thw266 KU

A region of suppressed recombination misleads neoavian phylogenomics

Mirarab, S., Rivas-González, I., Feng, S., Stiller, Josefin, Fang, Q., Mai, U., Hickey, G., Chen, G., Brajuka, N., Fedrigo, O., Formenti, G., Wolf, J. B. W., Howe, K., Antunes, A., Schierup, M. H., Paten, B., Jarvis, E. D., KU, thw266 & Braun, E. L., 1 Apr 2024, In: Proceedings of the National Academy of Sciences. 121, 15, 10 p., e2319506121.

Research output: Contribution to journal › Journal article › Research › peer-review

Complexity of avian evolution revealed by family-level genomes

Stiller, J., Feng, S., Chowdhury, A-A., Rivas-González, I., Duchêne, D. A., Fang, Q., Deng, Y., Kozlov, A., Stamatakis, A., Claramunt, S., Nguyen, J. M. T., Ho, S. Y. W., Faircloth, B. C., Haag, J., Houde, P., Cracraft, J., Balaban, M., Mai, U., Chen, G., Gao, R. & 32 others, Zhou, C., Xie, Y., Huang, Z., Cao, Z., Yan, Z., Ogilvie, H. A., Nakhleh, L., Lindow, Bent Erik Kramer, Morel, B., Fjeldså, Jon, Hosner, Peter Andrew, da Fonseca, R. R., Petersen, Bent, Tobias, J. A., Székely, T., Kennedy, J. D., Reeve, A. H., Liker, A., Stervander, M., Antunes, A., Tietze, D. T., Bertelsen, Mads, Lei, F., Rahbek, Carsten, Graves, G. R., Schierup, M. H., Warnow, T., Braun, E. L., Gilbert, M Thomas P, Jarvis, E. D., Mirarab, S. & KU, thw266, 1 Apr 2024, In: Nature.

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Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time

McComish, B. J., Charleston, M. A., Parks, M., Baroni, C., Salvatore, M. C., Li, R., KU, thw266, Millar, C. D., Holland, B. R. & Lambert, D. M., 2024, In: Genome Biology and Evolution. 16, 3, 11 p., evae017.

Research output: Contribution to journal › Journal article › Research › peer-review

ETV2 induces endothelial, but not hematopoietic, lineage specification in birds

Weng, W., Deng, Y., Deviatiiarov, R., Hamidi, S., Kajikawa, E., Gusev, O., Kiyonari, H., KU, thw266 & Sheng, G., 2024, In: Life Science Alliance. 7, 6, 12 p., e202402694.

Research output: Contribution to journal › Journal article › Research › peer-review

Identification of constrained sequence elements across 239 primate genomes

Kuderna, L. F. K., Ulirsch, J. C., Rashid, S., Ameen, M., Sundaram, L., Hickey, G., Cox, A. J., Gao, H., Kumar, A., Aguet, F., Christmas, M. J., Clawson, H., Haeussler, M., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., Manu, S., Valenzuela, A., Bergman, J. & 72 others, Rouselle, M., Silva, F. E., Agueda, L., Blanc, J., Gut, M., de Vries, D., Goodhead, I., Harris, R. A., Raveendran, M., Jensen, A., Chuma, I. S., Horvath, J. E., Hvilsom, C., Juan, D., Frandsen, P., Schraiber, J. G., de Melo, F. R., Bertuol, F., Byrne, H., Sampaio, I., Farias, I., Valsecchi, J., Messias, M., da Silva, M. N. F., Trivedi, M., Rossi, R., Hrbek, T., Andriaholinirina, N., Rabarivola, C. J., Zaramody, A., Jolly, C. J., Phillips-Conroy, J., Wilkerson, G., Abee, C., Simmons, J. H., Fernandez-Duque, E., Kanthaswamy, S., Shiferaw, F., Wu, D., Zhou, L., Shao, Y., KU, thw266, Keyyu, J. D., Knauf, S., Le, M. D., Lizano, E., Merker, S., Navarro, A., Nadler, T., Khor, C. C., Lee, J., Tan, P., Lim, W. K., Kitchener, A. C., Zinner, D., Gut, I., Melin, A. D., Guschanski, K., Schierup, M. H., Beck, R. M. D., Karakikes, I., Wang, K. C., Umapathy, G., Roos, C., Boubli, J. P., Siepel, A., Kundaje, A., Paten, B., Lindblad-Toh, K., Rogers, J., Marques Bonet, T. & Farh, K. K. H., 2024, In: Nature. 625, p. 735–742 8 p.

Research output: Contribution to journal › Journal article › Research › peer-review

A global catalog of whole-genome diversity from 233 primate species

Kuderna, L. F. K., Gao, H., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., Manu, S., Valenzuela, A., Bergman, J., Rousselle, M., Silva, F. E., Agueda, L., Blanc, J., Gut, M., de Vries, D., Goodhead, I., Harris, R. A., Raveendran, M., Jensen, A., Chuma, I. S. & 55 others, Horvath, J. E., Hvilsom, C., Juan, D., Frandsen, P., Schraiber, J. G., de Melo, F. R., Bertuol, F., Byrne, H., Sampaio, I., Farias, I., Valsecchi, J., Messias, M., da Silva, M. N. F., Trivedi, M., Rossi, R., Hrbek, T., Andriaholinirina, N., Rabarivola, C. J., Zaramody, A., Jolly, C. J., Phillips-Conroy, J., Wilkerson, G., Abee, C., Simmons, J. H., Fernandez-Duque, E., Kanthaswamy, S., Shiferaw, F., Wu, D., Zhou, L., Shao, Y., KU, thw266, Keyyu, J. D., Knauf, S., Le, M. D., Lizano, E., Merker, S., Navarro, A., Nadler, T., Khor, C. C., Lee, J., Tan, P., Lim, W. K., Kitchener, A. C., Zinner, D., Gut, I., Melin, A. D., Guschanski, K., Schierup, M. H., Beck, R. M. D., Umapathy, G., Roos, C., Boubli, J. P., Rogers, J., Farh, K. K. H. & Marques Bonet, T., 2023, In: Science (New York, N.Y.). 380, 6648, p. 906-913 8 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Comparative genomics reveals the hybrid origin of a macaque group

Zhang, B. L., Chen, W., Wang, Z., Pang, W., Luo, M. T., Wang, S., Shao, Y., He, W. Q., Deng, Y., Zhou, L., Chen, J., Yang, M. M., Wu, Y., Wang, L., Fernández-Bellon, H., Molloy, S., Meunier, H., Wanert, F., Kuderna, L., Marques-Bonet, T. & 10 others, Roos, C., Qi, X. G., Li, M., Liu, Z., Schierup, M. H., Cooper, D. N., Liu, J., Zheng, Y. T., KU, thw266 & Wu, D. D., 2023, In: Science Advances. 9, 22, 13 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast

Shen, Y., Gao, F., Wang, Y., Wang, Y., Zheng, J., Gong, J., Zhang, J., Luo, Z., Schindler, D., Deng, Y., Ding, W., Lin, T., Swidah, R., Zhao, H., Jiang, S., Zeng, C., Chen, S., Chen, T., Wang, Y., Luo, Y. & 11 others, Mitchell, L., Bader, J. S., KU, thw266, Shen, X., Wang, J., Fu, X., Dai, J., Boeke, J. D., Yang, H., Xu, X. & Cai, Y., 2023, In: Cell Genomics. 3, 11, 19 p., 100364.

Research output: Contribution to journal › Journal article › Research › peer-review

Eighty million years of rapid evolution of the primate Y chromosome

Zhou, Y., Zhan, X., Jin, J., Zhou, L., Bergman, J., Li, X., Rousselle, M. M. C., Belles, M. R., Zhao, L., Fang, M., Chen, J., Fang, Q., Kuderna, L., Marques-Bonet, T., Kitayama, H., Hayakawa, T., Yao, Y. G., Yang, H., Cooper, D. N., Qi, X. & 3 others, Wu, D. D., Schierup, M. H. & KU, thw266, 2023, In: Nature Ecology and Evolution. 7, 20 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Evolution of the germline mutation rate across vertebrates

Bergeron, Lucie Adrienne, Besenbacher, S., Zheng, J., Li, P., Bertelsen, Mads Frost, Quintard, B., Hoffman, J. I., Li, Z., Leger, J. S., Shao, C., Stiller, Josefin, Gilbert, M Thomas P, Schierup, M. H. & KU, thw266, 2023, In: Nature. 615, p. 285-291

Research output: Contribution to journal › Journal article › Research › peer-review

Harvesting the fruits of the first stage of the Primate Genome Project

Guo, Y. T., Shao, Y., Bi, X., Zhang, B. L., Wu, H., Zhou, Y., Li, M. L., Yu, L., KU, thw266, Wu, D. D. & Qi, X. G., 2023, In: Zoological research. 44, 4, p. 725-728 4 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros

Sánchez-Barreiro, F., Westbury, Binia De Cahsan, Westbury, Michael Vincent, Sun, Xin, Margaryan, Ashot, Fontsere, Claudia, Bruford, M. W., Russo, I. M., Kalthoff, D. C., Sicheritz-Pontén, Thomas, Petersen, Bent, Dalén, L., KU, thw266, Marquès-Bonet, T., Gilbert, M Thomas P & Moodley, Y., 2023, In: Molecular Biology and Evolution. 40, 9, 19 p., msad180.

