ReviewBriefings in bioinformatics2018
Computational pan-genomics: status, promises and challenges.
Review in Briefings in bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
168 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
- Privacy-preserving pangenome graphs.Nature communications · 2026Article
- SURE-Pipe: a pipeline to compare genomes and extract shared and unique regions.NAR genomics and bioinformatics · 2026Article
- Theseus: fast and optimal affine-gap sequence-to-graph alignment.Bioinformatics (Oxford, England) · 2026Article
- PangyPlot: multi-scale interactive visualization of pangenome variation graphs.Bioinformatics (Oxford, England) · 2026Article
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping.Briefings in bioinformatics · 2026Article
- Panorama: A robust pangenome-based method for predicting and comparing biological systems across species.PLoS computational biology · 2026Article
- Lossless pangenome indexing using tag arrays.Algorithms for molecular biology : AMB · 2026Article
- A novel Vector-Symbolic Architecture for graph encoding and its application to viral pangenome-based species classification.BioData mining · 2026Article
- Pattern matching with Elastic-Degenerate strings and Elastic-Founder graphs.Algorithms for molecular biology : AMB · 2026Article
- LCPAN: efficient variation graph construction using locally consistent parsing.Genome biology · 2026Article
- Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.bioRxiv : the preprint server for biology · 2026Article
- Celebrating 25 years of briefings in bioinformatics: a comprehensive bibliometric analysis.Briefings in bioinformatics · 2026Article
- Compressive pangenomics using mutation-annotated networks.Nature genetics · 2026Article
- Lossless Pangenome Indexing Using Tag Arrays.Research square · 2026Article
- From one genome to thousands, and beyond.FEMS yeast research · 2026Review
- From few to many: How non-model organisms' genomics broadened our understanding of molecular evolution.Genetics and molecular biology · 2026Article
- Conserved accessory genes link a phylogenetically distinct Bacillus subtilis strain from Indian bekang to the Japanese natto clade.Scientific reports · 2025Article
108 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.
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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.