Browsing by author "Choudhary, Jyoti"
Now showing items 21-40 of 85
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Cyclin B1-Cdk1 facilitates MAD1 release from the nuclear pore to ensure a robust spindle checkpoint.
Jackman, M; Marcozzi, C; Barbiero, M; Pardo, M; Yu, L; et al. (ROCKEFELLER UNIV PRESS, 2020-06-01)How the cell rapidly and completely reorganizes its architecture when it divides is a problem that has fascinated researchers for almost 150 yr. We now know that the core regulatory machinery is highly conserved in eukaryotes, ... -
Delineating the HMGB1 and HMGB2 interactome in prostate and ovary epithelial cells and its relationship with cancer.
Barreiro-Alonso, A; Lamas-Maceiras, M; García-Díaz, R; Rodríguez-Belmonte, E; Yu, L; et al. (Impact Journals, LLC, 2018-04-10)High Mobility Group B (HMGB) proteins are involved in cancer progression and in cellular responses to platinum compounds used in the chemotherapy of prostate and ovary cancer. Here we use affinity purification coupled to ... -
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 ... -
EPEC-induced activation of the Ca2+ transporter TRPV2 leads to pyroptotic cell death.
Zhong, Q; Chatterjee, S; Choudhary, JS; Frankel, G (WILEY, 2022-02-01)The enteropathogenic Escherichia coli (EPEC) type III secretion system effector Tir, which mediates intimate bacterial attachment to epithelial cells, also triggers Ca2+ influx followed by LPS entry and caspase-4-dependent ... -
Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity.
Thomas, DC; Clare, S; Sowerby, JM; Pardo, M; Juss, JK; et al. (ROCKEFELLER UNIV PRESS, 2017-04-03)The phagocyte respiratory burst is crucial for innate immunity. The transfer of electrons to oxygen is mediated by a membrane-bound heterodimer, comprising gp91phox and p22phox subunits. Deficiency of either subunit leads ... -
EROS is a selective chaperone regulating the phagocyte NADPH oxidase and purinergic signalling.
Randzavola, LO; Mortimer, PM; Garside, E; Dufficy, ER; Schejtman, A; et al. (eLIFE SCIENCES PUBL LTD, 2022-11-24)EROS (essential for reactive oxygen species) protein is indispensable for expression of gp91phox, the catalytic core of the phagocyte NADPH oxidase. EROS deficiency in humans is a novel cause of the severe immunodeficiency, ... -
Evaluation of a Dual Isolation Width Acquisition Method for Isobaric Labeling Ratio Decompression.
Roumeliotis, TI; Weisser, H; Choudhary, JS (AMER CHEMICAL SOC, 2019-03-01)Isobaric labeling is a highly precise approach for protein quantification. However, due to the isolation interference problem, isobaric tagging suffers from ratio underestimation at the MS2 level. The use of narrow isolation ... -
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 ... -
Evolution of complexity in the zebrafish synapse proteome.
Bayés, À; Collins, MO; Reig-Viader, R; Gou, G; Goulding, D; et al. (NATURE PUBLISHING GROUP, 2017-03-02)The proteome of human brain synapses is highly complex and is mutated in over 130 diseases. This complexity arose from two whole-genome duplications early in the vertebrate lineage. Zebrafish are used in modelling human ... -
Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis.
Yeung, ATY; Hale, C; Lee, AH; Gill, EE; Bushell, W; et al. (NATURE PUBLISHING GROUP, 2017-04-25)Chlamydia trachomatis remains a leading cause of bacterial sexually transmitted infections and preventable blindness worldwide. There are, however, limited in vitro models to study the role of host genetics in the response ... -
Faecal neutrophil elastase-antiprotease balance reflects colitis severity.
Barry, R; Ruano-Gallego, D; Radhakrishnan, ST; Lovell, S; Yu, L; et al. (NATURE PUBLISHING GROUP, 2020-03-01)Given the global burden of diarrheal diseases on healthcare it is surprising how little is known about the drivers of disease severity. Colitis caused by infection and inflammatory bowel disease (IBD) is characterised by ... -
Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes.
Schlaffner, CN; Pirklbauer, GJ; Bender, A; Choudhary, JS (CELL PRESS, 2017-08-23)Current tools for visualization and integration of proteomics with other omics datasets are inadequate for large-scale studies and capture only basic sequence identity information. Furthermore, the frequent reformatting ... -
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 ... -
Global, site-specific analysis of neuronal protein S-acylation.
Collins, MO; Woodley, KT; Choudhary, JS (NATURE PORTFOLIO, 2017-07-05)Protein S-acylation (palmitoylation) is a reversible lipid modification that is an important regulator of dynamic membrane-protein interactions. Proteomic approaches have uncovered many putative palmitoylated proteins ... -
HMGB1 Protein Interactions in Prostate and Ovary Cancer Models Reveal Links to RNA Processing and Ribosome Biogenesis through NuRD, THOC and Septin Complexes.
Barreiro-Alonso, A; Lamas-Maceiras, M; Lorenzo-Catoira, L; Pardo, M; Yu, L; et al. (MDPI, 2021-09-18)This study reports the HMGB1 interactomes in prostate and ovary cancer cells lines. Affinity purification coupled to mass spectrometry confirmed that the HMGB1 nuclear interactome is involved in HMGB1 known functions such ... -
HSP90-CDC37-PP5 forms a structural platform for kinase dephosphorylation.
Oberoi, J; Guiu, XA; Outwin, EA; Schellenberger, P; Roumeliotis, TI; et al. (NATURE PORTFOLIO, 2022-11-29)Activation of client protein kinases by the HSP90 molecular chaperone system is affected by phosphorylation at multiple sites on HSP90, the kinase-specific co-chaperone CDC37, and the kinase client itself. Removal of ... -
A HUWE1 defect causes PARP inhibitor resistance by modulating the BRCA1-∆11q splice variant.
Pettitt, SJ; Shao, N; Zatreanu, D; Frankum, J; Bajrami, I; et al. (SPRINGERNATURE, 2023-09-01)Although PARP inhibitors (PARPi) now form part of the standard-of-care for the treatment of homologous recombination defective cancers, de novo and acquired resistance limits their overall effectiveness. Previously, ...