Paul A. Khavari - Publications

Stanford University, Palo Alto, CA 
Molecular Biology

48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, Chang HY. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nature Methods. PMID 27643841 DOI: 10.1038/nmeth.3999  0.72
2016 Winge MC, Ohyama B, Dey CN, Boxer LM, Li W, Ehsani-Chimeh N, Truong AK, Wu D, Armstrong AW, Makino T, Davidson M, Starcevic D, Kislat A, Nguyen NT, Hashimoto T, ... ... Khavari PA, et al. RAC1 activation drives pathologic interactions between the epidermis and immune cells. The Journal of Clinical Investigation. PMID 27294528 DOI: 10.1172/JCI85738  0.72
2016 Zarnegar BJ, Flynn RA, Shen Y, Do BT, Chang HY, Khavari PA. irCLIP platform for efficient characterization of protein-RNA interactions. Nature Methods. PMID 27111506 DOI: 10.1038/nmeth.3840  0.72
2016 Flynn RA, Do BT, Rubin AJ, Calo E, Lee B, Kuchelmeister H, Rale M, Chu C, Kool ET, Wysocka J, Khavari PA, Chang HY. 7SK-BAF axis controls pervasive transcription at enhancers. Nature Structural & Molecular Biology. PMID 26878240 DOI: 10.1038/nsmb.3176  0.72
2015 Bao X, Rubin AJ, Qu K, Zhang J, Giresi PG, Chang HY, Khavari PA. A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome Biology. 16: 284. PMID 26683334 DOI: 10.1186/s13059-015-0840-9  0.72
2015 Bhaduri A, Ungewickell A, Boxer LD, Lopez-Pajares V, Zarnegar BJ, Khavari PA. Network Analysis Identifies Mitochondrial Regulation of Epidermal Differentiation by MPZL3 and FDXR. Developmental Cell. 35: 444-57. PMID 26609959 DOI: 10.1016/j.devcel.2015.10.023  0.72
2015 Siprashvili Z, Webster DE, Johnston D, Shenoy RM, Ungewickell AJ, Bhaduri A, Flockhart R, Zarnegar BJ, Che Y, Meschi F, Puglisi JD, Khavari PA. The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer. Nature Genetics. PMID 26595770 DOI: 10.1038/ng.3452  0.72
2015 Ungewickell A, Bhaduri A, Rios E, Reuter J, Lee CS, Mah A, Zehnder A, Ohgami R, Kulkarni S, Armstrong R, Weng WK, Gratzinger D, Tavallaee M, Rook A, Snyder M, ... ... Khavari PA, et al. Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2. Nature Genetics. PMID 26258847 DOI: 10.1038/ng.3370  0.72
2015 Lopez-Pajares V, Qu K, Zhang J, Webster DE, Barajas BC, Siprashvili Z, Zarnegar BJ, Boxer LD, Rios EJ, Tao S, Kretz M, Khavari PA. A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. Developmental Cell. 32: 693-706. PMID 25805135 DOI: 10.1016/j.devcel.2015.01.028  0.72
2015 Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY. Dissecting noncoding and pathogen RNA-protein interactomes. Rna (New York, N.Y.). 21: 135-43. PMID 25411354 DOI: 10.1261/rna.047803.114  0.72
2014 Lee CS, Bhaduri A, Mah A, Johnson WL, Ungewickell A, Aros CJ, Nguyen CB, Rios EJ, Siprashvili Z, Straight A, Kim J, Aasi SZ, Khavari PA. Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma. Nature Genetics. 46: 1060-2. PMID 25194279 DOI: 10.1038/ng.3091  0.72
2014 Noderer WL, Flockhart RJ, Bhaduri A, Diaz de Arce AJ, Zhang J, Khavari PA, Wang CL. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Molecular Systems Biology. 10: 748. PMID 25170020 DOI: 10.15252/msb.20145136  0.72
2014 Zheng GX, Do BT, Webster DE, Khavari PA, Chang HY. Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs. Nature Structural & Molecular Biology. 21: 585-90. PMID 24929436 DOI: 10.1038/nsmb.2842  0.72
2013 Jameson KL, Mazur PK, Zehnder AM, Zhang J, Zarnegar B, Sage J, Khavari PA. IQGAP1 scaffold-kinase interaction blockade selectively targets RAS-MAP kinase-driven tumors. Nature Medicine. 19: 626-30. PMID 23603816 DOI: 10.1038/nm.3165  0.72
2013 Bao X, Tang J, Lopez-Pajares V, Tao S, Qu K, Crabtree GR, Khavari PA. ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent induction of KLF4. Cell Stem Cell. 12: 193-203. PMID 23395444 DOI: 10.1016/j.stem.2012.12.014  0.72
