The DOI matches its Crossref record; 152 of the 152 references it cites were found in a registry or an index.
Computational pan-genomics: status, promises and challenges
Open accessPublished version of a preprint
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Self-citationInitial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247
Self-citationThe sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Self-citationStructure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., & Barton, G. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp033 · Cited by 10,235
Analysis of protein-coding genetic variation in 60,706 humans
Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049
dbSNP: the NCBI database of genetic variation
Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502
Research works printed but not linked: 11
- Sigaux, 2000, Cancer genome or the development of molecular portraits of tumors [in French], Bull Acad Natl Med, 184, 1441
- Kafarski, 2012, Rainbow code of biotechnology, Chemik, 66, 811
- 10.3389/fmicb.2015.00224 · doi:10.3389/fmicb.2015.00224
- 10.1093/bioinformatics/btp377 · doi:10.1093/bioinformatics/btp377
- 10.1038/nrmicro1477 · doi:10.1038/nrmicro1477
- 10.1186/1471-2105-14-102 · DOI
- Beller T Ohlebusch E. Efficient construction of a compressed de Bruijn graph for Pan-genome analysis. In: Cicalese F Porat E Vaccaro U (eds), Combinatorial Pattern Matching, number 9133 in Lecture Notes in Computer Science. Springer International Publishing, Switzerland, 2015, 40–51. · doi:10.1007/978-3-319-19929-0_4
- Ernst C Rahmann S. PanCake: a data structure for pangenomes. In: Beißbarth T Kollmar M Leha A Morgenstern B Schultz AK Waack S Wingender E (eds), German Conference on Bioinformatics 2013. volume 34 of OpenAccess Series in Informatics (OASIcs) . Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, 2013, 35–45.
- Beckstein C Böcker S Bogdan M , . Explorative analysis of heterogeneous, unstructured, and uncertain data: a computer science perspective on biodiversity research. In: Helfert M Holzinger A Belo O Francalanci C (eds), Proceedings of the 3rd International Conference on Data Management Technologies and Applications, DATA 2014, Vienna, Austria. SCITEPRESS, 2014, 251–57. · doi:10.5220/0005098402510257
- 10.1371/journal.pcbi.1003502 · DOI
- 10.1371/journal.pone.0138259 · doi:10.1371/journal.pone.0138259
Cited by
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies
Goel, M., Sun, H., Jiao, W.-B., & Schneeberger, K. (2019) · Genome Biology · doi:10.1186/s13059-019-1911-0 · Cited by 1,045
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702
Self-citationThe Human Pangenome Project: a global resource to map genomic diversity
Wang, T., Antonacci-Fulton, L., Howe, K., Lawson, H. A., Lucas, J. K., Phillippy, A. M., Popejoy, A. B., Asri, M., Carson, C., Chaisson, M. J. P., et al. (2022) · Nature · doi:10.1038/s41586-022-04601-8 · Cited by 494
The design and construction of reference pangenome graphs with minigraph
Li, H., Feng, X., & Chu, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02168-z · Cited by 455
Metadata
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-10-21
- Volume
- 19
- Issue
- 1
- Pages
- bbw089
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- OpenAlex
- W2952366981
- Cited by
- 287
- References
- 152
- FWCI
- 11.14
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Computational pan-genomics: status, promises and challenges. https://app.cochat.ai/papers/10.1093/bib/bbw089
- The paper
- Computational pan-genomics: status, promises and challenges. (2016). Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbw089
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
