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List of works by Jyoti Choudhary

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Knockout Screen of ApiAP2 Genes Reveals Networks of Interacting Transcriptional Regulators Controlling the Plasmodium Life Cycle

scientific article published on January 2017

A Plasmodium calcium-dependent protein kinase controls zygote development and transmission by translationally activating repressed mRNAs

scientific article

A comprehensive survey of protein palmitoylation in late blood-stage Plasmodium falciparum

A comprehensive survey of protein palmitoylation in late blood-stage Plasmodium falciparum.

scientific article

A conserved acetyl esterase domain targets diverse bacteriophages to the Vi capsular receptor of Salmonella enterica serovar Typhi

scientific article published on 3 September 2010

A molecular quantitative trait locus map for osteoarthritis

scientific article published on 26 February 2021

A new method to determine in vivo interactomes reveals binding of the Legionella pneumophila effector PieE to multiple rab GTPases

scientific article published on 12 August 2014

A polygenic burden of rare disruptive mutations in schizophrenia

scientific article

A quantitative proteomic screen of the Campylobacter jejuni flagellar-dependent secretome

scientific article

A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

scientific article

APC15 drives the turnover of MCC-CDC20 to make the spindle assembly checkpoint responsive to kinetochore attachment

scientific article

Accurate and sensitive peptide identification with Mascot Percolator

scientific article published on June 2009

Activation of the Aryl Hydrocarbon Receptor Interferes with Early Embryonic Development

scientific article published on 24 October 2017

An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules

scientific article published in Nature Communications

An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules

An expanded Oct4 interaction network: implications for stem cell biology, development, and disease

scientific article

Analysis of protein palmitoylation reveals a pervasive role in Plasmodium development and pathogenesis

scientific article published on August 2012

Analysis of protein phosphorylation on a proteome-scale

scientific article published on August 2007

Aneuploidy tolerance caused by BRG1 loss allows chromosome gains and recovery of fitness

scientific article published on 01 April 2022

Applications of protein mass spectrometry in cell biology.

scientific article

Arc Requires PSD95 for Assembly into Postsynaptic Complexes Involved with Neural Dysfunction and Intelligence. ⬇️

scientific article published in October 2017

Assignment of Protein Interactions from Affinity Purification/Mass Spectrometry Data ⬇️

scientific article published on February 10, 2012

Autoinhibition Mechanism of the Ubiquitin-Conjugating Enzyme UBE2S by Autoubiquitination

scientific article published on 20 June 2019

Broad-Spectrum Regulation of Nonreceptor Tyrosine Kinases by the Bacterial ADP-Ribosyltransferase EspJ.

scientific article published on 10 April 2018

C9orf72 arginine-rich dipeptide proteins interact with ribosomal proteins in vivo to induce a toxic translational arrest that is rescued by eIF1A

article

CRISPR activation screen in mice identifies novel membrane proteins enhancing pulmonary metastatic colonisation

scientific article published on 23 March 2021

Cell-type-specific visualisation and biochemical isolation of endogenous synaptic proteins in mice

scientific article published on 06 November 2019

Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells

scientific article published on 29 December 2015

Characterization of the proteome, diseases and evolution of the human postsynaptic density.

scientific article published on 19 December 2010

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

scientific article

Citrobacter rodentium induces rapid and unique metabolic and inflammatory responses in mice suffering from severe disease

scientific article published on 30 October 2019

Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux

scientific article published in April 2011

Clustering of Tir during enteropathogenic E. coli infection triggers calcium influx-dependent pyroptosis in intestinal epithelial cells

scientific article published on 30 December 2020

Comparative study of human and mouse postsynaptic proteomes finds high compositional conservation and abundance differences for key synaptic proteins

scientific article

Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold

scientific article

Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation

scientific article published on 21 March 2014

Coordinating cell cycle progression via cyclin specificity

scientific article published on 15 December 2011

Crosstalk between PKA and PKG controls pH-dependent host cell egress of Toxoplasma gondii.

scientific article published on 13 October 2017

Cyclic diGMP regulates production of sortase substrates of Clostridium difficile and their surface exposure through ZmpI protease-mediated cleavage

scientific article published on 17 August 2015

De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia.

scientific article

DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics

scientific article

Delineating the HMGB1 and HMGB2 interactome in prostate and ovary epithelial cells and its relationship with cancer.

scientific article published on 10 April 2018

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

scientific article published on 19 September 2019

Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator

scientific article

Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity

scientific article published on 28 March 2017

Evaluation of a Dual Isolation Width Acquisition Method for Isobaric Labeling Ratio Decompression

scientific article published on 03 January 2019

Evolution of complexity in the zebrafish synapse proteome.

scientific article published on 02 March 2017

Evolutionary expansion and anatomical specialization of synapse proteome complexity.

scientific article published on 8 June 2008

Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis

scientific article published on 25 April 2017

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

scientific article

Faecal neutrophil elastase-antiprotease balance reflects colitis severity

scientific article published on 26 November 2019

Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes

scientific article published on August 2017

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics

scientific article

Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism

scientific article

GENCODE reference annotation for the human and mouse genomes

scientific article published on 01 January 2019

Genome-wide analysis of the heat stress response in Zebu (Sahiwal) cattle

scientific article

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

scientific article published on August 2017

Global, site-specific analysis of neuronal protein S-acylation

scientific article published on 5 July 2017

Human post-mortem synapse proteome integrity screening for proteomic studies of postsynaptic complexes

scientific article

Identification of protein complexes that bind to histone H3 combinatorial modifications using super-SILAC and weighted correlation network analysis

scientific article

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

scientific article

Inhibition of somatosensory mechanotransduction by annexin A6

scientific article published on 19 June 2018

Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis.

