Explanipedia

DeepTarget predicts anti-cancer mechanisms of action of small molecules by integrating drug and genetic screens Open

Sanju Sinha, Neelam Sinha, Marlenne Perales, Adi V Tarrab, Trinh Nguyen , et al. · 2025

Identifying the mechanisms of action (MOA) driving a drug's anti-cancer efficacy is critical for its clinical success, guiding the search for its best biomarkers, indications and combinations. Yet, systematically identifying MOAs remains c…

1113 TIME_ACT: pan-cancer prediction of tumor immune activation and response to immune checkpoint blockade from tumor transcriptomics and histopathology Open

Sumit Mukherjee, Sumeet Patiyal, Lipika R. Pal, Tiangen Chang, Sutapa Biswas Majee , et al. · 2025

A machine learning framework for supervised treatment response prediction from tumor transcriptomics: A large-scale pan-cancer study Open

Lipika R. Pal, E. Michael Gertz, Nishanth Ulhas Nair, Sumit Mukherjee, Sumeet Patiyal , et al. · 2025

Precision oncology aims to guide treatment decisions using biomarkers. While DNA-based panels are increasingly applied, RNA transcriptomics remain underused due to limited datasets and the absence of robust models. We assembled the largest…

Accelerating Cough-Based Algorithms for Pulmonary Tuberculosis Screening: Results From the CODA TB DREAM Challenge Open

Devan Jaganath, Solveig K. Sieberts, Mihaja Raberahona, Sophie Huddart, Larsson Omberg , et al. · 2025

Background Open-access data challenges can accelerate innovation in artificial intelligence–based tools. In the Cough Diagnostic Algorithm for Tuberculosis (CODA TB) DREAM Challenge, we developed and independently validated cough sound–bas…

Longitudinal liquid biopsy identifies an early predictive biomarker of immune checkpoint blockade response in head and neck squamous cell carcinoma Open

Binbin Wang, Robert Saddawi‐Konefka, Lauren Clubb, Shiqi Tang, Di Wu , et al. · 2025

Network-based approach identifies key genes associated with tumor heterogeneity in HPV positive and negative head and neck cancer patients Open

Sumeet Patiyal, Piyush Agrawal · 2025

Head and Neck Squamous Cell Carcinoma (HNSCC) is the seventh most prevalent cancer worldwide and is classified as human papillomavirus (HPV) positive or negative. Substantial heterogeneity has been observed in the two groups, posing a sign…

NfκBin: a machine learning based method for screening TNF-α induced NF-κB inhibitors Open

Shipra Jain, Ritu Tomer, Sumeet Patiyal, Gajendra P. S. Raghava · 2025

Introduction Nuclear Factor kappa B (NF-κB) is a transcription factor whose upregulation is associated in chronic inflammatory diseases, including rheumatoid arthritis, inflammatory bowel disease, and asthma. In order to develop therapeuti…

The synthetic lethal interaction between CDS1 and CDS2 is a vulnerability in uveal melanoma and across multiple tumor types Open

Pui Ying Chan, Diana Alexander, Ishan Mehta, Larissa Satiko Alcântara Sekimoto Matsuyama, Victoria Harle , et al. · 2025

Metastatic uveal melanoma is an aggressive disease with limited effective therapeutic options. To comprehensively map monogenic and digenic dependencies, we performed CRISPR–Cas9 screening in ten extensively profiled human uveal melanoma c…

Pan-cancer prediction of tumor immune activation and response to immune checkpoint blockade from tumor transcriptomics and histopathology Open

Sumit Mukherjee, Sumeet Patiyal, Lipika R. Pal, Tiangen Chang, Sutapa Biswas Majee , et al. · 2025

Accurately predicting which patients will respond to immune checkpoint blockade (ICB) remains a major challenge. Here, we present TIME_ACT, an unsupervised 66-gene transcriptomic signature of tumor immune activation derived from TCGA melan…

PEPlife2: A Updated Repository of the Half-life of Peptides Open

Urooj Alam, Kunal Chaudhary, Nishant Kumar, Ritu Tomer, Sumeet Patiyal , et al. · 2025

