Vivofold Research

Research questions behind our work

Name: Vivofold
Price range: ₹₹

Seven areas of research, from the reliability of genomic analyses and structure-based drug design to machine learning for biology and validated scientific software. Each area lists the questions we are asking and the methods we use.

Research areas Collaborate

A workflow as a directed acyclic graph, in nf-core process naming: every step is versioned, containerised and re-runnable.

Research areas

7 areas

Validated Methods & Scientific Software

Clean-room implementations of published algorithms, tested against known answers and shipped as browser software.

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Genomics & Transcriptomics

Robust analysis of bulk, single-cell and spatial transcriptomes and genomic variation.

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Structural Bioinformatics & Computational Drug Discovery

Validation-first docking, QSAR and structure analysis for early drug discovery.

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AI & Machine Learning for Biology

Trustworthy machine learning for sequences, molecules and omics: baselines, honest splits and stated limits.

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Microbial Genomics & Antimicrobial Resistance

Genomic epidemiology of resistance using public bacterial genomes and open tools.

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Spatial & Health Data Science

Geoinformatics and health-data standards applied to public health, agriculture and ecology.

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Molecular & Cell Biology (Wet Lab)

Bench research linking experiments with computation, alongside Vedicgen’s laboratory training.

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Research output

The methods library

Published algorithms we have re-implemented clean-room, tested against known answers and shipped in Nayancode software.

Nayancode software

Method	Area	Where	How it is checked
Global and local alignment (affine gaps, BLOSUM62)	Sequence	Sequence Studio	Unit-tested for global, local and protein alignment
Primer design, in-silico PCR, cloning (restriction, Golden Gate, Gibson)	Sequence	Sequence Studio	Designed products re-derived; invalid assemblies refused with a reason
CRISPR guide search and off-target scan	Sequence	Sequence Studio	Finds planted mismatched sites; PAM handling tested
Progressive multiple alignment	Phylogenetics	Phylogenetics	Keeps every residue; places a simple indel correctly
Neighbour-joining, UPGMA + bootstrap	Phylogenetics	Phylogenetics	Recovers an additive tree and planted bootstrap-supported clades
Maximum-likelihood trees (JC69, K80, HKY85, Poisson, ±Γ)	Phylogenetics	Phylogenetics	Matches closed-form likelihoods; recovers the true topology on simulated data
MinHash ANI	Genome	Genome Studio	Zero distance for identical genomes; estimates ANI of diverged ones
Read mapping & SNV calling (minimap2 + samtools, WebAssembly)	Genome	Genome Studio	End-to-end test recovers 5 of 5 planted variants, no false positives
Moderated-t differential expression	Expression	Expression Studio	Recovers planted genes with controlled FDR; BH matches R
ComBat batch correction	Expression	Expression Studio	Removes a planted batch shift and keeps the biological effect
ORA and preranked GSEA	Expression	Expression Studio	Detects planted sets; planted pathway ranks first end to end
SNN-Louvain clustering, clean-room UMAP / t-SNE	Single-cell	Single-Cell Studio	Recovers four planted cell types (ARI > 0.9)
NMF mutational signatures (no COSMIC)	Variants	Variant Studio	Recovers two planted signatures (cosine > 0.95)
Weighted / unweighted UniFrac, PERMANOVA	Microbiome	Microbiome Studio	Matches hand-computed values; detects a planted effect, not a shuffled one
Random forest / kNN / ridge QSAR, Butina clustering	Chemistry	Chemistry Studio	Learns a known function; Y-randomisation collapses performance
Interaction profiling, pockets, SASA, Kabsch + TM-score	Structure	Structure Studio	Engineered-site tests; SASA and superposition recover known values; checked on PDB 1HSG

Open projects

Projects open to collaborators and student researchers

Research training

Validated Methods & Scientific Software

Browser-scale read mapping benchmarks

Characterise accuracy, memory and runtime of WebAssembly mapping across genome sizes and devices.

Validated Methods & Scientific Software

Numerical regression suites for analysis kernels

Extend planted-truth tests to every statistical kernel and publish the suite.

Validated Methods & Scientific Software

Accessible scientific visualisation

Keyboard and screen-reader access for interactive plots of large datasets.

Genomics & Transcriptomics

Robustness of RNA-seq conclusions

Re-analyse published RNA-seq studies under alternative, defensible pipelines and measure how conclusions change.

Genomics & Transcriptomics

Batch correction in small designs

Benchmark correction methods on simulated and public data with known batch structure.

Genomics & Transcriptomics

Annotation agreement in single-cell data

Quantify agreement between automated cell-type annotation methods across public atlases.

Structural Bioinformatics & Computational Drug Discovery

Docking validation audit

Systematically test docking protocols on public targets with known actives and decoys.

Structural Bioinformatics & Computational Drug Discovery

QSAR split study

Quantify performance inflation from random splits across ChEMBL targets.

Structural Bioinformatics & Computational Drug Discovery

Predicted structures for docking

Compare docking outcomes on experimental and predicted structures of the same targets.

AI & Machine Learning for Biology

Leakage in biological ML benchmarks

Re-evaluate public benchmarks with biologically aware splits.

AI & Machine Learning for Biology

Literature extraction accuracy

Measure how well LLM pipelines extract experimental parameters from methods sections.

AI & Machine Learning for Biology

Communicating uncertainty

Design and test ways of showing model applicability to bench scientists.

Collaborate

Work on a research question with us

We welcome collaborations with laboratories, clinicians and companies, and research projects with students.