Khavari, Paul A.

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., Satpathy, A. T., Rubin, A. J., Montine, K. S., Wu, B., et al. (2017) · Nature Methods

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 2,496

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) · Nature Methods

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,139

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., Guo, M. G., George, B. M., Mollbrink, A., Bergenstråhle, J., et al. (2020) · Cell

Nonmelanoma Skin Cancer StudiesSingle-cell and spatial transcriptomics

Cited by 1,117

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

Longo, S. K., Guo, M. G., Ji, A. L., & Khavari, P. A. (2021) · Nature Reviews Genetics

Single-cell and spatial transcriptomicsBiotin and Related Studies

Cited by 1,059

Advances in skin grafting and treatment of cutaneous wounds

Sun, B. K., Siprashvili, Z., & Khavari, P. A. (2014) · Science

Wound Healing and TreatmentsTissue Engineering and Regenerative Medicine

Cited by 972

NF-κB blockade and oncogenic Ras trigger invasive human epidermal neoplasia

Dajee, M., Lazarov, M., Zhang, J. Y., Cai, T., Green, C. L., Russell, A. J., Marinkovich, M. P., Tao, S., Lin, Q., Kubo, Y., et al. (2003) · Nature

NF-κB Signaling PathwaysProtein Kinase Regulation and GTPase Signaling

Cited by 535

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., Nguyen, M. L., Rubin, A. J., Granja, J. M., Kazane, K. R., et al. (2017) · Nature Genetics

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 490

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., Mumbach, M. R., Ji, A. L., Kim, D. S., Cho, S. W., et al. (2019) · Cell

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 314

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., Kim, D. S., Boxer, L. D., Cairns, J., Spivakov, M., et al. (2017) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 293

BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration

Flockhart, R. J., Webster, D. E., Qu, K., Mascarenhas, N., Kovalski, J., Kretz, M., & Khavari, P. A. (2012) · Genome Research

Melanoma and MAPK PathwaysCancer-related molecular mechanisms research

Cited by 277

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., Johnston, D., Siprashvili, Z., & Khavari, P. A. (2012) · Developmental Cell

Skin and Cellular Biology ResearchKruppel-like factors research

Cited by 246

Invasive three-dimensional organotypic neoplasia from multiple normal human epithelia

Ridky, T. W., Chow, J. M., Wong, D. J., & Khavari, P. A. (2010) · Nature Medicine

Cancer Cells and Metastasis3D Printing in Biomedical Research

Cited by 217

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., Zarnegar, B. J., Boxer, L. D., Rios, E. J., Tao, S., et al. (2015) · Developmental Cell

Skin and Cellular Biology ResearchHair Growth and Disorders

Cited by 194

Super-resolved spatial transcriptomics by deep data fusion

Bergenstråhle, L., He, B., Bergenstråhle, J., Abalo, X., Mirzazadeh, R., Thrane, K., Ji, A. L., Andersson, A., Larsson, L., Stakenborg, N., et al. (2022) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 188

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) · Molecular Systems Biology

RNA and protein synthesis mechanismsRNA Research and Splicing

Cited by 178

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) · Genome Biology

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 164

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) · Molecular Cell

Protein Kinase Regulation and GTPase SignalingPI3K/AKT/mTOR signaling in cancer

Cited by 154

Transcript-indexed ATAC-seq for precision immune profiling

Satpathy, A. T., Saligrama, N., Buenrostro, J. D., Wei, Y., Wu, B., Rubin, A. J., Granja, J. M., Lareau, C. A., Li, R., Qi, Y., et al. (2018) · Nature Medicine

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 152

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) · Genes & Development

Kruppel-like factors researchGenomics and Chromatin Dynamics

Cited by 147

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., Nguyen, C. B., Rios, E. J., Siprashvili, Z., Straight, A., et al. (2014) · Nature Genetics

Nonmelanoma Skin Cancer StudiesChromatin Remodeling and Cancer

Cited by 143

Sustainable correction of junctional epidermolysis bullosa via transposon‐mediated nonviral gene transfer

Ortiz-Urda, S., Lin, Q., Yant, S. R., Keene, D., Kay, M. A., & Khavari, P. A. (2003) · Gene Therapy

Skin and Cellular Biology ResearchVirus-based gene therapy research

Cited by 118

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., Cassarino, D., Chang, H. Y., & Khavari, P. A. (2009) · Cancer Cell

Bioinformatics and Genomic NetworksCancer Cells and Metastasis

Cited by 88

Network Analysis Identifies Mitochondrial 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) · Developmental Cell

Bioinformatics and Genomic NetworksSkin and Cellular Biology Research

Cited by 60