This manuscript presents an updated version of PEPlife, a manually curated database that provides comprehensive information on peptide half-life. The updated version, PEPlife2, includes 4,412 entries, compared to 2,229 entries in the previ…

MAP Format for Representing Chemical Modifications, Annotations, and Mutations in Protein Sequences: An Extension of the FASTA Format Open

Aditi Shendre, Naman Kumar Mehta, Anand Singh Rathore, Nishant Kumar, Sumeet Patiyal , et al. · 2025

Several formats, including FASTA, PIR, GenBank, EMBL, and GCG, have been developed for representing protein sequences composed of natural amino acids. Among these, FASTA remains the most widely used due to its simplicity and human readabil…

A systematic evaluation of the therapeutic potential of endogenous-ADAR editors in cancer prevention and treatment Open

Rona Merdler-Rabinowicz, Ariel Dadush, Sumeet Patiyal, Padma Sheila Rajagopal, Gulzar N. Daya , et al. · 2025

Adenosine deaminases acting on RNA (ADAR) enzymes constitute a natural cellular mechanism that induces A-to-I(G) editing, introducing genetic changes at the RNA level. Recently, interest in the endogenous-ADAR editor has emerged for correc…

NfκBin: A Machine Learning based Method for Screening Nf-κB Inhibitors Open

Shipra Jain, Ritu Tomer, Sumeet Patiyal, Gajendra P. S. Raghava · 2025

Nuclear Factor kappa B (NF-κB) is a transcription factor whose upregulation is associated in chronic inflammatory diseases, including rheumatoid arthritis, inflammatory bowel disease, and asthma. In order to develop therapeutic strategies …

A hybrid method for discovering interferon-gamma inducing peptides in human and mouse Open

Anjali Dhall, Sumeet Patiyal, Gajendra P. S. Raghava · 2024

A hybrid approach for predicting transcription factors Open

Sumeet Patiyal, Palak Tiwari, Mohit Ghai, Aman Dhapola, Anjali Dhall , et al. · 2024

Transcription factors are essential DNA-binding proteins that regulate the transcription rate of several genes and control the expression of genes inside a cell. The prediction of transcription factors with high precision is important for …

A deep learning method for classification of HNSCC and HPV patients using single-cell transcriptomics Open

Akanksha Jarwal, Anjali Dhall, Akanksha Arora, Sumeet Patiyal, Aman Srivastava , et al. · 2024

Background Head and Neck Squamous Cell Carcinoma (HNSCC) is the seventh most highly prevalent cancer type worldwide. Early detection of HNSCC is one of the important challenges in managing the treatment of the cancer patients. Existing tec…

MRSLpred—a hybrid approach for predicting multi-label subcellular localization of mRNA at the genome scale Open

Shubham Choudhury, Nisha Bajiya, Sumeet Patiyal, Gajendra P. S. Raghava · 2024

In the past, several methods have been developed for predicting the single-label subcellular localization of messenger RNA (mRNA). However, only limited methods are designed to predict the multi-label subcellular localization of mRNA. Furt…

HLA-DR4Pred2: An improved method for predicting HLA- DRB1*04:01 binders Open

Sumeet Patiyal, Anjali Dhall, Nishant Kumar, Gajendra P. S. Raghava · 2024

Background HLA-DRB1*04:01 is associated with many diseases including sclerosis, arthritis, diabetes, and Covid19. Thus, it is important to scan binders of HLA-DRB1*04:01 in an antigen to develop immunotherapy, vaccines, and protection agai…

Multi‐perspectives and challenges in identifying B‐cell epitopes Open

Nishant Kumar, Nisha Bajiya, Sumeet Patiyal, Gajendra P. S. Raghava · 2023

The identification of B‐cell epitopes (BCEs) in antigens is a crucial step in developing recombinant vaccines or immunotherapies for various diseases. Over the past four decades, numerous in silico methods have been developed for predictin…

A Deep Learning method for classification of HNSCC and HPV patients using single-cell transcriptomics Open

Akanksha Jarwal, Anjali Dhall, Akanksha Arora, Sumeet Patiyal, Aman Srivastava , et al. · 2023

