The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
The Genome 10K Project: A Way Forward
Open accessAbstract
The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species.
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“The Vertebrate Genomes Project38 led by the Genome 10K39 and the Earth BioGenome Project40, among others, aim to release thousands of new, high-quality genome assemblies over the next decade.”
From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [39]
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“Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to the development of long-read sequencing technologies like the Pacific Biosciences and Oxford Nanopore platforms (52); the development of DNA proximity ligation sequencing techniques, like Hi-C, for genome scaffolding (53–55); and the efforts of genome sequencing consortia (1, 2, 4, 56)”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [56]
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“The number of whole-genome assemblies for species throughout the tree of life continues to grow at a very fast rate , and efforts are underway to produce thousands more (Koepfli et al. 2015;Lewin et al. 2018).”
From RepeatModeler2 for automated genomic discovery of transposable element families (2020) · cites this paper as Koepfli et al. 2015
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STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
The 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
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
The zebrafish reference genome sequence and its relationship to the human genome.
Howe, K., Clark, M. D., Torroja, C. F., Torrance, J., Berthelot, C., Muffato, M., Collins, J. E., Humphray, S., McLaren, K., Matthews, L., et al. (2013) · Nature · doi:10.1038/nature12111 · Cited by 5,100
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971
The global diversity of birds in space and time
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K., & Mooers, A. O. (2012) · Nature · doi:10.1038/nature11631 · Cited by 3,934
Research works printed but not linked: 239
- 10.1093/jhered/esp086 · DOI
- 10.1038/462021a · DOI
- 10.1126/science.326_794 · DOI
- 10.1186/2047-217X-1-8 · DOI
- 10.1101/gr.131383.111 · DOI
- 10.1038/nrg3174 · DOI · Paper page
- 10.1101/gr.126599.111 · DOI
- 10.1186/2047-217X-2-10 · DOI
- Azvolinsky A, 2014, The Scientist
- 10.1038/nature09796 · DOI
- 10.1186/gb-2011-12-8-125 · DOI
- 10.1038/507294a · DOI
- 10.1038/nature12826 · DOI
- 10.1038/ng.2835 · DOI
- 10.1016/j.margen.2012.02.002 · DOI
- 10.1101/gr.101360.109 · DOI
- 10.1109/MSPEC.2013.6545119 · DOI
- 10.1101/gr.094557.109 · DOI
- 10.1038/nrg3367 · DOI · Paper page
- 10.1093/bioinformatics/bti769 · DOI
- 10.1038/ng.3121 · DOI
- 10.1093/bioinformatics/bts723 · DOI
- 10.1186/1756-0500-6-334 · DOI
- 10.1186/gb-2013-14-1-r8 · DOI
- 10.1186/1471-2164-15-439 · DOI
- 10.1101/gr.168450.113 · DOI
- 10.1038/nbt.2833 · DOI
- 10.1038/nmeth.2474 · DOI · Paper page
- 10.1186/gb-2013-14-9-r101 · DOI
- 10.1186/gb-2013-14-6-405 · DOI
- 10.1038/nbt.2280 · DOI
- 10.1126/science.1229112 · DOI
- 10.1016/j.cell.2012.06.030 · DOI
- 10.1101/gr.144600.112 · DOI
- 10.1038/nbt.2478 · DOI
- 10.1038/nbt.2303 · DOI
- 10.1371/journal.pone.0055864 · DOI
- 10.1186/1471-2105-13-189 · DOI
- 10.1186/1471-2164-14-604 · DOI
- 10.1038/nature11247 · DOI · Paper page
- 10.1186/1471-2105-14-274 · DOI
- 10.1038/nmeth.2714 · DOI · Paper page
- 10.1101/gr.7128207 · DOI
- 10.1101/gr.157503.113 · DOI
- 10.1073/pnas.1318948111 · DOI
- 10.1093/nar/gkt1196 · DOI
- 10.1093/nar/gkt1168 · DOI · Paper page
- Earl D, 2014, bioRxiv.
