title: De novo ChIP-seq analysis.
abstract: Methods for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data start by aligning the short reads to a reference genome. While often successful, they are not appropriate for cases where a reference genome is not available. Here we develop methods for de novo analysis of ChIP-seq data. Our methods combine de novo assembly with statistical tests enabling motif discovery without the use of a reference genome. We validate the performance of our method using human and mouse data. Analysis of fly data indicates that our method outperforms alignment based methods that utilize closely related species.
authors.affiliation: Department of Human Genetics, The University of Chicago, 920 E. 58th Street, CLSC, Chicago, IL, 60637, USA. xinhe@uchicago.edu.
authors.forename: Xin
authors.initials: X
authors.lastname: He
authors.affiliation: Computational Biology Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, 15213, USA. cicek@cs.cmu.edu.|Department of Computer Engineering, Bilkent University, Ankara, 06800, Turkey. cicek@cs.cmu.edu.
authors.forename: A Ercument
authors.initials: AE
authors.lastname: Cicek
authors.affiliation: Computer Science and Artificial Intelligence Laboratory, 32 Vassar Street, MIT, Cambridge, MA, 02139, USA. yuhaow@mit.edu.
authors.forename: Yuhao
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Multimodal Computing and Interaction, Saarland University & Max Planck Institute for Informatics, Saarbrücken, 66123, Saarland, Germany. mschulz@mmci.uni-saarland.de.
authors.forename: Marcel H
authors.initials: MH
authors.lastname: Schulz
authors.affiliation: Computational Biology Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, 15213, USA. hple+@cs.cmu.edu.
authors.forename: Hai-Son
authors.initials: HS
authors.lastname: Le
authors.affiliation: Computational Biology Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, 15213, USA. zivbj@cs.cmu.edu.
authors.forename: Ziv
authors.initials: Z
authors.lastname: Bar-Joseph
mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004330:Drosophila / Q000235:genetics; D053595:Embryonic Stem Cells / Q000378:metabolism; D006801:Humans; D051379:Mice; D059372:Nucleotide Motifs; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors