Ishaan Gupta

K-MARVEL is a computational tool that accurately identifies antimicrobial resistance genes and mutations from short and long-read sequencing data, outperforming existing methods in speed and accuracy.

The paper catalogs mobile element insertions in 82 Indian populations, revealing population-specific variants not present in European databases and highlighting their potential impact on disease associations.

NANOTAXI provides a user-friendly Shiny-based GUI for real-time classification and analysis of 16S rRNA nanopore reads, supporting multiple classifiers and databases.

The paper investigates alternative splicing of microexons in human peripheral tissues using transcriptomic data, finding that microexon dysregulation may reflect a broader splicing homeostasis collapse rather than a primary disease driver.

The paper identifies 354,937 novel lncRNAs across 13 cancer types using single-cell and spatial transcriptomics, revealing their cell-type specificity, spatial distribution, and potential functional roles.

The paper presents a comprehensive genomic atlas of Indian populations, identifying novel variants and highlighting genetic diversity and pharmacogenomic implications.

The paper identifies 13 lncRNA regions involved in zebrafish caudal fin regeneration and positional memory using RNA-seq and computational methods, showing their differential expression across time and position.

This study identifies underrepresentation of ESKAPE pathogens from developing regions in 16S rRNA sequencing due to primer bias.

This paper introduces an automated eight-stage classifier for Drosophila melanogaster using transfer-learning CNNs, achieving 85% accuracy and deploying it for mobile live-inference.

SpliceCoord identifies coordinated exon splicing events from long-read transcriptome data using a count matrix and GTF file.

The paper analyzes RNA methylation and alternative splicing in Plasmodium falciparum and P. vivax clinical isolates using Nanopore sequencing to reveal transcriptome diversity and regulatory mechanisms.

This study shows that host evolution against coinfections is influenced by the growth and virulence dynamics of individual pathogens, with fast-acting pathogens hindering adaptive success.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

This study uses deep learning models to classify Drosophila melanogaster gender with high accuracy and integrates the models into a mobile app for real-time analysis.

The paper introduces MIST, a cost-effective spatial transcriptomics method combining tissue microarrays with Visium, and presents AnnotateMap for analyzing multiple ROIs.

The paper presents a long-read RNA sequencing atlas across mammals, revealing conserved transcript complexity and m6A modifications, and their evolutionary roles.

The paper identifies 689 novel lncRNAs in zebrafish brain regeneration after traumatic injury and links them to specific biological pathways involved in wound healing and cell adhesion.

This study identifies PfAP2-MRP as a master regulator controlling parasite growth, chromatin structure, and var gene expression during malaria parasite blood stages.

The paper uses long-read sequencing to identify novel Ori-proximal transcripts in herpesviruses, revealing regulatory complexity in DNA replication and transcription.

The paper identifies spurious off-target signals from lncRNAs in 10X Visium FFPE spatial transcriptomics data and recommends excluding affected genes.

This study identifies two distinct molecular signatures in postmortem lung tissue from severe COVID-19 patients, associated with different pathological mechanisms and microbiome profiles.

This study identifies intronless genes differentially expressed across eight cancers, highlighting their role in epigenetic regulation and interactome rewiring in specific tumor types.

The paper computes polygenic risk scores for COVID-19 severity in Indian sub-populations using GWAS summary statistics and finds a positive correlation between genetic risk scores and mortality.

This study identifies Rpb4 and Puf3 as regulators of mRNA stability and imprinting in yeast through genome-wide analysis and functional interactions.

The paper identifies 129 differentially expressed genes in the PFC of alcoholics and links them to pathways and modules associated with alcohol dependence and consumption.

The paper introduces ScISOr-Seq, a method combining single-cell full-length cDNA amplification with short-read and long-read sequencing to identify isoforms in cerebellar cell types across thousands of cells.

This study identifies splicing variations in aging brains linked to Alzheimer’s Disease, finds genetic regulation of splicing, and highlights shared pathways with other neurodegenerative diseases.