Research output: Contribution to journal › Journal article › Research › peer-review

How genomics can help biodiversity conservation

The European Reference Genome Atlas Consortium, T. E. R. G. A. C., 2023, In: Trends in Genetics. 39, 7, 15 p.

Research output: Contribution to journal › Review › Research › peer-review

Lineage-specific accelerated sequences underlying primate evolution

Bi, X., Zhou, L., Zhang, J., Feng, S., Hu, M., Cooper, D. N., Lin, J., Li, J., Wu, D. & KU, thw266, 2023, In: Science Advances. 9, 22, 12 p., eadc9507.

Research output: Contribution to journal › Journal article › Research › peer-review

On the origin and evolution of RNA editing in metazoans

Zhang, P., Zhu, Y., Guo, Q., Li, J., Zhan, X., Yu, H., Xie, N., Tan, H., Lundholm, Nina, Garcia-Cuetos, L., Martin, M. D., Subirats, M. A., Su, Y., Ruiz-Trillo, I., Martindale, M. Q., Yu, J., Gilbert, M Thomas P, KU, thw266 & Li, Q., 2023, In: Cell Reports. 42, 2, 22 p., 112112.

Research output: Contribution to journal › Journal article › Research › peer-review

Parallel evolution of fish bi-modal breathing and expansion of olfactory receptor (OR) genes: toward a universal ORs nomenclature

Silva, L., Mendes, T., Ramos, L., KU, thw266 & Antunes, A., 2023, In: Journal of Genetics and Genomics. 50, 8, 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Pervasive incomplete lineage sorting illuminates speciation and selection in primates

Rivas-González, I., Rousselle, M., Li, F., Zhou, L., Dutheil, J. Y., Munch, K., Shao, Y., Wu, D., Schierup, M. H. & KU, thw266, 2023, In: Science (New York, N.Y.). 380, 6648, 10 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Phylogenomic analyses provide insights into primate evolution

Shao, Y., Zhou, L., Li, F., Zhao, L., Zhang, B. L., Shao, F., Chen, J. W., Chen, C. Y., Bi, X., Zhuang, X. L., Zhu, H. L., Hu, J., Sun, Z., Li, X., Wang, D., Rivas-González, I., Wang, S., Wang, Y. M., Chen, W., Li, G. & 23 others, Lu, H. M., Liu, Y., Kuderna, L. F. K., Farh, K. K. H., Fan, P. F., Yu, L., Li, M., Liu, Z. J., Tiley, G. P., Yoder, A. D., Roos, C., Hayakawa, T., Marques-Bonet, T., Rogers, J., Stenson, P. D., Cooper, D. N., Schierup, M. H., Yao, Y. G., Zhang, Y. P., Wang, W., Qi, X. G., KU, thw266 & Wu, D. D., 2023, In: Science (New York, N.Y.). 380, 6648, p. 913-924 12 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Species-specific traits mediate avian demographic responses under past climate change

Germain, Ryan Ross, Feng, S., Chen, G., Graves, G. R., Tobias, J. A., Rahbek, Carsten, Lei, F., Fjeldså, Jon, Hosner, Peter Andrew, Gilbert, M Thomas P, KU, thw266 & Nogues, David Bravo, 2023, In: Nature Ecology and Evolution. 7, 6, p. 862-872 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights

Shao, C., Sun, S., Liu, K., Wang, J., Li, S., Liu, Q., Deagle, B. E., Seim, I., Biscontin, A., Wang, Q., Liu, X., Kawaguchi, S., Liu, Y., Jarman, S., Wang, Y., Wang, H. Y., Huang, G., Hu, J., Feng, B., De Pittà, C. & 29 others, Liu, S., Wang, R., Ma, K., Ying, Y., Sales, G., Sun, T., Wang, X., Zhang, Y., Zhao, Y., Pan, S., Hao, X., Wang, Y., Xu, J., Yue, B., Sun, Y., Zhang, H., Xu, M., Liu, Y., Jia, X., Zhu, J., Liu, S., Ruan, J., KU, thw266, Yang, H., Xu, X., Wang, J., Zhao, X., Meyer, B. & Fan, G., 2023, In: Cell. 186, 6, p. 1279-1294.e19 36 p.

Research output: Contribution to journal › Journal article › Research › peer-review

The landscape of tolerated genetic variation in humans and primates

Gao, H., Hamp, T., Ede, J., Schraiber, J. G., McRae, J., Singer-Berk, M., Yang, Y., Dietrich, A. S. D., Fiziev, P. P., Kuderna, L. F. K., Sundaram, L., Wu, Y., Adhikari, A., Field, Y., Chen, C., Batzoglou, S., Aguet, F., Lemire, G., Reimers, R., Balick, D. & 77 others, Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Manu, S., Valenzuela, A., Bergman, J., Rousselle, M., Silva, F. E., Agueda, L., Blanc, J., Gut, M., de Vries, D., Goodhead, I., Harris, R. A., Raveendran, M., Jensen, A., Chuma, I. S., Horvath, J. E., Hvilsom, C., Juan, D., Frandsen, P., de Melo, F. R., Bertuol, F., Byrne, H., Sampaio, I., Farias, I., do Amaral, J. V., Messias, M., da Silva, M. N. F., Trivedi, M., Rossi, R., Hrbek, T., Andriaholinirina, N., Rabarivola, C. J., Zaramody, A., Jolly, C. J., Phillips-Conroy, J., Wilkerson, G., Abee, C., Simmons, J. H., Fernandez-Duque, E., Kanthaswamy, S., Shiferaw, F., Wu, D., Zhou, L., Shao, Y., KU, thw266, Keyyu, J. D., Knauf, S., Le, M. D., Lizano, E., Merker, S., Navarro, A., Bataillon, T., Nadler, T., Khor, C. C., Lee, J., Tan, P., Lim, W. K., Kitchener, A. C., Zinner, D., Gut, I., Melin, A., Guschanski, K., Schierup, M. H., Beck, R. M. D., Umapathy, G., Roos, C., Boubli, J. P., Lek, M., Sunyaev, S., O'Donnell-Luria, A., Rehm, H. L., Xu, J., Rogers, J., Marques-Bonet, T. & Farh, K. K. H., 2023, In: Science (New York, N.Y.). 380, 6648, 13 p.

Research output: Contribution to journal › Journal article › Research › peer-review

A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics

Mao, Y. & KU, thw266, 2022, In: Nature Methods. 19, 6, p. 635-638 4 p.

Research output: Contribution to journal › Comment/debate › Research › peer-review

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Toh, H., Yang, C., Formenti, G., Raja, K., Yan, L., Tracey, A., Chow, W., Howe, K., Bergeron, L. A., Zhang, G., Haase, B., Mountcastle, J., Fedrigo, O., Fogg, J., Kirilenko, B., Munegowda, C., Hiller, M., Jain, A., Kihara, D., Rhie, A. & 9 others, Phillippy, A. M., Swanson, S. A., Jiang, P., Clegg, D. O., Jarvis, E. D., Thomson, J. A., Stewart, R., Chaisson, M. J. P. & Bukhman, Y. V., 2022, In: BMC Biology. 20, 21 p., 245.

Research output: Contribution to journal › Journal article › Research › peer-review

A single-cell transcriptomic atlas tracking the neural basis of division of labour in an ant superorganism

Li, Q., Wang, M., Zhang, P., Liu, Y., Guo, Q., Zhu, Y., Wen, T., Dai, X., Zhang, X., Nagel, M., Dethlefsen, B. H., Xie, N., Zhao, J., Jiang, W., Han, L., Wu, L., Zhong, W., Wang, Z., Wei, X., Dai, W. & 9 others, Liu, L., Xu, X., Lu, H., Yang, H., Wang, J., Boomsma, Jacobus J., Liu, C., KU, thw266 & Liu, W., 2022, In: Nature Ecology & Evolution. 6, 8, p. 1191-1204

Research output: Contribution to journal › Journal article › Research › peer-review

Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors

Fiddaman, S. R., Vinkler, M., Spiro, S. G., Levy, H., Emerling, C. A., Boyd, A. C., Dimopoulos, E. A., Vianna, J. A., Cole, T. L., Pan, H., Fang, M., KU, thw266, Hart, T., Frantz, L. A. F. & Smith, A. L., 2022, In: Molecular Biology and Evolution. 39, 1, 17 p., msab354.

Research output: Contribution to journal › Journal article › Research › peer-review

Ancient proteins resolve controversy over the identity of Genyornis eggshell

Demarchi, B., Stiller, Josefin, Grealy, A., Mackie, Meaghan, Deng, Y., Gilbert, M Thomas P, Clarke, J., Legendre, L. J., Boano, R., Sicheritz-Pontén, Thomas, Magee, J., KU, thw266, Bunce, M., Collins, Matthew James & Miller, G., 2022, In: PNAS. 119, 43, 9 p., e2109326119.

