Browsing by author "Wright, James"

Now showing items 1-14 of 14

    • Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo. 

      Berger, CN; Crepin, VF; Roumeliotis, TI; Wright, JC; Carson, D; et al. (CELL PRESS, 2017-11-07)
      The intestinal epithelial cells (IECs) that line the gut form a robust line of defense against ingested pathogens. We investigated the impact of infection with the enteric pathogen Citrobacter rodentium on mouse IEC ...

    • Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. 

      Mudge, JM; Jungreis, I; Hunt, T; Gonzalez, JM; Wright, JC; et al. (COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2019-12-01)
      The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify ...

    • Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. 

      Khan, YA; Jungreis, I; Wright, JC; Mudge, JM; Choudhary, JS; et al. (BMC, 2020-03-06)
      BACKGROUND: POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria ...

    • Flexible Data Analysis Pipeline for High-Confidence Proteogenomics. 

      Weisser, H; Wright, JC; Mudge, JM; Gutenbrunner, P; Choudhary, JS (AMER CHEMICAL SOC, 2016-12-02)
      Proteogenomics leverages information derived from proteomic data to improve genome annotations. Of particular interest are "novel" peptides that provide direct evidence of protein expression for genomic regions not previously ...

    • GENCODE 2021. 

      Frankish, A; Diekhans, M; Jungreis, I; Lagarde, J; Loveland, JE; et al. (OXFORD UNIV PRESS, 2021-01-08)
      The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation ...

    • GENCODE reference annotation for the human and mouse genomes. 

      Frankish, A; Diekhans, M; Ferreira, A-M; Johnson, R; Jungreis, I; et al. (OXFORD UNIV PRESS, 2019-01-08)
      The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 ...

    • Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells. 

      Roumeliotis, TI; Williams, SP; Gonçalves, E; Alsinet, C; Del Castillo Velasco-Herrera, M; et al. (CELL PRESS, 2017-08-29)
      Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labeling to characterize the proteomic landscapes of 50 ...

    • Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow. 

      Wright, JC; Mudge, J; Weisser, H; Barzine, MP; Gonzalez, JM; et al. (NATURE PORTFOLIO, 2016-06-02)
      Complete annotation of the human genome is indispensable for medical research. The GENCODE consortium strives to provide this, augmenting computational and experimental evidence with manual annotation. The rapidly developing ...

    • Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever. 

      Blohmke, CJ; Darton, TC; Jones, C; Suarez, NM; Waddington, CS; et al. (ROCKEFELLER UNIV PRESS, 2016-05-30)
      Enteric fever, caused by Salmonella enterica serovar Typhi, is an important public health problem in resource-limited settings and, despite decades of research, human responses to the infection are poorly understood. In ...

    • Perspectives on ENCODE. 

      ENCODE Project Consortium,; Snyder, MP; Gingeras, TR; Moore, JE; Weng, Z; et al. (NATURE RESEARCH, 2020-07-30)
      The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated ...

    • SF3B1 hotspot mutations confer sensitivity to PARP inhibition by eliciting a defective replication stress response. 

      Bland, P; Saville, H; Wai, PT; Curnow, L; Muirhead, G; et al. (NATURE PORTFOLIO, 2023-08-01)
      SF3B1 hotspot mutations are associated with a poor prognosis in several tumor types and lead to global disruption of canonical splicing. Through synthetic lethal drug screens, we identify that SF3B1 mutant (SF3B1MUT) cells ...

    • The Citrobacter rodentium type III secretion system effector EspO affects mucosal damage repair and antimicrobial responses. 

      Berger, CN; Crepin, VF; Roumeliotis, TI; Wright, JC; Serafini, N; et al. (PUBLIC LIBRARY SCIENCE, 2018-10-01)
      Infection with Citrobacter rodentium triggers robust tissue damage repair responses, manifested by secretion of IL-22, in the absence of which mice succumbed to the infection. Of the main hallmarks of C. rodentium infection ...

    • The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. 

      Rozowsky, J; Gao, J; Borsari, B; Yang, YT; Galeev, T; et al. (CELL PRESS, 2023-03-30)
      Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 ...

    • Using Deep Learning to Extrapolate Protein Expression Measurements. 

      Barzine, MP; Freivalds, K; Wright, JC; Opmanis, M; Rituma, D; et al. (WILEY, 2020-11-01)
      Mass spectrometry (MS)-based quantitative proteomics experiments typically assay a subset of up to 60% of the ≈20 000 human protein coding genes. Computational methods for imputing the missing values using RNA expression ...