Search Results - "Mikkelsen, Tarjei S."

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells by Trapnell, Cole, Cacchiarelli, Davide, Grimsby, Jonna, Pokharel, Prapti, Li, Shuqiang, Morse, Michael, Lennon, Niall J, Livak, Kenneth J, Mikkelsen, Tarjei S, Rinn, John L

“…An algorithm uncovers transcriptome dynamics during differentiation by ordering RNA-Seq data from single cells. Defining the transcriptional dynamics of a…”
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Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells by Shalem, Ophir, Sanjana, Neville E., Hartenian, Ella, Shi, Xi, Scott, David A., Mikkelsen, Tarjei S., Heckl, Dirk, Ebert, Benjamin L., Root, David E., Doench, John G., Zhang, Feng

“…The simplicity of programming the CRISPR (clustered regularly interspaced short palindromic repeats)–associated nuclease Cas9 to modify specific genomic loci…”
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Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells by Semrau, Stefan, Goldmann, Johanna E., Soumillon, Magali, Mikkelsen, Tarjei S., Jaenisch, Rudolf, van Oudenaarden, Alexander

“…Gene expression heterogeneity in the pluripotent state of mouse embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast, exit from…”
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Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites by Schwartz, Schraga, Mumbach, Maxwell R., Jovanovic, Marko, Wang, Tim, Maciag, Karolina, Bushkin, G. Guy, Mertins, Philipp, Ter-Ovanesyan, Dmitry, Habib, Naomi, Cacchiarelli, Davide, Sanjana, Neville E., Freinkman, Elizaveta, Pacold, Michael E., Satija, Rahul, Mikkelsen, Tarjei S., Hacohen, Nir, Zhang, Feng, Carr, Steven A., Lander, Eric S., Regev, Aviv

“…N6-methyladenosine (m6A) is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins…”
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Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay by Tewhey, Ryan, Kotliar, Dylan, Park, Daniel S., Liu, Brandon, Winnicki, Sarah, Reilly, Steven K., Andersen, Kristian G., Mikkelsen, Tarjei S., Lander, Eric S., Schaffner, Stephen F., Sabeti, Pardis C.

“…Although studies have identified hundreds of loci associated with human traits and diseases, pinpointing causal alleles remains difficult, particularly for…”
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Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing by Replogle, Joseph M., Norman, Thomas M., Xu, Albert, Hussmann, Jeffrey A., Chen, Jin, Cogan, J. Zachery, Meer, Elliott J., Terry, Jessica M., Riordan, Daniel P., Srinivas, Niranjan, Fiddes, Ian T., Arthur, Joseph G., Alvarado, Luigi J., Pfeiffer, Katherine A., Mikkelsen, Tarjei S., Weissman, Jonathan S., Adamson, Britt

“…Single-cell CRISPR screens enable the exploration of mammalian gene function and genetic regulatory networks. However, use of this technology has been limited…”
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Mapping and analysis of chromatin state dynamics in nine human cell types by Ernst, Jason, Kheradpour, Pouya, Mikkelsen, Tarjei S., Shoresh, Noam, Ward, Lucas D., Epstein, Charles B., Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael, Ku, Manching, Durham, Timothy, Kellis, Manolis, Bernstein, Bradley E.

“…Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the…”
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Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits by Ulirsch, Jacob C., Nandakumar, Satish K., Wang, Li, Giani, Felix C., Zhang, Xiaolan, Rogov, Peter, Melnikov, Alexandre, McDonel, Patrick, Do, Ron, Mikkelsen, Tarjei S., Sankaran, Vijay G.

“…Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but…”
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Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions by Ernst, Jason, Melnikov, Alexandre, Zhang, Xiaolan, Wang, Li, Rogov, Peter, Mikkelsen, Tarjei S, Kellis, Manolis

“…The activating and repressing nucleotides of regulatory regions are identified at a genome-wide scale using tiling reporter assays. Massively parallel reporter…”
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Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis by Soumillon, Magali, Necsulea, Anamaria, Weier, Manuela, Brawand, David, Zhang, Xiaolan, Gu, Hongcang, Barthès, Pauline, Kokkinaki, Maria, Nef, Serge, Gnirke, Andreas, Dym, Martin, de Massy, Bernard, Mikkelsen, Tarjei S., Kaessmann, Henrik

“…Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide…”
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Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay by Melnikov, Alexandre, Murugan, Anand, Zhang, Xiaolan, Tesileanu, Tiberiu, Wang, Li, Rogov, Peter, Feizi, Soheil, Gnirke, Andreas, Callan, Curtis G, Kinney, Justin B, Kellis, Manolis, Lander, Eric S, Mikkelsen, Tarjei S

