G10K Community Member Publications

Members of the G10K Community of Scientists (G10KCOS) have submitted the following publications and bibliographies from their laboratories. If you are a G10KCOS participant or affiliate and want to be listed here, please send your citations and links to your bibliographies to: G10K webmaster.

Publications

Annabel C Beichman, Klaus-Peter Koepfli, Gang Li, William Murphy, Pasha Dobrynin, Sergei Kilver, M Tim Tinker, Michael J Murray, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K Karlsson, Kirk E Lohmueller, Robert K Wayne, Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter and giant otter, Molecular Biology and Evolution, msz101.

Annabel C Beichman, Klaus-Peter Koepfli, Gang Li, William Murphy, Pasha Dobrynin, Sergei Kilver, M Tim Tinker, Michael J Murray, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K Karlsson, Kirk E Lohmueller, Robert K Wayne, Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter and giant otter, Molecular Biology and Evolution, msz101.

Chen, Lei and Qiu, Qiang and Jiang, Yu and Wang, Kun and Lin, Zeshan and Li, Zhipeng and Bibi, Faysal and Yang, Yongzhi and Wang, Jinhuan and Nie, Wenhui and Su, Weiting and Liu, Guichun and Li, Qiye and Fu, Weiwei and Pan, Xiangyu and Liu, Chang and Yang, Jie and Zhang, Chenzhou and Yin, Yuan and Wang, Yu and Zhao, Yue and Zhang, Chen and Wang, Zhongkai and Qin, Yanli and Liu, Wei and Wang, Bao and Ren, Yandong and Zhang, Ru and Zeng, Yan and da Fonseca, Rute R. and Wei, Bin and Li, Ran and Wan, Wenting and Zhao, Ruoping and Zhu, Wenbo and Wang, Yutao and Duan, Shengchang and Gao, Yun and Zhang, Yong E. and Chen, Chunyan and Hvilsom, Christina and Epps, Clinton W. and Chemnick, Leona G. and Dong, Yang and Mirarab, Siavash and Siegismund, Hans Redlef and Ryder, Oliver A. and Gilbert, M. Thomas P. and Lewin, Harris A. and Zhang, Guojie and Heller, Rasmus and Wang, Wen. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 21 June 2019. doi 10.1126/science.aav6202.

Klaus-Peter Koepfli, Gaik Tamazian, David Wildt, Pavel Dobrynin, Changhoon Kim, Paul B. Frandsen, Raquel Godinho, Andrey A. Yurchenko, Aleksey Komissarov, Ksenia Krasheninnikova, Sergei Kliver, Sofia Kolchanova, Margarida Gonçalves, Miguel Carneiro, Pedro Vaz Pinto, Nuno Ferrand, Jesús E. Maldonado, Gina M. Ferrie, Leona Chemnick, Oliver A. Ryder, Warren E. Johnson, Pierre Comizzoli, Stephen J. O’Brien and Budhan S. Pukazhenthi. Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations. G3: GENES, GENOMES, GENETICS. Volume 9 Issue 5, May 2019 

Ravi, V and Venkatesh, B. The divergent genomes of teleosts. Annual Review of Animal Biosciences. Vol. 6:47-68, pp 47-68.

Sergej NowoshilowSiegfried SchloissnigJi-Feng FeiAndreas DahlAndy W. C. PangMartin PippelSylke WinklerAlex R. HastieGeorge YoungJuliana G. RoscitoFrancisco FalconDunja KnappSean PowellAlfredo CruzHan CaoBianca Habermann, Michael HillerElly M. Tanaka & Eugene W. Myers. The axolotl genome and the evolution of key tissue formation regulators. Nature Biotechnology. 2018 Jan 24.

Wolf, J.B. & Ellegren, H. Making sense of genomic islands of differentiation in the light of speciation.Nature Reviews Genetics, doi:10.1038/nrg.2016.133.

Ellegren, H. & Galtier, N. Determinants of genetic diversity. Nature Reviews Genetics 2016 Jul;17(7):422-33. doi: 10.1038/nrg.2016.58.

Zijun Xiong, Fang Li, Qiye Li, Long Zhou, Tony Gamble, Jiao Zheng, Ling Kui, Cai Li, Shengbin Li, Huanming Yang and Guojie Zhang. Draft genome of the leopard gecko, Eublepharis macularius. GigaScience. 2016 Oct 26;5:47

Pan, H., Yu, H., Ravi, V., et al. The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate. GigaScience (2016) 5:36.

Bian, C., Venkatesh, B., et al. The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. Sci. Rep. (2016) 6: 24501.

Luca Cornetti, Luis Valente, Luke T. Dunning, Xueping Quan, Richard A. Black, Olivier Hébert, and Vincent Savolainen. The genome of the ‘great speciator’ provides insights into bird diversification. Genome Biol Evol. 2015 Sept 2.

Klaus-Peter Koepfli, Benedict Paten, the Genome 10K Community of Scientists, and Stephen J. O’Brien. The Genome 10K Project: a way forward. Annual Review of Animal Biosciences. February 2015.

Andrew D Foote, Yue Liu, et al. Convergent evolution of the genomes of marine mammals. Nature Genetics. 2015 January 26.

You, X., Venkatesh, B., et al. Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes. Nat. Commun. (2014) 5:5594.

Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature. 2014 Sep 28.

Ho SYW. The changing face of the molecular evolutionary clock. Trends in Ecology and Evolution. 2014 September.

