Mikkelsen, Tarjei S.

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature

Genomics and Phylogenetic StudiesGenetic Associations and Epidemiology

Cited by 24,216

Massively parallel digital transcriptional profiling of single cells

Zheng, G. X. Y., Terry, J. M., Belgrader, P., Ryvkin, P., Bent, Z. W., Wilson, R., Ziraldo, S. B., Wheeler, T. D., McDermott, G. P., Zhu, J., et al. (2017) · Nature Communications

Single-cell and spatial transcriptomicsInnovative Microfluidic and Catalytic Techniques Innovation

Cited by 7,353

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 7,314

A bivalent chromatin structure marks key developmental genes in embryonic stem cells

Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 5,361

Genome-scale CRISPR-Cas9 knockout screening in human cells

Shalem, O., Sanjana, N. E., Hartenian, E., Shi, X., Scott, D. A., Mikkelsen, T. S., Heckl, D., Ebert, B. L., Root, D. E., Doench, J. G., et al. (2014) · Science

CRISPR and Genetic EngineeringChromatin Remodeling and Cancer

Cited by 5,234

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 4,129

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

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

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 2,536

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

Positive Natural Selection in the Human Lineage

Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., Palma, A., Mikkelsen, T. S., Altshuler, D., & Lander, E. S. (2006) · Science

Evolution and Genetic DynamicsForensic and Genetic Research

Cited by 1,157

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Broad Institute Genome Sequencing Platform, Mikkelsen, T. S., Broad Institute Whole Genome Assembly Team, Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., Garber, M., Gentles, A. J., et al. (2007) · Nature

Chromosomal and Genetic VariationsGenomics and Phylogenetic Studies

Cited by 711

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Melnikov, A., Murugan, A., Zhang, X., Tesileanu, T., Wang, L., Rogov, P., Feizi, S., Gnirke, A., Callan, C. G., Kinney, J. B., et al. (2012) · Nature Biotechnology

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 711

Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN

Sievers, Q. L., Petzold, G., Bunker, R. D., Renneville, A., Słabicki, M., Liddicoat, B. J., Abdulrahman, W., Mikkelsen, T., Ebert, B. L., & Thomä, N. H. (2018) · Science

Protein Degradation and InhibitorsUbiquitin and proteasome pathways

Cited by 537

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

Tewhey, R., Kotliar, D., Park, D. S., Liu, B., Winnicki, S., Reilly, S. K., Andersen, K. G., Mikkelsen, T. S., Lander, E. S., Schaffner, S. F., et al. (2016) · Cell

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Cited by 480

Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq

Replogle, J. M., Xu, A., Norman, T. M., Meer, E. J., Terry, J. M., Riordan, D., Srinivas, N., Mikkelsen, T. S., Weissman, J. S., & Adamson, B. (2018) · Nature Biotechnology

CRISPR and Genetic EngineeringSingle-cell and spatial transcriptomics

Cited by 465

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

Replogle, J. M., Norman, T. M., Xu, A., Hussmann, J. A., Chen, J., Cogan, J. Z., Meer, E. J., Terry, J. M., Riordan, D. P., Srinivas, N., et al. (2020) · Nature Biotechnology

CRISPR and Genetic EngineeringSingle-cell and spatial transcriptomics

Cited by 465

Progenitor identification and SARS-CoV-2 infection in human distal lung organoids

Salahudeen, A. A., Choi, S. S., Rustagi, A., Zhu, J., van Unen, V., de la O, S. M., Flynn, R. A., Margalef-Català, M., Santos, A. J. M., Ju, J., et al. (2020) · Nature

SARS-CoV-2 and COVID-19 ResearchNeonatal Respiratory Health Research

Cited by 416

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

Ulirsch, J. C., Nandakumar, S. K., Wang, L., Giani, F. C., Zhang, X., Rogov, P., Melnikov, A., McDonel, P., Do, R., Mikkelsen, T. S., et al. (2016) · Cell

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Cited by 328

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

Kheradpour, P., Ernst, J., Melnikov, A., Rogov, P., Wang, L., Zhang, X., Alston, J., Mikkelsen, T. S., & Kellis, M. (2013) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 315

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites

Xie, X., Mikkelsen, T. S., Gnirke, A., Lindblad-Toh, K., Kellis, M., & Lander, E. S. (2007) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 305

Prospective functional classification of all possible missense variants in PPARG

UK Monogenic Diabetes Consortium, Majithia, A. R., Myocardial Infarction Genetics Consortium, UK Congenital Lipodystrophy Consortium, Tsuda, B., Agostini, M., Gnanapradeepan, K., Rice, R., Peloso, G., Patel, K. A., et al. (2016) · Nature Genetics

Genomics and Rare DiseasesPeroxisome Proliferator-Activated Receptors

Cited by 227

Systematic dissection of genomic features determining transcription factor binding and enhancer function

Grossman, S. R., Zhang, X., Wang, L., Engreitz, J., Melnikov, A., Rogov, P., Tewhey, R., Isakova, A., Deplancke, B., Bernstein, B. E., et al. (2017) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 165