Bioinformatics and Computational Biology Consulting

From Atoms to Systems

We convert complex biological data into clear scientific answers. Molecular simulations, AI-driven design, and multi-omics analysis — rigorous, reproducible, and built to publish.

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About Us

From Molecules to Microbiomes

Computational bottlenecks should not stall biological discovery. Led by Dr. Bharat Manna, Manna Omics Solutions integrates molecular dynamics, AI-driven structural biology, and genome-resolved multi-omics to decode biological systems across scales — from atomic interactions to ecosystem dynamics. We work with academic research groups and industry teams to deliver rigorous, publication-quality analytics that drive real scientific progress.

28+ Peer-reviewed publications
450+ Citations
15 h-index
8+ International conferences

Reflecting the scientific track record of our founder, Dr. Bharat Manna.

Services

What We Do

Specialized computational services spanning molecular, genomic, and systems scales. Built for research groups and industry teams who need rigorous, reproducible, publication-ready outputs.

Research & Computational Services

Molecular Dynamics & AI-Driven Design

From protein–ligand binding to de novo molecular design. We run all-atom and coarse-grained simulations, free energy calculations, and enhanced sampling — combined with AlphaFold, RFdiffusion, and generative AI tools for structure prediction, design, and validation. Every result is reproducible and built for publication.

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(Meta)genomics & Multi-Omics

Comprehensive multi-omics services including 16S/ITS amplicon profiling, whole-genome shotgun sequencing, (meta)transcriptomics, (meta)proteomics, and metabolomics. Core capabilities include genome assembly, MAG reconstruction, taxonomic and functional annotation, metabolic pathway reconstruction, and cross-omics network analysis. Data analyzed individually or integrated for systems-level biological interpretation.

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Resistome & AMR Profiling

Comprehensive antimicrobial resistance gene profiling, mobile genetic element tracking, and resistome dynamics characterization across environmental, clinical, and agricultural samples. Applied within a One Health framework linking microbial ecology to public health.

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Academic & Writing Support

Scientific Writing & Grant Support

Support for publication and funding. We help with results interpretation, data visualization, and manuscript preparation for peer-reviewed journals. We also assist with grant proposals — specific aims, computational methods sections, and proposal strategy for national and international funding bodies.

Training & Workshops

Hands-on training in bioinformatics, metagenomics analysis, R programming, and molecular simulation workflows. Designed for research groups, graduate students, and professionals from non-computational backgrounds. Available as one-day workshops or structured multi-session courses, delivered remotely or on-site.

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Internship & Dissertation Support

Personalized one-on-one mentorship for undergraduate, postgraduate, and doctoral students. Final year project guidance, MSc dissertation support, PhD computational mentorship, and structured research internships — designed for students who need a computational mentor, not just a course.

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Featured Work

Representative Research and Methodology

Selected projects from Dr. Bharat Manna's collaborative academic research, demonstrating the analytical expertise that underpins Manna Omics Solutions.

Your Treatment Plant May Be Building the Resistance It's Meant to Remove

The Challenge: Conventional activated sludge processes are designed to reduce biological hazards. However, there is a critical unknown: is the treatment environment itself, specifically high-intensity aeration, actively generating the resistant bacteria that eventually dissipate into receiving water bodies?

The Solution: Using shotgun metagenomics and SWATH-metaproteomics across full-scale treatment plants, this Water Research (2025) study proved that aeration-induced ROS drives the de novo emergence of ~22% of the enriched resistome within the system. Crucially, the plant operation, not the incoming wastewater, determines up to 75% of the antibiotic resistance genes discharged into the environment.

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Your Biocatalyst Is Being Sabotaged by Its Own Product

The Challenge: Beta-glucosidases are the final bottleneck in lignocellulosic biofuel production, yet they are feedback-inhibited by the very glucose they produce. The molecular mechanism behind this remained unknown.

The Solution: Atomistic MD simulations, protein structure network analysis, and molecular docking identified six secondary glucose binding sites as the structural basis of uncompetitive inhibition, providing actionable targets for rational enzyme engineering. This ACS Sustainable Chemistry and Engineering (2021) study delivers the first molecular-level roadmap for glucose-tolerant biocatalyst design.

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Is Your Next Antiviral Already on the Shelf?

The Challenge: Drug development for emerging pathogens like SARS-CoV-2 is too slow. By the time a new drug clears trials, the window has passed.

