A5067192427- vaccines and immunoinformatics approaches
- Chromatin Remodeling and Cancer
- Glioma Diagnosis and Treatment
- Monoclonal and Polyclonal Antibodies Research
- Computational Drug Discovery Methods
- Immunotherapy and Immune Responses
- Bioinformatics and Genomic Networks
- Bacterial Infections and Vaccines
- Cancer Genomics and Diagnostics
- Hepatitis B Virus Studies
- interferon and immune responses
- Antimicrobial Peptides and Activities
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Herpesvirus Infections and Treatments
- Gene expression and cancer classification
- Malaria Research and Control
- Viral Infections and Vectors
- Cytomegalovirus and herpesvirus research
- Cancer Mechanisms and Therapy
- T-cell and B-cell Immunology
- Mosquito-borne diseases and control
- Peripheral Neuropathies and Disorders
- Neuroblastoma Research and Treatments
St. Jude Children's Research Hospital
2020-2025
La Jolla Institute for Immunology
2017-2024
Saveetha University
2022
Institute of Microbial Technology
2013-2018
Council of Scientific and Industrial Research
2013-2016
Indian Agricultural Statistics Research Institute
2016
The Immune Epitope Database (IEDB, iedb.org) captures experimental data confined in figures, text and tables of the scientific literature, making it freely available easily searchable to public. scope IEDB extends across immune epitope related all species studied includes antibody, T cell, MHC binding contexts associated with infectious, allergic, autoimmune, transplant diseases. Having been publicly accessible for >10 years, recent focus has improved query reporting functionality meet needs...
Abstract Background The generation of interferon-gamma (IFN-γ) by MHC class II activated CD4 + T helper cells play a substantial contribution in the control infections such as caused Mycobacterium tuberculosis . In past, numerous methods have been developed for predicting binders that can activate T-helper cells. Best author’s knowledge, no method has so far predict type cytokine will be secreted these Class or epitopes. this study, an attempt made to IFN-γ inducing peptides. main dataset...
Abstract The Immune Epitope Database Analysis Resource (IEDB-AR, http://tools.iedb.org/) is a companion website to the IEDB that provides computational tools focused on prediction and analysis of B T cell epitopes. All are freely available through public many also REST API and/or downloadable command-line tool. A virtual machine image entire site for non-commercial use contains most site. Here, we describe functionalities in IEDB-AR, focusing 10 new have been added since last report 2012 NAR...
The secretion of Interleukin-4 (IL4) is the characteristic T-helper 2 responses. IL4 a cytokine produced by CD4+ T cells in response to helminthes and other extracellular parasites. It has critical role guiding antibody class switching, hematopoiesis inflammation, development appropriate effector T-cell In this study, it first time an attempt been made understand whether possible predict inducing peptides. data set used study comprises 904 experimentally validated 742 noninducing MHC II...
In the past, numerous methods have been developed to predict MHC class II binders or T-helper epitopes for designing epitope-based vaccines against pathogens. contrast, limited attempts made develop predicting epitopes/peptides that can induce a specific type of cytokine. This paper describes method, interleukin-10 (IL-10) inducing peptides, cytokine responsible suppressing immune system. All models were trained and tested on experimentally validated 394 IL-10 848 non-inducing peptides. It...
SATPdb (http://crdd.osdd.net/raghava/satpdb/) is a database of structurally annotated therapeutic peptides, curated from 22 public domain peptide databases/datasets including 9 our own. The current version holds 19192 unique experimentally validated sequences having length between 2 and 50 amino acids. It covers peptides natural, non-natural modified residues. These were systematically grouped into 10 categories based on their major function or property like 1099 anticancer, 10585...
Prediction of T cell immunogenicity is a topic considerable interest, both in terms basic understanding the mechanisms cells responses and practical applications. HLA binding affinity often used to predict epitopes, since key requisite for human immunogenicity. However, at population it complicated by high level variability molecules, potential other factors beyond as well frequent lack typing data. To overcome those issues, we explored an alternative approach identify common characteristics...
The conventional approach for designing vaccine against a particular disease involves stimulation of the immune system using whole pathogen responsible disease. In post-genomic era, major challenge is to identify antigenic regions or epitopes that can stimulate different arms system. past two decades, numerous methods and databases have been developed immunotherapy various pathogen-causing diseases. This review describes computational resources important subunit vaccines epitope-based...
