The paper identifies synaptic gene networks specific to MDD in women by analyzing peripheral blood and brain transcriptomes, finding shared transcriptional signals across human and mouse models.

DOI 10.64898/2026.08.24.746654

humanmouse

BioinformaticsbioRxivPreprintMar 26, 2025

Systematic Comparative Analysis of Pathway Databases from a User-Perspective

Moushumi Goswami, Divya Dosemane, Sravanthi Davuluri…·Kshitish K. Acharya

The paper systematically compares pathway databases by querying them with genes, pathways, and conditions, finding that PathDIP and Reactome perform best depending on the query type.

DOI 10.1101/2025.03.26.645364

humanstatistical model

BioinformaticsbioRxivPreprintMar 26, 2024

Comparative Analysis of DNA Structural Parameters and the Corresponding Computational Tools to Differentiate Regulatory DNA Motifs and Promoters

Vasumathi Manivelan, Kavyashree Basavaraju, Bindu Sadanandan…·Kshitish K. Acharya

The paper evaluates DNA structural parameters and tools to differentiate regulatory DNA motifs and promoters, identifying effective combinations for various analyses.

1 citation

humanDNA methylation

Developmental BiologybioRxivPreprintSep 23, 2019

Listing candidate diagnostic markers and exploring the molecular basis of human spermatogenesis and a type of male infertility (Non-Obstructive Azoospermia), with transcriptomics via the next generation sequencing methods

Balagannavar Govindkumar, Kavyashree Basavaraju, Akhilesh Kumar Bajpai…·K Acharya Kshitish

The paper identifies 100+ genes associated with NOA and spermatogenesis through transcriptomics and shortlists 20 RNA molecules for diagnostic applications.

5 citations

humanbulk RNA-seq

BioinformaticsbioRxivPreprintMar 3, 2019

How helpful are the protein-protein interaction databases and which ones?

Akhilesh Kumar Bajpai, Sravanthi Davuluri, Kriti Tiwary…·Kshitish K. Acharya

The paper evaluates 375 PPI databases, compares 16 for human PPIs, and recommends STRING and hPRINT for comprehensive PPI coverage.

7 citations

humanprotein structure

Evolutionary BiologybioRxivPreprintJan 12, 2018

SYSTEMATIC ANALYSES OF AUTOSOMAL RECOMBINATION RATES FROM THE 1000 GENOMES PROJECT UNCOVERS THE GLOBAL RECOMBINATION LANDSCAPE IN HUMANS

Shivakumara Manu, Kshitish K Acharya, Saravanamuthu Thiyagarajan

The paper analyzes recombination rates across 20 human populations using 1000 Genomes Project data to uncover global recombination hotspots and coldspots.

DOI 10.1101/246702

humanGWAS summary statistics