“…An improved understanding of enhancers in mammalian genomes could facilitate the design of new regulatory elements. Melnikov et al . synthesize thousands of…”
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Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay by Kheradpour, Pouya, Ernst, Jason, Melnikov, Alexandre, Rogov, Peter, Wang, Li, Zhang, Xiaolan, Alston, Jessica, Mikkelsen, Tarjei S, Kellis, Manolis

“…Genome-wide chromatin annotations have permitted the mapping of putative regulatory elements across multiple human cell types. However, their experimental…”
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Dissecting direct reprogramming through integrative genomic analysis by Meissner, Alexander, Mikkelsen, Tarjei S, Hanna, Jacob, Zhang, Xiaolan, Ku, Manching, Wernig, Marius, Schorderet, Patrick, Bernstein, Bradley E, Jaenisch, Rudolf, Lander, Eric S

“…Somatic cells can be reprogrammed to a pluripotent state through the ectopic expression of defined transcription factors. Understanding the mechanism and…”
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Systematic dissection of genomic features determining transcription factor binding and enhancer function by Grossman, Sharon R., Zhang, Xiaolan, Wang, Li, Engreitz, Jesse, Melnikov, Alexandre, Rogov, Peter, Tewhey, Ryan, Isakova, Alina, Deplancke, Bart, Bernstein, Bradley E., Mikkelsen, Tarjei S., Lander, Eric S.

“…Enhancers regulate gene expression through the binding of sequence-specific transcription factors (TFs) to cognate motifs. Various features influence TF…”
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Genome-scale DNA methylation maps of pluripotent and differentiated cells by Jaenisch, Rudolf, Lander, Eric S, Meissner, Alexander, Mikkelsen, Tarjei S, Gu, Hongcang, Wernig, Marius, Hanna, Jacob, Sivachenko, Andrey, Zhang, Xiaolan, Bernstein, Bradley E, Nusbaum, Chad, Jaffe, David B, Gnirke, Andreas

“…DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide…”
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Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains by Ku, Manching, Koche, Richard P, Rheinbay, Esther, Mendenhall, Eric M, Endoh, Mitsuhiro, Mikkelsen, Tarjei S, Presser, Aviva, Nusbaum, Chad, Xie, Xiaohui, Chi, Andrew S, Adli, Mazhar, Kasif, Simon, Ptaszek, Leon M, Cowan, Chad A, Lander, Eric S, Koseki, Haruhiko, Bernstein, Bradley E

“…In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4…”
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Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals by Kellis, Manolis, Feldser, David, Cassady, John P, Amit, Ido, Lander, Eric S, Zuk, Or, Lin, Michael F, Carey, Bryce W, Garber, Manuel, Mikkelsen, Tarjei S, Jacks, Tyler, Hacohen, Nir, Guttman, Mitchell, French, Courtney, Cabili, Moran N, Huarte, Maite, Regev, Aviv, Rinn, John L, Jaenisch, Rudolf, Bernstein, Bradley E

“…There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts. However, the functional significance of these…”
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Phenotypic Characterization of a Comprehensive Set of MAPK1/ERK2 Missense Mutants by Brenan, Lisa, Andreev, Aleksandr, Cohen, Ofir, Pantel, Sasha, Kamburov, Atanas, Cacchiarelli, Davide, Persky, Nicole S., Zhu, Cong, Bagul, Mukta, Goetz, Eva M., Burgin, Alex B., Garraway, Levi A., Getz, Gad, Mikkelsen, Tarjei S., Piccioni, Federica, Root, David E., Johannessen, Cory M.

“…Tumor-specific genomic information has the potential to guide therapeutic strategies and revolutionize patient treatment. Currently, this approach is limited…”
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Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution by Meissner, Alexander, Gu, Hongcang, Bock, Christoph, Mikkelsen, Tarjei S, Jäger, Natalie, Smith, Zachary D, Tomazou, Eleni, Gnirke, Andreas, Lander, Eric S

“…Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We…”
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Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues by Kadoki, Motohiko, Patil, Ashwini, Thaiss, Cornelius C., Brooks, Donald J., Pandey, Surya, Deep, Deeksha, Alvarez, David, von Andrian, Ulrich H., Wagers, Amy J., Nakai, Kenta, Mikkelsen, Tarjei S., Soumillon, Magali, Chevrier, Nicolas

“…A fundamental challenge in immunology is to decipher the principles governing immune responses at the whole-organism scale. Here, using a comparative infection…”
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