@article{Sakabe10022012,
author = {Sakabe, Noboru J. and Aneas, Ivy and Shen, Tao and Shokri, Leila and Park, Soo-Young and Bulyk, Martha L. and Evans, Sylvia M. and Nobrega, Marcelo A.}, 
title = {Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function}, 
year = {2012}, 
doi = {10.1093/hmg/dds034}, 
abstract ={The ongoing requirement in adult heart for transcription factors with key roles in cardiac development is not well understood. We recently demonstrated that TBX20, a transcriptional regulator required for cardiac development, has key roles in the maintenance of functional and structural phenotypes in adult mouse heart. Conditional ablation of Tbx20 in adult cardiomyocytes leads to a rapid onset and progression of heart failure, with prominent conduction and contractility phenotypes that lead to death. Here we describe a more comprehensive molecular characterization of the functions of TBX20 in adult mouse heart. Coupling genome-wide chromatin immunoprecipitation and transcriptome analyses (RNA-Seq), we identified a subset of genes that change expression in Tbx20 adult cardiomyocyte-specific knockout hearts which are direct downstream targets of TBX20. This analysis revealed a dual role for TBX20 as both a transcriptional activator and a repressor, and that each of these functions regulates genes with very specialized and distinct molecular roles. We also show how TBX20 binds to its targets genome-wide in a context-dependent manner, using various cohorts of co-factors to either promote or repress distinct genetic programs within adult heart. Our integrative approach has uncovered several novel aspects of TBX20 and T-box protein function within adult heart.Sequencing data accession number (http://www.ncbi.nlm.nih.gov/geo): GSE30943.}, 
URL = {http://hmg.oxfordjournals.org/content/early/2012/02/23/hmg.dds034.abstract}, 
eprint = {http://hmg.oxfordjournals.org/content/early/2012/02/23/hmg.dds034.full.pdf+html}, 
journal = {Human Molecular Genetics} 
}
@article{Bowtie19261174,
author = {Langmead, Ben and Trapnell, Cole and Pop, Mihai and Salzberg, Steven},
title = {Ultrafast and memory-efficient alignment of short DNA sequences to the human genome},
journal = {Genome Biology},
volume = {10},
year = {2009},
number = {3},
pages = {R25},
url = {http://genomebiology.com/2009/10/3/R25},
doi = {10.1186/gb-2009-10-3-r25},
PubMedID = {19261174},
ISSN = {1465-6906},
abstract = {Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu webcite.},
}
@article{Barrett01012011,
author = {Barrett, Tanya and Troup, Dennis B. and Wilhite, Stephen E. and Ledoux, Pierre and Evangelista, Carlos and Kim, Irene F. and Tomashevsky, Maxim and Marshall, Kimberly A. and Phillippy, Katherine H. and Sherman, Patti M. and Muertter, Rolf N. and Holko, Michelle and Ayanbule, Oluwabukunmi and Yefanov, Andrey and Soboleva, Alexandra}, 
title = {NCBI GEO: archive for functional genomics data sets - 10 years on}, 
volume = {39}, 
number = {suppl 1}, 
pages = {D1005-D1010}, 
year = {2011}, 
doi = {10.1093/nar/gkq1184}, 
abstract ={A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20â€‰000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.}, 
url = {http://nar.oxfordjournals.org/content/39/suppl_1/D1005.abstract}, 
eprint = {http://nar.oxfordjournals.org/content/39/suppl_1/D1005.full.pdf+html}, 
journal = {Nucleic Acids Research} 
}
@article{Fujita18102010,
author = {Fujita, Pauline A. and Rhead, Brooke and Zweig, Ann S. and Hinrichs, Angie S. and Karolchik, Donna and Cline, Melissa S. and Goldman, Mary and Barber, Galt P. and Clawson, Hiram and Coelho, Antonio and Diekhans, Mark and Dreszer, Timothy R. and Giardine, Belinda M. and Harte, Rachel A. and Hillman-Jackson, Jennifer and Hsu, Fan and Kirkup, Vanessa and Kuhn, Robert M. and Learned, Katrina and Li, Chin H. and Meyer, Laurence R. and Pohl, Andy and Raney, Brian J. and Rosenbloom, Kate R. and Smith, Kayla E. and Haussler, David and Kent, W. James}, 
title = {The UCSC Genome Browser database: update 2011}, 
year = {2010}, 
doi = {10.1093/nar/gkq963}, 
abstract ={The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a Ômean+whiskersÕ windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.}, 
URL = {http://nar.oxfordjournals.org/content/early/2010/10/18/nar.gkq963.abstract}, 
eprint = {http://nar.oxfordjournals.org/content/early/2010/10/18/nar.gkq963.full.pdf+html}, 
journal = {Nucleic Acids Research} 
}