Research output: Contribution to journal › Journal article › Research › peer-review

Canalized gene expression during development mediates caste differentiation in ants

Qiu, Bitao, Dai, X., Li, P., Larsen, Rasmus Stenbak, Li, Ruyan, Price, A. L., Ding, G., Texada, Michael James, Zhang, X., Zuo, D., Gao, Q., Jiang, W., Wen, T., Pontieri, L., Guo, C., Rewitz, Kim, Li, Q., Liu, W., Boomsma, Jacobus J. & KU, thw266, 2022, In: Nature Ecology and Evolution. 6, 11, p. 1753-1765

Research output: Contribution to journal › Journal article › Research › peer-review

Comparative phylogeography study reveals introgression and incomplete lineage sorting during rapid diversification of Rhodiola

You, J., Lougheed, S. C., Zhao, Y., KU, thw266, Liu, W., Lu, F., Wang, Y., Zhang, W., Yang, J., Qiong, L. & Song, Z., 2022, In: Annals of Botany. 129, 2, p. 185-200 16 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Conservation genomics of the endangered Seychelles Magpie-Robin (Copsychus sechellarum): a unique insight into the history of a precious endemic bird

Cavill, Emily Louisa, Gopalakrishnan, Shyam, Puetz, Lara Christine, Ribeiro, Â. M., Mak, Sarah Siu Tze, Rodrigues da Fonseca, Rute Andreia, Antunes Pacheco, George, Dunlop, B., Accouche, W., Shah, N., Zora, A., Calabrese, L., Genner, M., Jones, G., Guo, C., KU, thw266 & Gilbert, M Thomas P, 2022, In: Ibis. 164, 2, p. 396-410 15 p.

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Draft genome assemblies of four manakins

Li, X., Gao, R., Chen, G., Price, A. L., Øksnebjerg, Daniel Bilyeli, Hosner, Peter Andrew, Zhou, Y., KU, thw266 & Feng, S., 2022, In: Scientific Data. 9, 11 p., 564.

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False gene and chromosome losses in genome assemblies caused by GC content variation and repeats

Kim, J., Lee, C., Ko, B. J., Yoo, D. A., Won, S., Phillippy, A. M., Fedrigo, O., KU, thw266, Howe, K., Wood, J., Durbin, R., Formenti, G., Brown, S., Cantin, L., Mello, C. V., Cho, S., Rhie, A., Kim, H. & Jarvis, E. D., 2022, In: Genome Biology. 23, 29 p., 204.

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Functional Diversity and Evolution of Bitter Taste Receptors in Egg-Laying Mammals

Itoigawa, A., Hayakawa, T., Zhou, Y., Manning, A. D., KU, thw266, Grutzner, F. & Imai, H., 2022, In: Molecular Biology and Evolution. 39, 6, 9 p., msac107.

Research output: Contribution to journal › Journal article › Research › peer-review

Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises

Li, M. L., Wang, S., Xu, P., Tian, H. Y., Bai, M., Zhang, Y. P., Shao, Y., Xiong, Z. J., Qi, X. G., Cooper, D. N., KU, thw266, Zhu, H. H. & Wu, D. D., 2022, In: Proceedings of the National Academy of Sciences of the United States of America. 119, 40, 10 p., e2123030119.

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Genomic insights into the secondary aquatic transition of penguins

Cole, T. L., Zhou, C., Fang, M., Pan, H., Ksepka, D. T., Fiddaman, S. R., Emerling, C. A., Thomas, D. B., Bi, X., Fang, Q., Ellegaard, M. R., Feng, S., Smith, A. L., Heath, T. A., Tennyson, A. J. D., Borboroglu, P. G., Wood, J. R., Hadden, P. W., Grosser, S., Bost, C. A. & 20 others, Cherel, Y., Mattern, T., Hart, T., Sinding, Mikkel Holger Strander, Shepherd, L. D., Phillips, R. A., Quillfeldt, P., Masello, J. F., Bouzat, J. L., Ryan, P. G., Thompson, D. R., Ellenberg, U., Dann, P., Miller, G., Dee Boersma, P., Zhao, R., Gilbert, M Thomas P, Yang, H., Zhang, D. & KU, thw266, 2022, In: Nature Communications. 13, 13 p., 3912.

Research output: Contribution to journal › Journal article › Research › peer-review

Incomplete lineage sorting and phenotypic evolution in marsupials

Feng, S., Bai, M., Rivas-González, I., Li, C., Liu, S., Tong, Y., Yang, H., Chen, G., Xie, D., Sears, K. E., Franco, L. M., Gaitan-Espitia, J. D., Nespolo, R. F., Johnson, W. E., Yang, H., Brandies, P. A., Hogg, C. J., Belov, K., Renfree, M. B., Helgen, K. M. & 3 others, Boomsma, Jacobus J., Schierup, M. H. & KU, thw266, 2022, In: Cell. 185, 10, p. 1646-1660.e18

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Initiation of the Primate Genome Project

Wu, D., Qi, X., Yu, L., Li, M., Liu, Z., Yoder, A. D., Roos, C., Hayakawa, T., Rogers, J., Marques-Bonet, T., Su, B., Yao, Y., Zhang, Y. & KU, thw266, 2022, In: Zoological research. 43, 2, p. 147-149 3 p.

Research output: Contribution to journal › Comment/debate › Research › peer-review

Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates

Li, Y., KU, thw266 & Cui, J., 2022, In: Viruses. 14, 7, 14 p., 1370.

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Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds

Ji, Y., Feng, S., Wu, L., Fang, Q., Brüniche-Olsen, Anna, DeWoody, J. A., Cheng, Y., Zhang, D., Hao, Y., Song, G., Qu, Y., Suh, A., KU, thw266, Hackett, S. J. & Lei, F., 2022, In: Science Advances. 8, 35, 11 p., eabo0099.

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Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation

Li, F., Rane, R. V., Luria, V., Xiong, Z., Chen, J., Li, Z., Catullo, R. A., Griffin, P. C., Schiffer, M., Pearce, S., Lee, S. F., McElroy, K., Stocker, A., Shirriffs, J., Cockerell, F., Coppin, C., Sgrò, C. M., Karger, A., Cain, J. W., Weber, J. A. & 5 others, Santpere, G., Kirschner, M. W., Hoffmann, A. A., Oakeshott, J. G. & KU, thw266, 2022, In: Molecular Ecology Resources. 22, 4, p. 1559-1581 23 p.

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Phylogeny and sex chromosome evolution of palaeognathae

Wang, Z., Zhang, J., Xu, X., Witt, C., Deng, Y., Chen, G., Meng, G., Feng, S., Xu, L., Szekely, T., KU, thw266 & Zhou, Q., 2022, In: Journal of Genetics and Genomics. 49, 2, p. 109-119 11 p.

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Probing the genomic limits of de-extinction in the Christmas Island rat

Lin, J., Duchene, David, Carøe, C., Smith, O., Ciucani, M. M., Niemann, Jonas, Richmond, D., Greenwood, A. D., MacPhee, R., KU, thw266, Gopalakrishnan, Shyam & Gilbert, M Thomas P, 2022, In: Current Biology. 32, 7, p. 1650-1656.e3

Research output: Contribution to journal › Journal article › Research › peer-review

Standards recommendations for the Earth BioGenome Project

Lawniczak, M. K. N., Durbin, R., Flicek, P., Lindblad-Toh, K., Wei, X., Archibald, J. M., Baker, W. J., Belov, K., Blaxter, M. L., Bonet, T. M., Childers, A. K., Coddington, J. A., Crandall, K. A., Crawford, A. J., Davey, R. P., Palma, F. D., Fang, Q., Haerty, W., Hall, N., Hoff, K. J. & 25 others, Howe, K., Jarvis, E. D., Johnson, W. E., Johnson, R. N., Kersey, P. J., Liu, X., Lopez, J. V., Myers, E. W., Pettersson, O. V., Phillippy, A. M., Poelchau, M. F., Pruitt, K. D., Rhie, A., Castilla-Rubio, J. C., Sahu, S. K., Salmon, N. A., Soltis, P. S., Swarbreck, D., Thibaud-Nissen, F., Wang, S., Wegrzyn, J. L., KU, thw266, Zhang, H., Lewin, H. A. & Richards, S., 2022, In: PNAS. 119, 4, 8 p., e2115639118.

Research output: Contribution to journal › Journal article › Research › peer-review

The Earth BioGenome Project 2020: Starting the clock

Lewin, H. A., Richards, S., Aiden, E. L., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, M. L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S. M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A. & 65 others, Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M Thomas P, Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J. H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O’Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D. & KU, thw266, 2022, In: PNAS. 119, 4, 7 p., e2115635118.

Research output: Contribution to journal › Review › Research › peer-review

The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

Bergeron, Lucie Adrienne, Besenbacher, S., Turner, T. N., Versoza, C. J., Wang, R. J., Price, A. L., Armstrong, E., Riera, M., Carlson, J., Chen, Hwei-Yen, Hahn, M. W., Harris, K., Kleppe, A. S., López-Nandam, E. H., Moorjani, P., Pfeifer, S. P., Tiley, G. P., Yoder, A. D., KU, thw266 & Schierup, M. H., 2022, In: eLife. 11, 28 p., e73577.

Research output: Contribution to journal › Journal article › Research › peer-review

The era of reference genomes in conservation genomics

Formenti, G., Theissinger, K., Fernandes, C., Bista, I., Bombarely, A., Bleidorn, C., Ciofi, C., Crottini, A., Godoy, J. A., Höglund, J., Malukiewicz, J., Mouton, A., Oomen, R. A., Paez, S., Palsbøll, P. J., Pampoulie, C., Ruiz-López, M. J., Svardal, H., Theofanopoulou, C., de Vries, J. & 8 others, Waldvogel, A. M., KU, thw266, Mazzoni, C. J., Jarvis, E., Bálint, M., Gilbert, M Thomas P, tsr259, tsr259 & European Reference Genome Atlas (ERGA) Consortium, E. R. G. A. (. C., 2022, In: Trends in Ecology and Evolution. 37, 3, p. 197-202 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Ferrández-Peral, L., Zhan, X., Alvarez-Estape, M., Chiva, C., Esteller-Cucala, P., García-Pérez, R., Julià, E., Lizano, E., Fornas, Ò., Sabidó, E., Li, Q., Marquès-Bonet, T., Juan, D. & KU, thw266, 2022, In: Genome Research. 32, 8, p. 1448-1462 15 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Unparalleled details of soft tissues in a Cretaceous ant

Zhuang, Y., Xu, W., KU, thw266, Mai, H., Li, X., He, H., Ran, H. & Liu, Y., 2022, In: BMC Ecology and Evolution. 22, 1, 10 p., 146.