The Solution: Combining virtual screening of 1918 FDA-approved drugs with transcriptomic signature reversal analysis, Indomethacin was identified and validated in-vitro at ICMR-NIV Pune with an IC50 of 12 μM. This Computers in Biology and Medicine (2022) study shows how computational repurposing pipelines can cut discovery timelines dramatically, turning existing drug libraries into actionable antiviral candidates before the next outbreak peaks.

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Technical Expertise

Our work is grounded in industry-standard and cutting-edge computational platforms, ensuring reproducibility, scalability, and methodological rigor across every project.

Molecular Simulation Suite

End-to-end MD simulation workflows, from system preparation and force field parameterization to production runs and thermodynamic analysis.

AMBERGROMACSNAMDCHARMMOpenMM PackmolAutoDockCPPTRAJ VMDPyMOLANI-2xDeePMD-kitPLUMED

AI/ML & Structural Biology Suite

State-of-the-art AI tools for protein structure prediction, molecular design, and generative biology pipelines.

AlphaFoldESM-2ProteinMPNNRFdiffusionBoltzGenBoltz-2 REINVENT4DiffDockOpenFE

Genomics & Metagenomics Suite

Genome-resolved metagenomics from raw sequencing data to binning, taxonomy, and functional annotation at population scale.

FastQCTrimmomaticMEGAHITProdigalDIAMOND Bowtie2MaxBin2MetaBAT2CONCOCTCheckM GTDB-TkKraken2MetaPhlAnHUMAnN3 METABOLICmetaGEMbreseqsnippy QIIME2KEGGeggNOGCAZy

Integrated Multi-Omics Suite

Cross-platform integration of metaproteomics, metabolomics, and transcriptomics data for systems-level biological interpretation.

STARSalmonfeatureCountsDESeq2edgeR WGCNADIA-NNMetaboAnalystMS-DIALmixOmics

Resistome & AMR Analytics

Antimicrobial resistance gene detection, mobile genetic element tracking, and horizontal gene transfer analysis across environmental and clinical datasets.

CARD-RGIAMRFinderPlusMetaCHIPResFinder

Computing & Workflow Automation

Scalable, reproducible pipelines built for HPC environments with version-controlled, documented workflows.

RPythonBashLinux SnakemakeNextflowSLURM / HPCGitDocker
Founder
Dr. Bharat Manna

Dr. Bharat Manna

Founder & Principal Scientist

Dr. Bharat Manna is a computational biologist with a Ph.D. from IIT Kharagpur and postdoctoral training at the University of Auckland, New Zealand. His research sits at the intersection of oxidative stress, microbial ecology, and antimicrobial resistance — an area of growing relevance to global One Health challenges.

His expertise spans two scales: atomistic molecular dynamics simulations of protein systems, and genome-resolved multi-omics analysis of complex environmental microbiomes. This dual fluency — from force fields to metagenomes — is the foundation on which Manna Omics Solutions was built.

With 28+ peer-reviewed publications in Water Research, ACS Sustainable Chemistry & Engineering, and Journal of Physical Chemistry B, and research presented across four continents, Dr. Manna brings scientific depth and international perspective to every engagement.

Gold Medalist, M.Tech Bioinformatics. Winner, SAMHAR-COVID19 Hackathon (C-DAC, DST, NVIDIA).

Google Scholar ORCID ResearchGate LinkedIn
Founder's Publications

Selected Publications

A selection from Dr. Bharat Manna's 28+ peer-reviewed publications.

Water Research (IF: 12.4)

ROS-Induced Oxidative Stress Causes Enrichment and Emergence of Antibacterial Resistance in Conventional Activated Sludge Process

Manna B, Zhou X, Singhal N. (2025)

Water Research (IF: 12.4)

L-norepinephrine Induces Community Shift, Oxidative Stress Response, Metabolic Reprogramming, and Virulence Potential in Wastewater Microbiomes

Bains A*, Dahal S*, Manna B*, Lyte M, Yang L, Singhal N. (2025)

J. Phys. Chem. B (IF: 3.3)

Elucidating the Ionic Liquid Induced Mixed Inhibition of GH1 Beta-Glucosidase H0HC94

Manna B*, Chanda P*, Datta S, Ghosh A. (2023)

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Get in Touch

Let's Work Together

Tell us about your project and we'll respond with a scope outline and estimate within 48 hours.

or
  info@mannaomics.com

  Kolkata, India

  Remote consulting worldwide

  Response within 48 hours

Academic collaborations, industry projects, and grant-linked consulting — all enquiries welcome.