- 10.1101/gr.1933104 · DOI · Paper page
- 10.1093/nar/gkr334 · DOI
- 10.1093/bioinformatics/btn630 · DOI
- 10.1038/366265a0 · DOI
- 10.1126/science.1072104 · DOI · Paper page
- 10.1038/nature05846 · DOI · Paper page
- 10.1038/nature10944 · DOI
- 10.1038/ng.2604 · DOI
- 10.1093/molbev/mss194 · DOI
- 10.1093/bfgp/elt046 · DOI
- 10.1641/0006-3568(2005)055[0693:NAAGCA]2.0.CO;2 · DOI
- 10.1126/science.1183670 · DOI
- 10.1046/j.1095-8312.2003.00191.x · DOI
- 10.1007/s10577-011-9248-x · DOI
- 10.1093/aob/mci009 · DOI
- 10.1093/gbe/evr139 · DOI
- 10.1086/655116 · DOI
- Ryan MJ, 1985, The Túngara Frog: A Study in Sexual Selection and Communication
- 10.1002/1521-1878(200103)23:3<233::AID-BIES1033>3.0.CO;2-Q · DOI
- 10.1126/science.1146035 · DOI
- 10.1111/j.1365-294X.2012.05644.x · DOI
- 10.1111/j.1748-1090.2008.00043.x · DOI
- 10.1093/molbev/msr269 · DOI
- 10.1017/S0006323197005045 · DOI
- 10.1111/j.1744-7429.2005.00026.x · DOI
- 10.1073/pnas.1106893108 · DOI
- Hedges SB, 2009, The Timetree of Life, 383, 10.1093/oso/9780199535033.003.0053 · DOI
- 10.1146/annurev-genom-082410-101518 · DOI
- 10.1007/s10577-011-9266-8 · DOI
- 10.1371/journal.pbio.1001643 · DOI
- 10.1007/978-90-481-2770-2_21 · DOI
- 10.1159/000295177 · DOI
- 10.1093/icb/icn046 · DOI
- 10.1038/nature10390 · DOI
- 10.1093/gbe/evr072 · DOI
- 10.1186/1471-2164-14-49 · DOI
- 10.1186/gb-2011-12-7-406 · DOI
- 10.1073/pnas.1314475110 · DOI
- 10.1073/pnas.1314702110 · DOI
- 10.1126/science.1254449 · DOI · Paper page
- 10.1038/cr.2013.104 · DOI
- 10.1186/gb-2013-14-3-r28 · DOI
- 10.1038/ng.2615 · DOI
- 10.1146/annurev.genom.9.081307.164356 · DOI
- 10.1007/s10577-005-1010-9 · DOI
- 10.1126/science.1135925 · DOI
- Feduccia A, 1999, The Origin and Evolution of Birds
- 10.1093/sysbio/syt110 · DOI
- 10.1038/nature08819 · DOI
- 10.1126/science.1157704 · DOI · Paper page
- 10.1093/molbev/msr014 · DOI
- 10.1371/journal.pone.0054848 · DOI
- 10.1641/B580706 · DOI
- 10.1186/2047-217X-3-26 · DOI
- 10.1186/2047-217X-3-32 · DOI
- 10.1126/science.1253451 · DOI · Paper page
- 10.1126/science.1251385 · DOI · Paper page
- 10.1126/science.1122277 · DOI
- 10.1038/nrg3707 · DOI
- 10.1038/nature12228 · DOI
- 10.1038/nature11584 · DOI
- 10.1038/ncomms3212 · DOI
- 10.1186/1471-2164-14-567 · DOI
- 10.1146/annurev-animal-031412-103636 · DOI
- 10.1073/pnas.1102838108 · DOI
- 10.1126/science.1188021 · DOI · Paper page
- 10.1038/nature07446 · DOI
- 10.1126/science.1236573 · DOI · Paper page
- 10.1038/ng.2890 · DOI
- 10.1101/gr.403602 · DOI
- 10.1101/gr.094607.109 · DOI
- 10.1093/bioinformatics/btt637 · DOI
- 10.1073/pnas.1315760110 · DOI
- 10.1038/ng.2568 · DOI
- 10.1093/gbe/evr041 · DOI
- 10.1038/nature10342 · DOI · Paper page
- 10.1016/j.gene.2012.09.064 · DOI
- 10.1073/pnas.1302051110 · DOI
- 10.1038/ncomms4657 · DOI
- 10.1126/science.1254432 · DOI
- 10.1038/ng.3098 · DOI
- 10.1038/ncomms6307 · DOI
- 10.1038/ncomms6227 · DOI
- 10.1038/ncomms6594 · DOI
- 10.1038/nature12027 · DOI
- 10.1101/gr.158105.113 · DOI
- 10.1098/rspb.2014.1122 · DOI
- 10.1186/2047-217X-1-14 · DOI
- 10.1038/ng.2657 · DOI
- 10.1371/journal.pone.0062415 · DOI
- 10.1016/j.ygeno.2013.03.006 · DOI
- 10.1038/ng.2588 · DOI
- 10.1186/1471-2164-14-95 · DOI
- 10.1186/2047-217X-3-11 · DOI
- 10.1186/gb-2013-14-3-r29 · DOI
- 10.1038/ncomms3071 · DOI
- 10.1371/journal.pone.0095599 · DOI
- 10.1371/journal.pone.0090240 · DOI
- 10.1126/science.1253226 · DOI
- 10.1186/1471-2164-15-180 · DOI
- Callicrate T, Dikow R, Thomas JW, Mullikin JC, NISC Comp. Seq. Progr., et al. 2014. Genomic resources for the endangered Hawaiian honeycreepers.BMC Genomics15:1098 · DOI
- 10.1038/35057062 · DOI · Paper page
