Search Results - "Pimentel, Harold"

Differential analysis of RNA-seq incorporating quantification uncertainty by Pimentel, Harold, Bray, Nicolas L, Puente, Suzette, Melsted, Páll, Pachter, Lior

“…By using bootstraps that estimate inferential variance, the sleuth method and software provide fast and highly accurate differential gene expression analysis…”
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Identification of novel transcripts in annotated genomes using RNA-Seq by ROBERTS, Adam, PIMENTEL, Harold, TRAPNELL, Cole, PACHTER, Lior

“…We describe a new 'reference annotation based transcript assembly' problem for RNA-Seq data that involves assembling novel transcripts in the context of an…”
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Accounting for isoform expression increases power to identify genetic regulation of gene expression by LaPierre, Nathan, Pimentel, Harold

“…A core problem in genetics is molecular quantitative trait locus (QTL) mapping, in which genetic variants associated with changes in the molecular phenotypes…”
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Gene-level differential analysis at transcript-level resolution by Yi, Lynn, Pimentel, Harold, Bray, Nicolas L, Pachter, Lior

“…Compared to RNA-sequencing transcript differential analysis, gene-level differential expression analysis is more robust and experimentally actionable. However,…”
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Intron retention is a source of neoepitopes in cancer by Smart, Alicia C, Margolis, Claire A, Pimentel, Harold, He, Meng Xiao, Miao, Diana, Adeegbe, Dennis, Fugmann, Tim, Wong, Kwok-Kin, Van Allen, Eliezer M

“…Neoepitopes derived from intron retention events are processed and presented on MHC I in cancer cell lines. We present an in silico approach to identifying…”
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A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis by Pimentel, Harold, Parra, Marilyn, Gee, Sherry L, Mohandas, Narla, Pachter, Lior, Conboy, John G

“…Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster…”
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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions by Kim, Daehwan, Pertea, Geo, Trapnell, Cole, Pimentel, Harold, Kelley, Ryan, Salzberg, Steven L

“…TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant…”
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Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways by Yi, Lynn, Pimentel, Harold, Pachter, Lior

“…A recent study of the gene expression patterns of Zika virus (ZIKV) infected human neural progenitor cells (hNPCs) revealed transcriptional dysregulation and…”
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A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis by Pimentel, Harold, Parra, Marilyn, Gee, Sherry, Ghanem, Dana, An, Xiuli, Li, Jie, Mohandas, Narla, Pachter, Lior, Conboy, John G

“…Alternative pre-messenger RNA splicing remodels the human transcriptome in a spatiotemporal manner during normal development and differentiation. Here we…”
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Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage by Rao, Jingyou, Xin, Ruiqi, Macdonald, Christian, Howard, Matthew K, Estevam, Gabriella O, Yee, Sook Wah, Wang, Mingsen, Fraser, James S, Coyote-Maestas, Willow, Pimentel, Harold

“…Deep mutational scanning (DMS) measures the effects of thousands of genetic variants in a protein simultaneously. The small sample size renders classical…”
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Erratum: Near-optimal probabilistic RNA-seq quantification by Bray, Nicolas L, Pimentel, Harold, Melsted, Páll, Pachter, Lior

“…Nat. Biotechnol. 34, 525–527 (2016); published online 4 April 2016; corrected after print 27 July 2016 In the version of this article initially published, in…”
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Near-optimal probabilistic RNA-seq quantification by Bray, Nicolas L, Pimentel, Harold, Melsted, Páll, Pachter, Lior

“…A pseudoalignment-based method enables faster quantification and measurement of uncertainty in RNA-seq experiments. We present kallisto, an RNA-seq…”
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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks by Trapnell, Cole, Roberts, Adam, Goff, Loyal, Pertea, Geo, Kim, Daehwan, Kelley, David R, Pimentel, Harold, Salzberg, Steven L, Rinn, John L, Pachter, Lior

“…Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay…”
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Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase by Catania, Sandra, Dumesic, Phillip A., Pimentel, Harold, Nasif, Ammar, Stoddard, Caitlin I., Burke, Jordan E., Diedrich, Jolene K., Cooke, Sophie, Shea, Terrance, Gienger, Elizabeth, Lintner, Robert, Yates, John R., Hajkova, Petra, Narlikar, Geeta J., Cuomo, Christina A., Pritchard, Jonathan K., Madhani, Hiten D.

“…Cytosine methylation of DNA is a widespread modification of DNA that plays numerous critical roles. In the yeast Cryptococcus neoformans, CG methylation occurs…”
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An evolved AAV variant enables efficient genetic engineering of murine T cells by Nyberg, William A., Ark, Jonathan, To, Angela, Clouden, Sylvanie, Reeder, Gabriella, Muldoon, Joseph J., Chung, Jing-Yi, Xie, William H., Allain, Vincent, Steinhart, Zachary, Chang, Christopher, Talbot, Alexis, Kim, Sandy, Rosales, Alan, Havlik, L. Patrick, Pimentel, Harold, Asokan, Aravind, Eyquem, Justin

“…Precise targeting of large transgenes to T cells using homology-directed repair has been transformative for adoptive cell therapies and T cell biology…”
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Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits by Patel, Roshni A., Musharoff, Shaila A., Spence, Jeffrey P., Pimentel, Harold, Tcheandjieu, Catherine, Mostafavi, Hakhamanesh, Sinnott-Armstrong, Nasa, Clarke, Shoa L., Smith, Courtney J., Durda, Peter P., Taylor, Kent D., Tracy, Russell, Liu, Yongmei, Johnson, W. Craig, Aguet, Francois, Ardlie, Kristin G., Gabriel, Stacey, Smith, Josh, Nickerson, Deborah A., Rich, Stephen S., Rotter, Jerome I., Tsao, Philip S., Assimes, Themistocles L., Pritchard, Jonathan K.

“…Despite the growing number of genome-wide association studies (GWASs), it remains unclear to what extent gene-by-gene and gene-by-environment interactions…”
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kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq by Sullivan, Delaney K, Min, Kyung Hoi Joseph, Hjörleifsson, Kristján Eldjárn, Luebbert, Laura, Holley, Guillaume, Moses, Lambda, Gustafsson, Johan, Bray, Nicolas L, Pimentel, Harold, Booeshaghi, A Sina, Melsted, Páll, Pachter, Lior

“…The term 'RNA-seq' refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, single cells or…”
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Erratum: near-optimal probabilistic RNA-seq quantification by Bray, Nicolas L, Pimentel, Harold, Melsted, Pall, Pachter, Lior

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The Lair: a resource for exploratory analysis of published RNA-Seq data by Pimentel, Harold, Sturmfels, Pascal, Bray, Nicolas, Melsted, Páll, Pachter, Lior

“…Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can,…”
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Abstract 5719: RNA-based tumor neoantigens from intron retention by Margolis, Claire A., Smart, Alicia C., Adeegbe, Dennis, Miao, Diana, He, Meng Xiao, Pimentel, Harold, Fugmann, Tim, Wong, Kwok-Kin, Allen, Eliezer M. Van

“…Background: Tumor neoantigens contribute to cancer immunity and may influence selective immune checkpoint inhibitor response. Translation of nonsynonymous…”
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