Browsing Other ICR Research by author "Choudhary, Jyoti"
Now showing items 1-20 of 31
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.
Schlaffner, CN; Pirklbauer, GJ; Bender, A; Steen, JAJ; Choudhary, JS (2018-05-22)Cross-talk between genes, transcripts, and proteins is the key to cellular responses; hence, analysis of molecular levels as distinct entities is slowly being extended to integrative studies to enhance the understanding ... -
A Knockout Screen of ApiAP2 Genes Reveals Networks of Interacting Transcriptional Regulators Controlling the Plasmodium Life Cycle.
Modrzynska, K; Pfander, C; Chappell, L; Yu, L; Suarez, C; et al. (CELL PRESS, 2017-01-11)A family of apicomplexa-specific proteins containing AP2 DNA-binding domains (ApiAP2s) was identified in malaria parasites. This family includes sequence-specific transcription factors that are key regulators of development. ... -
A molecular quantitative trait locus map for osteoarthritis.
Steinberg, J; Southam, L; Roumeliotis, TI; Clark, MJ; Jayasuriya, RL; et al. (NATURE PORTFOLIO, 2021-02-26)Osteoarthritis causes pain and functional disability for over 500 million people worldwide. To develop disease-stratifying tools and modifying therapies, we need a better understanding of the molecular basis of the disease ... -
A quantitative proteomic screen of the Campylobacter jejuni flagellar-dependent secretome.
Scanlan, E; Yu, L; Maskell, D; Choudhary, J; Grant, A (ELSEVIER SCIENCE BV, 2017-01-30)UNLABELLED: Campylobacter jejuni is the leading cause of bacterial gastroenteritis in the world. A number of factors are believed to contribute to the ability of C. jejuni to cause disease within the human host including ... -
Arc Requires PSD95 for Assembly into Postsynaptic Complexes Involved with Neural Dysfunction and Intelligence.
Fernández, E; Collins, MO; Frank, RAW; Zhu, F; Kopanitsa, MV; et al. (CELL PRESS, 2017-10-17)Arc is an activity-regulated neuronal protein, but little is known about its interactions, assembly into multiprotein complexes, and role in human disease and cognition. We applied an integrated proteomic and genetic ... -
Broad-Spectrum Regulation of Nonreceptor Tyrosine Kinases by the Bacterial ADP-Ribosyltransferase EspJ.
Pollard, DJ; Berger, CN; So, EC; Yu, L; Hadavizadeh, K; et al. (AMER SOC MICROBIOLOGY, 2018-04-10)Tyrosine phosphorylation is key for signal transduction from exogenous stimuli, including the defense against pathogens. Conversely, pathogens can subvert protein phosphorylation to control host immune responses and ... -
Cell-type-specific visualisation and biochemical isolation of endogenous synaptic proteins in mice.
Zhu, F; Collins, MO; Harmse, J; Choudhary, JS; Grant, SGN; et al. (WILEY, 2020-02-01)In recent years, the remarkable molecular complexity of synapses has been revealed, with over 1,000 proteins identified in the synapse proteome. Although it is known that different receptors and other synaptic proteins are ... -
Citrobacter rodentium induces rapid and unique metabolic and inflammatory responses in mice suffering from severe disease.
Carson, D; Barry, R; Hopkins, EGD; Roumeliotis, TI; García-Weber, D; et al. (WILEY-HINDAWI, 2020-01-01)The mouse pathogen Citrobacter rodentium is used to model infections with enterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC). Pathogenesis is commonly modelled in mice developing mild disease (e.g., ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
Identification of protein complexes that bind to histone H3 combinatorial modifications using super-SILAC and weighted correlation network analysis.
Kunowska, N; Rotival, M; Yu, L; Choudhary, J; Dillon, N (OXFORD UNIV PRESS, 2015-02-18)The large number of chemical modifications that are found on the histone proteins of eukaryotic cells form multiple complex combinations, which can act as recognition signals for reader proteins. We have used peptide capture ... -
Intestinal Epithelial Cells and the Microbiome Undergo Swift Reprogramming at the Inception of Colonic Citrobacter rodentium Infection.
Hopkins, EGD; Roumeliotis, TI; Mullineaux-Sanders, C; Choudhary, JS; Frankel, G (AMER SOC MICROBIOLOGY, 2019-04-02)We used the mouse attaching and effacing (A/E) pathogen Citrobacter rodentium, which models the human A/E pathogens enteropathogenic Escherichia coli and enterohemorrhagic E. coli (EPEC and EHEC), to temporally resolve ... -
OpenMS: a flexible open-source software platform for mass spectrometry data analysis.
Röst, HL; Sachsenberg, T; Aiche, S; Bielow, C; Weisser, H; et al. (NATURE PORTFOLIO, 2016-08-30)High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing ... -
Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner.
Bianco, JN; Bergoglio, V; Lin, Y-L; Pillaire, M-J; Schmitz, A-L; et al. (NATURE PUBLISHING GROUP, 2019-02-22)Oncogene-induced replication stress (RS) promotes cancer development but also impedes tumor growth by activating anti-cancer barriers. To determine how cancer cells adapt to RS, we have monitored the expression of different ...