- 10.1038/nature02426 · DOI
- 10.1101/gr.6380007 · DOI · Paper page
- 10.1038/nbt.1992 · DOI
- 10.1038/nature05805 · DOI · Paper page
- 10.1186/gb-2009-10-4-r42 · DOI
- 10.1038/srep04958 · DOI
- 10.1111/j.1365-2052.2010.02100.x · DOI
- 10.1038/nbt.2645 · DOI · Paper page
- 10.1038/nbt.2624 · DOI · Paper page
- 10.1186/gb-2012-13-7-r58 · DOI
- 10.1186/gb-2011-12-8-r81 · DOI
- 10.1371/journal.pone.0015811 · DOI
- 10.1038/nature09687 · DOI
- 10.1016/j.cell.2011.11.065 · DOI
- 10.1038/ncomms6188 · DOI
- 10.1093/jhered/esr153 · DOI
- 10.1038/ncomms2192 · DOI
- 10.1093/gbe/evr132 · DOI
- 10.1073/pnas.1211990110 · DOI
- 10.1038/nature10842 · DOI
- 10.1126/science.1230835 · DOI
- 10.1038/nature11128 · DOI · Paper page
- 10.1186/2047-217X-1-16 · DOI
- 10.1038/nature11622 · DOI
- 10.1038/nature12511 · DOI
- 10.1038/ncomms3708 · DOI
- 10.1038/ncomms2860 · DOI
- 10.1038/ncomms2416 · DOI
- 10.1038/ng.3042 · DOI
- 10.1093/molbev/msu104 · DOI
- 10.1038/ncomms4966 · DOI · Paper page
- 10.1016/j.cell.2014.03.054 · DOI · Paper page
- 10.1038/nature13679 · DOI
- 10.1038/ng.3137 · DOI
- 10.1073/pnas.1017351108 · DOI
- 10.1186/2047-217X-1-18 · DOI
- 10.1006/jmbi.1997.0951 · DOI
- 10.1093/nar/gkl200 · DOI · Paper page
- 10.1101/gr.1865504 · DOI · Paper page
- 10.1186/1471-2105-6-31 · DOI
- 10.1186/1745-6150-3-20 · DOI
- 10.1093/bioinformatics/btp352 · DOI · Paper page
- 10.1093/bioinformatics/btr330 · DOI
- 10.1101/gr.107524.110 · DOI · Paper page
- 10.1038/nmeth.1363 · DOI
- 10.1093/bioinformatics/btq216 · DOI
- 10.1038/ng.1028 · DOI
- 10.1093/bioinformatics/bts601 · DOI
- 10.1093/nar/gks003 · DOI
- 10.1093/bioinformatics/bti774 · DOI
200 of 239 shown
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“The Vertebrate Genomes Project 38 led by the Genome 10K 39 and the Earth BioGenome Project 40 , among others, aim to release thousands of new, high-quality genome assemblies over the next decade.”
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Metadata
- Authors
- Koepfli, K.-P., Paten, B., Scientists, T. G. 1. C. O., & O’Brien, S. J.
- Affiliations
- St Petersburg University (RU)
- New England Biolabs (United States) (US)
- Venue
- Annual Review of Animal Biosciences
- Publisher
- Annual Reviews
- Published
- 2015-02-16
- Volume
- 3
- Issue
- 1
- Pages
- 57-111
- ISSN
- 2165-8102 (ISSN-L)
- 2165-8110
- PMC
- PMC5837290
- OpenAlex
- W2152882637
- Cited by
- 311
- References
- 35
- Citations by year
- 2026: 9 · 2025: 11 · 2024: 16 · 2023: 15 · 2022: 30 · 2021: 41 · 2020: 36 · 2019: 32 · 2018: 43 · 2017: 33 · 2016: 34 · 2015: 11
- FWCI
- 3.96
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Annual Review of Animal Biosciences (publishedVersion)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (acceptedVersion)
- NSUWorks (Nova Southeastern University) (submittedVersion)
- University of Canberra Research Portal (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion)
- Funders
- National Human Genome Research Institute (U54HG007990)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Keywords
- vertebrate genomes, genome sequencing, species selection
- MeSH terms
- Animals, Forecasting, Humans, Species Specificity, Vertebrates, Genome, Computational Biology, Genomics
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- CoChat. (2026). Citation check: The Genome 10K Project: A Way Forward. https://app.cochat.ai/papers/10.1146/annurev-animal-090414-014900
- The paper
- Koepfli, K.-P., Paten, B., Scientists, T. G. 1. C. O., & O’Brien, S. J. (2015). The Genome 10K Project: A Way Forward. Annual Review of Animal Biosciences. https://doi.org/10.1146/annurev-animal-090414-014900
