Autarchy of the Private Cave

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    Archive for May 20th, 2008

    Gene regulatory network reconstruction from microarray data

    20th May 2008

    The title of this post is my current – “forthcome”, as in “done” – field of interest.

    First article on topic: Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data.

    Another one, on combining different high-throughput data sources to get higher-quality results: Uncovering signal transduction networks from high-throughput data by integer linear programming.

    I’m especially interested in time-series network reconstruction algorithms. If you have a good advice to share with a newcomer to the networks field – don’t hesitate :)

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    Posted in Bioinformatics, Links, Science | No Comments »

    COTRASIF: conservation-aided transcription factor binding site finder

    20th May 2008

    With this post, I’m finally announcing the opening of the (mostly) functional COTRASIF web-tool, created for the genome-wide identification of promoter regulatory sequences (transcription factor binding sits, TFBS). You can learn more from the About and Help pages. For an example of use, see the Supplement page (article is currently being prepared; as soon as it’s ready, I’ll make it available).

    If you are interested – have a look at the News page, where there is information on joining COTRASIF Google group. For non-public enquiries, please use my contact page.

    Note: the problem of identifying eukaryotic transcription factor binding sites stays acute for many years in a row – see e.g. the most recent Eukaryotic transcription factor binding sites – modelling and integrative search methods.

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    Posted in Bioinformatics, Links, Science, Software, Web | 6 Comments »