Jyoti S. Choudhary
A5017408001- Advanced Proteomics Techniques and Applications
- DNA Repair Mechanisms
- Ubiquitin and proteasome pathways
- Protein Degradation and Inhibitors
- Endoplasmic Reticulum Stress and Disease
- Genomics and Phylogenetic Studies
- Peptidase Inhibition and Analysis
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- Genomics and Chromatin Dynamics
- Cancer Research and Treatments
- Mass Spectrometry Techniques and Applications
- Microtubule and mitosis dynamics
- RNA and protein synthesis mechanisms
- Monoclonal and Polyclonal Antibodies Research
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- RNA modifications and cancer
- Malaria Research and Control
- PARP inhibition in cancer therapy
- Melanoma and MAPK Pathways
- Cellular transport and secretion
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Cancer Genomics and Diagnostics
Institute of Cancer Research
2017-2025
Lovely Professional University
2023-2025
Institute of Cancer Research
2019-2025
University of Delhi
2022-2025
Maulana Azad Medical College
2025
Cancer Research UK
2021-2023
Armed Forces Medical College
2023
Wellcome Sanger Institute
2011-2022
Gandhi Medical College
2022
Gurukul Kangri Vishwavidyalaya
2022
The accurate identification and description of the genes in human mouse genomes is a fundamental requirement for high quality analysis data informing both genome biology clinical genomics. Over last 15 years, GENCODE consortium has been producing reference gene annotations to provide this foundational resource. includes experimental computational groups who work together improve extend annotation. Specifically, we generate primary data, create bioinformatics tools support expert manual...
Abstract The human and mouse genomes contain instructions that specify RNAs proteins govern the timing, magnitude, cellular context of their production. To better delineate these elements, phase III Encyclopedia DNA Elements (ENCODE) Project has expanded analysis cell tissue repertoires RNA transcription, chromatin structure modification, methylation, looping, occupancy by transcription factors RNA-binding proteins. Here we summarize efforts, which have produced 5,992 new experimental...
Abstract The GENCODE project annotates human and mouse genes transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology clinical genomics. annotation processes make use of primary bioinformatic tools analysis generated both within the consortium externally to support creation transcript structures determination their function. Here, we present improvements our infrastructure, bioinformatics tools, analysis, advances they in...
A small number of rare, recurrent genomic copy variants (CNVs) are known to substantially increase susceptibility schizophrenia. As a consequence the low fecundity in people with schizophrenia and other neurodevelopmental phenotypes which these CNVs contribute, large effects on risk likely be rapidly removed from population by natural selection. Accordingly, such must frequently occur as de novo mutations. In sample 662 proband-parent trios, we found that rare CNV mutations were...
Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal plant samples of different cell types, organism parts, developmental stages, diseases other conditions. It consists selected microarray RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality processed using standardised analysis methods. Since the last update, has grown seven-fold (1572 as August 2015),...
Characterization of the composition postsynaptic proteome (PSP) provides a framework for understanding overall organization and function synapse in normal pathological conditions. We have identified 698 proteins from terminal mouse CNS synapses using series purification strategies analysis by liquid chromatography tandem mass spectrometry large-scale immunoblotting. Some 620 were found purified densities (PSDs), nine AMPA-receptor immuno-purifications, 100 isolates an antibody against NMDA...
Sound scoring methods for sequence database search algorithms such as Mascot and Sequest are essential sensitive accurate peptide protein identifications from proteomic tandem mass spectrometry data. In this paper, we present a software package that interfaces with Percolator, well performing machine learning method rescoring results, demonstrate it to be amenable both low high accuracy data, outperforming all available schemes providing reliable significance measures. Percolator can readily...
The transcription factor Oct4 is key in embryonic stem cell identity and reprogramming. Insight into its partners should illuminate how the pluripotent state established regulated. Here, we identify a considerably expanded set of Oct4-binding proteins mouse cells. We find that associates with varied including regulators gene expression modulators function. Half are transcriptionally regulated by itself or other factors, whereas one-third display significant change upon differentiation....
