Titlebook: Regulatory Genomics; RECOMB 2004 Internat Eleazar Eskin,Christopher Workman Conference proceedings 2005 Springer-Verlag Berlin Heidelberg 2

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Application of Kernel Method to Reveal Subtypes of TF Binding Motifs, novel sensitive method based on kernel estimations that is able to reveal subtypes of TF binding sites. The developed method produces patterns in form of positional weight matrices for the individual subtypes and has been tested on simulated data and compared with several other methods of pattern d

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Learning Regulatory Network Models that Represent Regulator States and Roles,transcriptional regulation than previous methods. Our approach involves learning Bayesian network models using both gene-expression and genomic-sequence data. One key aspect of our approach is that our models represent . of regulators in addition to their expression levels. For example, the state of

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Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs,ere are two major approaches to incorporating expression data into the discovery of TFBS. The first approach clusters genes according to their expression patterns. Then, over-represented sequences are sought, in the promoter regions of co-expressed genes [31, 15, 14]. A second approach uses a single

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Parameter Landscape Analysis for Common Motif Discovery Programs, problem in computational biology. Although many motif detection programs have been developed so far, they still seem to be immature practically. In particular the choice of tunable parameters is often critical to success. Thus knowledge regarding which parameter settings are most appropriate for va

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Parameter Landscape Analysis for Common Motif Discovery Programs,is more stable. We present recommended parameter settings for GS optimized for four different motif lengths. Thus, running GS four times with these settings should significantly decrease the risk of overlooking subtle motifs.

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Manuel Middendorf,Anshul Kundaje,Chris Wiggins,Yoav Freund,Christina Leslieation throughout the world.Contains case studies, practical Is it a sign of the times that last year the Nobel committee chose to award the Nobel Peace prize to Wangari Maathai for having planted 30 million trees? We believe so.We think that while in the 20th century conservation made signi?cant pro