Nguyen N, et al. Comparative assembly hubs: web accessible browsers for comparative genomics. Bioinformatics. 2014 Aug 18.

Wolfgang E. Comparative genomics of brain size evolution. PWC. 2014 May 21.

Chen S, Zhang G, Shao C, et al. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet. 2014 Feb 2. doi: 10.1038/ng.2890.

Venkatesh B, Lee AP, Ravi V, et al. Elephant shark genome provides unique insights into gnathostome evolution. Nature. 2014 Jan 9;505(7482):174-9.

Schrago CG, Menezes AN, Furtado C, Bonvicino CR, Seuanez HN. Multispecies coalescent analysis of the early diversification of neotropical primates: phylogenetic inference under strong gene trees/species tree conflict. Genome Biology and Evolution. 2014;6(11):3105-3114.

Vonk FJ, Casewell NR, Henkel CV, et al. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proc Natl Acad Sci U S A. 2013 Dec 2.

Castoe TA, de Koning AP, Hall KT, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proc Natl Acad Sci U S A. 2013 Dec 2.

Yim HS, Cho YS, Guang X, et al. Minke whale genome and aquatic adaptation in cetaceans. Nat Genet. 2013 Nov 24.

Menezes AN, Viana MC, Furtado C, Schrago CG, Seuánez HN. Positive selection along the evolution of primate mitogenomes. Mitochondrion. 2013 Nov;13(6):846-51.

Zhou X, Sun F, Xu S, et al. Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations. Nat Commun. 2013 Oct 29;4:2708.

Mehta TK, Ravi V, Yamasaki S, et al. Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16044-9.

Edwards RA, Haggerty JM, Cassman N, et al. Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era. BMC Genomics. 2013 Sep 4.

Cho YS, Hu L, Hou H, et al. The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun. 2013;4:2433.

Bradnam KR, Fass JN, Alexandrov A, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013 Jul 22;2(1):10.

Amemiya CT, Alföldi J, Lee AP, et al. The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013 Apr 18;496(7445):311-6.

Hickey G, et al. HAL: A hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics. 2013 Mar 16.

Ewing AD, et al. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol. 2013 Mar 13;14(3):R22.

Kim J. et al. Reference-assisted chromosome assembly. Proc Natl Acad Sci USA. 2013 Jan 29;110(5):1785-90.

Ge RL, Cai Q, Shen YY, et al. Draft genome sequence of the Tibetan antelope. Nat Commun. 2013;4:1858.

Brenner S. The revolution in the Life Sciences. Science Magazine. 2012 Dec 14.

Hiller M, Schaar BT, Indjeian VB, et al. A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species. Cell Reports. 2012 October 25.

Lowe CB, Haussler D. 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS One. 2012;7(8):e43128.

Vezzi F, Narzisi G, Mishra B. Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons. PLoS One. 2012;7(12):e52210.

O’Brien SJ. Genome empowerment for the Puerto Rican parrot–Amazona vittata. Gigascience. 2012 Sep 28;1(1):13.

Wong PB, Wiley EO, Johnson WE, et al. Tissue sampling methods and standards for vertebrate genomics. Gigascience. 2012 Jul 12;1(1):8.

Koren S, Schatz MC, Walenz BP, et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol. 2012 Jul 1;30(7):693-700.

Qiu Q, Zhang G, Ma T, et al. The yak genome and adaptation to life at high altitude. Nat Genet. 2012 Jul 1;44(8):946-9.

Bernardi G, et al. The fishes of Genome 10K, Mar Genomics. 2012 Sep;7:3-6.

St John JA, Braun EL, Isberg SR, et al. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology. 2012 January 31.

Ezaz T, Marshall Graves JA. Foreword: sex and sex chromosomes—new clues from nonmodel species. Chromosome Research. 2012 January 25.

Earl D, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011. Dec;21(12):2224-41.

Schrago CG, Menezes AN, Moreira MA, Pissinatti A, Seuánez HN. Chronology of deep nodes in the neotropical primate phylogeny: insights from mitochondrial genomes. PLoS One. 2012;7(12):e51699.

Lindblad-Toh K, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82.

Alföldi J, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011 Aug 31;477(7366):587-91.

Romanenko SA, Perelman PL, Trifonov VA, Graphodatsky AS. Chromosomal evolution in Rodentia. Heredity. 2011 November 16.

Paten B, et al. Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 2011 Sep;21(9):1512-28.

Cooper GM, Shendure J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Reviews Genetics. 2011 September.

Lowe CB, et al. Three periods of regulatory innovation during vertebrate evolution. Science. 2011 Aug 19;333(6045):1019-24.

Castoe TA, de Koning AP, Hall KT, et al. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biology. 2011 July 28.

Locke DP, et al. Comparative and demographic analysis of orangutan genomes. Nature. 2011 Jan 27;469(7331):529-33.
Lowe CB et al. Endangered species hold clues to human evolution. J Hered. 2010 Jul-Aug;101(4):437-47.

Kern AD, Haussler D. A population genetic hidden Markov model for detecting genomic regions under selection. Mol Biol Evol. 2010 Jul;27(7):1673-85.

Janes DE, Organ CL, Fujita MK, et al. Genome evolution in Reptilia, the sister group of mammals. 2010 June 29.

Genome 10K Community of Scientists. A proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 2009 Nov 4;100:659-674.