Research output: Contribution to journal › Journal article › Research › peer-review

Validation of Potential Reference Genes for Real-Time qPCR Analysis in Pharaoh Ant, Monomorium pharaonis (Hymenoptera: Formicidae)

Ding, G., Gao, Q., Chen, J., Zhao, J., KU, thw266 & Liu, W., 2022, In: Frontiers in Physiology. 13, 9 p., 852357.

Research output: Contribution to journal › Journal article › Research › peer-review

Why sequence all eukaryotes?

Blaxter, M., Archibald, J. M., Childers, A. K., Coddington, J. A., Crandall, K. A., Di Palma, F., Durbin, R., Edwards, S. V., Graves, J. A. M., Hackett, K. J., Hall, N., Jarvis, E. D., Johnson, R. N., Karlsson, E. K., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Lindblad-Toh, K., Lopez, J. V., Moran, N. A. & 7 others, Robinson, G. E., Ryder, O. A., Shapiro, B., Soltis, P. S., Warnow, T., KU, thw266 & Lewin, H. A., 2022, In: Proceedings of the National Academy of Sciences of the United States of America. 119, 4, 9 p., e2115636118.

Research output: Contribution to journal › Journal article › Research › peer-review

Callithrix jacchus (the common marmoset)

Yang, Chentao & KU, thw266, 2021, In: Trends in Genetics. 37, 10, p. 948-949 2 p.

Research output: Contribution to journal › Letter › Research › peer-review

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

Li, J., Zhang, J., Liu, J., Zhou, Y., Cai, C., Xu, L., Dai, X., Feng, S., Guo, C., Rao, J., Wei, K., Jarvis, E. D., Jiang, Y., Zhou, Z., KU, thw266 & Zhou, Q., 2021, In: GigaScience. 10, 1, 15 p., giaa142.

Research output: Contribution to journal › Journal article › Research › peer-review

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes

Liu, J., Wang, Z., Li, J., Xu, L., Liu, J., Feng, S., Guo, C., Chen, S., Ren, Z., Rao, J., Wei, K., Chen, Y., Jarvis, E. D., KU, thw266 & Zhou, Q., 2021, In: Genome Research. 31, 3, p. 497-511 15 p.

Research output: Contribution to journal › Journal article › Research › peer-review

African lungfish genome sheds light on the vertebrate water-to-land transition

Wang, K., Wang, J., Zhu, C., Yang, L., Ren, Y., Ruan, J., Fan, G., Hu, J., Xu, W., Bi, X., Zhu, Y., Song, Y., Chen, H., Ma, T., Zhao, R., Jiang, H., Zhang, B., Feng, C., Yuan, Y., Gan, X. & 16 others, Li, Y., Zeng, H., Liu, Q., Zhang, Y., Shao, F., Hao, S., Zhang, H., Xu, X., Liu, X., Wang, D., Zhu, M., KU, thw266, Zhao, W., Qiu, Q., He, S. & Wang, W., 2021, In: Cell. 184, 5, p. 1362-1376.e18 33 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Ancestral developmental potentials in early bony fish contributed to vertebrate water-to-land transition

Bi, X. & KU, thw266, 2021, In: Zoological research. 42, 2, p. 135-137 3 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

Liu, S., Westbury, M. V., Dussex, N., Mitchell, K. J., Sinding, M. H. S., Heintzman, P. D., Duchêne, D. A., Kapp, J. D., von Seth, J., Heiniger, H., Sánchez-Barreiro, F., Margaryan, A., André-Olsen, R., De Cahsan, B., Meng, G., Yang, C., Chen, L., van der Valk, T., Moodley, Y., Rookmaaker, K. & 19 others, Bruford, M. W., Ryder, O., Steiner, C., Sonsbeek, L. G. R. B., Vartanyan, S., Guo, C., Cooper, A., Kosintsev, P., Kirillova, I., Lister, A. M., Marques-Bonet, T., Gopalakrishnan, Shyam, Dunn, Rob, Lorenzen, Eline, Shapiro, B., KU, thw266, Antoine, P. O., Dalén, L. & Gilbert, M Thomas P, 2021, In: Cell. 184, 19, p. 4874-4885.e16

Research output: Contribution to journal › Journal article › Research › peer-review

Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds

Wang, Z., Chen, G., KU, thw266 & Zhou, Q., 2021, In: Zoological Research. 42, 1, p. 51-61 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Evolutionary and biomedical insights from a marmoset diploid genome assembly

Yang, C., Zhou, Y., Marcus, S., Formenti, G., Bergeron, L. A., Song, Z., Bi, X., Bergman, J., Rousselle, M. M. C., Zhou, C., Zhou, L., Deng, Y., Fang, M., Xie, D., Zhu, Y., Tan, S., Mountcastle, J., Haase, B., Balacco, J., Wood, J. & 13 others, Chow, W., Rhie, A., Pippel, M., Fabiszak, M. M., Koren, S., Fedrigo, O., Freiwald, W. A., Howe, K., Yang, H., Phillippy, A. M., Schierup, M. H., Jarvis, E. D. & KU, thw266, 2021, In: Nature. 594, p. 227-233

Research output: Contribution to journal › Journal article › Research › peer-review

Evolutionary history of the extinct Sardinian dhole

Ciucani, M. M., Jensen, J. K., Sinding, M. S., Smith, O., Lucenti, S. B., Rosengren, E., Rook, L., Tuveri, C., Arca, M., Cappellini, Enrico, Galaverni, M., Randi, E., Guo, C., KU, thw266, Sicheritz-Pontén, Thomas, Dalén, L., Gilbert, M Thomas P & Gopalakrishnan, Shyam, 2021, In: Current Biology. 31, 24, p. 5571-5579.e6 16 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication

Puetz, Lara Christine, Delmont, T. O., Aizpurua Arrieta, Ostaizka, Guo, C., KU, thw266, Katajamaa, R., Jensen, P. & Gilbert, M Thomas P, 2021, In: Advanced Genetics. 2, 4, 12 p., 2100018.

Research output: Contribution to journal › Journal article › Research › peer-review

Hairs distinguish castes and sexes: identifying the early ontogenetic building blocks of a fungus-farming superorganism (Hymenoptera: Formicidae)

Adams, R. M. M., Larsen, Rasmus Stenbak, Stylianidi, N., Cheung, D., Qiu, Bitao, Murray, S. K., KU, thw266 & Boomsma, Jacobus J., 2021, In: Myrmecological News. 31, p. 201-216 16 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

Sánchez-Barreiro, F., Gopalakrishnan, Shyam, Ramos Madrigal, Jazmin, Westbury, Michael Vincent, de Manuel, M., Margaryan, Ashot, Ciucani, M. M., Vieira, Filipe Garrett, Patramanis, Ioannis, Kalthoff, D. C., Timmons, Z., Sicheritz-Pontén, Thomas, Dalén, L., Ryder, O. A., KU, thw266, Marques-Bonet, T., Moodley, Y. & Gilbert, M Thomas P, 2021, In: Molecular Ecology. 30, 23, p. 6355-6369 15 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Labour classified by cervical dilatation & fetal membrane rupture demonstrates differential impact on RNA-seq data for human myometrium tissues

Lai, P. F., Lei, K., Zhan, X., Sooranna, G., Li, J. K. H., Georgiou, E. X., Das, A., Singh, N., Li, Q., Stanfield, Z., KU, thw266, Tribe, R. M., Mesiano, S. & Johnson, M. R., 2021, In: PLoS ONE. 16, 11, 22 p., e0260119.

Research output: Contribution to journal › Journal article › Research › peer-review

Large-scale genomic analysis reveals the genetic cost of chicken domestication

Wang, M-S., Zhang, J-J., Guo, X., Li, M., Meyer, R., Ashari, H., Zheng, Z-Q., Wang, S., Peng, M-S., Jiang, Y., Thakur, M., Suwannapoom, C., Esmailizadeh, A., Hirimuthugoda, N. Y., Zein, M. S. A., Kusza, S., Kharrati-Koopaee, H., Zeng, L., Wang, Y-M., Yin, T-T. & 23 others, Yang, M., Li, M., Lu, X., Lasagna, E., Ceccobelli, S., Gunwardana, H. G. T. N., Senasig, T. M., Feng, S., Zhang, H., Bhuiyan, A. K. F. H., Khan, M. S., Silva, G. L. L. P., Thuy, L. T., Mwai, O. A., Ibrahim, M. N. M., KU, thw266, Qu, K., Hanotte, O., Shapiro, B., Bosse, M., Wu, D., Han, J. & Zhang, Y., 2021, In: BMC Biology. 19, 16 p., 118.

