Sunday, May 18, 2014

Re: Uppsala ICM seminar -- request for title and abstract

Great Mark!



Jan Komorowski, Professor of Bioinformatics
Program in Computational and Systems Biology
Department of Cell and Molecular Biology
Uppsala University
Institute of Computer Science, PAN, Warsaw

On 17 maj 2014, at 22:14, Mark Gerstein <> wrote:

> The ENCODE and modENCODE consortia have generated a resource
> containing large amounts of transcriptomic data, extensive mapping of
> chromatin states, as well as the binding locations of over 300
> transcription-regulatory factors for human, worm and fly. We performed
> extensive data integration by constructing genome-wide co-expression
> networks and transcriptional regulatory models, revealing fundamental
> principles of transcription and network organization that are
> conserved across the three highly divergent animals. In particular:
> (1) We developed a novel cross-species clustering algorithm to
> integrate the co-expression networks of the three species, resulted at
> conserved modules shared between the organisms. These modules are
> enriched in developmental genes and exhibited hourglass behavior. They
> were then used to align the stages in worm and fly development,
> finding the normal embryo-to-embryo and larvae-to-larvae pairings in
> addition to a novel pairing between worm embryo and fly pupae.
> (2) We developed a global optimization algorithm to examine the
> hierarchical organization of the regulatory network. We found that,
> despite extensive rewiring of binding targets, high-level organization
> principles such as a three-layer heirarchy are conserved across the
> three species.
> (3) We found the gene expression levels in the organisms, both coding
> and non-coding, can be predicted consistently based on their upstream
> histone marks. In fact, a "universal model" with a single set of
> cross-organism parameters can predict expressionlevel for both protein
> coding genes and ncRNAs.
> (4) Finally, we found that the extent of the non-coding, non-canonical
> transcription is consistent between worm, fly and human.
> ==
> cmptxn,i0se14

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