Re: Invited Talk at 2014 NIPS Workshop on Machine Learning in Computational Biology

Hi Mark,

I'm sorry. I didn't check my gmail yesterday.

Best,
Martin Renqiang

发自我的 iPhone

在 Nov 6, 2014，11:13 AM，Mark Gerstein <mark@gersteinlab.org> 写道：

> Title: Comparative Genome Analysis
>
> Abstract:
>
> 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. The
> consortium performed
> extensive data integration on this data set. Here
> I will give an overview of the data and some of the key analyses.
> In particular:
>
> (1) Conservation & Divergence of Transcription
>
> (1a) A novel cross-species clustering algorithm to
> integrate the co-expression networks of the three species, resulting in
> conserved modules shared between the organisms. These modules are
> enriched in developmental genes and exhibited hourglass behavior.
>
> (1b) The extent of the non-coding, non-canonical
> transcription is consistent between worm, fly and human.
>
> (1c) In contrast, analyses of pseudogene (fossil genes) show that they
> diverged greatly between the organisms, much more so than genes.
> Nevertheless, they had a consistent amount of residual transcription.
>
> (2) Conservation of Regulation
>
> (2a) A global optimization algorithm to examine the
> hierarchical organization of the regulatory network.
> Despite extensive rewiring of binding targets, high-level organization
> principles such as a three-layer hierarchy are conserved across the
> three species.
>
> (2b) 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 expression level for both protein
> coding genes and ncRNAs.
>
>
> encodenets.gersteinlab.org
> encodeproject.org/comparative
> pseudogene.org/psicube
>
> ==
>
> i0nips