Nebula-a web-server for advanced ChIP-seq data analysis

Bioinformatics

Volumn 28, Issue 19, 2012, Pages 2517-2519

  Boeva, Valentina ^a,b,c   Lermine, Alban ^a,b,c   Barette, Camille ^a,b,c   Guillouf, Christel ^a,d   Barillot, Emmanuel ^a,b,c  

^a INSTITUT CURIE   (France)

^b INSERM   (France)

^c PSL RESEARCH UNIVERSITY   (France)

^d INSTITUT CURIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; BIOLOGY; CHROMATIN IMMUNOPRECIPITATION; COMPUTER PROGRAM; HIGH THROUGHPUT SEQUENCING; INTERNET; METHODOLOGY;

BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; SOFTWARE;

EID: 84867325570     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts463     Document Type: Article

References (15)

1. Boeva, V. et al. (2010) De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. Nucleic Acids Res., 38, e126.
2. Fejes, A. et al. (2008) FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics, 24, 729-1730.
3. Goecks, J. et al. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
4. Homer, N. et al. (2009) BFAST: an alignment tool for large scale genome resequencing. PLoS One, 4, e7767.
5. Ji, H. et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol., 26, 1293-1300.
6. Ji, X. et al. (2006) CEAS: cis-regulatory element annotation system. Nucleic Acids Res., 34 (Web Server issue), W551-W554.
7. Kulakovskiy, I. et al. (2010) Deep and wide digging for binding motifs in ChIP-Seq data. Bioinformatics, 26, 2622-2623.
8. Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
9. Li, H. et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
10. Liu, T. et al. (2011) Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol., 12, R83.
11. Pruitt, K.D. et al. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40 (Database issue), D130-D135.
12. Ridinger-Saison, M. et al. (2012) Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia. Nucleic Acids Res., [Epub ahead of print] PubMed
13. Shin, H. et al. (2009) CEAS: cis-regulatory element annotation system. Bioinformatics, 25, 2605-2606.
14. Zhang, Y. et al. (2008)Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
15. Wilbanks, E.G. and Facciotti, M.T. (2010) Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One, 5, e11471.