GNOMATIX

Consulting · Since 2013

Overview

GNOMATIX was established to provide experienced project support services in bioinformatics & research IT.

We’re ready to work with you in finding practical, pragmatic solutions to help realize your project goals.

If you happen to be a PI or other project leader, we’d love to hear about your project’s objectives & technical challenges, whether you’re presently in need of project support or not.

Drop us a note right now at: helpdesk@gnomatix.com

Services

“GNOMATIX” launched in 2013 providing services in Genomics/Informatics. Our vision is now focused on being a community-minded organization applying best-practice research & engineering solutions to grand challenge projects worldwide.

Working with teams of every size & projects of every scope, we’ve innovated & engineered robust, scalable — even “gold-standard” — production systems & methods. The publications & project success stories speak for themselves.

Available support includes

Engineering DesignUX ResearchIT ConsultingVirtual AssistanceTechnical SupportStrategic PlanningGhostwritingSoftware TestingCustom Software DevelopmentResearch Skills

Engineering Research Advisory Support Writing

Artificial Teams ][ Real Intelligence

Contactinfo@gnomatix.com LinkedIn

US$200M+ in “Big Science” projects // 100% shipped

PGDx · LabCorp FDA · CMS 2018–2020 $90M+ VC raised
$575M LabCorp acquisition FDA 510(k) · PGDx elio

PGDx elio PlatformFDA Approved

Invented a microhaplotype-based contamination detection method and wrote the software for LabCorp's PGDx elio™ platform — detecting ≥0.2% contamination in unpaired clinical plasma (ctDNA) and tissue (FFPE) tumor samples. Performed the complete failure-mode audit of the elio™ platform prior to FDA submission. Authored technical documents for the successful FDA 510(k) filing. Clinically validated, FDA-approved, covered under Medicare and Medicaid. The platform sequences liquid and solid tumor genomes, diagnoses cancer sub-type, identifies approved targeted therapies, and pre-qualifies patients for experimental drug trials — matching people to studies likely to produce positive outcomes based on their personal genomic data.

Invented the method · wrote the software · did the FDA audit · people are alive because of this

OICR ICGC · NCI 2011–2013 $30M DCC initial
$30M renewal Genome Canada / OICR · ICGC DCC

ICGC DCC → NCI Genomic Data Commons Cancer Moonshot

The ICGC is one of the most ambitious biomedical research efforts since the Human Genome Project — a global collaboration to map 25,000 cancer genomes across 50 tumor types. The Data Coordination Centre managed data standards, open and controlled access, and community support for 53 member projects across 16 countries, featured in The Scientist, "Combing the Cancer Genome" (March 2012). The ICGC Data Portal paper is a co-authored publication in Database (Oxford, 2011).

25,000 cancer genomes · 16 countries · The Scientist · Biomedical Commons Cloud — organizational meeting (April 2013) · NCI GDC · Cancer Moonshot

MSU · Buell Lab DOE JGI · USDA NIFA 2008–2011 SCGR my MSU project · USDA NIFA
$5.4M SolCAP CAP
DOE JGI sequencing (in-kind) SCGR: USDA NIFA 2008-35300-18671

Potato Genome · SolCAP SNPs · Solanaceae Comparative Genomics Resource · Pythium ultimumNature July 2011 (Cover)

The potato is the world's most important non-grain food crop. An international consortium of 29 research groups across 14 countries sequenced its 844-megabase genome, predicting 39,031 protein-coding genes — the first sequenced asterid. The result made the cover of Nature in July 2011, drew international media attention including Al Jazeera, and the genome browser and public data release website that researchers worldwide used to access the data were built here. The gene annotation and manual curation of the published genome were done here. This was a side project. My MSU project was the Solanaceae Comparative Genomics Resource (SCGR) — a USDA-funded comparative-genomics platform for the Solanaceae family; code archive at brettwhitty/bw-msu-sites. Also co-authored the Pythium ultimum genome (Genome Biology 2010), a necrotrophic plant-pathogen genome with original pathogenicity mechanisms and effector repertoire. Separately, the USDA-funded Solanaceae Coordinated Agricultural Project (SolCAP) produced the genome-wide SNP array now used worldwide for marker-assisted breeding of potato and tomato — enabling blight-resistant varieties and accelerating crop improvement globally. The work received the USDA Secretary's Honor Award, the Department's highest recognition, for helping America promote sustainable agricultural production and food security.

Nature cover · global press coverage · USDA Secretary's Honor Award · SCGR · Pythium ultimum (Genome Biology 2010) · global food security

TIGR / JCVI NIAID MSC · NIAID BRC for Biodefense · Moore Foundation 2005–2008 $24.5M CAMERA · Moore Foundation (7-year)
NIAID Microbial Sequencing Center at TIGR
NIAID Bioinformatics Resource Center for Biodefense MSC: NIAID Contract HHSN266200400001C

Biodefense · Amerithrax · Global Ocean SamplingNIAID

TIGR — later JCVI — was the NIAID Microbial Genome Center and Bioinformatics Resource Center for Biodefense, funded under Fauci's National Institute of Allergy and Infectious Diseases. The work included preliminary data analysis on Project Amerithrax, the FBI's forensic genomics investigation of the 2001 anthrax letter attacks, under Jacques Ravel. Separately, CAMERA (Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis) was a $24.5M, 7-year Gordon and Betty Moore Foundation grant — Gordon Moore, co-founder of Intel — to build the computational infrastructure at Calit2 for the Sorcerer II Global Ocean Sampling Expedition. Craig Venter sailed his research yacht 32,000 nautical miles across 23 countries; Discovery Channel made a documentary about it (Cracking the Ocean Code, 2005). The metagenomic annotation pipeline that processed the resulting sequence data — an unprecedented volume, exceeding what existed in all public databases at the time — was created from scratch in roughly two months. It became JCVI's standard operating procedure for metagenomic annotation and was later deployed on the NIH Human Microbiome Project. Ergatis — the web-based workflow engine behind these and other TIGR/JCVI production annotation pipelines — is software we wrote; I'm a core developer and co-author on its Bioinformatics (2010) paper.

Amerithrax · biodefense · Human Microbiome Project · more data than all public databases

McMaster University Biology 2002–2005 $5.8M GASM · Genome Canada Genome Canada · GASM

Sinorhizobium · Thellungiella · Molecular Evolution

The Genome Canada–funded Genomics Analysis of Soil Microorganisms project ($5.8M) studied Sinorhizobium meliloti, a nitrogen-fixing soil bacterium associated with many Canadian crops — research aimed at improving agricultural practices and helping the environment. Separately, functional annotation and EST analysis of Thellungiella (salt cress), a model extremophile plant that thrives in extreme salinity and cold. Co-first-authored the expressed sequence tag characterization published in Plant Molecular Biology (2005). Phylogenomics-based prediction of novel functional associations in conserved hypothetical proteins.

Genome Canada · Plant Molecular Biology · Plant Physiology · J. Mol. Evolution