Models for transcript quantification from RNA-Seq
Explore this paper's citation graph
Summary
This work focuses on the quantification problem of RNA-Seq, and describes the models and the different approaches to inference, and shows how inference with many of the models results in identical estimates of relative abundances, even though model formulations can be very different.
- Type
- preprint
- Published
- 2011-04-19
- Cited by
- 197
- References
- 70
- Access
- Open access
- OpenAlex
- https://openalex.org/W1617443829
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:14558903
Keywords
Inference, RNA-Seq, Computer science, Computational biology, Relative species abundance
References
- Modeling and automation of sequencing-based characterization of RNA structure
- On the comparison of multinomial and Poisson log-linear models
- RNA sequencing and quantitation using the Helicos Genetic Analysis System.
- Real-time DNA sequencing from single polymerase molecules.
- Analysis and design of RNA sequencing experiments for identifying isoform regulation
- Variation in Transcription Factor Binding Among Humans
- Computation for ChIP-seq and RNA-seq studies
- Polygenic and directional regulatory evolution across pathways in Saccharomyces
- Repeat-aware modeling and correction of short read errors
- RNA-Seq: a revolutionary tool for transcriptomics
- Methods for Allocating Ambiguous Short-reads
- Statistical Design and Analysis of RNA Sequencing Data
- How to map billions of short reads onto genomes
- Making cancer transcriptome sequencing assays practical for the research and clinical scientist
- Recovering frequencies of known haplotype blocks from single-nucleotide polymorphism allele frequencies.
- Cloud-scale RNA-sequencing differential expression analysis with Myrna
- Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing.
- Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq.
- Modeling non-uniformity in short-read rates in RNA-Seq data
- Understanding mechanisms underlying human gene expression variation with RNA sequencing
Cited by
- Computational approaches for isoform detection and estimation: good and bad news
- Prognostic and immunological potential of PPM1G in lung adenocarcinoma
- Algorithms And Tools For Computational Analysis Of Human Transcriptome Using Rna-Seq
- Robust estimation of isoform expression with RNA-Seq data
- Statistical algorithms in the study of mammalian DNA methylation
- Increasing the Evidential Value of Biological evidence
- Assessing Dissimilarity Measures for Sample-Based Hierarchical Clustering of RNA Sequencing Data Using Plasmode Datasets
- Realistic simulations reveal extensive sample-specificity of RNA-seq biases
- A penalized likelihood approach for robust estimation of isoform expression
- Methods to study splicing from high-throughput RNA sequencing data.
- Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap
- Avances en el conocimiento de la fermentación maloláctica de vinos tintos elaborados en Castilla-La Mancha
- Isoform reconstruction using short RNA-Seq reads by maximum likelihood is NP-hard
- An island-based approach for RNA-SEQ differential expression analysis.
- Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis
- CEDER: Accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq
- FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions
- ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq
- Cardiovascular Transcriptomics and Epigenomics Using Next-Generation Sequencing: Challenges, Progress, and Opportunities
- Evaluating statistical analysis models for RNA sequencing experiments
Related papers
- Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
- TopHat: discovering splice junctions with RNA-Seq
- RNA-Seq gene expression estimation with read mapping uncertainty
- Statistical inferences for isoform expression in RNA-Seq
- Differential expression analysis for sequence count data
- Fast gapped-read alignment with Bowtie 2
- Alternative Isoform Regulation in Human Tissue Transcriptomes