GENCODE produces high quality gene and transcript annotation for the human mouse genomes. All is supported by experimental data serves as a reference genome biology clinical genomics. The consortium generates targeted data, develops bioinformatic tools carries out analyses that, along with externally produced methods, support identification of structures determination their function. Here, we present an update on genes, including developments in tools, major collaborations which underpin...
Prmt5 , an arginine methyltransferase, has multiple roles in germ cells, and possibly pluripotency. Here we show that loss of function is early embryonic-lethal due to the abrogation pluripotent cells blastocysts. also up-regulated cytoplasm during derivation embryonic stem (ES) together with Stat3, where they persist maintain association Mep50 methylates cytosolic histone H2A (H2AR3me2s) repress differentiation genes ES cells. Loss or results derepression genes, indicating significance...
Article19 May 2009Open Access Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins Esperanza Fernández Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Cambridge, UK Search for more papers by this author Mark O Collins Proteomic Mass Spectrometry, Rachel T Uren Maksym V Kopanitsa Noboru H Komiyama Mike D R Croning Lysimachos Zografos School Informatics, Edinburgh University, Edinburgh, J Douglas...
Lung cancer in East Asia is characterized by a high percentage of never-smokers, early onset and predominant EGFR mutations. To illuminate the molecular phenotype this demographically distinct disease, we performed deep comprehensive proteogenomic study on prospectively collected cohort Taiwan, representing stage, predominantly female, non-smoking lung adenocarcinoma. Integrated genomic, proteomic, phosphoproteomic analysis delineated attributes hallmarks tumor progression. Mutational...
Abstract Naïve CD4 + T cells coordinate the immune response by acquiring an effector phenotype in to cytokines. However, cytokine responses memory remain largely understudied. Here we use quantitative proteomics, bulk RNA-seq, and single-cell RNA-seq of over 40,000 human naïve show that cytokines differ substantially between these cell types. Memory are unable differentiate into Th2 phenotype, acquire a Th17-like iTreg polarization. Single-cell analyses constitute transcriptional continuum...
Chemical genetics and a global comparative analysis of phosphorylation phospholipids in vivo shows that PKG is the upstream regulator induces calcium signals enables Plasmodium to progress through its complex life cycle.
A family of apicomplexa-specific proteins containing AP2 DNA-binding domains (ApiAP2s) was identified in malaria parasites. This includes sequence-specific transcription factors that are key regulators development. However, functions for the majority ApiAP2 genes remain unknown. Here, a systematic knockout screen Plasmodium berghei ten were essential mosquito transmission: four critical formation infectious ookinetes, and three required sporogony. We describe non-essential AP2-O AP2-SP blood...
The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal developing a comprehensive map functional elements human genome. These included genes, biochemical regions associated gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) transcript isoforms. marks serve as sites for candidate cis-regulatory (cCREs) that may roles regulating expression1. project has been extended to model organisms, particularly mouse. In...
Abstract Poly (ADP-ribose) polymerase (PARP) inhibitors elicit antitumour activity in homologous recombination-defective cancers by trapping PARP1 a chromatin-bound state. How cells process trapped remains unclear. Using wild-type and trapping-deficient mutant combined with rapid immunoprecipitation mass spectrometry of endogenous proteins Apex2 proximity labelling, we delineated spectrometry-based interactomes non-trapped PARP1. These analyses identified an interaction between the...
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on single haploid reference genome. Here, we present the EN-TEx resource 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating catalog >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes less conserved...
Malaria transmission to mosquitoes requires a developmental switch in asexually dividing blood-stage parasites sexual reproduction. In Plasmodium berghei, the transcription factor AP2-G is required and sufficient for this switch, but how particular sex determined haploid parasite remains unknown. Using global screen of barcoded mutants, we here identify genes essential formation either male or female forms validate their importance transmission. High-resolution single-cell transcriptomics...
Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) functions as a critical stress sentinel that coordinates cell survival, inflammation, and immunogenic death (ICD). Although the catalytic function of RIPK1 is required to trigger death, its non-catalytic scaffold mediates strong pro-survival signaling. Accordingly, cancer cells can hijack block necroptosis evade immune detection. We generated small-molecule proteolysis-targeting chimera (PROTAC) selectively degraded human murine...