2013 Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, ... ... Khavari PA, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 493: 231-5. PMID 23201690 DOI: 10.1038/nature11661  0.72
2013 Lopez-Pajares V, Yan K, Zarnegar BJ, Jameson KL, Khavari PA. Genetic pathways in disorders of epidermal differentiation. Trends in Genetics : Tig. 29: 31-40. PMID 23141808 DOI: 10.1016/j.tig.2012.10.005  0.72
2012 Siprashvili Z, Webster DE, Kretz M, Johnston D, Rinn JL, Chang HY, Khavari PA. Identification of proteins binding coding and non-coding human RNAs using protein microarrays. Bmc Genomics. 13: 633. PMID 23157412 DOI: 10.1186/1471-2164-13-633  0.72
2012 Lee CS, Ungewickell A, Bhaduri A, Qu K, Webster DE, Armstrong R, Weng WK, Aros CJ, Mah A, Chen RO, Lin M, Sundram U, Chang HY, Kretz M, Kim YH, ... Khavari PA, et al. Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. Blood. 120: 3288-97. PMID 22936659 DOI: 10.1182/blood-2012-04-423061  0.72
2012 Zarnegar BJ, Webster DE, Lopez-Pajares V, Vander Stoep Hunt B, Qu K, Yan KJ, Berk DR, Sen GL, Khavari PA. 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: 435-43. PMID 22922031 DOI: 10.1016/j.ajhg.2012.07.007  0.72
2012 Bhaduri A, Qu K, Lee CS, Ungewickell A, Khavari PA. Rapid identification of non-human sequences in high-throughput sequencing datasets. Bioinformatics (Oxford, England). 28: 1174-5. PMID 22377895 DOI: 10.1093/bioinformatics/bts100  0.72
2012 Sen GL, Boxer LD, Webster DE, Bussat RT, Qu K, Zarnegar BJ, Johnston D, Siprashvili Z, Khavari PA. ZNF750 is a p63 target gene that induces KLF4 to drive terminal epidermal differentiation. Developmental Cell. 22: 669-77. PMID 22364861 DOI: 10.1016/j.devcel.2011.12.001  0.72
2012 Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GX, Chow J, Kim GE, Rinn JL, Chang HY, Siprashvili Z, Khavari PA. Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes & Development. 26: 338-43. PMID 22302877 DOI: 10.1101/gad.182121.111  0.72
2010 Ridky TW, Chow JM, Wong DJ, Khavari PA. Invasive three-dimensional organotypic neoplasia from multiple normal human epithelia. Nature Medicine. 16: 1450-5. PMID 21102459 DOI: 10.1038/nm.2265  0.72
2010 Sen GL, Reuter JA, Webster DE, Zhu L, Khavari PA. DNMT1 maintains progenitor function in self-renewing somatic tissue. Nature. 463: 563-7. PMID 20081831 DOI: 10.1038/nature08683  0.72
2009 Reuter JA, Ortiz-Urda S, Kretz M, Garcia J, Scholl FA, Pasmooij AM, Cassarino D, Chang HY, Khavari PA. Modeling inducible human tissue neoplasia identifies an extracellular matrix interaction network involved in cancer progression. Cancer Cell. 15: 477-88. PMID 19477427 DOI: 10.1016/j.ccr.2009.04.002  0.72
2009 Dumesic PA, Scholl FA, Barragan DI, Khavari PA. Erk1/2 MAP kinases are required for epidermal G2/M progression. The Journal of Cell Biology. 185: 409-22. PMID 19414607 DOI: 10.1083/jcb.200804038  0.72
2009 Scholl FA, Dumesic PA, Barragan DI, Harada K, Charron J, Khavari PA. Selective role for Mek1 but not Mek2 in the induction of epidermal neoplasia. Cancer Research. 69: 3772-8. PMID 19383924 DOI: 10.1158/0008-5472.CAN-08-1963  0.72
2008 Sen GL, Webster DE, Barragan DI, Chang HY, Khavari PA. Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3. Genes & Development. 22: 1865-70. PMID 18628393 DOI: 10.1101/gad.1673508  0.72
2007 Zhang JY, Adams AE, Ridky TW, Tao S, Khavari PA. Tumor necrosis factor receptor 1/c-Jun-NH2-kinase signaling promotes human neoplasia. Cancer Research. 67: 3827-34. PMID 17440097 DOI: 10.1158/0008-5472.CAN-06-4017  0.72
2007 Scholl FA, Dumesic PA, Barragan DI, Harada K, Bissonauth V, Charron J, Khavari PA. Mek1/2 MAPK kinases are essential for Mammalian development, homeostasis, and Raf-induced hyperplasia. Developmental Cell. 12: 615-29. PMID 17419998 DOI: 10.1016/j.devcel.2007.03.009  0.72