Research output: Contribution to journal › Journal article › Research › peer-review

Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal

Feuerborn, T. R., Carmagnini, A., Losey, R. J., Nomokonova, T., Askeyev, A., Askeyev, I., Askeyev, O., Antipina, E. E., Appelt, M., Bachura, O. P., Beglane, F., Bradley, D. G., Daly, K. G., Gopalakrishnan, S., Gregersen, K. M., Guo, C., Gusev, A. V., Jones, C., Kosintsev, P. A., Kuzmin, Y. V. & 17 others, Mattiangeli, V., Perri, A. R., Plekhanov, A. V., Ramos Madrigal, Jazmin, Schmidt, A. L., Shaymuratova, D., Smith, O., Yavorskaya, L. V., KU, thw266, Willerslev, Eske, Meldgaard, Morten, Gilbert, M Thomas P, Larson, G., Dalén, L., Hansen, Anders Johannes, Sinding, Mikkel Holger Strander & Frantz, L., 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 39, e2100338118.

Research output: Contribution to journal › Journal article › Research › peer-review

Modes of genetic adaptations underlying functional innovations in the rumen

Pan, X., Cai, Y., Li, Z., Chen, X., Heller, R., Wang, N., Wang, Y., Zhao, C., Wang, Y., Xu, H., Li, S., Li, M., Li, C., Hu, S., Li, H., Wang, K., Chen, L., Wei, B., Zheng, Z., Fu, W. & 20 others, Yang, Y., Zhang, T., Hou, Z., Yan, Y., Lv, X., Sun, W., Li, X., Huang, S., Liu, L., Mao, S., Liu, W., Hua, J., Li, Z., KU, thw266, Chen, Y., Wang, X., Qiu, Q., Dalrymple, B. P., Wang, W. & Jiang, Y., 2021, In: Science China Life Sciences. 64, 1, p. 1-21 21 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles

Andreu-Sánchez, S., Chen, W., Stiller, Josefin & KU, thw266, 2021, In: GigaScience. 10, 1, 11 p., giaa161.

Research output: Contribution to journal › Journal article › Research › peer-review

Platypus and echidna genomes reveal mammalian biology and evolution

Zhou, Y., Shearwin-Whyatt, L., Li, J., Song, Z., Hayakawa, T., Stevens, D., Fenelon, J. C., Peel, E., Cheng, Y., Pajpach, F., Bradley, N., Suzuki, H., Nikaido, M., Damas, J., Daish, T., Perry, T., Zhu, Z., Geng, Y., Rhie, A., Sims, Y. & 22 others, Wood, J., Haase, B., Mountcastle, J., Fedrigo, O., Li, Q., Yang, H., Wang, J., Johnston, S. D., Phillippy, A. M., Howe, K., Jarvis, E. D., Ryder, O. A., Kaessmann, H., Donnelly, P., Korlach, J., Lewin, H. A., Graves, J., Belov, K., Renfree, M. B., Grutzner, F., Zhou, Q. & KU, thw266, 2021, In: Nature. 592, 7856, p. 756-762

Research output: Contribution to journal › Journal article › Research › peer-review

Relaxed selection underlies genome erosion in socially parasitic ant species

Schrader, Lukas, Pan, H., Bollazzi, M., Schiøtt, M., Larabee, F. J., Bi, X., Deng, Y., KU, thw266, Boomsma, Jacobus J. & Rabeling, C., 2021, In: Nature Communications. 12, 13 p., 2918.

Research output: Contribution to journal › Journal article › Research › peer-review

Response of an Afro-Palearctic bird migrant to glaciation cycles

Thorup, Kasper, Pedersen, L., Rodrigues da Fonseca, Rute Andreia, Naimi, B., Nogues, David Bravo, Krapp, M., Manica, A., Willemoes, M., Sjöberg, Sissel, Feng, S., Chen, G., Rey de la Iglesia, Alba, Campos, P. F., Beyer, R., Araújo, M. B., Hansen, Anders Johannes, KU, thw266, Tøttrup, Anders P. & Rahbek, Carsten, 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 52, 8 p., e2023836118.

Research output: Contribution to journal › Journal article › Research › peer-review

Studying mutation rate evolution in primates - a need for systematic comparison of computational pipelines

Bergeron, Lucie Adrienne, Besenbacher, S., Schierup, M. H. & KU, thw266, 2021, In: GigaScience. 10, 10, 4 p., giab072.

Research output: Contribution to journal › Review › Research › peer-review

Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts

O'Brien, P. A., Andreakis, N., Tan, S., Miller, D. J., Webster, N. S., KU, thw266 & Bourne, D. G., 2021, In: Molecular Ecology. 30, 15, p. 3768-3782 15 p.

Research output: Contribution to journal › Journal article › Research › peer-review

The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai–Tibet Plateau

Qu, Y., Chen, C., Chen, X., Hao, Y., She, H., Wang, M., Ericson, P. G. P., Lin, H., Cai, T., Song, G., Jia, C., Chen, C., Zhang, H., Li, J., Liang, L., Wu, T., Zhao, J., Gao, Q., Zhang, G., Zhai, W. & 3 others, Zhang, C., Zhang, Y. E. & Lei, F., 2021, In: PNAS. 118, 13, 10 p., e2012398118.

Research output: Contribution to journal › Journal article › Research › peer-review

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

Bergeron, Lucie Adrienne, Besenbacher, S., Bakker, J., Zheng, J., Li, P., Antunes Pacheco, George, Sinding, Mikkel Holger Strander, Kamilari, M., Gilbert, M Thomas P, Schierup, M. H. & KU, thw266, 2021, In: GigaScience. 10, 5, 14 p., giab029.

Research output: Contribution to journal › Journal article › Research › peer-review

Towards complete and error-free genome assemblies of all vertebrate species

Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., Lee, C., Ko, B. J., Chaisson, M., Gedman, G. L., Cantin, L. J., Thibaud-Nissen, F., Haggerty, L., Bista, I., Smith, M., Haase, B. & 107 others, Mountcastle, J., Winkler, S., Paez, S., Howard, J., Vernes, S. C., Lama, T. M., Grutzner, F., Warren, W. C., Balakrishnan, C. N., Burt, D., George, J. M., Biegler, M. T., Iorns, D., Digby, A., Eason, D., Robertson, B., Edwards, T., Wilkinson, M., Turner, G., Meyer, A., Kautt, A. F., Franchini, P., Detrich, H. W., Svardal, H., Wagner, M., Naylor, G. J. P., Pippel, M., Malinsky, M., Mooney, M., Simbirsky, M., Hannigan, B. T., Pesout, T., Houck, M., Misuraca, A., Kingan, S. B., Hall, R., Kronenberg, Z., Sović, I., Dunn, C., Ning, Z., Hastie, A., Lee, J., Selvaraj, S., Green, R. E., Putnam, N. H., Gut, I., Ghurye, J., Garrison, E., Sims, Y., Collins, J., Pelan, S., Torrance, J., Tracey, A., Wood, J., Dagnew, R. E., Guan, D., London, S. E., Clayton, D. F., Mello, C. V., Friedrich, S. R., Lovell, P. V., Osipova, E., Al-Ajli, F. O., Secomandi, S., Kim, H., Theofanopoulou, C., Hiller, M., Zhou, Y., Harris, R. S., Makova, K. D., Medvedev, P., Hoffman, J., Masterson, P., Clark, K., Martin, F., Howe, K., Flicek, P., Walenz, B. P., Kwak, W., Clawson, H., Diekhans, M., Nassar, L., Paten, B., Kraus, R. H. S., Crawford, A. J., Gilbert, M Thomas P, KU, thw266, Venkatesh, B., Murphy, R. W., Koepfli, K., Shapiro, B., Johnson, W. E., Di Palma, F., Marques-Bonet, T., Teeling, E. C., Warnow, T., Graves, J. M., Ryder, O. A., Haussler, D., O’Brien, S. J., Korlach, J., Lewin, H. A., Howe, K., Myers, E. W., Durbin, R., Phillippy, A. M. & Jarvis, E. D., 2021, In: Nature. 592, 7856, p. 737-746 10 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes

Bi, X., Wang, K., Yang, L., Pan, H., Jiang, H., Wei, Q., Fang, M., Yu, H., Zhu, C., Cai, Y., He, Y., Gan, X., Zeng, H., Yu, D., Zhu, Y., Jiang, H., Qiu, Q., Yang, H., Zhang, Y. E., Wang, W. & 3 others, Zhu, M., He, S. & KU, thw266, 2021, In: Cell. 184, 5, p. 1377-1391, e1-e14

Research output: Contribution to journal › Journal article › Research › peer-review

Variation in predicted COVID-19 risk among lemurs and lorises

Melin, A. D., Orkin, J. D., Janiak, M. C., Valenzuela, A., Kuderna, L., Marrone, F., Ramangason, H., Horvath, J. E., Roos, C., Kitchener, A. C., Khor, C. C., Lim, W. K., Lee, J. G. H., Tan, P., Umapathy, G., Raveendran, M., Alan Harris, R., Gut, I., Gut, M., Lizano, E. & 19 others, Nadler, T., Zinner, D., Le, M. D., Manu, S., Rabarivola, C. J., Zaramody, A., Andriaholinirina, N., Johnson, S. E., Jarvis, E. D., Fedrigo, O., Wu, D., KU, thw266, Farh, K. K., Rogers, J., Marques-Bonet, T., Navarro, A., Juan, D., Arora, P. S. & Higham, J. P., 2021, In: American Journal of Primatology. 83, 6, 12 p., e23255.

