Genomiverse

Uncovering Diverse Microbial Mechanisms via AI

Home DNAProteinBinding MicrobiomeConnectome JeffsKnowledgeGraph Publications News AnniBot Our Team Contact Us Game
We make microbes more useful to our society.

We decode their behavior and design microbes to follow instructions: Sensing environmental molecules & releasing products accordingly.

What do we do?

  • AI models to predict how proteins interact with DNA and ligands (coming soon).
  • MicrobiomeConnectome: knowledge graph for candidate drug prediction!

How we do it?

We build AI from biological principles and generate training data from data we already have:

  • >3M microbial genomes and >30K microbial species
  • 143K microbiome literature
Contact us!

Who are we?

We are a team of microbiologists and software engineers previously from MIT and Google.

Other tools

Genomiverse lab members & collaborators

Highlighted discoveries & publications

ARG Risk Mapping
Nature Communications

Antibiotic Resistance Gene (ARG) Risk

Antibiotic resistance genes (ARGs) are everywhere, but enrichment in human-associated environments is considered a requirement to be the highest risk (Rank I - red bars).

Read Publication →
ARG Prevalence Graph
Microbiome

ARG Prevalence & Spread

ARGs are highly prevalent in bacterial genomes. Specifically, ARGs in Gammaproteobacteria are spreading by horizontal gene transfer via class 1 integrons (i.e. intI1).

Read Publication →
QuickVariants Speed Chart
BMC Biology

QuickVariants - Variant Detection

A novel algorithm (QuickVariants) for genetic variant identification that is 9x faster than existing tools, while producing fewer false positives and false negatives.

Read Publication →
Mapper k-mer alignment
Genome Biology

Mapper - Sequence Aligner

Our tool, Mapper, dynamically incorporates k-mers of various sizes and gaps (gapped x-mers) to significantly improve sequence alignment quality.

Read Publication →
CRISPR Gut Defense Mechanism
Cell Genomics

Gut CRISPR Immunology

Gut microbiomes share CRISPR systems through horizontal gene transfer to dynamically update their phage defense. Selected as Cover Image and reported by MIT News.

Read Publication →
CRISPR horizontal gene transfer
Cell Genomics Analysis

CRISPR Adaptation

A highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in 15 persons from the United States and Europe

Read Publication →