Gajendra Pal Singh Raghava

Gajendra Pal Singh Raghava
Indraprastha Institute of Information Technology | IIITD · Department of Computational Biology

M.Tech, PhD
Development of Computational Resources in the field of Biomedicine

About

543
Publications
532,940
Reads
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19,389
Citations
Introduction
Prof Raghava is a Head, Department of Computational Biology, IIIT Delhi, India. For more information see web sites http://www.iiitd.edu.in/raghava/ and alternate web site http://raghavagps.github.io/
Additional affiliations
February 2017 - present
Indraprastha Institute of Information Technology
Position
  • Professor (Full)
Description
  • Working as professor at Department of Computational Biology, IIIT Delhi
April 2007 - present
Institute of Microbial Technology
Position
  • Project Investigator (PI, OSDD)
Description
  • Develop and maintain computational resources for drug discovery an insilco module of OSDD
March 2006 - September 2006
University of Arkansas for Medical Sciences
Position
  • Bioinformatics Specialist
Education
July 1992 - July 1996
Panjab University
Field of study
July 1984 - January 1986
July 1982 - June 1984
Chaudhary Charan Singh University
Field of study
  • Physics (Sp Electronics)

Publications

Publications (543)
Preprint
This paper describes a method Pprint2, which is an improved version of Pprint developed for predicting RNA-interacting residues in a protein. Training and validation datasets used in this study comprises of 545 and 161 non-redundant RNA-binding proteins, respectively. All models were trained on training dataset and evaluated on the validation datas...
Preprint
Phage therapy is a viable alternative to antibiotics for treating microbial infections, particularly managing drug-resistant strains of bacteria. One of the major challenges in designing phage based therapy is to identify the most appropriate phage to treat a bacterial infection. In this study, an attempt has been made to predict phage-host interac...
Article
Identification of somatic mutations with high precision is one of the major challenges in the prediction of high-risk liver-cancer patients. In the past, number of mutations calling techniques have been developed that include MuTect2, MuSE, Varscan2, and SomaticSniper. In this study, an attempt has been made to benchmark the potential of these tech...
Article
Proteins/peptides have shown to be promising therapeutic agents for a variety of diseases. However, toxicity is one of the obstacles in protein/peptide-based therapy. The current study describes a web-based tool, ToxinPred2, developed for predicting the toxicity of proteins. This is an update of ToxinPred developed mainly for predicting toxicity of...
Article
Human leukocyte antigens (HLA) regulate various innate and adaptive immune responses and play a crucial immunomodulatory role. Recent studies revealed that non-classical HLA-(HLA-E & HLA-G) based immunotherapies have many advantages over traditional HLA-based immunotherapy, particularly against cancer and COVID-19 infection. In the last two decades...
Article
Full-text available
Healthcare is the most important component in the life of all human beings as each individual wish to have happy, healthy, and wealthy life‐span. Most of the branches of science are dedicated to improve the healthcare. In the era of knowledge mining, informatics is playing a crucial role in different branches of research. Thus, a wide range of info...
Preprint
Influenza A is a contagious viral disease responsible for four pandemics in the past and a major public health concern. Being zoonotic in nature, the virus can cross the species barrier and transmit from wild aquatic bird reservoirs to humans via intermediate hosts. Virus gradually undergoes host adaptive mutations in their genome and proteins, res...
Article
Full-text available
Background Interleukin 13 (IL-13) is an immunoregulatory cytokine, primarily released by activated T-helper 2 cells. IL-13 induces the pathogenesis of many allergic diseases, such as airway hyperresponsiveness, glycoprotein hypersecretion, and goblet cell hyperplasia. In addition, IL-13 inhibits tumor immunosurveillance, leading to carcinogenesis....
Chapter
Full-text available
Immunotherapy is a rapidly growing therapy for cancer which have numerous benefits over conventional treatments like surgery, chemotherapy, and radiation. Overall survival of cancer patients has improved significantly due to the use of immunotherapy. It acts as a novel pillar for treating different malignancies from their primary to the metastatic...
Chapter
In the past few decades, a large number of cell-penetrating peptides (CPPs) have been discovered. These CPPs have a wide range of applications including drug delivery vehicles. Numerous in silico tools have been developed over the years to design and predict the cell-penetrating peptides that contain natural amino acids. The majority of natural cel...
