khavari, P. A. (2016). Regulation of epidermal differentiation by MAF and MAFB. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 136(5), S59.

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.

The ATP2C1 golgi ATPase is required for Ras-driven human epidermal neoplasia
Kimmel, R., & Khavari, P. (2004). The ATP2C1 golgi ATPase is required for Ras-driven human epidermal neoplasia. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 122(3), A89.

Mek1, but not Mek2, alters epidermal growth and differentiation
Scholl, F. A., Dumesic, P. A., Charron, J., & Khavari, P. (2004). Mek1, but not Mek2, alters epidermal growth and differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 122(3), A77.

Class II PI3-kinase mediates cell cycle inhibition and terminal differentiation in epidermis
Cai, T., Harada, K., Yang, E., & Khavari, P. (2004). Class II PI3-kinase mediates cell cycle inhibition and terminal differentiation in epidermis. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 122(3), A77.

Unbiased proteomic-genomic investigation of MHC class I peptide ligands reveals unconventional translation origins
Scharf, A. N. D., Flockhart, R. J., Olsson, N. E., Devabhaktuni, A., Zhang, J., Zhao, X., … Elias, J. E. (2015). Unbiased proteomic-genomic investigation of MHC class I peptide ligands reveals unconventional translation origins. MOLECULAR IMMUNOLOGY, 68(2), 135–36.

DeltaNp63 expression is reduced in aged and photoexposed human epidermis, and down regulated in reconstructed epidermis by aged dermal fibroblasts secretome
Boulgana, R., Leblanc-Noblesse, E., Juan, M., Sobilo, L., Bernois, A., Lopez-Pajares, V., … Dumas, M. (2015). DeltaNp63 expression is reduced in aged and photoexposed human epidermis, and down regulated in reconstructed epidermis by aged dermal fibroblasts secretome. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 135, S47.

ZNF750 expression is reduced in photoexposed sites of the epidermis, by replicative senescence, retinoic acid, and increased by calcium treatment
Boulgana, R., Soyer, M., Leblanc-Noblesse, E., Jeronimo-Monteiro, V., Bernois, A., Lopez-Pajares, V., … Dumas, M. (2015). ZNF750 expression is reduced in photoexposed sites of the epidermis, by replicative senescence, retinoic acid, and increased by calcium treatment. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 135, S47.

DNMT1 expression is down-regulated in human keratinocytes during differentiation and senescence and by the secretome of aged dermal fibroblasts
Boulgana, R., Soyer, M., Jeronimo-Monteiro, V., Leblanc-Noblesse, E., Marteau, C., Lopez-Pajares, V., … Dumas, M. (2015). DNMT1 expression is down-regulated in human keratinocytes during differentiation and senescence and by the secretome of aged dermal fibroblasts. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 135, S47.

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.

Calmodulin-like 5 interacts with 14-3-3-sigma/stratifin to regulate late epidermal differentiation
Sun, B., Ransohoff, J., Qu, K., Lopez-Pajares, V., Boxer, L. D., & Khavari, P. (2015). Calmodulin-like 5 interacts with 14-3-3-sigma/stratifin to regulate late epidermal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 135, S67.

Network analysis identifies MPZL3 as an essential regulator of epidermal differentiation that binds FDXR to induce reactive oxygen species
Bhaduri, A., Ungewickell, A., & Khavari, P. (2015). Network analysis identifies MPZL3 as an essential regulator of epidermal differentiation that binds FDXR to induce reactive oxygen species. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 135, S59.

BAF53A enforces the epidermal progenitor state by re-targeting the SWI/SNF/BAF chromatin remodeling complex away from differentiation gene promoters
Bao, X., Tang, J., Lopez-Pajares, V., Tao, S., Qu, K., Crabtree, G. R., & Khavari, P. A. (2012). BAF53A enforces the epidermal progenitor state by re-targeting the SWI/SNF/BAF chromatin remodeling complex away from differentiation gene promoters. MOLECULAR BIOLOGY OF THE CELL, 23.

BAF53A enforces the epidermal progenitor state by re-targeting the SWI/SNF/BAF chromatin remodeling complex away from differentiation gene promoters
Bao, X., Tang, J., Lopez-Pajares, V., Tao, S., Qu, K., Crabtree, G. R., & Khavari, P. A. (2012). BAF53A enforces the epidermal progenitor state by re-targeting the SWI/SNF/BAF chromatin remodeling complex away from differentiation gene promoters. MOLECULAR BIOLOGY OF THE CELL, 23.

