Statistical modeling of isoform splicing dynamics from RNA-seq time series data

Yuanhua Huang, Guido Sanguinetti


Isoformquantification is an important goal of RNA-seq experiments, yet it remains problematic for genes with low expression or several isoforms. These difficulties may in principle be ameliorated by exploiting correlated experimental designs, such as time series or dosage response experiments. Time series RNA-seq experiments, in particular, are becoming increasingly popular, yet there are no methods that explicitly leverage the experimental design to improve isoform quantification. Here we present DICEseq, the first isoform quantification method tailored to correlated RNAseq experiments. DICEseq explicitly models the correlations between different RNA-seq experiments to aid the quantification of isoforms across experiments. Numerical experiments on simulated data sets show that DICEseq yields more accurate results than state-of-the-art methods, an advantage that can become considerable at low coverage levels. On real data sets, our results show that DICEseq provides substantially more reproducible and robust quantifications, increasing the correlation of estimates from replicate data sets by up to 10% on genes with low or moderate expression levels (bottom third of all genes). Furthermore, DICEseq permits to quantify the trade-...Continue Reading


Feb 15, 2001·Trends in Genetics : TIG·B R Graveley
Jul 15, 2006·Cell·Benjamin J Blencowe
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Oliver StegleKarsten M Borgwardt
Nov 9, 2010·Nature Methods·Yarden KatzChristopher B Burge
Mar 18, 2011·Genome Biology·Adam RobertsLior Pachter
Apr 21, 2011·Algorithms for Molecular Biology : AMB·Marius NicolaeAlex Zelikovsky
Jul 19, 2012·Nature Reviews. Genetics·Ziv Bar-JosephItamar Simon
Oct 29, 2014·Proceedings of the National Academy of Sciences of the United States of America·Ray ZhangJohn B Hogenesch
Jan 15, 2015·Genome Biology·Brian Tjaden
Jan 30, 2015·Genome Biology·Olivier GevaertSylvia K Plevritis
Mar 10, 2015·Nature Methods·Daehwan KimSteven L Salzberg
Apr 4, 2015·PloS One·Birk Diedenhofen, Jochen Musch
Oct 7, 2015·Proceedings of the National Academy of Sciences of the United States of America·Antti HonkelaMagnus Rattray
Nov 25, 2015·Nature Reviews. Genetics·Marina M Scotti, Maurice S Swanson
Feb 18, 2016·Molecular Systems Biology·Philipp EserJulien Gagneur


Jun 29, 2017·Genome Biology·Yuanhua Huang, Guido Sanguinetti

Related Concepts

Protein Isoforms
Research Study
Sequence Determinations, RNA
Protein Expression
Nucleic Acid Sequencing
Statistical Technique

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.