scientific article

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

scientific article published on 23 May 2016

Interrogating the human genome using uninterpreted mass spectrometry data ⬇️

scientific article published on May 1, 2001

Intestinal Epithelial Cells and the Microbiome Undergo Swift Reprogramming at the Inception of Colonic Citrobacter rodentium Infection

scientific article published on 02 April 2019

Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality.

scientific article published on 6 August 2019

Mapping multiprotein complexes by affinity purification and mass spectrometry

scientific article published on 16 July 2008

Matching peptide mass spectra to EST and genomic DNA databases ⬇️

scientific article published on October 1, 2001

Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome

scientific article (publication date: April 2006)

Molecular characterization of the Salmonella enterica serovar Typhi Vi-typing bacteriophage E1.

scientific article

Multiple short windows of calcium-dependent protein kinase 4 activity coordinate distinct cell cycle events during Plasmodium gametogenesis

scientific article

Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy

scientific article published on 23 July 2020

Myst2/Kat7 histone acetyltransferase interaction proteomics reveals tumour-suppressor Niam as a novel binding partner in embryonic stem cells

scientific article

Nbeal2 interacts with Dock7, Sec16a, and Vac14.

scientific article published on 29 November 2017

Neurotransmitters drive combinatorial multistate postsynaptic density networks.

scientific article published on 28 April 2009

Nuclear receptor binding protein 1 regulates intestinal progenitor cell homeostasis and tumour formation

scientific article

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

scientific article

Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner

scientific article published on 22 February 2019

Palmitoylation and palmitoyl-transferases in Plasmodium parasites

scientific article published on April 2015

Paxillin associates with poly(A)-binding protein 1 at the dense endoplasmic reticulum and the leading edge of migrating cells

scientific article

Phosphoinositide metabolism links cGMP-dependent protein kinase G to essential Ca²⁺ signals at key decision points in the life cycle of malaria parasites

scientific article (publication date: March 2014)

Phosphoproteomic Analysis of the Mouse Brain Cytosol Reveals a Predominance of Protein Phosphorylation in Regions of Intrinsic Sequence Disorder

scientific article

Precision Medicine in Pancreatic Disease-Knowledge Gaps and Research Opportunities: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases Workshop

scientific article published on 01 November 2019

Prmt5 is essential for early mouse development and acts in the cytoplasm to maintain ES cell pluripotency

scientific article published on December 2010

Proteomic analysis of NMDA receptor-adhesion protein signaling complexes

scientific article (publication date: July 2000)

Proteomic analysis of extracellular vesicles from a Plasmodium falciparum Kenyan clinical isolate defines a core parasite secretome.

scientific article published on 17 July 2017

Proteomic analysis of in vivo phosphorylated synaptic proteins.

scientific article published on 30 November 2004

Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores

scientific article published on 19 June 2009

Proteomic navigation using proximity-labeling

scientific article published on 04 April 2019

Proteomics characterization of abundant Golgi membrane proteins

scientific article (publication date: 16 February 2001)

Proteomics in postgenomic neuroscience: the end of the beginning.

scientific article published on May 2004

Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome

scientific article published on 4 August 2011

Quantitative proteomic analysis of Shigella flexneri and Shigella sonnei Generalized Modules for Membrane Antigens (GMMA) reveals highly pure preparations

scientific article published on 23 December 2015

Quantitative proteomics reveals the basis for the biochemical specificity of the cell-cycle machinery

scientific article published in August 2011

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

scientific article published on April 2017

Robust enrichment of phosphorylated species in complex mixtures by sequential protein and peptide metal-affinity chromatography and analysis by tandem mass spectrometry.

scientific article published on 23 August 2005

Scoring and Validation of Tandem MS Peptide Identification Methods

article published in 2009

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

scientific article

Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines

scientific article published on 14 April 2020

Structural basis for the modulation of MRP2 activity by phosphorylation and drugs

scientific article published in 2024

Study of Plasmodium falciparum DHHC palmitoyl transferases identifies a role for PfDHHC9 in gametocytogenesis

scientific article (publication date: November 2016)

Sub-minute Phosphoregulation of Cell Cycle Systems during Plasmodium Gamete Formation

scientific article published in November 2017

Sub-minute phosphoregulation of cell-cycle systems during Plasmodium gamete formation

SynGAP isoforms exert opposing effects on synaptic strength

scientific article

Targeted Feature Detection for Data-Dependent Shotgun Proteomics

scientific article

Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

scientific journal article

The BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC Differentiation

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

scientific article published on 26 October 2018

The OMSSAPercolator: an automated tool to validate OMSSA results.

scientific article

The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre

scientific article published on 09 October 2019

The midbody interactome reveals unexpected roles for PP1 phosphatases in cytokinesis

scientific article published on 04 October 2019

The three-dimensional structure and X-ray sequence reveal that trichomaglin is a novel S-like ribonuclease.

scientific article

Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice.

scientific article

UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs

scientific article published on 07 May 2018

Ubiquitylation of MLKL at lysine 219 positively regulates necroptosis-induced tissue injury and pathogen clearance

scientific article published on 07 June 2021

Widespread epigenomic, transcriptomic and proteomic differences between hip osteophytic and articular chondrocytes in osteoarthritis

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