Kellis, Manolis

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

The GTEx Consortium atlas of genetic regulatory effects across human tissues

The GTEx Consortium, Aguet, F., Anand, S., Ardlie, K. G., Gabriel, S., Getz, G. A., Graubert, A., Hadley, K., Handsaker, R. E., Huang, K. H., et al. (2020) · Science

Genetic Associations and EpidemiologyRNA Research and Splicing

Cited by 5,547

GENCODE: The reference human genome annotation for The ENCODE Project

Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 4,585

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature

Cancer-related molecular mechanisms researchGenomics and Chromatin Dynamics

Cited by 4,098

The repertoire of mutational signatures in human cancer

Alexandrov, L. B., Kim, J., Haradhvala, N. J., Huang, M. N., Tian Ng, A. W., Wu, Y., Boot, A., Covington, K. R., Gordenin, D. A., Bergstrom, E. N., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,496

Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,064

Mapping and analysis of chromatin state dynamics in nine human cell types

Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 2,898

Genome sequence, comparative analysis and haplotype structure of the domestic dog

members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., et al. (2005) · Nature

Human-Animal Interaction StudiesGenetic and phenotypic traits in livestock

Cited by 2,568

Single-cell transcriptomic analysis of Alzheimer’s disease

Mathys, H., Davila-Velderrain, J., Peng, Z., Gao, F., Mohammadi, S., Young, J. Z., Menon, M., He, L., Abdurrob, F., Jiang, X., et al. (2019) · Nature

Single-cell and spatial transcriptomicsAlzheimer's disease research and treatments

Cited by 2,568

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 2,533

Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila

Brennecke, J., Aravin, A. A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., & Hannon, G. J. (2007) · Cell

Chromosomal and Genetic VariationsRNA Interference and Gene Delivery

Cited by 2,524

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

Ward, L. D., & Kellis, M. (2012) · Nucleic Acids Research

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Cited by 2,229

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

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., et al. (2004) · Nature

Chromosomal and Genetic VariationsGenome Rearrangement Algorithms

Cited by 1,966

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use

23andMe Research Team, Liu, M., Psychiatry, H. A.-I., Jiang, Y., Wedow, R., Li, Y., Brazel, D. M., Chen, F., Datta, G., Davila-Velderrain, J., et al. (2019) · Nature Genetics

Genetic Associations and EpidemiologySmoking Behavior and Cessation

Cited by 1,896

The NIH Roadmap Epigenomics Mapping Consortium

Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M. A., Beaudet, A. L., Ecker, J. R., et al. (2010) · Nature Biotechnology

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 1,892

Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., & Kellis, M. (2005) · Nature

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 1,872

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

Wisdom of crowds for robust gene network inference

The DREAM5 Consortium, Marbach, D., Costello, J. C., Küffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., Allison, K. R., Kellis, M., Collins, J. J., et al. (2012) · Nature Methods

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 1,667

GENCODE 2021

Frankish, A., Diekhans, M., Jungreis, I., Lagarde, J., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Armstrong, J., Barnes, I., et al. (2021) · Nucleic Acids Research

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 1,334

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

Claussnitzer, M., Dankel, S. N., Kim, K.-H., Quon, G., Meuleman, W., Haugen, C., Glunk, V., Sousa, I. S., Beaudry, J. L., Puviindran, V., et al. (2015) · New England Journal of Medicine

Adipose Tissue and MetabolismGenetic Associations and Epidemiology

Cited by 1,332

A high-resolution map of human evolutionary constraint using 29 mammals

Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 1,108

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

Butler, G., Rasmussen, M. D., Lin, M. F., Santos, M. A. S., Sakthikumar, S., Munro, C. A., Rheinbay, E., Grabherr, M., Forche, A., Reedy, J. L., et al. (2009) · Nature

Fungal and yeast genetics researchYeasts and Rust Fungi Studies

Cited by 1,065

The evolutionary history of 2,658 cancers

Gerstung, M., Jolly, C., Leshchiner, I., Dentro, S. C., Gonzalez, S., Rosebrock, D., Mitchell, T. J., Rubanova, Y., Anur, P., Yu, K., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 1,057