Summary Epitopes identified in large‐scale screens of overlapping peptides often share significant levels sequence identity, complicating the analysis epitope‐related data. Clustering algorithms are used to facilitate these analyses, but available methods generally insufficient their capacity define biologically meaningful epitope clusters context immune response. To fulfil this need we developed an algorithm that generates based on representative or consensus sequences. This tool allows...
In this study, we investigated drug profile of 24 anticancer drugs tested against a large number cell lines in order to understand the relation between resistance and altered genomic features cancer line. We detected frequent mutations, high expression copy variations certain genes both resistant sensitive lines. It was observed that few drugs, like Panobinostat, are effective almost all types lines, whereas only limited type Tissue-specific preference also seen where is more belonging...
Members of the flavivirus genus share a high level sequence similarity and often circulate in same geographical regions. However, whether T cells induced by one viral species cross-react with other related flaviviruses has not been globally addressed. In this study, we tested pools epitopes derived from dengue (DENV), Zika (ZIKV), Japanese encephalitis (JEV), West Nile (WNV), yellow fever (YFV) viruses intracellular cytokine staining (ICS) using peripheral blood mononuclear (PBMCs)...
Report relevance of molecular groups to clinicopathologic features, germline
Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining the carotenoids is scattered throughout literature. Furthermore, about genes/proteins involved biosynthesis of has tremendously increased post-genomic era. A web server providing microbial a structured manner required will be valuable resource for scientific community working with carotenoids.Here, we created manually...
Abstract Background Identification of drug-like molecules is one the major challenges in field drug discovery. Existing approach like Lipinski rule 5 (Ro5), Operea have their own limitations. Thus, there a need to develop computational method that can predict drug-likeness molecule with precision. In addition, algorithm for screening chemical library properties. Results this study, we used 1347 approved and 3206 experimental drugs developing knowledge-based model predicting molecule. We...
Abstract Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes fever illness ranging from severe autoimmune to neurological complications humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR ( http://bioinfo.imtech.res.in/manojk/zikavr/ ), dedicated the ZIKV genomic, proteomic therapeutic...
CD4+ T cells have a major role in regulating immune responses. They are activated by recognition of peptides mostly generated from exogenous antigens through the histocompatibility complex (MHC) class II pathway. Identification epitopes is important and computational prediction used widely to save time resources. Although there algorithms predict binding affinity MHC molecules, no accurate methods exist which ligands as result natural antigen processing. We utilized dataset around 14,000...
Abstract Motivation Datasets that are derived from different studies (e.g. MHC ligand elution, binding, B/T cell epitope screening etc.) often vary in terms of experimental approaches, sizes peptides tested, including partial and or nested overlapping the number donors tested. Results We present a customized application Immune Epitope Database’s ImmunomeBrowser tool, which can be used to effectively aggregate visualize heterogeneous immunological data. User provided peptide sets associated...
Abstract Background FOXR2 activation is regarded as pathognomonic for CNS neuroblastoma (NB). However, a comprehensive understanding of the landscape tumors exhibiting lacking. Methods Histopathologic, molecular, imaging, and clinical data 42 with overexpression identified through screening institutional datasets published cases were analyzed. Results Among tumors, 21 (50.0%) high-grade gliomas (HGGs), 18 (42.9%) embryonal tumors. The HGGs included ten H3 K27M-mutant diffuse midline (DMGs)...
Abstract Medulloblastoma (MB) is one of the most malignant pediatric brain tumors. Molecularly, MB separates into four subgroups—WNT, SHH, Group 3 (G3), and 4 (G4)—each with unique clinical features genetic profiles. WNT tumors have best survival outcomes low metastatic potential, whereas G3 exhibit highest malignancy poorest outcomes. While SHH are highly distinct, G4 interrelated when grouped together, these referred to as G3/G4 These genetically complex, a constellation molecular...
Overexpression of EGFR is responsible for causing a number cancers, including lung cancer as it activates various downstream signaling pathways. Thus, important to control function in order treat the patients. It well established that inhibiting ATP binding within kinase domain regulates its function. The existing quinazoline derivative based drugs used treating inhibits wild type EGFR. In this study, we have made systematic attempt develop QSAR models designing derivatives could inhibit and...