Analysis Priorities

Analysis Priorities

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Integrative Analysis of molecular datatypes for a given sample

A sample could be analyzed for DNA sequence variations, structural variations, CNVs, Gene or transcript isoform expression, genome-wide methylation patterns, ChIP-seq for specific transcription factors, metabolomic or proteomic analysis, and other molecular profiles. A framework that allows a researcher to readily identify all molecular data types associated with a particular sample and integrate the results of such analyses ...more »

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Education and usability

Provide a series of online short videos and short courses that will help users adopt the new tools and instructors to incorporate into courses. (Maybe this is obvious, but high-quality tutorials and case studies take significant time to develop.)

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Construct background mutation rate

Construct background mutation rate (noise) based on the correlation of mutation frequency and expression levels or replication time. It has been shown that longer replication time and lower expression levels imply higher mutation rates among the genome (http://www.nature.com/nature/journal/v499/n7457/full/nature12213.html). Transcription-coupled DNA repair results in high expression levels and low mutation rate. So I ...more »

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CANCER whole genomes codon populations analysis

In this main open access article

http://fr.scribd.com/doc/169323556/7401586of18september2013

published in october 2013 by APPLIED MATHEMATICS (BIOMATHEMATICS issue http://www.scirp.org/journal/am/ ) we show how our human genome MUST be considedred as a NUMERICAL WHOLE. The idea is now to run this kind of analysis on complete genomes DNA from CANCER CELLS (LOH) at individual chromosomes and whole genome scales.

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