Shyam Gopalakrishnan

Shyam Gopalakrishnan

Associate Professor

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    ORCID: 0000-0002-2004-6810

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    1. Published

      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

    2. Published

      Promises and pitfalls of using high-throughput sequencing for diet analysis

      Alberdi, Antton, Aizpurua Arrieta, Ostaizka, Bohmann, Kristine, Gopalakrishnan, Shyam, Lynggaard, Christina Islas, Nielsen, M. & Gilbert, M Thomas P, Mar 2019, In: Molecular Ecology Resources. 19, 2, p. 327-348

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

    3. Published

      Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic

      Ameen, C., Feuerborn, T. R., Brown, S. K., Linderholm, A., Hulme-Beaman, A., Lebrasseur, O., Sinding, M-H. S., Lounsberry, Z. T., Lin, A. T., Appelt, M., Bachmann, L., Betts, M., Britton, K., Darwent, J., Dietz, R., Fredholm, M., Gopalakrishnan, S., Goriunova, O. I., Grønnow, B., Haile, J. & 39 others, Hallsson, J. H., Harrison, R., Heide-Jørgensen, M. P., Knecht, R., Losey, R. J., Masson-MacLean, E., McGovern, T. H., McManus-Fry, E., Meldgaard, Morten, Midtdal, Å., Moss, M. L., Nikitin, I. G., Nomokonova, T., Pálsdóttir, A. H., Perri, A., Popov, A. N., Rankin, L., Reuther, J. D., Sablin, M., Schmidt, A. L., Shirar, S., Smiarowski, K., Sonne, C., Stiner, M. C., Vasyukov, M., West, C. F., Ween, G. B., Wennerberg, S. E., Wiig, Ø., Woollett, J., Dalén, L., Hansen, Anders Johannes, Gilbert, M Thomas P, Sacks, B. N., Frantz, L., Larson, G., Dobney, K., Darwent, C. M. & Evin, A., 2019, In: Proceedings. Biological sciences. 286, 1916, p. 20191929

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

    4. Published

      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.e6

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

    5. Published

      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

    6. Published

      Grey wolf genomic history reveals a dual ancestry of dogs

      Bergström, A., Stanton, D. W. G., Taron, U. H., Frantz, L., Sinding, M. H. S., Ersmark, E., Pfrengle, S., Cassatt-Johnstone, M., Lebrasseur, O., Girdland-Flink, L., Fernandes, D. M., Ollivier, M., Speidel, L., Gopalakrishnan, S., Westbury, M. V., Ramos-Madrigal, J., Feuerborn, T. R., Reiter, E., Gretzinger, J., Münzel, S. C. & 61 others, Swali, P., Conard, N. J., Carøe, C., Haile, James Seymour, Linderholm, A., Androsov, S., Barnes, I., Baumann, C., Benecke, N., Bocherens, H., Brace, S., Carden, R. F., Drucker, D. G., Fedorov, S., Gasparik, M., Germonpré, M., Grigoriev, S., Groves, P., Hertwig, S. T., Ivanova, V. V., Janssens, L., Jennings, R. P., Kasparov, A. K., Kirillova, I. V., Kurmaniyazov, I., Kuzmin, Y. V., Kosintsev, P. A., Lázničková-Galetová, M., Leduc, C., Nikolskiy, P., Nussbaumer, M., O’Drisceoil, C., Orlando, L., Outram, A., Pavlova, E. Y., Perri, A. R., Pilot, M., Pitulko, V. V., Plotnikov, V. V., Protopopov, A. V., Rehazek, A., Sablin, M., Seguin-Orlando, A., Storå, J., Verjux, C., Zaibert, V. F., Zazula, G., Crombé, P., Hansen, Anders Johannes, Willerslev, Eske, Leonard, J. A., Götherström, A., Pinhasi, R., Schuenemann, V. J., Hofreiter, M., Gilbert, M Thomas P, Shapiro, B., Larson, G., Krause, J., Dalén, L. & Skoglund, P., 2022, In: Nature. 607, 7918, p. 313-320

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

    7. Published

      Uncovering the genomic basis of an extraordinary plant invasion

      Bieker, V. C., Battlay, P., Petersen, B., Sun, X., Wilson, J., Brealey, J. C., Bretagnolle, F., Nurkowski, K., Lee, C., Barreiro, F. S., Owens, G. L., Lee, J. Y., Kellner, F. L., van Boheeman, L., Gopalakrishnan, S., Gaudeul, M., Mueller-Schaerer, H., Lommen, S., Karrer, G., Chauvel, B. & 8 others, Sun, Y., Kostantinovic, B., Dalén, L., Poczai, P., Rieseberg, L. H., Gilbert, M Thomas P, Hodgins, K. A. & Martin, M. D., 2022, In: Science Advances. 8, 34, 18 p., eabo5115.

