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Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
Genome Biology 9 (9), R137 (17 Sep 2008)
info:doi/10.1186/gb-2008-9-9-r137
Posted by eldfors and 3 others to ChIP-seq Bioinformatics on Sat Sep 20 2008 at 12:27 UTC | info | related
 
F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags
Alan Boyle et al.
Bioinformatics, (10 Sep 2008)
info:pmid/18784119 | info:doi/10.1093/bioinformatics/btn480
Posted by eldfors to nextgen sequencing ChIP-seq Bioinformatics on Sat Sep 13 2008 at 10:42 UTC | info | related
 
PLoS Computational Biology: Modeling ChIP Sequencing In Silico with Applications
www.ploscompbiol.org
Posted by eldfors and 2 others to nextgen sequencing ChIP-seq illumina Chromatin Immunoprecipitation on Mon Sep 08 2008 at 12:22 UTC | info | related
 
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Heng Li, Jue Ruan, and Richard Durbin
Genome Research, (19 Aug 2008)
info:pmid/18714091 | info:doi/10.1101/gr.078212.108
http://maq.sourceforge.net/
Posted by eldfors and 4 others to nextgen sequencing read mapping Alignment algorithm Bioinformatics on Sun Aug 24 2008 at 08:32 UTC | info | related
 
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
Anton Valouev et al.
Nature methods, (17 Aug 2008)
info:pmid/18711362 | info:doi/10.1038/nmeth.1246
Posted by eldfors and 6 others to GABP nextgen sequencing ChIP-seq illumina SRF NRSF on Fri Aug 22 2008 at 08:12 UTC | info | related
 
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome.
Yutao Fu et al.
PLoS genetics 4 (7), e1000138 (Jul 2008)
info:pmid/18654629 | info:doi/10.1371/journal.pgen.1000138
Posted by eldfors to nextgen sequencing ChIP-seq ctcf illumina on Thu Aug 14 2008 at 16:49 UTC | info | related
 
How to assess a stem cell genome
Nature Reports Stem Cells, (2008)
info:doi/10.1038/stemcells.2008.85
Posted by eldfors to genome stability Stem Cell on Thu Aug 14 2008 at 12:32 UTC | info | related
 
Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells
Alexander Marson et al.
Cell 134 (3), 521-33 (08 Aug 2008)
info:pmid/18692474 | info:doi/10.1016/j.cell.2008.07.020
GEO accession #: GSE11724
Posted by eldfors and 4 others to nextgen sequencing ChIP-seq Tcf3 illumina Nanog Sox2 Stem Cell Oct4 RNA-seq miRNA on Wed Aug 13 2008 at 09:47 UTC | info | related
 
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
Raja Jothi et al.
Nucleic Acids Research 36 (16), 5221-31 (06 Aug 2008)
info:pmid/18684996 | info:doi/10.1093/nar/gkn488
Algorithm and datasets: http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/
Posted by eldfors and 5 others to nextgen sequencing ChIP-seq Chromatin Immunoprecipitation ctcf NRSF STAT1 ChIP-locus TFBS algorithm Bioinformatics on Sat Aug 09 2008 at 06:38 UTC | info | related
 
FindPeaks 3.1: A Tool for Identifying Areas of Enrichment from Massively Parallel Short-Read Sequencing Technology
FindPeaks 31 a tool for identifying areas of enrichment from massively parallel shortread sequencing technology
Bioinformatics (Oxford, England) 24 (15), 1729-30 (01 Aug 2008)
info:pmid/18599518 | info:doi/10.1093/bioinformatics/btn305
Posted by eldfors and 6 others to nextgen sequencing ChIP-seq Bioinformatics on Mon Jul 14 2008 at 17:01 UTC | info | related

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