Preprint
Full-text available
Purpose Identification of somatic mutations with high precision is one of the major challenges in prediction of high-risk liver-cancer patients. In the past number of mutation calling techniques have been developed that include MuTect2, MuSE, Varscan2, and SomaticSniper. In this study an attempt has been made to benchmark potential of these techniq...
Preprint
Full-text available
In the past few decades, public repositories on nucleotides have increased with exponential rates. This pose a major challenge to researchers to predict the structure and function of nucleotide sequences. In order to annotate function of nucleotide sequences it is important to compute features/attributes for predicting function of these sequences u...
Preprint
In the last two decades, ample of methods have been developed to predict the classical HLA binders in an antigen. In contrast, limited attempts have been made to develop methods for predicting binders for non-classical HLA; due to the scarcity of sufficient experimental data and lack of community interest. Of Note, non-classical HLA plays a crucial...
Article
Full-text available
Prostate cancer (PCa) is the second lethal malignancy in men worldwide. In the past, numerous research groups investigated the omics profiles of patients and scrutinized biomarkers for the diagnosis and prognosis of PCa. However, information related to the biomarkers is widely scattered across numerous resources in complex textual format, which pos...
Article
Full-text available
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...
Article
Full-text available
The blood–brain barrier poses major hurdles in the treatment of brain-related ailments. Over the past decade, interest in peptides-based therapeutics has thrived a lot because of their higher benefit to risk ratio. However, a complete knowledgebase providing a well-annotated picture of the peptide as a therapeutic molecule to cure brain-related ail...
Article
Full-text available
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...
Article
Full-text available
Background: Postoperative tumor recurrence is one of the major concerns associated with the poor prognosis of hepatocellular carcinoma (HCC) patients. There is yet to elucidate a standard surveillance system for HCC recurrence risk owing to complexity of this malignancy. Generation of multi-omics data from patients facilitate the identification of...
Article
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...
Preprint
Full-text available
Interleukin 13 (IL-13) is an immunoregulatory cytokine that is primarily released by activated T-helper 2 cells. It induces the pathogenesis of many allergic diseases, such as airway hyperresponsiveness, glycoprotein hypersecretion and goblet cell hyperplasia. IL-13 also inhibits tumor immunosurveillance, which leads to carcinogenesis. In recent st...
Preprint
Triple-negative breast cancer (TNBC) is more prone to metastasis and recurrence than other breast cancer subtypes. This study aimed to identify genes that can act as diagnostic biomarkers for predicting lymph node metastasis in TNBC patients. The transcriptomic data of TNBC with or without lymph node metastasis was acquired from TCGA, and the diffe...
Article
Background Allergy is the abrupt reaction of the immune system that may occur after the exposure to allergens such as proteins, peptides, or chemicals. In the past, various methods have been generated for predicting allergenicity of proteins and peptides. In contrast, there is no method that can predict allergenic potential of chemicals. In this pa...
Article
Full-text available
The blood–brain barrier is a major obstacle in treating brain-related disorders, as it does not allow the delivery of drugs into the brain. We developed a method for predicting blood–brain barrier penetrating peptides to facilitate drug delivery into the brain. These blood–brain barrier penetrating peptides (B3PPs) can act as therapeutics, as well...
Preprint
DNA-protein interaction is one of the most crucial interactions in the biological system, which decide the fate of many processes such as transcription, regulation of gene expression, splicing, and many more. Though many computational approaches exist that can predict the DNA interacting residues from the protein sequences, there is still a signifi...
Article
Background Proinflammatory cytokines are correlated with the severity of disease in patients with COVID-19. IL6-mediated activation of STAT3 proliferates proinflammatory responses that lead to cytokine storm promotion. Thus, STAT3 inhibitors may play a crucial role in managing the COVID-19 pathogenesis. The present study discusses a method for pred...
Preprint
Full-text available
Number of beta-lactamase variants have ability to deactivate ceftazidime antibiotic, which is the most commonly used antibiotic for treating infection by Gram-negative bacteria. In this study an attempt has been made to develop a method that can predict ceftazidime resistant strains of bacteria from amino acid sequence of beta-lactamases. We obtain...
