Shyam Gopalakrishnan
Associate Professor
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A 5700 year-old human genome and oral microbiome from chewed birch pitch
Jensen, T. Z. T., Niemann, J., Iversen, K. H., Fotakis, A. K., Gopalakrishnan, S., Vågene, Å. J., Pedersen, M. W., Sinding, M-H. S., Ellegaard, M. R., Allentoft, M. E., Lanigan, L. T., Taurozzi, A. J., Nielsen, S. H., Dee, M. W., Mortensen, M. N., Christensen, M. C., Sørensen, S. A., Collins, M. J., Gilbert, M. T. P., Sikora, M. & 2 others, , 2019, In: Nature Communications. 10, 10 p., 5520.Research output: Contribution to journal › Journal article › Research › peer-review
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A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)
Rasmussen, Jacob Agerbo, Villumsen, Kasper Rømer, Ernst, M., Hansen, M., Forberg, T., Gopalakrishnan, Shyam, Gilbert, M Thomas P, Bojesen, Anders Miki, Kristiansen, Karsten & Limborg, Morten Tønsberg, 2022, In: Microbiome. 10, 19 p., 21.Research output: Contribution to journal › Journal article › Research › peer-review
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Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
Gileta, A. F., Gao, J., Chitre, A. S., Bimschleger, H., St Pierre, C. L., Gopalakrishnan, Shyam & Palmer, A. A., 2020, In: G3: Genes, Genomes, Genetics (Bethesda). 10, 7, p. 2195-2205 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding
Aizpurua Arrieta, Ostaizka, Budinski, I., Georgiakakis, P., Gopalakrishnan, Shyam, Ibanez, C., Mata, V., Rebelo, H., Russo, D., Szodoray-Paradi, F., Zhelyazkova, V., Zrncic, V., Gilbert, M Thomas P & Alberdi, Antton, 2018, In: Molecular Ecology. 27, 3, p. 815-825 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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An Anthropocene map of genetic diversity
Miraldo, A., Li, Sen, Borregaard, Michael Krabbe, Florez Rodriguez, A., Gopalakrishnan, Shyam, Rizvanovic, M., Wang, Z., Rahbek, Carsten, Marske, K. A. & Nogues, David Bravo, 2016, In: Science. 353, 6307, p. 1532-1535 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility
Zou, J., Gopalakrishnan, Shyam, Parker, C. C., Nicod, J., Mott, R., Cai, N., Lionikas, A., Davies, R. W., Palmer, A. A. & Flint, J., 2022, In: G3: Genes, Genomes, Genetics. 12, 1, 13 p., jkab394.Research output: Contribution to journal › Journal article › Research › peer-review
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Ancient DNA reveals genetic admixture in China during tiger evolution
Sun, X., Liu, Y. C., Tiunov, M. P., Gimranov, D. O., Zhuang, Y., Han, Y., Driscoll, C. A., Pang, Y., Li, C., Pan, Y., Velasco, M. S., Gopalakrishnan, S., Yang, R. Z., Li, B. G., Jin, K., Xu, X., Uphyrkina, O., Huang, Y., Wu, X. H., Gilbert, M. T. P. & 3 others, , 2023, In: Nature Ecology and Evolution. 7, 11, p. 1914-1929 29 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Ancient Maltese genomes and the genetic geography of Neolithic Europe
Ariano, B., Mattiangeli, V., Breslin, E. M., Parkinson, E. W., McLaughlin, T. R., Thompson, J. E., Power, R. K., Stock, J. T., Mercieca-Spiteri, B., Stoddart, S., Malone, C., Gopalakrishnan, Shyam, Cassidy, L. M. & Bradley, D. G., 2022, In: Current Biology. 32, 12, p. 2668-2680.e6Research output: Contribution to journal › Journal article › Research › peer-review
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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, , 2021, In: Cell. 184, 19, p. 4874-4885.e16Research output: Contribution to journal › Journal article › Research › peer-review
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Ancient genomes from Iceland reveal the making of a human population
Ebenesersdóttir, S. S., Sandoval Velasco, M., Gunnarsdóttir, E. D., Jagadeesan, A., Guðmundsdóttir, V. B., Thordardóttir, E. L., Einarsdóttir, M. S., Moore, K. H. S., Sigurðsson, Á., Magnusdóttir, D. N., Jonsson, H., Snorradóttir, S., Hovig, E., Møller, P., Kockum, I., Olsson, T., Alfredsson, L., Hansen, T. F., Werge, T., Cavalleri, G. L. & 10 others, , 2018, In: Science. 360, 6392, p. 1028-1032 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Arctic-adapted dogs emerged at the Pleistocene-Holocene transition
Sinding, M. H. S., Gopalakrishnan, S., Ramos-Madrigal, J., de Manuel, M., Pitulko, V. V., Kuderna, L., Feuerborn, T. R., Frantz, L. A. F., Vieira, F. G., Niemann, J., Samaniego Castruita, J. A., Carøe, C., Andersen-Ranberg, E. U., Jordan, P. D., Pavlova, E. Y., Nikolskiy, P. A., Kasparov, A. K., Ivanova, V. V., Willerslev, E., Skoglund, P. & 15 others, , 2020, In: Science (New York, N.Y.). 368, 6498, p. 1495-1499 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions
Thuesen, N. H., Klausen, M. S., Gopalakrishnan, Shyam, Trolle, T. & Renaud, Gabriel, 2022, In: Frontiers in Immunology. 13, 15 p., 987655.Research output: Contribution to journal › Journal article › Research › peer-review
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Biodiversity Soup II: A bulk-sample metabarcoding pipeline emphasizing error reduction
