ArticleGenome research2004
The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
36 citing papers in PubMed.
- The splice of life: an isoform-centric view of disease, technology, and therapeutics.The Journal of clinical investigation · 2026Review
- rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data.Nature protocols · 2024Review
- Efficient Minimum Flow Decomposition via Integer Linear Programming.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Tasks, Techniques, and Tools for Genomic Data Visualization.Computer graphics forum : journal of the European Association for Computer Graphics · 2019Article
- A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.Bioinformatics (Oxford, England) · 2017Article
- Optimal antisense target reducing INS intron 1 retention is adjacent to a parallel G quadruplex.Nucleic acids research · 2014Article
- The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites.BMC genomics · 2014Article
- PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.Genomics, proteomics & bioinformatics · 2014Article
- On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly.BMC bioinformatics · 2014Article
- MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.Bioinformatics (Oxford, England) · 2013Article
- TMEM16A alternative splicing coordination in breast cancer.Molecular cancer · 2013Article
- A novel min-cost flow method for estimating transcript expression with RNA-Seq.BMC bioinformatics · 2013Article
- Generation and analysis of the expressed sequence tags from the mycelium of Ganoderma lucidum.PloS one · 2013Article
- RCDA: a highly sensitive and specific alternatively spliced transcript assembly tool featuring upstream consecutive exon structures.Genomics · 2012Article
- SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.Bioinformatics (Oxford, England) · 2012Article
- PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text.BMC bioinformatics · 2012Article
- SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.Genome biology · 2012Article
- SpliceDisease database: linking RNA splicing and disease.Nucleic acids research · 2012Article
- Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements.Frontiers in plant science · 2012Article
- Pediatric pharmacogenetic and pharmacogenomic studies: the current state and future perspectives.European journal of clinical pharmacology · 2011Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Recent evidence of abundant transcript variation (e.g., alternative splicing, alternative initiation, alternative polyadenylation) in complex genomes indicates that cataloging the complete set of transcripts from an organism is an important project. One challenge is the fact that most high-throughput experimental methods for characterizing transcripts (such as EST sequencing) give highly detailed information about short fragments of transcripts or protein products, instead of a complete characterization of a full-length form. We analyze this "multiassembly problem"-reconstructing the most likely set of full-length isoform sequences from a mixture of EST fragment data-and present a graph-based algorithm for solving it. In a variety of tests, we demonstrate that this algorithm deals appropriately with coupling of distinct alternative splicing events, increasing fragmentation of the input data and different types of transcript variation (such as alternative splicing, initiation, polyadenylation, and intron retention). To test the method's performance on pure fragment (EST) data, we removed all mRNA sequences, and found it produced no errors in 40 cases tested. Using this algorithm, we have constructed an Alternatively Spliced Proteins database (ASP) from analysis of human expressed and genomic sequences, consisting of 13,384 protein isoforms of 4422 genes, yielding an average of 3.0 protein isoforms per gene.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.