ArticleJournal of computational biology : a journal of computational molecular cell biology2015
Building a pan-genome reference for a population.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 54 citations in OpenAlex.
- PanDelos-plus: A parallel algorithm for computing sequence homology in pangenomic analysis.PLoS computational biology · 2026Article
- Reference-agnostic representation and visualization of pan-genomes.BMC bioinformatics · 2021Article
- Plant NLR diversity: the known unknowns of pan-NLRomes.The Plant cell · 2021Review
- A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes.BMC bioinformatics · 2021Article
- Article
- Estimating Pangenomes with Roary.Molecular biology and evolution · 2020Article
- Predicting transfer RNA gene activity from sequence and genome context.Genome research · 2020Article
- Genetic Variation, Comparative Genomics, and the Diagnosis of Disease.The New England journal of medicine · 2019Review
- Whole-Genome Alignment and Comparative Annotation.Annual review of animal biosciences · 2019Review
- Article
- PanDelos: a dictionary-based method for pan-genome content discovery.BMC bioinformatics · 2018Article
- A Flow Procedure for Linearization of Genome Sequence Graphs.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery.Genome biology · 2018Article
- Computational pan-genomics: status, promises and challenges.Briefings in bioinformatics · 2018Review
- Coordinate systems for supergenomes.Algorithms for molecular biology : AMB · 2018Article
- Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.Genome research · 2017Article
- Genome graphs and the evolution of genome inference.Genome research · 2017Review
- Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage.Algorithms for molecular biology : AMB · 2016Article
- Completing the human genome: the progress and challenge of satellite DNA assembly.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
A reference genome is a high quality individual genome that is used as a coordinate system for the genomes of a population, or genomes of closely related subspecies. Given a set of genomes partitioned by homology into alignment blocks we formalize the problem of ordering and orienting the blocks such that the resulting ordering maximally agrees with the underlying genomes' ordering and orientation, creating a pan-genome reference ordering. We show this problem is NP-hard, but also demonstrate, empirically and within simulations, the performance of heuristic algorithms based upon a cactus graph decomposition to find locally maximal solutions. We describe an extension of our Cactus software to create a pan-genome reference for whole genome alignments, and demonstrate how it can be used to create novel genome browser visualizations using human variation data as a test. In addition, we test the use of a pan-genome for describing variations and as a reference for read mapping.
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What OpenQuestion holds
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.