Mortazavi, Ali

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 15,556

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 13,696

Landscape of transcription in human cells

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature

Genomics and Chromatin DynamicsRNA Research and Splicing

Cited by 5,187

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 2,927

A survey of best practices for RNA-seq data analysis

Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 2,794

A comparative encyclopedia of DNA elements in the mouse genome

Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., et al. (2014) · Nature

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 1,781

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

Li, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., Poh, H. M., Goh, Y., Lim, J., Zhang, J., et al. (2012) · Cell

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,232

iPSC-derived human microglia-like cells to study neurological diseases

Abud, E. M., Ramirez, R. N., Martinez, E. S., Healy, L. M., Nguyen, C. H. H., Newman, S. A., Yeromin, A. V., Scarfone, V. M., Marsh, S. E., Fimbres, C., et al. (2017) · Neuron

Neuroinflammation and Neurodegeneration MechanismsPluripotent Stem Cells Research

Cited by 1,154

Regeneration of fat cells from myofibroblasts during wound healing

Plikus, M. V., Guerrero-Juarez, C. F., Ito, M., Li, Y. R., Dedhia, P. H., Zheng, Y., Shao, M., Gay, D. L., Ramos, R., Hsi, T.-C., et al. (2017) · Science

Wound Healing and TreatmentsHair Growth and Disorders

Cited by 584

Systematic phenotyping and characterization of the 5xFAD mouse model of Alzheimer’s disease.

Forner, S., Kawauchi, S., Balderrama-Gutierrez, G., Kramár, E. A., Matheos, D. P., Phan, J., Javonillo, D. I., Tran, K. M., Hingco, E., da Cunha, C., et al. (2021) · Scientific Data

Alzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

Cited by 501

An encyclopedia of mouse DNA elements (Mouse ENCODE)

Mouse ENCODE Consortium, Stamatoyannopoulos, J. A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D. M., Groudine, M., Bender, M., Kaul, R., et al. (2012) · Genome Biology

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 446

Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

Zhang, J. A., Mortazavi, A., Williams, B. A., Wold, B. J., & Rothenberg, E. V. (2012) · Cell

Genomics and Chromatin DynamicsT-cell and B-cell Immunology

Cited by 337

Systematic Phenotyping and Characterization of the 3xTg-AD Mouse Model of Alzheimer’s Disease

Javonillo, D. I., Tran, K. M., Phan, J., Hingco, E., Kramár, E. A., da Cunha, C., Forner, S., Kawauchi, S., Milinkeviciute, G., Gomez-Arboledas, A., et al. (2022) · Frontiers in Neuroscience

Alzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

Cited by 203

Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire

Mortazavi, A., Thompson, E. C. L., Garcia, S. T., Myers, R. M., & Wold, B. (2006) · Genome Research

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 159

Occupancy maps of 208 chromatin-associated proteins in one human cell type

Partridge, E. C., Chhetri, S. B., Prokop, J. W., Ramaker, R. C., Jansen, C. S., Goh, S.-T., Mackiewicz, M., Newberry, K. M., Brandsmeier, L. A., Meadows, S. K., et al. (2020) · Nature

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 154

NRSF-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilience

Singh-Taylor, A., Molet, J., Jiang, S., Korosi, A., Bolton, J. L., Noam, Y., Simeone, K., Cope, J., Chen, Y., Mortazavi, A., et al. (2018) · Molecular Psychiatry

Stress Responses and CortisolNeuroendocrine regulation and behavior

Cited by 115

A limited capacity for microglial repopulation in the adult brain

Najafi, A. R., Crapser, J., Jiang, S., Ng, W., Mortazavi, A., West, B. L., & Green, K. N. (2018) · Glia

Neuroinflammation and Neurodegeneration MechanismsNeurogenesis and neuroplasticity mechanisms

Cited by 99

Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network

Longabaugh, W. J. R., Zeng, W., Zhang, J. A., Hosokawa, H., Jansen, C. S., Li, L., Romero-Wolf, M., Liu, P., Kueh, H. Y., Mortazavi, A., et al. (2017) · Proceedings of the National Academy of Sciences

T-cell and B-cell ImmunologyGenomics and Chromatin Dynamics

Cited by 89

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

Rebboah, E., Reese, F., Williams, K., Balderrama-Gutierrez, G., McGill, C., Trout, D., Rodriguez, I., Liang, H., Wold, B. J., & Mortazavi, A. (2021) · Genome Biology

Single-cell and spatial transcriptomicsRNA Research and Splicing

Cited by 58

Swan: a library for the analysis and visualization of long-read transcriptomes

Reese, F., & Mortazavi, A. (2021) · Bioinformatics

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 29

5xFAD/Abi3S209F mice display distinct age‐dependent effects on amyloid beta pathology and microglia dynamics

Butler, C. A., O'Gara, K., Mendoza‐Arvilla, A., Milinkeviciute, G., Da Cunha, C., Kawauchi, S., Rezaie, N., Liang, H. Y., Thach, A., Wang, S., et al. (2024) · Alzheimer's & Dementia

Alzheimer's disease research and treatmentsNeuroinflammation and Neurodegeneration Mechanisms

Cited by 1