Research output: Contribution to journal › Journal article › Research › peer-review

863 genomes reveal the origin and domestication of chicken

Wang, M. S., Thakur, M., Peng, M-S., Jiang, Y., Frantz, L. A. F., Li, M., Zhang, J-J., Wang, S., Peters, J., Otecko, N. O., Suwannapoom, C., Guo, X., Zheng, Z-Q., Esmailizadeh, A., Hirimuthugoda, N. Y., Ashari, H., Suladari, S., Zein, M. S. A., Kusza, S., Sohrabi, S. & 37 others, Kharrati-Koopaee, H., Shen, Q., Zeng, L., Yang, M., Wu, Y., Yang, X., Lu, X., Jia, X., Nie, Q., Lamont, S. J., Lasagna, E., Ceccobelli, S., Gunwardana, H. G. T. N., Senasige, T. M., Feng, S., Si, J., Zhang, H., Jin, J., Li, M., Liu, Y., Chen, H., Ma, C., Dai, S., Bhuiyan, A. K. F. H., Khan, M. S., Silva, G. L. L. P., Le, T., Mwai, O. A., Ibrahim, M. N. M., Supple, M., Shapiro, B., Hanotte, O., KU, thw266, Larson, G., Han, J., Wu, D. & Zhang, Y., 2020, In: Cell Research. 30, 8, p. 693-701 9 p.

Research output: Contribution to journal › Journal article › Research › peer-review

A draft genome assembly of spotted hyena, Crocuta crocuta

Yang, C., Li, F., Xiong, Z., Koepfli, K., Ryder, O., Perelman, P., Li, Q. & KU, thw266, 2020, In: Scientific Data. 7, 10 p., 126.

Research output: Contribution to journal › Journal article › Research › peer-review

A draft genome sequence of the elusive giant squid, Architeuthis dux

da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, Â. M., Barrio-Hernandez, I., Hoving, H-J., Tafur-Jimenez, R., Chu, C., Frazão, B., Petersen, B., Peñaloza, F., Musacchia, F., Alexander, G. C. & 24 others, Osório, H., Winkelmann, I., Simakov, O., Rasmussen, Simon, Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., KU, thw266, Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Pontén, Thomas, Nielsen, Rasmus & Gilbert, M Thomas P, 2020, In: GigaScience. 9, 1, 12 p., giz152.

Research output: Contribution to journal › Journal article › Research › peer-review

A novel method for using RNA-seq data to identify imprinted genes in social Hymenoptera with multiply mated queens

Howe, Jack, Schiøtt, M., Li, Q., Wang, Z., KU, thw266 & Boomsma, Jacobus J., 2020, In: Journal of Evolutionary Biology. 33, 12, p. 1770-1782 13 p.

Research output: Contribution to journal › Journal article › Research › peer-review

An Indo-Pacific Humpback Dolphin Genome Reveals Insights into Chromosome Evolution and the Demography of a Vulnerable Species

Zhang, P., Zhao, Y., Li, C., Lin, M., Dong, L., Zhang, R., Liu, M., Li, K., Zhang, H., Liu, X., Zhang, Y., Yuan, Y., Liu, H., Seim, I., Sun, S., Du, X., Chang, Y., Li, F., Liu, S., Lee, S. M. Y. & 13 others, Wang, K., Wang, D., Wang, X., McGowen, M. R., Jefferson, T. A., Olsen, Morten Tange, Stiller, Josefin, KU, thw266, Xu, X., Yang, H., Fan, G., Liu, X. & Li, S., 2020, In: iScience. 23, 10, 52 p., 101640.

Research output: Contribution to journal › Journal article › Research › peer-review

Chromatin accessibility and transcriptome landscapes of Monomorium pharaonis brain

Wang, M., Liu, Y., Wen, T., Liu, W., Gao, Q., Zhao, J., Xiong, Z., Wang, Z., Jiang, W., Yu, Y., Wu, L., Yuan, Y., Wei, X., Xu, J., Cheng, M., Zhang, P., Li, P., Hou, Y., Yang, H., Zhang, G. & 3 others, Li, Q., Liu, C. & Liu, L., 2020, In: Scientific Data. 7, 10 p., 217.

Research output: Contribution to journal › Journal article › Research › peer-review

Dense sampling of bird diversity increases power of comparative genomics

Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Hart Reeve, A., Xie, D., Chen, G., Guo, C., Faircloth, B. C., Petersen, B., Wang, Z., Zhou, Q., Diekhans, M., Chen, W., Andreu-Sánchez, S., Margaryan, A., Howard, J. T., Parent, C., Pacheco, G. & 130 others, Sinding, Mikkel Holger Strander, Puetz, Lara Christine, Cavill, Emily Louisa, Ribeiro, Â. M., Eckhart, L., Fjeldså, Jon, Hosner, Peter Andrew, Brumfield, R. T., Christidis, L., Bertelsen, Mads Frost, Sicheritz-Pontén, Thomas, Tietze, D. T., Robertson, B. C., Song, G., Borgia, G., Claramunt, S., Lovette, I. J., Cowen, S. J., Njoroge, P., Dumbacher, J. P., Ryder, O. A., Fuchs, J., Bunce, M., Burt, D. W., Cracraft, J., Meng, G., Hackett, S. J., Ryan, P. G., Jønsson, Knud Andreas, Jamieson, I. G., Rodrigues da Fonseca, Rute Andreia, Braun, E. L., Houde, P., Mirarab, S., Suh, A., Hansson, B., Ponnikas, S., Sigeman, H., Stervander, M., Frandsen, P. B., van der Zwan, H., van der Sluis, R., Visser, C., Balakrishnan, C. N., Clark, A. G., Fitzpatrick, J. W., Bowman, R., Chen, N., Cloutier, A., Sackton, T. B., Edwards, S. V., Foote, D. J., Shakya, S. B., Sheldon, F. H., Vignal, A., Soares, A. E. R., Shapiro, B., González-Solís, J., Ferrer-Obiol, J., Rozas, J., Riutort, M., Tigano, A., Friesen, V., Dalén, L., Urrutia, A. O., Székely, T., Liu, Y., Campana, M. G., Corvelo, A., Fleischer, R. C., Rutherford, K. M., Gemmell, N. J., Dussex, N., Mouritsen, H., Thiele, N., Delmore, K., Liedvogel, M., Franke, A., Hoeppner, M. P., Krone, O., Fudickar, A. M., Milá, B., Ketterson, E. D., Fidler, A. E., Friis, G., Parody-Merino, Á. M., Battley, P. F., Cox, M. P., Lima, N. C. B., Prosdocimi, F., Parchman, T. L., Schlinger, B. A., Loiselle, B. A., Blake, J. G., Lim, H. C., Day, L. B., Fuxjager, M. J., Baldwin, M. W., Braun, M. J., Wirthlin, M., Dikow, R. B., Ryder, T. B., Camenisch, G., Keller, L. F., Dacosta, J. M., Hauber, M. E., Louder, M. I. M., Witt, C. C., McGuire, J. A., Mudge, J., Megna, L. C., Carling, M. D., Wang, B., Taylor, S. A., Del-Rio, G., Aleixo, A., Vasconcelos, A. T. R., Mello, C. V., Weir, J. T., Haussler, D., Li, Q., Yang, H., Wang, J., Lei, F., Rahbek, Carsten, Gilbert, M Thomas P, Graves, G. R., Jarvis, E. D., Paten, B. & KU, thw266, 2020, In: Nature. 587, 7833, p. 252-257

Research output: Contribution to journal › Journal article › Research › peer-review

Developmental plasticity shapes social traits and selection in a facultatively eusocial bee

Kapheim, K. M., Jones, B. M., Pan, H., Li, C., Harpur, B. A., Kent, C. F., Zayed, A., Ioannidis, P., Waterhouse, R. M., Kingwell, C., Stolle, E., Avalos, A., KU, thw266, McMillan, W. O. & Wcislo, W. T., 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 24, p. 13615-13625 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Diverse coral reef invertebrates exhibit patterns of phylosymbiosis

O'Brien, P. A., Tan, S., Yang, C., Frade, P. R., Andreakis, N., Smith, H. A., Miller, D. J., Webster, N. S., KU, thw266 & Bourne, D. G., 2020, In: ISME Journal. 14, 9, p. 2211-2222 12 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet

Gelabert, P., Sandoval-Velasco, M., Serres, A., de Manuel, M., Renom, P., Margaryan, A., Stiller, J., de-Dios, T., Fang, Q., Feng, S., Mañosa, S., Pacheco, G., Ferrando-Bernal, M., Shi, G., Hao, F., Chen, X., Petersen, B., Olsen, R-A., Navarro, A., Deng, Y. & 6 others, Dalén, L., Marquès-Bonet, T., KU, thw266, Antunes, A., Gilbert, M Thomas P & Lalueza-Fox, C., 2020, In: Current Biology. 30, 1, p. 108-114, e1-e5

Research output: Contribution to journal › Journal article › Research › peer-review

Genome and single-cell RNA-sequencing of the earthworm Eisenia andrei identifies cellular mechanisms underlying regeneration

Shao, Y., Wang, X., Zhang, J., Li, M. L., Wu, S., Ma, X., Wang, X., Zhao, H., Li, Y., Zhu, H. H., Irwin, D. M., Wang, D., KU, thw266, Ruan, J. & Wu, D., 2020, In: Nature Communications. 11, 15 p., 2656.

