https://project.iith.ac.in/sharmaglab/gscholarlens/
Manuscript Link: Authorship-contribution normalized Sh-index and citations are better research output indicators. Preprint at arXiV, 2025
To address several challenges in equitable academic evaluation, we have created GScholarLENS, a freely available browser extension designed to simplify bibliometric analyses. GScholarLENS seamlessly integrates with Google Scholar, enabling researchers to evaluate both primary and subsidiary contributions in publications. Along with providing contribution-specific publication count and citation details for each author profile, the tool introduces a contribution-normalized variant of the h-index, termed the Scholar h-index (Sh-index, Sharma-index), which adjusts citation counts based on authorship roles, assigning proportional weights (e.g., 100% for corresponding authors, 90% for first authors, 50% for second authors, and 10-25% for coauthors based on total number of authors per publication). By computing these normalized metrics, GScholarLENS provides a transparent representation of scholarly contributions, addressing issues in allocating academic credit. The tool also offers h-indices disaggregated by authorship categories and enables systematic analyses of researchers' cumulative impact, fostering discussions around equity and inclusivity in academic recognition.
The extension is still in development, and we will keep adding new features and bug fixes in the upcoming versions. Please try it out in Chrome or Mozilla and give us feedback about its features, usage, bugs, and suggestions. Please don't hesitate to share it with your national and international colleagues for their valuable input. The extension is available for Chrome and Firefox and can be easily downloaded via these links:
Google Chrome Extension link: https://chromewebstore.google.com/detail/gscholarlens/gkdjmplmnhobhaoobcgklnfkoclpebbn
Mozilla Extension link: https://addons.mozilla.org/en-US/firefox/addon/gscholarlens/
https://project.iith.ac.in/sharmaglab/rrnadatabase
Preprint at bioRXiv (Under revision in mSystems). 2025
16S-23S-5S rRNA database is an online database repository of all 16S, 23S, and 5S ribosomal RNA sequences from a curated dataset of ~5000 genomes. All available reference genomes of archeal and bacterial species from NCBI are included in this database.
Complete/chromosome level assemblies from NCBI
Representative genomes from NCBI
~5,000 genomes from 51 diverse phyla
>60,000 rRNA sequences information
Detailed user-friendly information for all 16S, 23S, and 5S rRNAs
Circos plot available for all genomes
Embedded NCBI sequence viewer for each replicon
Identity matrix and sequence alignment for all rRNAs per organism
Predicted secondary structure for each rRNA sequence
https://project.iith.ac.in/sharmaglab/alphafoldextractor/
Manuscript Link: AlphaFold Database Structure Extractor: A web server and API to download AlphaFold structures using common protein accessions. BMC Bioinformatics (Accepted). 2025.
The AlphaFoldDB Structure Extractor is an open-access web server and API toolkit designed to facilitate the bulk download of predicted protein structures from the AlphaFold Database using well-known accession numbers. Addressing the current limitations in extracting structures beyond a restricted list of model organisms and a threshold number, this tool accepts diverse input identifiers, such as NCBI Taxonomy ID, RefSeq accessions, locus tags, and UniProt or AlphaFold accessions and maps them to UniProt and AlphaFold IDs for structure retrieval. Users can download structure files in PDB, mmCIF, bCIF, or PAE JSON formats. The tool also generates an accompanying ID mapping file to trace input identifiers back to standard accession numbers and reports unmapped IDs separately. An API methodology is also provided for programmatic access, enabling integration into bioinformatics pipelines. AlphaFoldDB Structure Extractor streamlines the structure procurement process from AlphaFold database, empowering researchers in structural and functional genomics with minimal computational expertise.
Variantis is a user-friendly platform for calculating transition and transversion ratios. It generates a matrix for comparative analysis and provides insights into individual nucleotide changes.
This web-based tool has been developed using Flask, JavaScript, HTML, and CSS. It integrates advanced libraries to deliver a seamless and interactive user experience for sequence analysis.
https://project.iith.ac.in/sharmaglab/variantis/
Manuscript Link: 16S-23S-5S rRNA Database: a comprehensive integrated database of archaeal and bacterial rRNA sequences, alignments, intragenomic heterogeneity, and secondary structures. Preprint at bioRXiv (Under revision in mSystems). 2025
VARiantIS is a user-friendly web interface designed to calculate and visualize transitions and transversions in nucleotide sequences. It enables researchers to upload DNA sequence data, compute substitution statistics, and generate intuitive graphical representations for comparative genomics or molecular evolution studies. Developed for accessibility and precision, Variantis simplifies mutation pattern analysis without requiring advanced programming skills, supporting both educational and research applications.
https://project.iith.ac.in/sharmaglab/csspred/
Manuscript Link:
https://project.iith.ac.in/sharmaglab/novelbgc/
Manuscript Link:
https://project.iith.ac.in/sharmaglab/origenomi/
Manuscript Link: