+1 (858) 257-1860

Offices in San Diego and Belgium



image credit: `ili spatial data mapping


Explore Our Services

Clarity Genomics leverages high performance cloud computing with security and privacy compliance in accordance with HIPPA, and reproducibility and documentation for CLIA compliance.

Identification of molecules or species predictive of response

Statistical analysis to identify microbes, metabolites or proteins predictive of metadata responses (such as disease phenotype, sample time collection, protein measurements in blood). Microbe data can be in form of 16S, shotgun metagenomics, RNA-Seq or microarray.

Machine learning on control and disease cohorts

Predictive analytics models using machine learning and covariate analysis on public and private cohorts for specific disease types.

Genome, metagenome assembly and annotation

Alignment-based or de novo genome assembly for isolate genomes or metagenomes from Illumina or PacBio platforms. 

Untargeted metabolomics for novel molecule biomarker leads

Raw tandem MS/MS spectra from untargeted liquid or gas chromatography (LC/GC) mass spectrometry are converted into analyte feature tables and molecular annotations are explored beyond simple library matching using molecular networking and in silico screening.

Antibiotic resistance and virulence gene profiling

Whole-genome profiling for antibiotic resistance and virulence genes against public databases and putative phage identification. 

2D/3D molecular and microbial mapping

2D/3D molecular or microbiome cartography to view spatial distribution of molecules or microbes on the sample surface.

Microbiome-metabolome or proteome correlation analysis

Paired samples are analyzed to identify significant correlations between microbes, metabolites or proteins, yielding insight into microbial-derived metabolites and their metabolic pathways. Microbe data can be in form of 16S, shotgun metagenomics, RNA-Seq or microarray.

Cloud application development for microbiome analysis

Porting microbiome-based analysis workflows or applications to the cloud, such as data quality control, genome assembly or annotation.

Pan-genome and phylogeny analysis

Pan-genome analysis (core, accessory genes) and phylogenetic tree generation based on protein coding sequences. 


Meet the Experts

We bring together worldwide experts in mass spectrometry and next-generation sequencing to elucidate how human microbiota communicate with their host and provide valuable insights for clinical research.

Evguenia Kopylova, PhD

Managing Director

Creating advanced analytical algorithms to accelerate the development of microbiome-based therapeutics.

Alexey Melnik

Metabolomics Lead

Identifying potential therapeutics within complex microbial communities using modern mass spectrometry methods and advanced computational approaches.

Josh Daulton

Marketing & Analytics Lead

Accelerating the adoption of statistical programming to automate marketing processes and optimize the performance of sales enablement initiatives.

Rayan Chikhi, PhD

Genome Assembly Lead

Developing big data computation algorithms and optimizing tools for analysis of DNA sequencing data.

Zhenjiang Zech Xu, PhD

NGS Analysis Adviser

Utilizing machine learning techniques for predictive modeling and biomarker identification for metatranscriptome and metagenome sequencing data.

Ajay Kshatriya

Business Adviser

Pioneering genomics in new markets as founder/CEO. Formerly a VC at XSeed Capital and senior manager at Genentech.

Alexander Aksenov, PhD

Metabolomics Adviser

Researching bioanalytical chemistry with a focus on biomarker discovery and chemical aspects of biological processes.

Nicola Segata, PhD

NGS Analysis Adviser

Employing experimental meta'omic tools and novel computational approaches to study the diversity of the microbiome across conditions and populations.

Clarity Genomics is honored to collaborate with world-leading experts in microbiome analysis.

Featured Clients

Our clients include a top 5 pharmaceutical company, biotech and nutraceutical companies. We also offer services to hospitals and other healthcare institutions.