Preprint
Full-text available
Interleukin-2 (IL-2) based immunotherapy has been already approved to treat certain type of cancers as it plays vital role in immune system. Thus it is important to discover new peptides or epitopes that can induce IL-2 with high efficiency. We analyzed experimentally validated IL-2 inducing and non-inducing peptides and observed differ in average...
Preprint
Full-text available
Blood-brain-barrier is a major obstacle in treating brain-related disorders as it does not allow to deliver drugs in the brain. In order to facilitate delivery of drugs in brain, we developed a method for predicting blood-brain-barrier penetrating peptides. These blood-brain barriers penetrating peptides (B3PPs) can act as therapeutic as well as dr...
Preprint
Full-text available
Background: Prostate Cancer is the second lethal malignancy in men worldwide. In the past, numerous research groups investigated the omics profiles of patients and scrutinized biomarkers for the diagnosis and prognosis of prostate cancer. However, information related to the biomarkers is widely scattered across numerous resources in complex textual...
Preprint
Full-text available
In literature, several mRNA, miRNA, lncRNA based biomarkers are identified by genomic analysis to stratify the patients into high and low risk groups of pancreatic adenocarcinoma (PAAD). The identified biomarkers are of limited use in terms of sensitivity and prediction ability. Thus, we aimed to identify the prognostic alternative splicing events...
Preprint
Allergy is the abrupt reaction of the immune system that may occur after the exposure with allergens like protein/peptide or chemical allergens. In past number of methods of have been developed for classifying the protein/peptide based allergen. To the best of our knowledge, there is no method to classify the allergenicity of chemical compound. Her...
Preprint
Full-text available
It has been shown in the past that levels of cytokines, including interleukin 6 (IL6), is highly correlated with the disease severity of COVID-19 patients. IL6 mediated activation of STAT3 is responsible to proliferate proinflammatory responses that leads to promotion of cytokine storm. Thus, STAT3 inhibitors may play a crucial role in managing pat...
Article
Full-text available
Cancer is one of the most prevailing, deadly and challenging diseases worldwide. The advancement in technology led to the generation of different types of omics data at each genome level that may potentially improve the current status of cancer patients. These data have tremendous applications in managing cancer effectively with improved outcome in...
Article
Full-text available
Globally fermented foods are in demands due to their functional and nutritional benefits. These foods are sources of probiotic organisms and bioactive peptides, various amino acids, enzymes etc. that provides numerous health benefits. FermFooDb (https://webs.iiitd.edu.in/raghava/fermfoodb/) is a manually curated database of bioactive peptides deriv...
Article
Nanostructures generated by self-assembly of peptides yield nanomaterials that have many therapeutic applications, including drug delivery and biomedical engineering, due to their low cytotoxicity and higher uptake by targeted cells owing to their high affinity and specificity towards cell surface receptors. Despite the promising implications of th...
Article
This article reviews more than 50 computational resources developed in past two decades for forecasting of antibiotic resistance (AR)-associated mutations, genes and genomes. More than 30 databases have been developed for AR-associated information, but only a fraction of them are updated regularly. A large number of methods have been developed to f...
Preprint
Full-text available
Prostate-specific antigen (PSA) is a key biomarker, which is commonly used to screen patients of prostate cancer. There is a significant number of unnecessary biopsies that are performed every year, due to poor accuracy of PSA based biomarker. In this study, we identified alternate biomarkers based on gene expression that can be used to screen pros...
Preprint
Full-text available
Postoperative tumor recurrence is one of the major concerns associated with the poor prognosis of HCC patients. There is yet to elucidate a standard surveillance system for HCC recurrence risk owing to complexity of this malignancy. Generation of multi-omics data from patients facilitate the identification of robust signatures for various diseases....
Article
Globally, ~20% of cancer malignancies are associated with virus infections. Lung cancer is the most prevalent cancer and has a 10% 5-year survival rate when diagnosed at stage IV. Cancer vaccines and oncolytic immunotherapy are promising treatment strategies for better clinical outcomes in advanced-stage cancer patients. Here, we used a reverse vac...
Article
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...
Article
Full-text available
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...
Article
Full-text available
Interleukin 6 (IL-6) is a pro-inf lammatory cytokine that stimulates acute phase responses, hematopoiesis and specific immune reactions. Recently, it was found that the IL-6 plays a vital role in the progression of COVID-19, which is responsible for the high mortality rate. In order to facilitate the scientific community to fight against COVID-19,...