Inhibiting Oncogenic RAS in Multiple Myeloma By Targeting Scaffold-ERK Interactions Inhibiting Oncogenic RAS in Multiple Myeloma By Targeting Scaffold-ERK Interactions
Gocke, C. B., Wang, Q., McMillan, R., Penchev, V., Sage, J., Khavari, P. A., & Matsui, W. (2014). Inhibiting Oncogenic RAS in Multiple Myeloma By Targeting Scaffold-ERK Interactions Inhibiting Oncogenic RAS in Multiple Myeloma By Targeting Scaffold-ERK Interactions. BLOOD, 124(21).

Calmodulin-like 5 is a downstream effector of the TINCR long noncoding RNA and is required for late epidermal differentiation
Sun, B., Zhang, J., Qu, K., Lopez-Pajares, V., & Khavari, P. A. (2014). Calmodulin-like 5 is a downstream effector of the TINCR long noncoding RNA and is required for late epidermal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 134, S71.

ZNF750 binding to KLF4 and specific epigenetic regulators controls epidermal differentiation
Boxer, L. D., Barajas, B., Zhang, J., Zarnegar, B., & Khavari, P. (2014). ZNF750 binding to KLF4 and specific epigenetic regulators controls epidermal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 134, S68.

The protein arginine methyltransferase PRMT1 acts with the CSNK1a1 kinase to enforce the epidermal progenitor state in vivo
Bao, X., Zarnegar, B., Mah, A., Qu, K., Tao, S., & Khavari, P. (2014). The protein arginine methyltransferase PRMT1 acts with the CSNK1a1 kinase to enforce the epidermal progenitor state in vivo. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 134, S66.

A IncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation
Lopez-Pajares, V., Qu, K., Zhang, J., Webster, D., Barajas, B., Zarnegar, B., … Khavari, P. (2014). A IncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 134, S44.

New cancer models assessed via quantitative transcriptome analysis
Ridky, T. W., Chow, J. M., Wong, D. J., & Khavari, P. A. (2010). New cancer models assessed via quantitative transcriptome analysis. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 130, S31.

Restoration of full-length type VII collagen expression in RDEB via nonviral gene integration using the phiC31 integrase
Ortiz-Urda, S., Thyagarajan, B., Calos, M., & Khavari, P. (2002). Restoration of full-length type VII collagen expression in RDEB via nonviral gene integration using the phiC31 integrase. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 343.

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.

Oncogenic Ras and telomerase induce invasive human melanocytic neoplasia
Robbins, P., Sheu, S., Chudnovsky, J., Cai, T., & Khavari, P. (2002). Oncogenic Ras and telomerase induce invasive human melanocytic neoplasia. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 339.

Regulation of CDK4 expression levels by TGF beta, TNF alpha, IL-1, NF-kappa B and Ras determines cellular proliferative responses to these regulators of epidermal growth
Lazarov, M., Dajee, M., Kubo, Y., & Khavari, P. (2002). Regulation of CDK4 expression levels by TGF beta, TNF alpha, IL-1, NF-kappa B and Ras determines cellular proliferative responses to these regulators of epidermal growth. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 279.

Impact of Ras effectors RalGDS, Akt and Raf on epidermal growth and differentiation
Tarutani, M., Dajee, M., Lin, Q., & Khavari, P. (2002). Impact of Ras effectors RalGDS, Akt and Raf on epidermal growth and differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 279.

Upstream regulators of Ras function in epidermal cells
Cai, T., & Khavari, P. (2002). Upstream regulators of Ras function in epidermal cells. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 278.

Potential redundancy of MEK kinase impacts on epidermal growth and differentiation
Scholl, F., Dajee, M., Charron, J., & Khavari, P. (2002). Potential redundancy of MEK kinase impacts on epidermal growth and differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 279.

Regulated Ras function in transgenic skin demonstrates potent and reversible Ras effects on epidermal growth and differentiation
Tarutani, M., Dajee, M., Cai, T., & Khavari, P. (2002). Regulated Ras function in transgenic skin demonstrates potent and reversible Ras effects on epidermal growth and differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 254.

Laminin 5 integrin beta 4 are required for Ras-driven human epidermal tumorigenesis
Dajee, A. M., Lazarov, M., Russell, A., Marinkovich, P., Reuter, J., & Khavari, P. (2002). Laminin 5 integrin beta 4 are required for Ras-driven human epidermal tumorigenesis. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 229.

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.