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

    8. Published

      Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure

      Bohmann, Kristine, Gopalakrishnan, Shyam, Nielsen, M., Santos-Bay, Luisa, Jones, G., Streicker, D. G. & Gilbert, M Thomas P, 2018, In: Molecular Ecology Resources. 18, 5, p. 1050-1063 14 p.

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

    9. Published

      Single-tube library preparation for degraded DNA

      Carøe, C., Gopalakrishnan, Shyam, Vinner, Lasse, Mak, Sarah Siu Tze, Sinding, Mikkel Holger Strander, Samaniego, J. A., Wales, N., Sicheritz-Ponten, T. & Gilbert, M Thomas P, 2018, In: Methods in Ecology and Evolution. 9, 2, p. 410-419 10 p.

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

    10. Published

      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

    11. Published

      The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

      Ciucani, M. M., Ramos-Madrigal, J., Hernández-Alonso, G., Carmagnini, A., Aninta, S. G., Sun, X., Scharff-Olsen, C. H., Lanigan, L. T., Fracasso, I., Clausen, C. G., Aspi, J., Kojola, I., Baltrūnaitė, L., Balčiauskas, L., Moore, J., Åkesson, M., Saarma, U., Hindrikson, M., Hulva, P., Bolfíková, B. Č. & 19 others, Nowak, C., Godinho, R., Smith, S., Paule, L., Nowak, S., Mysłajek, R. W., Lo Brutto, S., Ciucci, P., Boitani, L., Vernesi, C., Stenøien, H. K., Smith, O., Frantz, L., Rossi, L., Angelici, F. M., Cilli, E., Sinding, Mikkel Holger Strander, Gilbert, M Thomas P & Gopalakrishnan, Shyam, 2023, In: iScience. 26, 8, 22 p., 107307.

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

    12. Published

      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

    13. Published

      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, Gilbert, E., Lalueza-Fox, C., Walser, J. ,. I., Kristjánsdóttir, S., Gopalakrishnan, Shyam, Árnadóttir, L., Magnússon, Ó. Þ., Gilbert, M Thomas P, Stefánsson, K. & Helgason, A., 2018, In: Science. 360, 6392, p. 1028-1032 5 p.

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

    14. Published

      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

    15. Published

      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

    16. Published

      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

    17. Published

      Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Euphrasia, Orobanchaceae)

      Garrett, P., Becher, H., Gussarova, G., dePamphilis, C. W., Ness, R. W., Gopalakrishnan, Shyam & Twyford, A. D., 2022, In: Frontiers in Plant Science. 13, 16 p., 869583.

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

    18. Published

      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

    19. Published

      The population genomic legacy of the second plague pandemic

      Gopalakrishnan, S., Ebenesersdóttir, S. S., Lundstrøm, I. K. C., Turner-Walker, G., Moore, K. H. S., Luisi, P., Margaryan, A., Martin, M. D., Ellegaard, M. R., Magnússon, Ó., Sigurðsson, Á., Snorradóttir, S., Magnúsdóttir, D. N., Laffoon, J. E., van Dorp, L., Liu, X., Moltke, I., Ávila-Arcos, M. C., Schraiber, J. G., Rasmussen, S. & 40 others, Juan, D., Gelabert, P., de-Dios, T., Fotaki, Anna Katerina, Iraeta Orbegozo, Miren, Vågene, Åshild Joanne, Denham, S. D., Christophersen, A., Stenøien, H. K., Vieira, Filipe Garrett, Liu, Shanlin, Günther, T., Kivisild, T., Moseng, O. G., Skar, B., Cheung, C., Sandoval-Velasco, Marcela, Wales, N., Schroeder, Hannes, Campos, P. F., Guðmundsdóttir, V. B., Sicheritz-Pontén, Thomas, Petersen, Bent, Halgunset, J., Gilbert, E., Cavalleri, G. L., Hovig, E., Kockum, I., Olsson, T., Alfredsson, L., Hansen, Thomas Folkmann, Werge, Thomas, Willerslev, Eske, Balloux, F., Marques-Bonet, T., Lalueza-Fox, C., Nielsen, Rasmus, Stefánsson, K., Helgason, A. & Gilbert, M Thomas P, 2022, In: Current Biology. 32, 21, p. 4743-4751.e6

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

    20. Published

      The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

      Gopalakrishnan, Shyam, Samaniego Castruita, J. A., Sinding, Mikkel Holger Strander, Kuderna, L. F. K., Räikkönen, J., Petersen, Bent, Sicheritz-Pontén, T., Larson, G., Orlando, L. A. A., Marques-Bonet, T., Hansen, Anders Johannes, Dalén, L. & Gilbert, M Thomas P, 2017, In: BMC Genomics. 18, 11 p., 495.

