Now showing items 1-5 of 5

    • Expression-Guided in Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells 

      Philippakis, Anthony Andrew; Busser, Brian W; Gisselbrecht, Stephen S; He, Fangxue Sherry; Estrada, Beatriz; Michelson, Alan D; Bulyk, Martha Leonia (Public Library of Science, 2006)
      While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need ...
    • Inferring Condition-Specific Transcription Factor Function from DNA Binding and Gene Expression Data 

      McCord, Rachel Patton; Berger, Michael F; Philippakis, Anthony Andrew; Bulyk, Martha Leonia (2007)
      Numerous genomic and proteomic datasets are permitting the elucidation of transcriptional regulatory networks in the yeast Saccharomyces cerevisiae. However, predicting the condition dependence of regulatory network ...
    • A Map of Human Genome Variation from Population Scale Sequencing 

      Altshuler, David Matthew; Lander, Eric Steven; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Lee, Charles; Mills, Ryan Edward; Shi, Xinghua; Daly, Mark Joseph; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon Rachel; Handsaker, Robert E; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; Nemesh, James C.; McKenna, Aaron; Philippakis, Anthony Andrew; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis Christine; Schaffner, Stephen; Shlyakhter, Ilya (Nature Publishing Group, 2010)
      The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot ...
    • Mapping Copy Number Variation by Population Scale Genome Sequencing 

      Mills, Ryan Edward; Handsaker, Robert E; Korn, Joshua; Nemesh, James; Shi, Xinghua; Lee, Charles; McCarroll, Steven A.; Altshuler, David Matthew; Gabriel, Stacey B.; Lander, Eric Steven; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Daly, Mark Joseph; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon Rachel; Handsaker, Robert E; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Li, Heng; Maguire, Jared R.; McKenna, Aaron; Philippakis, Anthony Andrew; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis Christine; Schaffner, Stephen; Shlyakhter, Ilya; DePristo, Mark A.; Wilkinson, Jane (Nature Publishing Group, 2011)
      Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of ...
    • Predicting the Binding Preference of Transcription Factors to Individual DNA \(\kappa\)-mers 

      Alleyne, Trevis M.; Peña-Castillo, Lourdes; Badis, Gwenael; Talukder, Shaheynoor; Berger, Michael F.; Gehrke, Andrew R.; Philippakis, Anthony Andrew; Bulyk, Martha Leonia; Morris, Quaid D.; Hughes, Timothy R. (Oxford University Press, 2008)
      Motivation: Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding preferences, however, are unknown or poorly characterized, in part due ...