ArticleBMC bioinformatics2013
A novel min-cost flow method for estimating transcript expression with RNA-Seq.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
- Minimum flow decomposition guided by saturating subflows.bioRxiv : the preprint server for biology · 2026Article
- Data-driven AI system for learning how to run transcript assemblers.Genome biology · 2026Article
- Open-Field Blast Injury Disrupts Corneal Gene Expression Linked to Ion Transport, Sensory Perception, and Neural Signaling.Investigative ophthalmology & visual science · 2025Article
- Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses.BMC genomics · 2024Article
- Transcriptomic landscape of quiescent and proliferating human corneal stromal fibroblasts.Experimental eye research · 2024Article
- RNA-Seq Analysis Unraveling Novel Genes and Pathways Influencing Corneal Wound Healing.Investigative ophthalmology & visual science · 2024Article
- Floria: fast and accurate strain haplotyping in metagenomes.Bioinformatics (Oxford, England) · 2024Article
- A safety framework for flow decomposition problems via integer linear programming.Bioinformatics (Oxford, England) · 2023Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- Phables: from fragmented assemblies to high-quality bacteriophage genomes.Bioinformatics (Oxford, England) · 2023Article
- Phables: from fragmented assemblies to high-quality bacteriophage genomes.bioRxiv : the preprint server for biology · 2023Article
- Improving RNA Assembly via Safety and Completeness in Flow Decompositions.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Efficient Minimum Flow Decomposition via Integer Linear Programming.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Tiglon enables accurate transcriptome assembly via integrating mappings of different aligners.iScience · 2022Article
- Accurate assembly of multi-end RNA-seq data with Scallop2.Nature computational science · 2022Article
- Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Article
- TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.Genome research · 2020Article
- A multi-sample approach increases the accuracy of transcript assembly.Nature communications · 2019Article
- Ryūtō: network-flow based transcriptome reconstruction.BMC bioinformatics · 2019Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThrough transcription and alternative splicing, a gene can be transcribed into different RNA sequences (isoforms), depending on the individual, on the tissue the cell is in, or in response to some stimuli. Recent RNA-Seq technology allows for new high-throughput ways for isoform identification and quantification based on short reads, and various methods have been put forward for this non-trivial problem.
resultsIn this paper we propose a novel radically different method based on minimum-cost network flows. This has a two-fold advantage: on the one hand, it translates the problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers; on the other hand, it is general enough to encompass many of the previous proposals under the least sum of squares model. Our method works as follows: in order to find the transcripts which best explain, under a given fitness model, a splicing graph resulting from an RNA-Seq experiment, we find a min-cost flow in an offset flow network, under an equivalent cost model. Under very weak assumptions on the fitness model, the optimal flow can be computed in polynomial time. Parsimoniously splitting the flow back into few path transcripts can be done with any of the heuristics and approximations available from the theory of network flows. In the present implementation, we choose the simple strategy of repeatedly removing the heaviest path.
conclusionsWe proposed a new very general method based on network flows for a multiassembly problem arising from isoform identification and quantification with RNA-Seq. Experimental results on prediction accuracy show that our method is very competitive with popular tools such as Cufflinks and IsoLasso. Our tool, called Traph (Transcrips in gRAPHs), is available at: http://www.cs.helsinki.fi/gsa/traph/.
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