Chakit Arora

Scuola Normale Superiore di Pisa | Normale · Faculty of Sciences

Risk assessment in cutaneous melanoma (CM) patients is one of the major challenges in the effective treatment of CM patients. Traditionally, clinico-pathological features such as Breslow thickness, American Joint Committee on Cancer (AJCC) tumor staging, etc. are utilized for this purpose. However, due to advancements in technology, most of the upc...

Numerous cancer-specific prognostic models have been developed in the past, wherein one model is applicable for only one type of cancer. In this study, an attempt has been made to identify universal or multi-cancer prognostic biomarkers and develop models for predicting survival risk across different types of cancer patients. In order to accomplish...

Aberrant expressions of apoptotic genes have been associated with papillary thyroid carcinoma (PTC) in the past, however, their prognostic role and utility as biomarkers remains poorly understood. In this study, we analysed 505 PTC patients by employing Cox-PH regression techniques, prognostic index models and machine learning methods to elucidate...

In the last three decades, a wide range of protein features have been discovered to annotate a protein. Numerous attempts have been made to integrate these features in a software package/platform so that the user may compute a wide range of features from a single source. To complement the existing methods, we developed a method, Pfeature, for compu...

We explored the dysregulation of GPCR ligand signaling systems in cancer transcriptomics datasets. We derived a network of interacting ligands and biosynthetic enzymes from public databases, that we combined with cognate GPCRs and downstream effectors to quantify GPCR signaling pathways. We found multiple GPCRs differentially regulated together wit...

EXPANSION (https://expansion.bioinfolab.sns.it/) is an integrated web-server to explore the functional consequences of protein-coding alternative splice variants. We combined information from Differentially Expressed (DE) protein-coding transcripts from cancer genomics, together with domain architecture, protein interaction network, and gene enrich...

We explored the dysregulation of GPCR ligand signaling systems in cancer transcriptomics datasets to uncover new therapeutics opportunities in oncology. We derived an interaction network of receptors with ligands and their biosynthetic enzymes, which revealed that multiple GPCRs are differentially regulated together with their upstream partners acr...

Defensins are host defense peptides present in nearly all living species, which play a crucial role in innate immunity. These peptides provide protection to the host, either by killing microbes directly or indirectly by activating the immune system. In the era of antibiotic resistance, there is a need to develop a fast and accurate method for predi...

Introduction: Uterine corpus endometrial carcinoma (UCEC) causes thousands of deaths per year. To improve the overall survival of patients with UCEC, there is a need to identify prognostic biomarkers and potential drugs. Objectives: The aim of this study was twofold: the identification of prognostic gene signatures from expression profiles of patte...

In this study, we attempted to identify prognostic biomarkers for predicting survival risk of uterine corpus endometrial cancer (UCEC) patients from the gene expression profile of pattern recognition receptors (PRRs). A wide range of feature selection techniques have been tried, including network-based methods to identify a small number of genes fr...

Objectives: Aberrant expression of apoptotic genes has been associated with papillary thyroid carcinoma (PTC) in the past, however, their prognostic role and utility as biomarkers remains poorly understood. Materials and methods: In this study, we analysed 505 PTC patients by employing Cox-PH regression techniques, prognostic index models and mach...

AlgPred 2.0 is a web server developed for predicting allergenic proteins and allergenic regions in a protein. It is an updated version of AlgPred developed in 2006. The dataset used for training, testing and validation consists of 10 075 allergens and 10 075 non-allergens. In addition, 10 451 experimentally validated immunoglobulin E (IgE) epitopes...

AlgPred 2.0 is a web server developed for predicting allergenic proteins and allergenic regions in a protein. It is an updated version of AlgPred developed in 2006. The dataset used for training, testing and validation consists of 10 075 allergens and 10 075 non-allergens. In addition, 10 451 experimentally validated immunoglobulin E (IgE) epitopes...

A web-based resource CoronaVIR (https://webs.iiitd.edu.in/raghava/coronavir/) has been developed to maintain the predicted and existing information on coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We have integrated multiple modules, including ''Genomics,'' ''Diagnosis,'' ''Immunotherapy,'' and ''Drug Designing'' to unde...

