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akundaje's conservation [3 articles]

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	Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes. Nature reviews. Genetics, Vol. 9, No. 4. (April 2008), pp. 303-313. by Elliott H. Margulies, Ewan Birney posted to comparative conservation review sequence by akundaje on 2009-04-18 20:02:05 along with 8 people gjuggler timflutre guhjy zwang mingzhi phoenixzxl ptrobajo natstreet Abstract Copy My Attachments My Copy Abstract The comparison of genomic sequences is now a common approach to identifying and characterizing functional regions in vertebrate genomes. However, for theoretical reasons and because of practical issues, the generation of these data sets is non-trivial and can have many pitfalls. We are currently seeing an explosion of comparative sequence data, the benefits and limitations of which need to be disseminated to the scientific community. This Review provides a critical overview of the different types of sequence data that are available ...
	Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome Science, Vol. 324, No. 5925. (17 April 2009), pp. 389-392. by Stephen C. J. Parker, Loren Hansen, Hatice O. Abaan, Thomas D. Tullius, Elliott H. Margulies posted to comparative conservation dna motif-discovery structure tfbs now by akundaje on 2009-04-18 19:58:46 along with 45 people and 6 groups nklee mox primordialstew dakelley arthegall provero rsaito daveGerrard operon sujaikumar antonkratz pradiptaray roys gjuggler benjaminsb gdb hagechouchin443 tomtullius scjparker psique orzenil emptyhb ilyashl coela VGreiff APRegier myzhang pkonings athma absterga rpatward timflutre stajich bpcusack jbhiatt djkt dhlbh friendpine dpollard inesdesantiago JustinCrocker aprasad maximilianh idonaldson kshundyak BergmanLab Mycology structural_bioinformatics RockmanLab EisenLab cis-regulatory-evolution Abstract Copy My Attachments My Copy Abstract The three-dimensional molecular structure of DNA, specifically the shape of the backbone and grooves of genomic DNA, can be dramatically affected by nucleotide changes, which can cause differences in protein-binding affinity and phenotype. We developed an algorithm to measure constraint on the basis of similarity of DNA topography among multiple species, using hydroxyl radical cleavage patterns to interrogate the solvent-accessible surface area of DNA. This algorithm found that 12% of bases in the human genome are evolutionarily constrained--double the number detected ...
	ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004) by A. Sandelin, W. W. Wasserman, B. Lenhard posted to conservation file-import-09-04-15 tfbs by akundaje on 2009-04-15 09:21:10 Abstract Copy My Attachments My Copy Abstract ConSite is a user-friendly, web-based tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering (phylogenetic footprinting). By incorporating evolutionary constraints, selectivity is increased by an order of magnitude as compared to single-sequence analysis. ConSite offers several unique features, including an interactive expert system for retrieving orthologous regulatory sequences. Programming modules and biological databases that form the foundation of the ConSite service are ...

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