Head and Neck Squamous Cell Carcinoma (HNSCC) is the seventh most highly prevalent cancer type worldwide. Early detection of HNSCC is one of the important challenges in managing the treatment of the cancer patients. Existing techniques for…

HLA-DR4Pred2: an improved method for predicting HLA-DRB1*04:01 binders Open

Sumeet Patiyal, Anjali Dhall, Nishant Kumar, Gajendra P. S. Raghava · 2023

HLA-DRB1*04:01 is associated with many disease that include sclerosis, arthritis, diabetes and Covid19. Thus, it is important to scan binders of HLA-DRB1*04:01 in an antigen to develop immunotherapy, vaccine and protection against these di…

Prediction of Alzheimer’s Disease from Single Cell Transcriptomics Using Deep Learning Open

Aman Srivastava, Anjali Dhall, Sumeet Patiyal, Akanksha Arora, Akanksha Jarwal , et al. · 2023

Alzheimer’s disease (AD) is a progressive neurological disorder characterized by brain cell death, brain atrophy, and cognitive decline. Early diagnosis of AD remains a significant challenge in effectively managing this debilitating diseas…

An ensemble method for prediction of phage-based therapy against bacterial infections Open

Suchet Aggarwal, Anjali Dhall, Sumeet Patiyal, Shubham Choudhury, Akanksha Arora , et al. · 2023

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 appropri…

A hybrid method for discovering interferon-gamma inducing peptides in human and mouse Open

Anjali Dhall, Sumeet Patiyal, Gajendra P. S. Raghava · 2023

A host-specific technique has been developed for annotating interferon-gamma (IFN-γ) inducing peptides, it is an updated version of IFNepitope. In this study, dataset used for developing prediction method contain experimentally validated 2…

Hmrbase2: A comprehensive database of hormones and their receptors Open

Dashleen Kaur, Akanksha Arora, Sumeet Patiyal, Gajendra P. S. Raghava · 2023

Background and objective Hormones are essential for cell communication and hence regulate various physiological processes. The discrepancies in the hormones or their receptors can break this communication and cause major endocrinological d…

A random forest model for predicting exosomal proteins using evolutionary information and motifs Open

Akanksha Arora, Sumeet Patiyal, Neelam Sharma, Leimarembi Devi Naorem, Dashleen Kaur , et al. · 2023

Identification of secretory proteins in body fluids is one of the key challenges in the development of non-invasive diagnostics. It has been shown in the part that a significant number of proteins are secreted by cells via exosomes called …

A method for predicting linear and conformational B-cell epitopes in an antigen from its primary sequence Open

Nishant Kumar, Sadhana Tripathi, Neelam Sharma, Sumeet Patiyal, Leimarembi Devi Naorem , et al. · 2023

B-cell is an essential component of the immune system that plays a vital role in providing the immune response against any pathogenic infection by producing antibodies. Existing methods either predict linear or conformational B-cell epitop…

A hybrid approach for predicting multi-label subcellular localization of mRNA at genome scale Open

Shubham Choudhury, Nisha Bajiya, Sumeet Patiyal, Gajendra P. S. Raghava · 2023

In the past, number of methods have been developed for predicting single label subcellular localization of mRNA in a cell. Only limited methods had been built to predict multi-label subcellular localization of mRNA. Most of the existing me…

Prediction of celiac disease associated epitopes and motifs in a protein Open

Ritu Tomer, Sumeet Patiyal, Anjali Dhall, Gajendra P. S. Raghava · 2023

Introduction Celiac disease (CD) is an autoimmune gastrointestinal disorder causes immune-mediated enteropathy against gluten. Gluten immunogenic peptides have the potential to trigger immune responses which leads to damage the small intes…

SalivaDB—a comprehensive database for salivary biomarkers in humans Open

Akanksha Arora, Dashleen Kaur, Sumeet Patiyal, Dilraj Kaur, Ritu Tomer , et al. · 2023

Saliva as a non-invasive diagnostic fluid has immense potential as a tool for early diagnosis and prognosis of patients. The information about salivary biomarkers is broadly scattered across various resources and research papers. It is imp…

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