Agarwal, Vikram

Predicting effective microRNA target sites in mammalian mRNAs

Agarwal, V., Bell, G. W., Nam, J.-W., & Bartel, D. P. (2015) · eLife

MicroRNA in disease regulationRNA Research and Splicing

Cited by 7,318

Effective gene expression prediction from sequence by integrating long-range interactions

Avsec, Ž., Agarwal, V., Visentin, D., Ledsam, J. R., Grabska-Barwinska, A., Taylor, K. R., Assael, Y., Jumper, J., Kohli, P., & Kelley, D. R. (2021) · Nature Methods

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 1,326

Impact of MicroRNA levels, target-site complementarity, and cooperativity on competing endogenous RNA-regulated gene expression

Denzler, R., McGeary, S. E., Title, A. C., Agarwal, V., Bartel, D. P., & Stoffel, M. (2016) · Molecular Cell

Cancer-related molecular mechanisms researchMicroRNA in disease regulation

Cited by 340

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation

Linder, J., Srivastava, D., Yuan, H., Agarwal, V., & Kelley, D. R. (2025) · Nature Genetics

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Cited by 265

Predicting mRNA abundance directly from genomic sequence using deep convolutional neural networks

Agarwal, V., & Shendure, J. (2018) · Cell Reports

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 243

Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

Agarwal, V., & Shendure, J. (2020) · Cell Reports

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 243

A systematic evaluation of the design and context dependencies of massively parallel reporter assays

Klein, J. C., Agarwal, V., Inoue, F., Keith, A., Martin, B., Kircher, M., Ahituv, N., & Shendure, J. (2020) · Nature Methods

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 226

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

Chen, W., McKenna, A., Schreiber, J., Haeussler, M., Yin, Y., Agarwal, V., Noble, W. S., & Shendure, J. (2019) · Nucleic Acids Research

CRISPR and Genetic EngineeringDNA Repair Mechanisms

Cited by 216

The genetic and biochemical determinants of mRNA degradation rates in mammals

Agarwal, V., & Kelley, D. R. (2022) · Genome Biology

RNA Research and SplicingRNA and protein synthesis mechanisms

Cited by 155

The genetic and biochemical determinants of mRNA degradation rates in mammals

Agarwal, V., & Kelley, D. (2022) · Genome biology

RNA Research and SplicingRNA and protein synthesis mechanisms

Cited by 155

Massively parallel characterization of transcriptional regulatory elements

Agarwal, V., Inoue, F., Schubach, M., Penzar, D., Martin, B. K., Dash, P. M., Keukeleire, P., Zhang, Z., Sohota, A., Zhao, J., et al. (2025) · Nature

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 146

Functional testing of thousands of osteoarthritis-associated variants for regulatory activity

Klein, J. C., Keith, A., Rice, S. J., Shepherd, C., Agarwal, V., Loughlin, J., & Shendure, J. (2019) · Nature Communications

Osteoarthritis Treatment and MechanismsGenetic Associations and Epidemiology

Cited by 92

Transcription factor binding site orientation and order are major drivers of gene regulatory activity

Georgakopoulos-Soares, I., Deng, C., Agarwal, V., Chan, C. S. Y., Zhao, J., Inoue, F., & Ahituv, N. (2023) · Nature Communications

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 82

Functional characterization of enhancer evolution in the primate lineage

Klein, J. C., Keith, A., Agarwal, V., Durham, T., & Shendure, J. (2018) · Genome Biology

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 63

Predicting the translation efficiency of messenger RNA in mammalian cells

Zheng, D., Persyn, L., Wang, J., Liu, Y., Montoya, F. U., Cenik, C., & Agarwal, V. (2024) · Nature Biotechnology

RNA and protein synthesis mechanismsRNA Research and Splicing

Cited by 52

Predicting the translation efficiency of messenger RNA in mammalian cells

Zheng, D., Persyn, L., Wang, J., Liu, Y., Ulloa-Montoya, F., Cenik, C., & Agarwal, V. (2026) · Nature Biotechnology

RNA and protein synthesis mechanismsRNA Research and Splicing

Cited by 52

Translation efficiency covariation identifies conserved coordination patterns across cell types

Liu, Y., Rao, S., Hoskins, I., Geng, M., Zhao, Q., Chacko, J., Ghatpande, V., Qi, K., Persyn, L., Wang, J., et al. (2026) · Nature Biotechnology

RNA and protein synthesis mechanismsRNA Research and Splicing

Cited by 15