PurposeIntra-tumor heterogeneity and high mortality among patients with non-small-cell lung carcinoma (NSCLC) emphasize the need to identify reliable prognostic markers unique to each subtype.Methods In this study, univariate cox regression and prognostic index (PI)-based approaches were used to develop models for predicting NSCLC patients’ subtype...

This is a python code for functional (Gene Ontology) enrichment and other types of enrichment (such as KEGG pathway, Pubmed, Interpro, Molecular function). All you have to do is use this script in google colab: https://github.com/chakitarora/compbio_utils/blob/master/GO_analysis.ipynb input= list of gene (protein) symbols output= a csv file

1 A web-based resource CoronaVIR (https://webs.iiitd.edu.in/raghava/coronavir/) has been 2 developed to maintain predicted and existing information on coronavirus SARS-CoV-2. We 3 have integrated multiple modules including "Genomics", "Diagnosis", "Immunotherapy" and 4 "Drug Designing" to understand the holistic view of this pandemic medical disast...

Human leukocyte antigen (HLA) are essential components of the immune system that stimulate immune cells to provide protection and defense against cancer. Thousands of HLA alleles have been reported in the literature, but only a specific set of HLA alleles are present in an individual. The capability of the immune system to recognize cancer-associat...

This study describes a method developed for predicting pattern recognition receptors (PRRs), which are an integral part of the immune system. The models developed here were trained and evaluated on the largest possible non-redundant PRRs, obtained from PRRDB 2.0, and non-pattern recognition receptors (Non-PRRs), obtained from Swiss-Prot. Firstly, a...

Human Leukocyte Antigen (HLA) is an essential component of the immune system which stimulates immune cells to provide protection and defense against cancer. More than thousands of HLA alleles have been reported in the literature; but, only a specific set of HLA alleles expressed in an individual. Recognition of cancer-associated mutations by the im...

This study describes a method developed for predicting pattern recognition receptors (PRRs), which are an integral part of the immune system. The models developed here were trained and evaluated on the largest possible non-redundant PRRs, and non-pattern recognition receptors (Non-PRRs) obtained from PRRDB 2.0. Firstly, a similarity-based approach...

One of the major challenges in managing the treatment of colorectal cancer (CRC) patients is to predict risk scores or level of risk for CRC patients. In past, several biomarkers, based on concentration of proteins involved in type-2/intrinsic/mitochondrial apoptotic pathway, have been identified for prognosis of colorectal cancer patients. Recentl...

One of the major challenges in managing the treatment of colorectal cancer (CRC) patients is to predict risk scores or level of risk for CRC patients. In past, several biomarkers, based on concentration of proteins involved in type-2/intrinsic/mitochondrial apoptotic pathway, have been identified for prognosis of colorectal cancer patients. Recentl...

Motivation In last three decades, a wide range of protein descriptors/features have been discovered to annotate a protein with high precision. A wide range of features have been integrated in numerous software packages (e.g., PROFEAT, PyBioMed, iFeature, protr, Rcpi, propy) to predict function of a protein. These features are not suitable to predic...

Cancer cells frequently evade immune attack possibly by utilizing slow stochastic signaling through the mitochondrial cell death pathway and thus keeping apoptotic activation immunologically silent. A key goal of this computational work is to find optimal strategy to induce apoptosis selectively in cancer cells in a rapid and deterministic manner u...

Cancer cells are stressed and “primed” for death yet inhibition of the intrinsic cell death pathway through over-expressed anti-apoptotic proteins is a mechanism for tumor progression and cancer chemoresistance generation. Slow kinetics of mitochondrial outer membrane permeabilization (MOMP), modulated by expression levels of affinity variant anti-...

Obesity, metabolic syndrome and premature ageing form a hugely researched and discussed area of interest these days. In the pathology of this cluster of conditions, adipose tissue is gaining attention as a major playground for interplay between metabolic stress, inflammation and accelerated ageing, and not merely being an energy storage tank. Drast...

Cells are equipped with a genetically programmed intrinsic death pathway for controlling variable cellular life spans in different tissues and for responding to cellular stress conditions. While the genes regulating the process are mostly known elucidating the biophysical mechanisms that underlie apoptotic phenotype generation remains a challenge....