Bypassing CDK4 suppression by oncogenic Ras leads to invasive human epidermal carcinoma capable of visceral dissemination
Lazarov, M., Kubo, Y., Dajee, M., Cai, T., & Khavari, P. (2002). Bypassing CDK4 suppression by oncogenic Ras leads to invasive human epidermal carcinoma capable of visceral dissemination. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 219.

NF-kappa B blockade and oncogenic Ras induce invasive human epidermal neoplasia by circumventing cell cycle arrest
Dajee, M., Lazarov, M., & Khavari, P. (2002). NF-kappa B blockade and oncogenic Ras induce invasive human epidermal neoplasia by circumventing cell cycle arrest. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 119(1), 220.

Identification of the core gene expression signature and key cell-signaling pathways associated with Ras driven squamous cell carcinoma invasion
Ridky, T. W., Wong, D., & Khavari, P. A. (2009). Identification of the core gene expression signature and key cell-signaling pathways associated with Ras driven squamous cell carcinoma invasion. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 129, S29.

Ras driven genetically defined invasive human carcinomas generated from primary human epidermal, head and neck, cervical, esophageal, prostate, and breast epithelial cells established within in a three-dimensional organotypic human tissue platform
Ridky, T. W., Chow, J., & Khavari, P. A. (2009). Ras driven genetically defined invasive human carcinomas generated from primary human epidermal, head and neck, cervical, esophageal, prostate, and breast epithelial cells established within in a three-dimensional organotypic human tissue platform. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 129, S29.

Sustainable systemic erythropoietin delivery via a single injection of lentivirus into human skin
Baek, S., Sheu, S., Lin, Q., Robbins, P., & Khavari, P. (2001). Sustainable systemic erythropoietin delivery via a single injection of lentivirus into human skin. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 549.

Molecular transporters facilitate topical protein transduction into the skin
Rothbard, J., Robbins, P., Sheu, S., Oliver, S., Goodnough, J., Wender, P., & Khavari, P. (2001). Molecular transporters facilitate topical protein transduction into the skin. JOURNAL OF INVESTIGATIVE DERMATOLOGY. BLACKWELL SCIENCE INC.

Impact of gene vs. protein replacement on genomic expression patterns in functional epidermolysis bullosa
Goodnough, J., Robbins, P., Sheu, S., & Khavari, P. (2001). Impact of gene vs. protein replacement on genomic expression patterns in functional epidermolysis bullosa. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 541.

Differential target gene induction mediates opposing growth effects of NF-kappa B in keratinocytes and fibroblasts
Hinata, K., & Khavari, P. (2001). Differential target gene induction mediates opposing growth effects of NF-kappa B in keratinocytes and fibroblasts. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 526.

Regulated induction of Ras and its effectors in epithelial cells
Tarutani, M., Dajee, M., & Khavari, P. (2001). Regulated induction of Ras and its effectors in epithelial cells. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 526.

Generation of inducible NF-kappa B subunits: Confirmation of a primary growth inhibitory role for NF-kappa B in epidermal cells
Zhang, Y., & Khavari, P. (2001). Generation of inducible NF-kappa B subunits: Confirmation of a primary growth inhibitory role for NF-kappa B in epidermal cells. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 525.

Induction of invasive human melanocytic neoplasia by defined genetic elements
Khavari, P., Sheu, S., Robbins, P., Kubo, Y., Dajee, M., & Goodnough, J. (2001). Induction of invasive human melanocytic neoplasia by defined genetic elements. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 483.

Impact of specific receptor tyrosine kinases on Ras in epithelial cells
Cai, T., & Khavari, P. (2001). Impact of specific receptor tyrosine kinases on Ras in epithelial cells. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 476.

I kappa B kinase (IKK) complex function inhibits epidermal growth via NF-kappa B and fails to alter epidermal differentiation
Goodnough, J., Robbins, P., Sheu, S., & Khavari, P. (2001). I kappa B kinase (IKK) complex function inhibits epidermal growth via NF-kappa B and fails to alter epidermal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 117(2), 403.

Durable laminin 5 01 beta 3 gene delivery vectors for gene therapy of junctional epidermolysis bullosa
Robbins, P., Alvarez-Saavedra, E., Lin, Q., Chen, X. J., & Khavari, P. (1999). Durable laminin 5 01 beta 3 gene delivery vectors for gene therapy of junctional epidermolysis bullosa. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 639.

NF-kappa B-directed transcription is normally localized to non-proliferating cells within epidermis and is strongly induced by ultraviolet injury but not by wounding
Gervin, A. M., Memet, S., Freiberg, R. A., Israel, A., & Khavari, P. A. (1999). NF-kappa B-directed transcription is normally localized to non-proliferating cells within epidermis and is strongly induced by ultraviolet injury but not by wounding. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 530.