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

    21. Published

      Interspecific Gene Flow Shaped the Evolution of the Genus Canis

      Gopalakrishnan, S., Sinding, M. H. S., Ramos-Madrigal, J., Niemann, J., Samaniego Castruita, J. A., Vieira, F. G., Carøe, C., Montero, M. D. M., Kuderna, L., Serres, A., González-Basallote, V. M., Liu, Y. H., Wang, G. D., Marques-Bonet, T., Mirarab, S., Fernandes, C., Gaubert, P., Koepfli, K. P., Budd, J., Rueness, E. K. & 7 others, Heide-Jørgensen, M. P., Petersen, Bent, Sicheritz-Ponten, T., Bachmann, L., Wiig, Ø., Hansen, Anders Johannes & Gilbert, M. T. P., 2018, In: Current Biology. 28, 21, p. 3441-3449

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

    22. Published

      Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences

      Hernández Alonso, Germán, Ramos Madrigal, Jazmin, van Grouw, H., Ciucani, Marta Maria, Cavill, Emily Louisa, Sinding, Mikkel Holger Strander, Gopalakrishnan, Shyam, Antunes Pacheco, George & Gilbert, M Thomas P, 2023, In: Molecular Biology and Evolution. 40, 11, 17 p., msad243.

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

    23. Published

      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, Gilbert, M Thomas P & Gopalakrishnan, Shyam, 2023, In: Ecology and Evolution. 13, 8, 15 p., e10404.

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

    24. Published

      Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes

      Iwanycki Ahlstrand, N., Gopalakrishnan, S., Vieira, F. G., Bieker, V. C., Meudt, H. M., Dunbar-Co, S., Rothfels, C. J., Martinez-Swatson, K. A., Maldonado, C., Hassemer, G., Shipunov, A., Bowers, M. D., Gardner, E., Xu, M., Ghorbani, A., Amano, M., Grace, O. M., Pringle, J. S., Bishop, M., Manzanilla, V. & 18 others, Cotrim, H., Blaney, S., Zubov, D., Choi, H., Yesil, Y., Bennett, B., Vimolmangkang, S., El-Seedi, H. R., Staub, P. O., Li, Z., Boldbaatar, D., Hislop, M., Caddy, L. J., Muasya, A. M., Saslis-Lagoudakis, C. H., Gilbert, M Thomas P, Zerega, N. J. C. & Rønsted, Nina, 2022, In: Frontiers in Plant Science. 13, 16 p., 838166.

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

    25. Published

      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, Rasmussen, Simon & Schroeder, Hannes, 2019, In: Nature Communications. 10, 10 p., 5520.

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

    26. Published

      The evolutionary history of dogs in the Americas

      Leathlobhair, M. N., Perri, A. R., Irving-Pease, E. K., Witt, K. E., Linderholm, A., Haile, J., Lebrasseur, O., Ameen, C., Blick, J., Boyko, A. R., Brace, S., Cortes, Y. N., Crockford, S. J., Devault, A., Dimopoulos, E. A., Eldridge, M., Enk, J., Gopalakrishnan, S., Gori, K., Grimes, V. & 30 others, Guiry, E., Hansen, Anders Johannes, Hulme-Beaman, A., Johnson, J., Kitchen, A., Kasparov, A. K., Kwon, Y., Nikolskiy, P. A., Lope, C. P., Manin, A., Martin, T., Meyer, M., Myers, K. N., Omura, M., Rouillard, J., Pavlova, E. Y., Sciulli, P., Sinding, M. S., Strakova, A., Ivanova, V. V., Widga, C., Willerslev, Eske, Pitulko, V. V., Barnes, I., Gilbert, M Thomas P, Dobney, K. M., Malhi, R. S., Murchison, E. P., Larson, G. & Frantz, L. A. F., 2018, In: Science. 361, 6397, p. 81-85 6 p.

