Links to the latest CytoGnomix products:

Applications and consulting in Geostatistical Epidemiology

Monitoring and discriminating infectious disease hotspots from high disease burden regions, eg. for COVID-19:

Zenodo repository:  Geostatistical Analysis of SARS-CoV-2 Positive Cases in the United States

Defence Canada IDEaS project: Locating emerging COVID19 hotspots in Ontario after community transmission by time-correlated, geospatial analysis 

Addressing large scale radiation incidents and accidents: 

Article in PLOS One: Meeting radiation dosimetry capacity requirements of population-scale exposures …. (Funded by High performance computing consortium: SOSCIP and CytoGnomix)

How to: Protocol for Geostatistical Determination of Radiation Dosimetry Maps of Population-Scale Exposures 

Large scale Radiation Biodosimetry

Capacity of supercomputer version of Automated Dicentric Chromosome Identifier and Dose Estimator  (ADCI) software: Automated Cytogenetic Biodosimetry at Population-Scale and Radiation, Radiation, 2021 (link to published article).

Scalable, democratized access to ADCI:

Overview of Cloud version- ADCI_Online

Presentation to the International Atomic Energy Agency (CRP E35010)

Gene Expression Signatures for Radiation Biodosimetry

Mucaki, E.J., Shirley, B.C. and Rogan, P.K., 2021. Improved radiation expression profiling in blood by sequential application of sensitive and specific gene signatures. International Journal of Radiation Biology,    Link to pdf: Improved radiation expression profiling…

Zhao, J.Z., Mucaki, E.J. and Rogan, P.K., 2018. Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning. F1000Research7(233), p.233.   Link to open access article:

Large Scale Repository of Cancer Splicing Mutations

Pan-cancer repository of validated natural and cryptic mRNA splicing mutations   (a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. )

Article in F1000Research: Pan-Cancer repository of …..

Presentation at the 2019 American College of Medical Genetics Annual Meeting:

Pan-cancer repository of validated natural and cryptic mRNA.ePoster

Interactive Website: Gene signatures for chemotherapy drug response

Demo (Windows): Automated Dicentric Chromosome Identifier and Dose Estimator  

Review on information theory-based splicing mutation analysis:

Caminsky et al. 2014, Videos describing this paper: short and long versions.

MutationForecaster system

Learn more

Automated Splice Site and Exon Definition Server

User manual (select link to open)
Peer reviewed publications:
Mucaki et. al. 2013
Nalla Rogan  2005
Literature citations
Videos:  YouTube Tutorial,    Wiley Video Abstracts
Brief Review of Molecular Information Theory

Shannon Pipeline for mRNA Splicing Mutation Analysis

Product sheet
Manual (Cytognomix Online Subscription):  Shannon mutation analysis documentation – webservice
User reference guide  (CLC Bio Genomics Workbench and Server)
Guide to installation of trial webserver 
White paper describing capabilities and features
Peer reviewed publications:
Shirley et al. 2013
Stephanie Dorman and Ben Shirley (hosted by CLC bio)
2012: BioIT World,   TechAlliance
2012 American Society of Human Genetics meeting, CLC bio Medical Genomics workshop
2013: Slides from Shannon Pipeline Webinar 2013 – presentation


Validate predicted splicing mutations with RNASeq
Peer reviewed publications:
Viner et al. 2014
2014: Coby Viner at Compute Ontario

Ab initio sc probes (FISH, NGS enrichment, genomic microarrays)

Peer reviewed publications:
Khan et al. 2015
Khan et al. 2014.
Dorman et al. 2013
Khan et al. 2012
Newkirk et al. 2005
Mora et al. 2005
Knoll and Rogan 2003
Rogan et al. 2001
Probe hybridization protocol for scFISH
Hybridization enrichment:  sequence capture protocol for Next Generation Sequencing library preparation

Cytogenetic Biodosimetry

Application note
Peer reviewed publications and patents:
Rogan et al. 2014
Subasinghe et al. 2013
Li et al. 2012
Subasinghe et al. 2011
Subasinghe et al. 2010
US Patent 8,605,981 and patents pending (PCT/US11/59257 ).