NF-kappa B function determiner localization and features of programmed cell death in epidermis
Seitz, C. S., Freiberg, R. A., & Khavari, P. A. (1999). NF-kappa B function determiner localization and features of programmed cell death in epidermis. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 526.

Sonic hedgehog opposes epithelial cell cycle arrest
Fan, H., Wee, S. A., & Khavari, P. A. (1999). Sonic hedgehog opposes epithelial cell cycle arrest. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 112(4), 525.

Sonic hedgehog regulates keratinocyte differentiation gene expression and cell cycle progression.
Fan, H., & Khavari, P. A. (1998). Sonic hedgehog regulates keratinocyte differentiation gene expression and cell cycle progression. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 110(4), 486.

Fas signal transduction effects in the skin differ by cellular target and magnitude of receptor activation.
Khavari, P., & Freiberg, R. (1996). Fas signal transduction effects in the skin differ by cellular target and magnitude of receptor activation. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 106(4), 634.

SPECIFIC TRIGGERING OF TNF RECEPTOR SUPERFAMILY SIGNAL-TRANSDUCTION PATHWAYS USING CYTOPLASMIC DOMAINS OF FAS AND TNF-R1
FREIBERG, R. A., DUH, H., SPENCER, D., SCHREIBER, S. L., CRABTREE, G. R., & KHAVARI, P. A. (1995). SPECIFIC TRIGGERING OF TNF RECEPTOR SUPERFAMILY SIGNAL-TRANSDUCTION PATHWAYS USING CYTOPLASMIC DOMAINS OF FAS AND TNF-R1. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 104(4), 560.

SPECIFIC GENE-REGULATION IN KERATINOCYTES AND FIBROBLASTS BY DOSE-DEPENDENT INTRACELLULAR MOLECULAR OLIGOMERIZATION
FREIBERG, R. A., HO, S., SPENCER, D. M., WANDLESS, T., SCHREIBER, S. L., CRABTREE, G. R., & KHAVARI, P. A. (1995). SPECIFIC GENE-REGULATION IN KERATINOCYTES AND FIBROBLASTS BY DOSE-DEPENDENT INTRACELLULAR MOLECULAR OLIGOMERIZATION. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 104(4), 559.

INTERACTION BETWEEN THE RETINOBLASTOMA PROTEIN AND THE HUMAN HOMOLOG OF BRAHMA, A REGULATOR OF HOMEOTIC GENES
DUNAIEF, J., KHAVARI, P., GUHA, S., ALIN, K., LUBAN, J., CRABTREE, G., & GOFF, S. (1994). INTERACTION BETWEEN THE RETINOBLASTOMA PROTEIN AND THE HUMAN HOMOLOG OF BRAHMA, A REGULATOR OF HOMEOTIC GENES. JOURNAL OF CELLULAR BIOCHEMISTRY, 175.

Methods to study RNA-protein interactions (vol 16, pg 225, 2019)
Ramanathan, M., Porter, D. F., & Khavari, P. A. (2019). Methods to study RNA-protein interactions (vol 16, pg 225, 2019). NATURE METHODS, 16(4), 351.

Profiling of rotavirus 3UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication
Ren, L., Ding, S., Song, Y., Li, B., Ramanathan, M., Co, J., … Greenberg, H. B. (2019). Profiling of rotavirus 3UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication. JOURNAL OF BIOLOGICAL CHEMISTRY, 294(15), 5993–6006.

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.

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. (2019). Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks. CELL, 176(1-2), 361-+.

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.

HiChIRP reveals RNA-associated chromosome conformation.
Mumbach, M. R., Granja, J. M., Flynn, R. A., Roake, C. M., Satpathy, A. T., Rubin, A. J., … Chang, H. Y. (2019). HiChIRP reveals RNA-associated chromosome conformation. Nature Methods.

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).

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.

A large-scale TF-DNA interaction map in primary keratinocytes and its relation to skin disease-linked regulatory variants
Porter, D. F., Reynolds, D. L., Miao, W., Meyers, R. M., Hong, A. W., Yang, X., … Khavari, P. A. (2024). A large-scale TF-DNA interaction map in primary keratinocytes and its relation to skin disease-linked regulatory variants. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC.

p63 cooperates with FOXK1 to mediate oncogenic 3D chromatin dynamics
Lopez-Pajares, V., Jung, N., Donohue, L., Guo, M., & Khavari, P. A. (2024). p63 cooperates with FOXK1 to mediate oncogenic 3D chromatin dynamics. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC.