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Paul A. Khavari

Stanford University · US
Area of research
Molecular Biology
Research interest
Research interests include RNA Research and Splicing, RNA modifications and cancer, Genomics and Chromatin Dynamics, and RNA and protein synthesis mechanisms.
h-index
83
citations
29,325
works
269
NIH funding
primary concept
Biology
email

Recent publications

irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein assemblies on RNA
Nature 2025cited by 13position: lastdoi
The adhesion GPCR ADGRL2 engages Gα13 to enable epidermal differentiation
Proceedings of the National Academy of Sciences 2025cited by 1position: lastdoi
Spatially resolved clonal copy number alterations in benign and malignant tissue
Nature 2022cited by 311position: middledoi
Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics
Nature Reviews Genetics 2021cited by 1,008position: lastdoi
Super-resolved spatial transcriptomics by deep data fusion
Nature Biotechnology 2021cited by 175position: middledoi
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
Cell 2020cited by 1,093position: lastdoi
Structural modularity of the XIST ribonucleoprotein complex
Nature Communications 2020cited by 96position: middledoi
Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation
eLife 2020cited by 58position: middledoi
The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2
Molecular Cell 2019cited by 151position: lastdoi
HiChIRP reveals RNA-associated chromosome conformation
Nature Methods 2019cited by 106position: middledoi
Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks
Cell 2018cited by 323position: lastdoi
Transcript-indexed ATAC-seq for precision immune profiling
Nature Medicine 2018cited by 161position: middledoi
Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment
Nature Genetics 2018cited by 62position: middledoi
Cancer-Associated Long Noncoding RNA SMRT-2 Controls Epidermal Differentiation
Journal of Investigative Dermatology 2018cited by 18position: lastdoi
1435 Dynamic morphogen-p63 chromatin interactions that guide epigenetic changes and p63 activity in surface ectoderm commitment
Journal of Investigative Dermatology 2018cited by 0position: middledoi
182 Single-cell RNA-sequencing reveals SCC intratumoral heterogeneity
Journal of Investigative Dermatology 2018cited by 0position: lastdoi
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
Nature Methods 2017cited by 2,724position: middledoi
The functions and unique features of long intergenic non-coding RNA
Nature Reviews Molecular Cell Biology 2017cited by 1,390position: lastdoi
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
Nature Genetics 2017cited by 553position: middledoi
Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation
Nature Genetics 2017cited by 325position: lastdoi
CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue
Developmental Cell 2017cited by 67position: lastdoi
519 Phase I/IIa clinical trial for recessive dystrophic epidermolysis bullosa using genetically corrected autologous keratinocytes
Journal of Investigative Dermatology 2017cited by 6position: middledoi
464 Dynamic and stable enhancer-promoter contacts regulate epidermal terminal differentiation
Journal of Investigative Dermatology 2017cited by 2position: lastdoi
408 Discovery of differential RNA binding and regulation by the APOL4 protein to disease-linked psoriasis CDSN gene variants using RaPID
Journal of Investigative Dermatology 2017cited by 1position: lastdoi
117 K-RAS oncogene activation is regulated by a snoRNA/SNARE protein axis that controls its subcellular transport
Journal of Investigative Dermatology 2017cited by 0position: lastdoi
121 The SNORD86 small non-coding RNA binds and regulates Rac1
Journal of Investigative Dermatology 2017cited by 0position: lastdoi
811 Attenuated netrin-1 receptor mediated regulation of tiam1 is required for rac1 mutant melanoma progression
Journal of Investigative Dermatology 2017cited by 0position: middledoi
123 RNA-protein interaction detection (RaPID) in living cells uncovers post-transcriptional regulation in carcinogenesis
Journal of Investigative Dermatology 2017cited by 0position: lastdoi
HiChIP: efficient and sensitive analysis of protein-directed genome architecture
Nature Methods 2016cited by 1,249position: middledoi
A LncRNA-MAF:MAFB Transcription Factor Network Regulates Epidermal Differentiation
Developmental Cell 2015cited by 204position: lastdoi

Grants

No grants ingested yet.

Frequent collaborators

Howard Y. Chang · Amgen (United States)16 papers (2012–2020)Adam J. Rubin · Broad Institute13 papers (2015–2020) · 9 papers (2012–2025)Maxwell R. Mumbach · Stanford University9 papers (2016–2019)Zurab Siprashvili · Palo Alto University9 papers (2012–2025)Kun Qu · PAX Scientific (United States)7 papers (2012–2017)William J. Greenleaf · Stanford Medicine7 papers (2016–2019)Dan E. Webster · AbbVie (United States)6 papers (2012–2018) · 6 papers (2013–2025)Andrew L. Ji · Centers for Disease Control and Prevention5 papers (2018–2021)Xiaomin Bao · Iowa State University4 papers (2013–2018)Ansuman T. Satpathy · Stanford University4 papers (2017–2019)Aparna Bhaduri · University of California, Berkeley4 papers (2017–2020)Markus Kretz · University of Regensburg4 papers (2012–2018)Yuning Wei · Dynamic Systems (United States)4 papers (2017–2020)Shiying Tao · Beijing University of Chinese Medicine4 papers (2013–2025) · 3 papers (2012–2012)Joanna Kovalski · University of California, San Francisco3 papers (2017–2019) · 3 papers (2015–2017)Yanyan Qi · Stanford University3 papers (2018–2019)