2007 Truong AB, Khavari PA. Control of keratinocyte proliferation and differentiation by p63. Cell Cycle (Georgetown, Tex.). 6: 295-9. PMID 17264679  0.72
2006 Adams AE, Chudnovsky Y, Khavari PA. Oxygen deprivation provokes melanoma. Nature Medicine. 12: 168-9. PMID 16462795 DOI: 10.1038/nm0206-168  0.72
2005 Harada K, Truong AB, Cai T, Khavari PA. The class II phosphoinositide 3-kinase C2beta is not essential for epidermal differentiation. Molecular and Cellular Biology. 25: 11122-30. PMID 16314532 DOI: 10.1128/MCB.25.24.11122-11130.2005  0.72
2005 Scholl FA, Dumesic PA, Khavari PA. Effects of active MEK1 expression in vivo. Cancer Letters. 230: 1-5. PMID 16253755 DOI: 10.1016/j.canlet.2004.12.013  0.72
2005 Chudnovsky Y, Adams AE, Robbins PB, Lin Q, Khavari PA. Use of human tissue to assess the oncogenic activity of melanoma-associated mutations. Nature Genetics. 37: 745-9. PMID 15951821 DOI: 10.1038/ng1586  0.72
2005 Chudnovsky Y, Khavari PA, Adams AE. Melanoma genetics and the development of rational therapeutics. The Journal of Clinical Investigation. 115: 813-24. PMID 15841168 DOI: 10.1172/JCI24808  0.72
2005 Ortiz-Urda S, Garcia J, Green CL, Chen L, Lin Q, Veitch DP, Sakai LY, Lee H, Marinkovich MP, Khavari PA. Type VII collagen is required for Ras-driven human epidermal tumorigenesis. Science (New York, N.Y.). 307: 1773-6. PMID 15774758 DOI: 10.1126/science.1106209  0.72
2004 Scholl FA, Dumesic PA, Khavari PA. Mek1 alters epidermal growth and differentiation. Cancer Research. 64: 6035-40. PMID 15342384 DOI: 10.1158/0008-5472.CAN-04-0017  0.72
2003 Siprashvili Z, Scholl FA, Oliver SF, Adams A, Contag CH, Wender PA, Khavari PA. Gene transfer via reversible plasmid condensation with cysteine-flanked, internally spaced arginine-rich peptides. Human Gene Therapy. 14: 1225-33. PMID 12952594 DOI: 10.1089/104303403767740768  0.72
2003 Ortiz-Urda S, Thyagarajan B, Keene DR, Lin Q, Calos MP, Khavari PA. PhiC31 integrase-mediated nonviral genetic correction of junctional epidermolysis bullosa. Human Gene Therapy. 14: 923-8. PMID 12828862 DOI: 10.1089/104303403765701204  0.72
2003 Hinata K, Gervin AM, Jennifer Zhang Y, Khavari PA. Divergent gene regulation and growth effects by NF-kappa B in epithelial and mesenchymal cells of human skin. Oncogene. 22: 1955-64. PMID 12673201 DOI: 10.1038/sj.onc.1206198  1
2003 Dajee M, Lazarov M, Zhang JY, Cai T, Green CL, Russell AJ, Marinkovich MP, Tao S, Lin Q, Kubo Y, Khavari PA. NF-kappaB blockade and oncogenic Ras trigger invasive human epidermal neoplasia. Nature. 421: 639-43. PMID 12571598 DOI: 10.1038/nature01283  0.32
2003 Ortiz-Urda S, Lin Q, Green CL, Keene DR, Marinkovich MP, Khavari PA. Injection of genetically engineered fibroblasts corrects regenerated human epidermolysis bullosa skin tissue. The Journal of Clinical Investigation. 111: 251-5. PMID 12531881 DOI: 10.1172/JCI17193  0.32
2002 Lazarov M, Kubo Y, Cai T, Dajee M, Tarutani M, Lin Q, Fang M, Tao S, Green CL, Khavari PA. CDK4 coexpression with Ras generates malignant human epidermal tumorigenesis. Nature Medicine. 8: 1105-14. PMID 12357246 DOI: 10.1038/nm779  0.32
2002 Ortiz-Urda S, Thyagarajan B, Keene DR, Lin Q, Fang M, Calos MP, Khavari PA. Stable nonviral genetic correction of inherited human skin disease Nature Medicine. 8: 1166-1170. PMID 12244305 DOI: 10.1038/nm766  0.72
2000 Seitz CS, Deng H, Hinata K, Lin Q, Khavari PA. Nuclear factor kappaB subunits induce epithelial cell growth arrest. Cancer Research. 60: 4085-92. PMID 10945614  1
2000 Seitz CS, Freiberg RA, Hinata K, Khavari PA. NF-kappaB determines localization and features of cell death in epidermis. The Journal of Clinical Investigation. 105: 253-60. PMID 10675350 DOI: 10.1172/JCI7630  1
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