Browsing by Author "Davis, Carrie A."

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  • A benchmark for RNA-seq quantification pipelines
    Teng, Mingxiang; Love, Michael I.; Davis, Carrie A.; Djebali, Sarah; Dobin, Alexander; Graveley, Brenton R.; Li, Sheng; Mason, Christopher E.; Olson, Sara; Pervouchine, Dmitri D.; Sloan, Cricket A.; Wei, Xintao; Zhan, Lijun; Irizarry, Rafael A. (BioMed Central, 2016)
    Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, ...
  • A limited set of transcriptional programs define major cell types
    Breschi, Alessandra, 1988-; Muñoz-Aguirre, Manuel; Wucher, Valentin; Davis, Carrie A.; Garrido Martín, Diego, 1992-; Djebali, Sarah; Gillis, Jesse; Pervouchine, Dmitri D.; Vlasova, Anna; Dobin, Alexander; Zaleski, Chris; Drenkow, Jorg; Danyko, Cassidy; Scavelli, Alexandra; Reverter, Ferran; Snyder, Michael; Gingeras, Thomas R.; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)
    We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, ...
  • Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
    Tilgner, Hagen, 1980-; Knowles, David G.; Johnson, Rory; Davis, Carrie A.; Chakrabortty, Sudipto; Djebali, Sarah; Curado, Joao; Snyder, Michael; Gingeras, Thomas R.; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Splicing remains an incompletely understood process. Recent findings suggest that chromatin structure participates in its regulation. Here, we analyze the RNA from subcellular fractions obtained through RNA-seq in the cell ...
  • Erratum to: A benchmark for RNA-seq quantification pipelines
    Teng, Mingxiang; Love, Michael I.; Davis, Carrie A.; Djebali, Sarah; Dobin, Alexander; Graveley, Brenton R.; Li, Sheng; Mason, Christopher E.; Olson, Sara; Pervouchine, Dmitri D.; Sloan, Cricket A.; Wei, Xintao; Zhan, Lijun; Irizarry, Rafael A. (BioMed Central, 2016)
    After the publication of this work [1] it was noticed that there were typographical errors in the following equations: equation 5 in column 2, equation 7 in column 2, equation 8 in column 1.
  • Gene-specific patterns of expression variation across organs and species
    Breschi, Alessandra, 1988-; Djebali, Sarah; Gillis, Jesse; Pervouchine, Dmitri D.; Dobin, Alexander; Davis, Carrie A.; Gingeras, Thomas R.; Guigó Serra, Roderic (BioMed Central, 2016)
    Background: A comparison of transcriptional profiles derived from different tissues in a given species or among different species assumes that commonalities reflect evolutionarily conserved programs and that differences ...
  • High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
    Lagarde, Julien; Uszczynska-Ratajczak, Barbara; Carbonell, Silvia; Pérez-Lluch, Sílvia; Davis, Carrie A.; Gingeras, Thomas R.; Frankish, Adam; Harrow, Jennifer; Guigó Serra, Roderic; Johnson, Rory (Nature Research, 2017)
    Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene ...
  • The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
    Derrien, Thomas; Johnson, Rory; Bussotti, Giovanni, 1983-; Tanzer, Andrea; Djebali, Sarah; Tilgner, Hagen, 1980-; Guernec, Gregory; Martin, David; Merkel, Angelika; Knowles, David G.; Lagarde, Julien; Veeravalli, Lavanya; Ruan, Xiaoan; Ruan, Yijun; Lassmann, Timo; Carninci, Piero; Brown, James B.; Lipovich, Leonard; González, José M.; Thomas, Mark; Davis, Carrie A.; Shiekhattar, Ramin; Gingeras, Thomas R.; Hubbard, Tim J.; Notredame, Cedric; Harrow, Jennifer; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to ...
  • Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    Cheng, Chao; Alexander, Roger; Min, Renqiang; Leng, Jing; Yip, Kevin Y.; Rozowsky, Joel S.; Yan, Koon-Kiu; Dong, Xianjun; Djebali, Sarah; Ruan, Yijun; Davis, Carrie A.; Carninci, Piero; Lassmann, Timo; Gingeras, Thomas R.; Guigó Serra, Roderic; Birney, Ewan; Weng, Zhiping; Snyder, Michael; Gerstein, Mark B. (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Statistical models have been used to quantify the relationship between gene expression and transcription factor (TF) binding signals. Here we apply the models to the large-scale data generated by the ENCODE project to study ...