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, doi.org/10.1080/09553002.2021.1998709 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. F1000Research, 7(233), p.233. Link to open access article: https://f1000research.com/articles/7-233
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 TheoryShannon 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 Videos Stephanie Dorman and Ben Shirley (hosted by CLC bio) 2012: BioIT World, TechAlliance Presentations 2012 American Society of Human Genetics meeting, CLC bio Medical Genomics workshop 2013: Slides from Shannon Pipeline Webinar 2013 – presentationVeridical
Validate predicted splicing mutations with RNASeq Peer reviewed publications: Viner et al. 2014 Video 2014: Coby Viner at Compute OntarioAb 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 ).