title: INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments.
abstract: BACKGROUND
  Cellular mRNA levels originate from the combined action of multiple regulatory processes, which can be recapitulated by the rates of pre-mRNA synthesis, pre-mRNA processing and mRNA degradation. Recent experimental and computational advances set the basis to study these intertwined levels of regulation. Nevertheless, software for the comprehensive quantification of RNA dynamics is still lacking.
  
  
  RESULTS
  INSPEcT is an R package for the integrative analysis of RNA- and 4sU-seq data to study the dynamics of transcriptional regulation. INSPEcT provides gene-level quantification of these rates, and a modeling framework to identify which of these regulatory processes are most likely to explain the observed mRNA and pre-mRNA concentrations. Software performance is tested on a synthetic dataset, instrumental to guide the choice of the modeling parameters and the experimental design.
  
  
  METHODS
  INSPEcT is submitted to Bioconductor and is currently available as Supplementary Additional File S1.
  
  
  BACKGROUND
  mattia.pelizzola@iit.it
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and.
authors.forename: Stefano
authors.initials: S
authors.lastname: de Pretis
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and.
authors.forename: Theresia
authors.initials: T
authors.lastname: Kress
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and.
authors.forename: Marco J
authors.initials: MJ
authors.lastname: Morelli
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and.
authors.forename: Giorgio E M
authors.initials: GE
authors.lastname: Melloni
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and.
authors.forename: Laura
authors.initials: L
authors.lastname: Riva
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and Department of Experimental Oncology, European Institute of Oncology (IEO), 20139, Milano, Italy.
authors.forename: Bruno
authors.initials: B
authors.lastname: Amati
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and.
authors.forename: Mattia
authors.initials: M
authors.lastname: Pelizzola
mesh_terms: D000465:Algorithms; D000818:Animals; D002478:Cells, Cultured; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D051379:Mice; D012313:RNA / Q000235:genetics*; D012322:RNA Precursors / Q000235:genetics*; D020871:RNA Stability / Q000235:genetics*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014158:Transcription, Genetic
chemical_list: D012322:RNA Precursors; D012333:RNA, Messenger; D012313:RNA