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

    27. Published

      The history of Coast Salish “woolly dogs” revealed by ancient genomics and Indigenous Knowledge

      Lin, A. T., Hammond-Kaarremaa, L., Liu, H-L., Stantis, C., McKechnie, I., Pavel, M., Pavel, S. S. M., Wyss, S. S., Sparrow, D. Q., Carr, K., Aninta, S. G., Perri, A., Hartt, J., Bergström, A., Carmagnini, A., Charlton, S., Dalén, L., Feuerborn, T. R., France, C. A. M., Gopalakrishnan, S. & 13 others, Grimes, V., Harris, A., Kavich, G., Sacks, B. N., Sinding, Mikkel Holger Strander, Skoglund, P., Stanton, D. W. G., Ostrander, E. A., Larson, G., Armstrong, C. G., Frantz, L. A. F., Hawkins, M. T. R. & Kistler, L., 2023, In: Science. 382, 6676, p. 1303-1309 7 p.

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

    28. Published

      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

    29. Published

      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

    30. Published

      Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites

      Liu, Y., Wang, L., Xu, T., Guo, X., Li, Y., Yin, T., Yang, H., Hu, Y., Adeola, A. C., Sanke, O. J., Otecko, N. O., Wang, M., Ma, Y., Charles, O. S., Sinding, M. S., Gopalakrishnan, S., Alfredo Samaniego, J., Hansen, A. J., Fernandes, C., Gaubert, P. & 10 others, Budd, J., Dawuda, P. M., Knispel Rueness, E., Jiang, L., Zhai, W., Gilbert, M Thomas P, Peng, M., Qi, X., Wang, G. & Zhang, Y., 1 Feb 2018, In: MOLECULAR BIOLOGY AND EVOLUTION . 35, 2, p. 287-298

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

    31. Published

      Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros

      Louis, Marie Georgette Yolande J, Skovrind, Mikkel, Samaniego Castruita, J. A., Garilao, C., Kaschner, K., Gopalakrishnan, Shyam, Haile, James Seymour, Lydersen, C., Kovacs, K. M., Garde, E., Heide-Jørgensen, M. P., Postma, L., Ferguson, S. H., Willerslev, Eske & Lorenzen, Eline, 2020, In: Proceedings of the Royal Society B: Biological Sciences. 287, 1925, 9 p., 20192964.

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

    32. Published

      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

    33. Published

      Mitochondrial genomes of Danish vertebrate species generated for the national DNA reference database, DNAmark

      Margaryan, Ashot, Noer, Christina, Richter, S. R., Restrup, M. E., Bülow‐hansen, J. L., Leerhøi, Frederik, Arfaoui, Emilia Marie Rolander, Gopalakrishnan, Shyam, Carøe, C., Gilbert, M Thomas P & Bohmann, Kristine, 2021, In: Environmental DNA. 3, 2, p. 472-480

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

    34. Published

      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

    35. Published

      Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros

      Moodley, Y., Westbury, M., Russo, I. M., Gopalakrishnan, Shyam, Rakotoarivelo, A., Olsen, R., Prost, S., Tunstall, T., Ryder, O. A., Dalén, L. & Bruford, M. W., 2020, In: Molecular Biology and Evolution. 37, 11, p. 3105-3117 13 p.

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

    36. Published

      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

    37. Published

      Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research

      Jessen, Lasse Nyholm, Koziol, Adam Leslie, Marcos, S., Botnen, A. B., Aizpurua Arrieta, Ostaizka, Gopalakrishnan, Shyam, Limborg, Morten Tønsberg, Gilbert, M Thomas P & Alberdi, Antton, 2020, In: iScience. 23, 8, p. 1-16 101414.

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

    38. Published

      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

    39. Published

      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, Evin, A., Gaubert, P., Gopalakrishnan, Shyam, Gower, Graham, Heiniger, H., Helgen, K. M., Kapp, J., Kosintsev, P. A., Linderholm, A., Ozga, A. T., Presslee, S., Salis, A. T., Saremi, N. F., Shew, C., Skerry, K., Taranenko, D. E., Thompson, M., Sablin, M. V., Kuzmin, Y. V., Collins, Matthew James, Sinding, M. S., Gilbert, M Thomas P, Stone, A. C., Shapiro, B., Van Valkenburgh, B., Wayne, R. K., Larson, G., Cooper, A. & Frantz, L. A. F., 2021, In: Nature. 591, p. 87-91

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

    40. Published

      Contrasting dates of rainforest fragmentation in Africa inferred from trees with different dispersal abilities

      Pineiro, R., Hardy, O. J., Tovar, C., Gopalakrishnan, Shyam, Vieira, Filipe Garrett & Gilbert, M Thomas P, 2019, 19 p. (bioRxiv).

