FOUNDER

Yevgeniy “Eugene” Antipin

Founder · Bioinformatics & Computational Biology

Fifteen years turning genomic and protein data into tools that clinicians and researchers rely on — across cancer diagnostics, variant interpretation, and machine learning for drug discovery. AlgoGenomics is his independent computational-biology practice.

Sema4 Mount Sinai Memorial Sloan Kettering

Get in touch → View bibliography

Eugene Antipin — Founder, AlgoGenomics LLC

EXPERIENCE

A track record in clinical and cancer genomics.

Before founding AlgoGenomics, Eugene led computational-biology and medical-informatics teams across clinical and academic cancer genomics. As Director of Medical Informatics at Sema4, he led software developers and bioinformaticians building the pipelines and web tools — for somatic mutations, inherited-syndrome germline variants, and copy-number changes — that inform oncologists on personalized treatment. At the Icahn Institute for Genomics & Multiscale Biology at Mount Sinai, he led the team behind a pipeline that analyzed individual cancer profiles for the Personalized Cancer Therapy Program. Earlier, in the Chris Sander Lab at Memorial Sloan Kettering, he created MutationAssessor and contributed the mutation analysis and visualization to cBioPortal.

EXPERTISE

From raw sequence to interpretable biology.

Variant functional impact

Predicting the effect of protein mutations, with 3D-structure stability analysis and genome-wide binding-site mapping.

Machine learning

Entropy-based methods, biomarker prediction, computational docking and high-throughput screening for drug discovery.

Data visualization

Interactive visualization of genetic and protein data — mutations, alignments, sub-families and specificity residues.

Database integration

Uniting UniProt, GENCODE, RefSeq, Pfam, PDB, KEGG, dbNSFP and 1000 Genomes into one coherent frame.

Pathway & expression analysis

Gene-expression analysis, cancer-subtype prediction, copy-number clustering and survival analysis.

Full-stack cloud platforms

End-to-end web services — front end, back end, databases and parallel computing — deployed on AWS & RDS.

SELECTED WORK

Tools used across cancer genomics.

LATEST AlgoGenomics flagship

Protein Function Genome Browser

Everything known about a protein in one view — from its chromosomal locus down to a single residue. PFGB consolidates 16 public databases and 3D structural context into a single, zoomable page.

See the product → human genome · in development

MutationAssessor

An evolution-based functional impact score for cancer mutations. Developed within The Cancer Genome Atlas; now integrated into cBioPortal, serving scores for ~4M somatic mutations across 320K+ tumor samples.

mutationassessor.org ↗

cBioPortal

Contributed the visualization and functional analysis of missense mutations to the open cancer-genomics portal.

cbioportal.org ↗

MSAViewer

A web tool for analysis and visualization of protein multiple-sequence alignments.

msaviewer.org ↗

SELECTED PUBLICATIONS

Peer-reviewed, and widely cited.

Comprehensive molecular characterization of human colon and rectal cancer

Nature · 2012

The cBio Cancer Genomics Portal: an open platform for exploring multidimensional cancer genomics data

Cancer Discovery · 2012

Predicting the functional impact of protein mutations: application to cancer genomics

Nucleic Acids Research · 2011

Determinants of protein function revealed by combinatorial entropy optimization

Genome Biology · 2007

Full bibliography on Google Scholar ↗

Let’s talk.

Reach out about collaborations, consulting, or a walkthrough of the Protein Function Genome Browser. Based in New York.

Send a message → Google Scholar ↗

AlgoGenomics LLC