Yang, C., Bohmann, Kristine, Wang, X., Cai, W., Wales, N., Ding, Z., Gopalakrishnan, Shyam & Yu, D. W., 2021, In: Methods in Ecology and Evolution. 12, 7, p. 1252-1264 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Circumpolar phylogeography and demographic history of beluga whales reflect past climatic fluctuations
Skovrind, M., Louis, M., Westbury, M. V., Garilao, C., Kaschner, K., Castruita, J. A. S., Gopalakrishnan, S., Knudsen, S. W., Haile, J. S., Dalén, L., Meshchersky, I. G., Shpak, O. V., Glazov, D. M., Rozhnov, V. V., Litovka, D. I., Krasnova, V. V., Chernetsky, A. D., Bel'kovich, V. M., Lydersen, C., Kovacs, K. M. & 4 others, , Jun 2021, In: Molecular Ecology. 30, 11, p. 2543-2559 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Mak, Sarah Siu Tze, Gopalakrishnan, Shyam, Carøe, C., Geng, C., Liu, Shanlin, Sinding, Mikkel Holger Strander, Kuderna, L. F. K., Zhang, W., Fu, S., Vieira, Filipe Garrett, Germonpré, M., Bocherens, H., Fedorov, S., Petersen, Bent, Sicheritz-Pontén, T., Marques-Bonet, T., KU, thw266, Jiang, H. & Gilbert, M Thomas P, Aug 2017, In: GigaScience. 6, 8, p. 1–13 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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.Research output: Contribution to journal › Journal article › Research › peer-review
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Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing
Hernández-Alonso, G., Ramos-Madrigal, J., Sun, X., Scharff-Olsen, C. H., Sinding, M. H. S., Martins, N. F., Ciucani, M. M., Mak, S. S. T., Lanigan, L. T., Clausen, C. G., Bhak, J., Jeon, S., Kim, C., Eo, K. Y., Cho, S. H., Boldgiv, B., Gantulga, G., Unudbayasgalan, Z., Kosintsev, P. A., Stenøien, H. K. & 2 others, , 2023, In: Ecology and Evolution. 13, 8, 15 p., e10404.Research output: Contribution to journal › Journal article › Research › peer-review
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Contrasting genetic signal of recolonization after rainforest fragmentation in African trees with different dispersal abilities
Piñeiro, R., Hardy, O. J., Tovar, C., Gopalakrishnan, Shyam, Vieira, Filipe Garrett & Gilbert, M Thomas P, 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 27, 9 p., e2013979118.Research output: Contribution to journal › Journal article › Research › peer-review
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Dealing with dimensionality: the application of machine learning to multi-omics data
Feldner-Busztin, D., Nisantzis, P. F., Edmunds, S. J., Boza, G., Racimo, Fernando, Gopalakrishnan, Shyam, Limborg, Morten Tønsberg, Lahti, L. & de Polavieja, G. G., 2023, In: Bioinformatics. 39, 2, 8 p., btad021.Research output: Contribution to journal › Journal article › Research › peer-review
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Dire wolves were the last of an ancient New World canid lineage
Perri, A. R., Mitchell, K. J., Mouton, A., Alvarez-Carretero, S., Hulme-Beaman, A., Haile, J., Jamieson, A., Meachen, J., Lin, A. T., Schubert, B. W., Ameen, C., Antipina, E. E., Bover, P., Brace, S., Carmagnini, A., Carøe, C., Samaniego Castruita, J. A., Chatters, J. C., Dobney, K., dos Reis, M. & 29 others, , 2021, In: Nature. 591, p. 87-91Research output: Contribution to journal › Journal article › Research › peer-review
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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
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Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshu
Niemann, Jonas, Gopalakrishnan, Shyam, Yamaguchi, N., Ramos Madrigal, Jazmin, Wales, N., Gilbert, M Thomas P & Sinding, M. S., 2021, In: iScience. 24, 25 p., 101904.Research output: Contribution to journal › Journal article › Research › peer-review
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Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication
Ramos Madrigal, Jazmin, Smith, B. D., Moreno Mayar, J. Víctor, Gopalakrishnan, Shyam, Ross-Ibarra, J., Gilbert, M Thomas P & Wales, N., 2016, In: Current Biology. 26, 23, p. 3195-3201 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice
Parker, C. C., Gopalakrishnan, Shyam, Carbonetto, P., Gonzales, N. M., Leung, E., Park, Y. J., Aryee, E., Davis, J., Blizard, D. A., Ackert-Bicknell, C. L., Lionikas, A., Pritchard, J. K. & Palmer, A. A., Aug 2016, In: Nature Genetics. 48, 8, p. 919-926 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
ID: 140603020
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Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Research output: Contribution to journal › Journal article › Research › peer-review
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331
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Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure
Research output: Contribution to journal › Journal article › Research › peer-review
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285
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The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics
Research output: Contribution to journal › Journal article › Research › peer-review
Published