      Research output: Working paper › Preprint › Research

    41. Published

      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

    42. Published

      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

    43. Published

      Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages

      Ramos-Madrigal, J., Sinding, M-H. S., Carøe, C., Mak, S. S. T., Niemann, J., Samaniego Castruita, J. A., Fedorov, S., Kandyba, A., Germonpré, M., Bocherens, H., Feuerborn, T. R., Pitulko, V. V., Pavlova, E. Y., Nikolskiy, P. A., Kasparov, A. K., Ivanova, V. V., Larson, G., Frantz, L. A. F., Willerslev, E., Meldgaard, M. & 7 others, Petersen, Bent, Sicheritz-Pontén, Thomas, Bachmann, L., Wiig, Ø., Hansen, Anders Johannes, Gilbert, M Thomas P & Gopalakrishnan, Shyam, 2020, In: Current biology : CB. 31, p. 198-206

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

    44. Published

      The rise of genomics in snake venom research: recent advances and future perspectives

      Rao, W. Q., Kalogeropoulos, K., Allentoft, Morten Erik, Gopalakrishnan, Shyam, Zhao, W., Workman, C. T., Knudsen, C., Jiménez-Mena, B., Seneci, L., Mousavi-Derazmahalleh, M., Jenkins, T. P., Rivera-de-Torre, E., Liu, S. Q. & Laustsen, A. H., 2022, In: GigaScience. 11, 16 p., giac024.

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

    45. Published

      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

    46. Published

      eDNA‐based biomonitoring at an experimental German vineyard to characterize how management regimes shape ecosystem diversity

      Rasmussen, Jacob Agerbo, Nielsen, M., Mak, Sarah Siu Tze, Döring, J., Klincke, F., Gopalakrishnan, Shyam, Dunn, Rob, Kauer, R. & Gilbert, M Thomas P, 2021, In: Environmental DNA. 3, 1, p. 70-82 12 p.

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

    47. Published

      The genetic history of Scandinavia from the Roman Iron Age to the present

      Rodríguez-Varela, R., Moore, K. H. S., Ebenesersdóttir, S. S., Kilinc, G. M., Kjellström, A., Papmehl-Dufay, L., Alfsdotter, C., Berglund, B., Alrawi, L., Kashuba, N., Sobrado, V., Lagerholm, V. K., Gilbert, E., Cavalleri, G. L., Hovig, E., Kockum, I., Olsson, T., Alfredsson, L., Hansen, T. F., Werge, T. & 24 others, Munters, A. R., Bernhardsson, C., Skar, B., Christophersen, A., Turner-Walker, G., Gopalakrishnan, Shyam, Daskalaki, E., Omrak, A., Pérez-Ramallo, P., Skoglund, P., Girdland-Flink, L., Gunnarsson, F., Hedenstierna-Jonson, C., Gilbert, M Thomas P, Lidén, K., Jakobsson, M., Einarsson, L., Victor, H., Krzewińska, M., Zachrisson, T., Storå, J., Stefánsson, K., Helgason, A. & Götherström, A., 2023, In: Cell. 186, 1, p. 32-46.e19

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

    48. Published

      HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph

      Rubin, J. D., Vogel, N. A., Gopalakrishnan, Shyam, Sackett, P. W. & Renaud, G., 2023, In: PLOS Computational Biology. 19, 6, 27 p., e1011148.

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

    49. Published

      The genetic origins of Saint Helena’s liberated Africans

      Sandoval-Velasco, Marcela, Jagadeesan, A., Ávila-Arcos, M. C., Gopalakrishnan, Shyam, Ramos Madrigal, Jazmin, Moreno Mayar, J. Víctor, Renaud, Gabriel, Cruz-Dávalos, D. I., Johannesdóttir, E., Watson, J., Robson-Brown, K., Pearson, A., Helgason, A., Gilbert, M Thomas P & Schroeder, Hannes, 2019, bioRxiv, 16 p.

      Research output: Working paper › Preprint › Research

    50. Published

      The ancestry and geographical origins of St Helena's liberated Africans

      Sandoval-Velasco, Marcela, Jagadeesan, A., Ramos Madrigal, Jazmin, Ávila-Arcos, M. C., Fortes-Lima, C. A., Watson, J., Johannesdóttir, E., Cruz-Dávalos, D. I., Gopalakrishnan, Shyam, Moreno Mayar, J. Víctor, Niemann, Jonas, Renaud, G., Brown, K. A. R., Bennett, H., Pearson, A., Helgason, A., Gilbert, M Thomas P & Schroeder, Hannes, 2023, In: American Journal of Human Genetics. 110, 9, p. 1590-1599 10 p.

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

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