Research output: Contribution to journal › Journal article › Research › peer-review

Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens

Barnett, R., Westbury, M. V., Sandoval-Velasco, M., Vieira, F. G., Jeon, S., Zazula, G., Martin, M. D., Ho, S. Y. W., Mather, N., Gopalakrishnan, S., Ramos-Madrigal, J., de Manuel, M., Zepeda-Mendoza, M. L., Antunes, A., Baez, A. C., De Cahsan, B., Larson, G., O’Brien, S. J., Eizirik, E., Johnson, W. E. & 11 others, Koepfli, K., Wilting, A., Fickel, J., Dalén, L., Lorenzen, Eline, Marques-Bonet, T., Hansen, Anders Johannes, KU, thw266, Bhak, J., Yamaguchi, N. & Gilbert, M Thomas P, 2020, In: Current Biology. 30, p. 5018-5025

Research output: Contribution to journal › Journal article › Research › peer-review

Genomic regions influencing aggressive behavior in honey bees are defined by colony allele frequencies

Avalos, A., Fang, M., Pan, H., Lluch, A. R., Lipka, A. E., Zhao, S. D., Giray, T., Robinson, G. E., KU, thw266 & Hudson, M. E., 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 29, p. 17135-17141 7 p.

Research output: Contribution to journal › Journal article › Research › peer-review

High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis

Gao, Q., Xiong, Z., Larsen, Rasmus Stenbak, Zhou, L., Zhao, J., Ding, G., Zhao, R., Liu, C., Ran, H. & KU, thw266, 2020, In: GigaScience. 9, 12, 14 p., giaa143.

Research output: Contribution to journal › Journal article › Research › peer-review

Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus

Fotaki, Anna Katerina, Denham, S. D., Mackie, Meaghan, Iraeta Orbegozo, Miren, Mylopotamitaki, Dorothea, Gopalakrishnan, Shyam, Sicheritz-Pontén, Thomas, Olsen, Jesper Velgaard, Cappellini, Enrico, KU, thw266, Christophersen, A., Gilbert, M Thomas P & Vågene, Åshild Joanne, 2020, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 375, 1812, 10 p., 20190584.

Research output: Contribution to journal › Journal article › Research › peer-review

Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros

Lord, E., Dussex, N., Kierczak, M., Díez-del-Molino, D., Ryder, O. A., Stanton, D. W. G., Gilbert, M. T. P., Sánchez-Barreiro, F., Zhang, G., Sinding, M. H. S., Lorenzen, E. D., Willerslev, E., Protopopov, A., Shidlovskiy, F., Fedorov, S., Bocherens, H., Nathan, S. K. S. S., Goossens, B., van der Plicht, J., Chan, Y. L. & 10 others, Prost, S., Potapova, O., Kirillova, I., Lister, A. M., Heintzman, P. D., Kapp, J. D., Shapiro, B., Vartanyan, S., Götherström, A. & Dalén, L., 2020, In: Current Biology. 30, 19, p. 3871-3879, e1-e7 16 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., Genereux, D., Johnson, J., Marinescu, V. D., Alföldi, J., Harris, R. S., Lindblad-Toh, K., Haussler, D., Karlsson, E., Jarvis, E. D., Zhang, G. & 1 others, Paten, B., 2020, In: Nature. 587, 7833, p. 246-251

Research output: Contribution to journal › Journal article › Research › peer-review

Rapid loss of endogenous DNA in pig bone buried in five different environments

Eriksen, A. M. H., Matthiesen, H., Kontopoulos, I., Gregory, D., Snoeck, C., KU, thw266, Collins, Matthew James & Gilbert, M Thomas P, 2020, In: Archaeometry. 62, 4, p. 827-846 20 p.

Research output: Contribution to journal › Review › Research › peer-review

The evolutionary history of extinct and living lions

de Manuel, M., Barnett, R., Sandoval-Velasco, M., Yamaguchi, N., Vieira, F. G., Mendoza, M. L. Z., Liu, S., Martin, M. D., Sinding, M-H. S., Mak, S. S. T., Caroe, C., Liu, S., Guo, C., Zheng, J., Zazula, G., Baryshnikov, G., Eizirik, E., Koepfli, K-P., Johnson, W. E., Antunes, A. & 9 others, Sicheritz-Pontén, Thomas, Gopalakrishnan, Shyam, Larson, G., Yang, H., O'Brien, S. J., Hansen, Anders Johannes, KU, thw266, Marques-Bonet, T. & Gilbert, M Thomas P, 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 20, p. 10927-10934 8 p.

Research output: Contribution to journal › Journal article › Research › peer-review

The gene expression network regulating queen brain remodeling after insemination and its parallel use in ants with reproductive workers

Nagel, M., Qiu, Bitao, Brandenborg, L. E., Larsen, Rasmus Stenbak, Ning, D., Boomsma, Jacobus J. & KU, thw266, 2020, In: Science Advances. 6, 38, 17 p., eaaz5772.

Research output: Contribution to journal › Journal article › Research › peer-review

The origin of domestication genes in goats

Zheng, Z., Wang, X., Li, M., Li, Y., Yang, Z., Wang, X., Pan, X., Gong, M., Zhang, Y., Guo, Y., Wang, Y., Liu, J., Cai, Y., Chen, Q., Okpeku, M., Colli, L., Cai, D., Wang, K., Huang, S., Sonstegard, T. S. & 16 others, Esmailizadeh, A., Zhang, W., Zhang, T., Xu, Y., Xu, N., Yang, Y., Han, J., Chen, L., Lesur, J., Daly, K. G., Bradley, D. G., Heller, Rasmus, KU, thw266, Wang, W., Chen, Y. & Jiang, Y., 2020, In: Science Advances. 6, 21, eaaz5216.

Research output: Contribution to journal › Journal article › Research › peer-review

Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys

Zhang, P., Chen, J-S., Li, Q-Y., Sheng, L-X., Gao, Y-X., Lu, B-Z., Zhu, W-B., Zhan, X-Y., Li, Y., Yuan, Z-B., Xu, G., Qiu, B-T., Yan, M., Guo, C-X., Wang, Y-Q., Huang, Y-J., Zhang, J-X., Liu, F-Y., Tang, Z-W., Lin, S-Z. & 7 others, Cooper, D. N., Yang, H., Wang, J., Gao, Y., Yin, W., KU, thw266 & Yan, G., 13 Dec 2019, In: Zoological research. 41, 1, p. 3-19 17 p.

Research output: Contribution to journal › Review › Research › peer-review

31º South: The physiology of adaptation to arid conditions in a passerine bird

Ribeiro, Â. M., Puetz, Lara Christine, Pattinson, N. B., Dalén, L., Deng, Y., KU, thw266, Rodrigues da Fonseca, Rute Andreia, Smit, B. & Gilbert, M Thomas P, 2019, In: Molecular Ecology. 28, 16, p. 3709-3721 13 p.

Research output: Contribution to journal › Journal article › Research › peer-review

A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari Desert

Farré, M., Li, Q., Zhou, Y., Damas, J., Chemnick, L. G., Kim, J., Ryder, O. A., Ma, J., KU, thw266, Larkin, D. M. & Lewin, H. A., 2019, In: GigaScience. 8, 2, p. 1-8 giy162.

Research output: Contribution to journal › Journal article › Research › peer-review

Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype

Borges, R., Fonseca, J., Gomes, C., Johnson, W. E., O'Brien, S. J., KU, thw266, Gilbert, M Thomas P, Jarvis, E. D. & Antunes, A., 2019, In: Genome Biology and Evolution. 11, 8, p. 2244-2255

Research output: Contribution to journal › Journal article › Research › peer-review

Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies

Stiller, Josefin & KU, thw266, 2019, In: Diversity. 11, 7, 19 p., 115.

Research output: Contribution to journal › Journal article › Research › peer-review

Comparative study on pattern recognition receptors in non-teleost ray-finned fishes and their evolutionary significance in primitive vertebrates

He, Y., Pan, H., KU, thw266 & He, S., 2019, In: Science China Life Sciences. 62, 4, p. 566-578

Research output: Contribution to journal › Journal article › Research › peer-review

Detoxification Genes Differ Between Cactus-, Fruit-, and Flower-Feeding Drosophila

Rane, R. V., Clarke, D. F., Pearce, S. L., KU, thw266, Hoffmann, A. A. & Oakeshott, J. G., 2019, In: The Journal of Heredity. 110, 1, p. 80-91 12 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi)

Kapheim, K. M., Pan, H., Li, C., Blatti, C., Harpur, B. A., Ioannidis, P., Jones, B. M., Kent, C. F., Ruzzante, L., Sloofman, L., Stolle, E., Waterhouse, R. M., Zayed, A., KU, thw266 & Wcislo, W. T., 2019, In: G3: Genes, Genomes, Genetics (Bethesda). 9, 3, p. 625-634

Research output: Contribution to journal › Journal article › Research › peer-review

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds

Xu, L., Auer, G., Peona, V., Suh, A., Deng, Y., Feng, S., KU, thw266, Blom, M. P. K., Christidis, L., Prost, S., Irestedt, M. & Zhou, Q., 2019, In: Nature Ecology and Evolution. 3, 5, p. 834-844 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

Farre, M., Kim, J., Proskuryakova, A. A., Zhang, Y., Kulemzina, A. I., Li, Q., Zhou, Y., Xiong, Y., Johnson, J. L., Perelman, P. L., Johnson, W. E., Warren, W. C., Kukekova, A. V., KU, thw266, O'Brien, S. J., Ryder, O. A., Graphodatsky, A. S., Ma, J., Lewin, H. A. & Larkin, D. M., 2019, In: Genome Research. 29, 4, p. 576-589

Research output: Contribution to journal › Journal article › Research › peer-review

Genetic basis of ruminant headgear and rapid antler regeneration

Wang, Y., Zhang, C., Wang, N., Li, Z., Heller, R., Liu, R., Zhao, Y., Han, J., Pan, X., Zheng, Z., Dai, X., Chen, C., Dou, M., Peng, S., Chen, X., Liu, J., Li, M., Wang, K., Liu, C., Lin, Z. & 18 others, Chen, L., Hao, F., Zhu, W., Song, C., Zhao, C., Zheng, C., Wang, J., Hu, S., Li, C., Yang, H., Jiang, L., Li, G., Liu, M., Sonstegard, T. S., KU, thw266, Jiang, Y., Wang, W. & Qiu, Q., 2019, In: Science. 364, 6446, p. 1153-+ eaav6335.

