Anupam Gautam

ProFinder: Candidate constitutive promoter prediction across the bacterial tree for genetic tool development in non-model species

ProFinder predicts constitutive promoters across bacterial species to aid genetic tool development, achieving high precision and robustness across diverse genomes.

Mettl3-catalyzed m6A methylation determines CD8+ T cell differentiation fate in tumor

This study identifies Mettl3-m6A methylation as a regulator of CD8+ T cell differentiation fate in tumors, showing its role in promoting terminal exhaustion and its potential as a target to enhance immunotherapy.

MMonitor: Software for Real-Time Monitoring of Microbial Communities Using Long Reads

MMonitor provides real-time analysis and visualization of metagenomic data, enabling dynamic microbiome research through automated pipelines and interactive dashboards.

A mechanistic study on the tolerance of PAM distal end mismatch by SpCas9

The paper investigates how mismatches at the PAM distal end affect SpCas9 activity through experimental and computational methods, finding that certain mismatches reduce activity due to conformational instability.

mgPGPT: Metagenomic analysis of plant growth-promoting traits

The paper extends the PGPT ontology to analyze metagenomic datasets, introducing mgPGPT-db and integrating it into MEGAN for PGPT-related gene identification.

TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data

TIPPo assembles organellar genomes using HiFi data without reference genomes or nuclear information, achieving complete chloroplast assemblies and improved mitochondrial results compared to existing tools.

Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.

MMIP integrates microbiome and metabolome data to identify features and predict metabolite signatures from amplicon sequencing data without requiring initial metabolomic analysis.

Megan Server: facilitating interactive access to metagenomic data on a server

Megan Server provides web-based interactive access to metagenomic data without requiring full data downloads.

MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction

MuLan-Methyl uses five transformer-based models to predict three types of DNA methylation sites, achieving good performance on a benchmark dataset.

DeepToA: An Ensemble Deep-Learning Approach to Predicting the Theater of Activity of a Microbiome

DeepToA predicts the theater of activity of a microbiome using taxonomic and functional profiles with high accuracy.

AUF-1 knock down in mice overarches butyrate driven hypo-cholesteraemia by conjuring AUF-1-Dicer-1-miR122 hierarchy

The paper investigates how butyrate affects cholesterol levels through the AUF-1-Dicer-1-miR122 pathway in mice, showing that AUF-1 knockdown increases miR122 and reduces serum cholesterol.

Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN

The paper analyzes fruit-waste fermentation samples to identify biosurfactant-producing microbes using metagenomic sequencing and integrates BiosurfDB into MEGAN for interactive exploration.

Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis

The paper demonstrates that using AnnoTree improves speed and assignment rates in DIAMOND+MEGAN microbiome analysis compared to NCBI-nr.

PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria

PLaBAse annotates bacterial genomes against a curated ontology of ∼6,900 plant growth-promoting traits; applied to 70,540 genomes, plant symbionts and rhizobacteria had the largest genomes and most traits.

Enhanced COVID-19 data for improved prediction of survival

The paper enhances a COVID-19 dataset by adding weather and research sentiment features, achieving 95% accuracy in survival prediction using XGBoost.