Research
Full-text available
Many vaccines are under clinical trials to fight against pandemic COVID-19. Here, we briefly reviewed vaccines under trial and their limitations, with a possible alternate solution to overcome these limitations. In most cases, vaccine targets are all viral proteins or a specific protein, mainly spike protein. As shown in previous studies on coronav...
Article
Full-text available
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...
Article
Increasing use of therapeutic peptides for treating cancer has received considerable attention of the scientific community in the recent years. The present study describes the in silico model developed for predicting and designing anticancer peptides (ACPs). ACPs residue composition analysis show the preference of A, F, K, L and W. Positional prefe...
Article
Full-text available
Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods to infer protein levels from other omics measurements, we leveraged crowdsourcing via the NCI-CPTAC DREAM proteo...
Article
Dengue virus (DENV) researchers often face challenges with the highly time-consuming process of collecting and curating information on known inhibitors during the standard drug discovery process. To this end, however, required collective information is not yet available on a single platform. Hence, we have developed the DenvInD database for experim...
Article
Dengue virus (DENV) researchers often face challenges with the highly time-consuming process of collecting and curating information on known inhibitors during the standard drug discovery process. To this end, however, required collective information is not yet available on a single platform. Hence, we have developed the DenvInD database for experim...
Preprint
Full-text available
Identification of pregnancies at risk of preterm birth (PTB), the leading cause of newborn deaths, remains challenging given the syndromic nature of the disease. We report a longitudinal multi-omics study coupled with a DREAM challenge to develop predictive models of PTB. We found that whole blood gene expression predicts ultrasound-based gestation...
Article
One of the emerging technologies to fight against cancer is oncolytic virus-based immunotherapy. Recently, the FDA approved an oncolytic virus T-vec for the treatment of melanoma. To facilitate the scientific community, we build a manually-curated repository of oncolytic viruses called OvirusTdb (https://webs.iiitd.edu.in/raghava/ovirustdb/). The r...
Article
CancerEnD is an integrated resource developed for annotating 8524 unique expressed enhancers, associated genes, somatic mutations and copy number variations of 8063 cancer samples from 18 cancer types of TCGA. Somatic mutation data was taken from the COSMIC repository. To delineate the relationship of change in copy number of enhancer elements with...
Article
Full-text available
Introduction Recently, the rise in the incidences of thyroid cancer worldwide renders it to be the sixth most common cancer among women. Commonly, Fine Needle Aspiration biopsy predominantly facilitates the diagnosis of the nature of thyroid nodules. However, it is inconsiderable in determining the tumor’s state, i.e., benign or malignant. This stu...
Preprint
Full-text available
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...
Article
Wild-type and genetically engineered oncolytic viruses (OVs) represent powerful therapeutic agents in cancer immunotherapy. Several OV species are in clinical trials for cancer treatment. Preclinical and clinical trials revealed several issues related to OV therapy in terms of viral delivery, spread, antiviral immune response, and tumor resistance....
Article
Full-text available
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...
Preprint
Full-text available
Increasing use of therapeutic peptides for treating cancer has received considerable attention of the scientific community in the recent years. The present study describes the in silico model developed for predicting and designing anticancer peptides (ACPs). ACPs residue composition analysis revealed the preference of A, F, K, L and W. Positional p...
Article
Full-text available
In the present study, a systematic effort has been made to predict the hemolytic potency of chemically modified peptides. All models have been trained, tested, and evaluated on a dataset that contains 583 modified hemolytic peptides and a balanced number of non-hemolytic peptides. Machine learning techniques have been used to build the classificati...
Article
Full-text available
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...
Article
Full-text available
Motivation: S-adenosyl-L-methionine (SAM) is an essential cofactor present in the biological system and plays a key role in many diseases. There is a need to develop a method for predicting SAM binding sites in a protein for designing drugs against SAM associated disease. To the best of our knowledge, there is no method that can predict the bindin...
Preprint
Full-text available
IndiaBioDb (https://webs.iiitd.edu.in/raghava/indiabiodb/) is a manually curated comprehensive repository of bioinformatics resources developed and maintained by Indian researchers. This repository maintains information about more than 550 freely accessible functional resources that include around 263 biological databases. Each entry provides a com...