title: RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints.
abstract: Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case-control studies are needed.
  
  
  
  We present a statistical framework and an analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency using both mRNA abundance and ribosome occupancy.
  
  
  
  RiboDiff webpage http://bioweb.me/ribodiff Source code including scripts for preprocessing the FASTQ data are available at http://github.com/ratschlab/ribodiff CONTACTS: zhongy@cbio.mskcc.org or raetsch@inf.ethz.chSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Computational Biology Program, Sloan Kettering Institute, New York, NY 1275, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhong
authors.affiliation: Computational Biology Program, Sloan Kettering Institute, New York, NY 1275, USA.
authors.forename: Theofanis
authors.initials: T
authors.lastname: Karaletsos
authors.affiliation: Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Drewe
authors.affiliation: Computational Biology Program, Sloan Kettering Institute, New York, NY 1275, USA.
authors.forename: Vipin T
authors.initials: VT
authors.lastname: Sreedharan
authors.affiliation: Computational Biology Program, Sloan Kettering Institute, New York, NY 1275, USA.
authors.forename: David
authors.initials: D
authors.lastname: Kuo
authors.affiliation: Cancer Biology Program, Sloan Kettering Institute, New York, NY, USA.
authors.forename: Kamini
authors.initials: K
authors.lastname: Singh
authors.affiliation: Cancer Biology Program, Sloan Kettering Institute, New York, NY, USA.
authors.forename: Hans-Guido
authors.initials: HG
authors.lastname: Wendel
authors.affiliation: Computational Biology Program, Sloan Kettering Institute, New York, NY 1275, USA.|Department of Computer Science, ETH Zurich, Universitatsstrasse 6, 8092 Zrich, Switzerland.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Rätsch
mesh_terms: D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012333:RNA, Messenger