Research output: Contribution to journal › Journal article › Research › peer-review

Genomic and transcriptomic investigations of the evolutionary transition from oviparity to viviparity

Gao, W., Sun, Y-B., Zhou, W-W., Xiong, Z-J., Chen, L., Li, H., Fu, T-T., Xu, K., Xu, W., Ma, L., Chen, Y-J., Xiang, X-Y., Zhou, L., Zeng, T., Zhang, S., Jin, J-Q., Chen, H-M., Zhang, G., Hillis, D. M., Ji, X. & 2 others, Zhang, Y. & Che, J., 2019, In: Proceedings of the National Academy of Sciences of the United States of America. 116, 9, p. 3646-3655

Research output: Contribution to journal › Journal article › Research › peer-review

Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species

Rane, R. V., Pearce, S. L., Li, F., Coppin, C., Schiffer, M., Shirriffs, J., Sgro, C. M., Griffin, P. C., KU, thw266, Lee, S. F., Hoffmann, A. A. & Oakeshott, J. G., 2019, In: BMC Genomics. 20, p. 1-22 52.

Research output: Contribution to journal › Journal article › Research › peer-review

High-coverage genomes to elucidate the evolution of penguins

Pan, H., Cole, T. L., Bi, X., Fang, M., Zhou, C., Yang, Z., Ksepka, D. T., Hart, T., Bouzat, J. L., Argilla, L. S., Bertelsen, M. F., Boersma, P. D., Bost, C. A., Cherel, Y., Dann, P., Fiddaman, S. R., Howard, P., Labuschagne, K., Mattern, T., Miller, G. & 26 others, Parker, P., Phillips, R. A., Quillfeldt, P., Ryan, P. G., Taylor, H., Thompson, D. R., Young, M. J., Ellegaard, M. R., Gilbert, M Thomas P, Sinding, Mikkel Holger Strander, Antunes Pacheco, George, Shepherd, L. D., Tennyson, A. J. D., Grosser, S., Kay, E., Nupen, L. J., Ellenberg, U., Houston, D. M., Reeve, A. H., Johnson, K., Masello, J. F., Stracke, T., McKinlay, B., Borboroglu, P. G., Zhang, D. X. & KU, thw266, 2019, In: GigaScience. 8, 9, p. 1-17

Research output: Contribution to journal › Journal article › Research › peer-review

Identification and evolution of avian endogenous foamy viruses

Chen, Y., Wei, X., KU, thw266, Holmes, E. C. & Cui, J., 2019, In: Virus Evolution. 5, 2, 6 p., vez049.

Research output: Contribution to journal › Journal article › Research › peer-review

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Chen, L., Qin, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., Su, W., Liu, G., Li, Q., Fu, W., Pan, X., Liu, C., Yang, J., Zhang, C., Yin, Y., Wang, Y. & 32 others, Zhao, Y., Zhang, C., Wang, Z., Qin, Y., Liu, W., Wang, B., Ren, Y., Zhang, R., Zeng, Y., Rodrigues da Fonseca, Rute Andreia, Wei, B., Li, R., Wan, W., Zhao, R., Zhu, W., Wang, Y., Duan, S., Gao, Y., Zhang, Y. E., Chen, C., Hvilsom, C., Epps, C. W., Chemnick, L. G., Doug, Y., Mirarab, S., Siegismund, Hans Redlef, Ryder, O. A., Gilbert, M Thomas P, Lewin, H. A., KU, thw266, Heller, Rasmus & Wang, W., 2019, In: Science. 364, 6446, p. 1152-

Research output: Contribution to journal › Journal article › Research › peer-review

Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation

Cole, T. L., Ksepka, D. T., Mitchell, K. J., Tennyson, A. J. D., Thomas, D. B., Pan, H., KU, thw266, Rawlence, N. J., Wood, J. R., Bover, P., Bouzat, J. L., Cooper, A., Fiddaman, S. R., Hart, T., Miller, G., Ryan, P. G., Shepherd, L. D., Wilmshurst, J. M. & Waters, J. M., 2019, In: MOLECULAR BIOLOGY AND EVOLUTION . 36, 4, p. 784-797 14 p.

Research output: Contribution to journal › Journal article › Research › peer-review

The Genomic Footprints of the Fall and Recovery of the Crested Ibis

Feng, S., Fang, Q., Barnett, R., Li, C., Han, S., Kuhlwilm, M., Zhou, L., Pan, H., Deng, Y., Chen, G., Gamauf, A., Woog, F., Prys-Jones, R., Marques-Bonet, T., Gilbert, M Thomas P & KU, thw266, 2019, In: Current Biology. 29, 2, p. 340-349, e1-e7

Research output: Contribution to journal › Journal article › Research › peer-review

The Vertebrate TLR Supergene Family Evolved Dynamically by Gene Gain/Loss and Positive Selection Revealing a Host-Pathogen Arms Race in Birds

Khan, I., Maldonado, E., Silva, L., Almeida, D., Johnson, W. E., O'Brien, S. J., KU, thw266, Jarvis, E. D., Gilbert, M Thomas P & Antunes, A., 2019, In: Diversity. 11, 8, 25 p., 131.

Research output: Contribution to journal › Journal article › Research › peer-review

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly

Rando, H. M., Farre, M., Robson, M. P., Won, N. B., Johnson, J. L., Buch, R., Bastounes, E. R., Xiang, X., Feng, S., Liu, S., Xiong, Z., Kim, J., KU, thw266, Trut, L. N., Larkin, D. M. & Kukekova, A. V., 2018, In: Genes. 9, 6, 21 p., 308.

Research output: Contribution to journal › Journal article › Research › peer-review

Earth BioGenome Project: sequencing life for the future of life

Lewin, H. A., Robinson, G. E., Kress, W. J., Baker, W. J., Coddington, J., Crandall, K. A., Durbin, R., Edwards, S. V., Forest, F., Gilbert, M. T. P., Goldstein, M. M., Grigoriev, I. V., Hackett, K. J., Haussler, D., Jarvis, E. D., Johnson, W. E., Patrinos, A., Richards, S., Castilla-Rubio, J. C., van Sluys, M-A. & 4 others, Soltis, P. S., Xu, X., Yang, H. & KU, thw266, 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 17, p. 4325-4333 9 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Genomic Takeover by Transposable Elements in the Strawberry Poison Frog

Rogers, R. L., Zhou, L., Chu, C., Márquez, R., Corl, A., Linderoth, T., Freeborn, L., MacManes, M. D., Xiong, Z., Zheng, J., Guo, C., Xun, X., Kronforst, M. R., Summers, K., Wu, Y., Yang, H., Richards-Zawacki, C. L., KU, thw266 & Nielsen, R., 2018, In: MOLECULAR BIOLOGY AND EVOLUTION . 35, 12, p. 2913-2927

Research output: Contribution to journal › Journal article › Research › peer-review

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

Zepeda Mendoza, M. L., Xiong, Z., Escalera-Zamudio, M., Runge, A. K. W., Thézé, J., Streicker, D., Frank, H. K., Loza-Rubio, E., Liu, S., Ryder, O. A., Castruita, J. A. S., Katzourakis, A., Pacheco, G. A., Taboada, B., Löber, U., Pybus, O. G., Li, Y., Rojas-Anaya, E., Bohmann, K., Carmona Baez, A. & 9 others, Arias, C. F., Liu, S., Greenwood, A. D., Bertelsen, Mads Frost, White, N. E., Bunce, M., KU, thw266, Sicheritz-Ponten, T. & Gilbert, M Thomas P, 2018, In: Nature Ecology & Evolution. 2, 4, p. 659-668 10 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours

Kukekova, A. V., Johnson, J. L., Xiang, X., Feng, S., Liu, S., Rando, H. M., Kharlamova, A. V., Herbeck, Y., Serdyukova, N. A., Xiong, Z., Beklemischeva, V., Koepfli, K-P., Gulevich, R. G., Vladimirova, A. V., Hekman, J. P., Perelman, P. L., Graphodatsky, A. S., O'Brien, S. J., Wang, X., Clark, A. G. & 3 others, Acland, G. M., Trut, L. N. & KU, thw266, 2018, In: Nature Ecology & Evolution. 2, 9, p. 1479-1491

Research output: Contribution to journal › Journal article › Research › peer-review

The bird's-eye view on chromosome evolution

KU, thw266, 2018, In: Genome Biology. 19, p. 1-3 201.

Research output: Contribution to journal › Journal article › Research › peer-review

The first AsiaEvo conference, connecting Asian evolutionary biologists to the world

KU, thw266, 2018, In: National Science Review. 5, 5, p. 614-616

Research output: Contribution to journal › Editorial › Research › peer-review