Kundaje, Anshul

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 6,368

Learning Important Features Through Propagating Activation Differences

Shrikumar, A., Greenside, P., & Kundaje, A. (2017) · arXiv

Explainable Artificial Intelligence (XAI)Neural Networks and Applications

Cited by 2,761

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

Opportunities and obstacles for deep learning in biology and medicine

Ching, T., Himmelstein, D. S., Beaulieu-Jones, B. K., Kalinin, A. A., Do, B. T., Way, G. P., Ferrero, E., Agapow, P.-M., Zietz, M., Hoffman, M. M., et al. (2018) · Journal of The Royal Society Interface

Machine Learning in HealthcareArtificial Intelligence in Healthcare and Education

Cited by 2,310

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 2,033

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

Amemiya, H. M., Kundaje, A., & Boyle, A. P. (2019) · Scientific Reports

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 1,831

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

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

Corces, M. R., Buenrostro, J. D., Wu, B., Greenside, P. G., Chan, S. M., Koenig, J. L., Snyder, M. P., Pritchard, J. K., Kundaje, A., Greenleaf, W. J., et al. (2016) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,151

Genome-wide enhancer maps link risk variants to disease genes

Nasser, J., Bergman, D. T., Fulco, C. P., Guckelberger, P., Doughty, B. R., Patwardhan, T. A., Jones, T. R., Nguyen, T. H., Ulirsch, J. C., Lekschas, F., et al. (2021) · Nature

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 669

Base-resolution models of transcription-factor binding reveal soft motif syntax

Avsec, Ž., Weilert, M., Shrikumar, A., Krueger, S., Alexandari, A., Dalal, K., Fropf, R., McAnany, C., Gagneur, J., Kundaje, A., et al. (2021) · Nature Genetics

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 610

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease

Gjoneska, E., Pfenning, A. R., Mathys, H., Quon, G., Kundaje, A., Tsai, L.-H., & Kellis, M. (2015) · Nature

Alzheimer's disease research and treatmentsNeuroinflammation and Neurodegeneration Mechanisms

Cited by 576

Transparency and reproducibility in artificial intelligence

Haibe-Kains, B., Adam, G. A., Hosny, A., Khodakarami, F., Massive Analysis Quality Control (MAQC) Society Board of Directors, Shraddha, T., Kusko, R., Sansone, S.-A., Tong, W., Wolfinger, R. D., et al. (2020) · Nature

Explainable Artificial Intelligence (XAI)Ethics and Social Impacts of AI

Cited by 540

H3K4me3 breadth is linked to cell identity and transcriptional consistency

Benayoun, B. A., Pollina, E. A., Ucar, D., Mahmoudi, S., Karra, K., Wong, E. D., Devarajan, K., Daugherty, A. C., Kundaje, A. B., Mancini, E., et al. (2014) · Cell

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 536

WILDS: A Benchmark of in-the-Wild Distribution Shifts

Koh, P. W., Sagawa, S., Marklund, H., Xie, S. M., Zhang, M., Balsubramani, A., Hu, W., Yasunaga, M., Phillips, R. L., Gao, I., et al. (2020) · arXiv

Domain Adaptation and Few-Shot LearningMachine Learning and Data Classification

Cited by 518

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

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

Trevino, A. E., Müller, F., Andersen, J., Sundaram, L., Kathiria, A., Shcherbina, A., Farh, K., Chang, H. Y., Pașca, A. M., Kundaje, A., et al. (2021) · Cell

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 478

Comparative analysis of metazoan chromatin organization

Ho, J. W. K., Jung, Y. L., Liu, T., Alver, B. H., Lee, S., Ikegami, K., Sohn, K.-A., Minoda, A., Tolstorukov, M. Y., Appert, A., et al. (2014) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 390

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

Benayoun, B. A., Pollina, E. A., Singh, P. P., Mahmoudi, S., Harel, I., Casey, K. M., Dulken, B. W., Kundaje, A., & Brunet, A. (2019) · Genome Research

Genomics and Chromatin DynamicsGenetics, Aging, and Longevity in Model Organisms

Cited by 360

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

Corces, M. R., Shcherbina, A., Kundu, S., Gloudemans, M. J., Frésard, L., Granja, J. M., Louie, B. H., Eulalio, T., Shams, S., Bagdatli, S. T., et al. (2020) · Nature Genetics

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Cited by 358

Extensive Variation in Chromatin States Across Humans

Kasowski, M., Kyriazopoulou-Panagiotopoulou, S., Grubert, F., Zaugg, J. B., Kundaje, A., Liu, Y., Boyle, A. P., Zhang, Q. C., Zakharia, F., Spacek, D. V., et al. (2013) · Science

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 339

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., Greenside, P., Srivas, R., Phanstiel, D. H., Pekowska, A., et al. (2015) · Cell

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 319

CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities

Han, K., Pierce, S. E., Li, A., Spees, K., Anderson, G. R., Seoane, J. A., Lo, Y.-H., Dubreuil, M., Olivas, M., Kamber, R. A., et al. (2020) · Nature

CRISPR and Genetic EngineeringCancer Genomics and Diagnostics

Cited by 311

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

Technical Note on Transcription Factor Motif Discovery from Importance Scores (TF-MoDISco) version 0.5.6.5

Shrikumar, A., Tian, K., Avsec, Ž., Shcherbina, A., Banerjee, A., Sharmin, M., Nair, S., & Kundaje, A. (2018) · arXiv

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 229