2023

• Bergeron, Lucie A.; Besenbacher, Søren; Zheng, Jiao; Li, Panyi; Bertelsen, Mads Frost; Quintard, Benoit; Hoffman, Joseph I.; Li, Zhipeng; St. Leger, Judy; Shao, Changwei; Stiller, Josefin; Gilbert, Marcus Thomas Pius; Schierup, Mikkel H.; Zhang, Guojie. (2023) Evolution of the germline mutation rate across vertebrates. Nature.
  Academic article
• Bolt Botnen, Amanda; Bjørnsen, Mads Bjørn; Alberdi, Antton; Gilbert, Marcus Thomas Pius; Aizpurua, Ostaizka. (2023) A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies. Heliyon. volum 9 (1).
  Academic article
• Cohen, Pnina; Bacilieri, Roberto; Ramos-Madrigal, Jazmín; Privman, Eyal; Boaretto, Elisabetta; Weber, Audrey; Fuks, Daniel; Weiss, Ehud; Erickson-Gini, Tali; Bucking, Scott; Tepper, Yotam; Cvikel, Deborah; Schmidt, Joshua; Gilbert, Marcus Thomas Pius; Wales, Nathan; Bar-Oz, Guy; Meiri, Meirav. (2023) Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage. Proceedings of the National Academy of Sciences of the United States of America. volum 120 (17).
  Academic article
• Díez-del-Molino, David; Dehasque, Marianne; Chacón-Duque, J. Camilo; Pečnerová, Patrícia; Tikhonov, Alexei; Protopopov, Albert; Plotnikov, Valeri; Kanellidou, Foteini; Nikolskiy, Pavel; Mortensen, Peter; Danilov, Gleb K.; Vartanyan, Sergey; Gilbert, Marcus Thomas Pius; Lister, Adrian M.; Heintzman, Peter D.; van der Valk, Tom; Dalén, Love. (2023) Genomics of adaptive evolution in the woolly mammoth. Current Biology. volum 33 (9).
  Academic article
• Germain, Ryan R.; Feng, Shaohong; Buffan, Lucas; Carmona, Carlos P.; Chen, Guangii; Graves, Gary R.; Tobias, Joseph A.; Rahbek, Carsten; Lei, Fumin; Fjeldså, Jon; Hosner, Peter A.; Gilbert, Marcus Thomas Pius; Zhang, Guojie; Nogués-Bravo, David. (2023) Changes in the functional diversity of modern bird species over the last million years. Proceedings of the National Academy of Sciences of the United States of America. volum 120 (7).
  Academic article
• Germain, Ryan R.; Feng, Shaohong; Chen, Guangji; Graves, Gary R.; Tobias, Joseph A.; Rahbek, Carsten; Lei, Fumin; Fjeldså, Jon; Hosner, Peter A.; Gilbert, Marcus Thomas Pius; Zhang, Guojie; Nogués-Bravo, David. (2023) Species-specific traits mediate avian demographic responses under past climate change. Nature Ecology and Evolution.
  Academic article
• Hansen, Charles Christian Riis; Láruson, Áki Jarl; Rasmussen, Jacob Agerbo; Chimal Ballesteros, Jesus Adrian; Sinding, Mikkel Holger Strander; Hallgrimsson, Gunnar T.; von Schmalensee, Menja; Stefansson, Robert A.; Skarphédinsson, Kristinn Haukur; Labansen, Aili Lage; Leivits, Madis; Sonne, Christian; Dietz, Rune; Skelmose, Kim; Boertmann, David; Eulaers, Igor; Martin, Michael David; Helgason, Agnar S.; Gilbert, Marcus Thomas Pius. (2023) Genomic diversity and differentiation between island and mainland populations of white-tailed eagles (Haliaeetus albicilla). Molecular Ecology. volum 32.
  Academic article
• Hansen, Søren B.; Bozzi, Davide; Mak, Sarah S.T.; Clausen, Cecilie G.; Nielsen, Tue K.; Kodama, Miyako; Hansen, Lars H.; Gilbert, Marcus Thomas Pius; Limborg, Morten T.. (2023) Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. Genomics. volum 115 (3).
  Academic article
• Rasmussen, Jacob A.; Kiilerich, Pia; Madhun, Abdullah Sami; Waagbø, Rune; Lock, Erik Jan Robert; Madsen, Lise; Gilbert, Marcus Thomas Pius; Kristiansen, Karsten; Limborg, Morten T.. (2023) Co-diversification of an intestinal Mycoplasma and its salmonid host. The ISME Journal.
  Academic article

2022

• Bergström, Anders; Stanton, David W. G.; Taron, Ulrike H.; Frantz, Laurent; Sinding, Mikkel Holger Strander; Ersmark, Erik; Pfrengle, Saskia; Cassatt-Johnstone, Molly; Lebrasseur, Ophélie; Girdland-Flink, Linus; Fernandes, Daniel M.; Ollivier, Morgane; Speidel, Leo; Gopalakrishnan, Shyam; Westbury, Michael V.; Ramos-Madrigal, Jazmin; Feuerborn, Tatiana R.; Reiter, Ella; Gretzinger, Joscha. (2022) Grey wolf genomic history reveals a dual ancestry of dogs. Nature. volum 607 (7918).
  Academic article
• Bieker, Vanessa Carina; Battlay, Paul; Petersen, Bent; Sun, Xin; Wilson, Jonathan; Brealey, Jaelle C.; Bretagnolle, François; Nurkowski, Kristin; Lee, Chris; Sánchez Barreiro, Fatima; Owens, Gregory; Lee, Jacqueline; Kellner, Fabian Laszlo; van Boheeman, Lotte; Gopalakrishnan, Shyam; Gaudeul, Myriam; Mueller-Schaerer, Heinz; Lommen, Suzanne; Karrer, Gerhard. (2022) Uncovering the genomic basis of an extraordinary plant invasion. Science Advances. volum 8 (34).
  Academic article
• Cerca, José; Petersen, Bent; Lazaro-Guevara, José Miguel; Rivera-Colón, Angel G.; Birkeland, Siri; Vizueta, Joel; Li, Siyu; Li, Qionghou; Loureiro, João; Kosawang, Chatchai; Jaramillo Díaz, Patricia; Rivas-Torres, Gonzalo; Fernández-Mazuecos, Mario; Vargas, Pablo; McCauley, Ross; Petersen, Gitte; Santos-Bay, Luisa; Wales, Nathan; Catchen, Julian M.. (2022) The genomic basis of the plant island syndrome in Darwin’s giant daisies. Nature Communications. volum 13.
  Academic article
• Cole, Theresa L.; Zhou, Chengran; Fang, Miaoquan; Pan, Hailin; Ksepka, Daniel T.; Fiddaman, Steven R.; Emerling, Christopher A.; Thomas, Daniel B.; Bi, Xupeng; Fang, Qi; Ellegaard, Martin Rene; Feng, Shaohong; Smith, Adrian L.; Heath, Tracy A.; Tennyson, Alan J. D.; Borboroglu, Pablo García; Wood, Jamie R.; Hadden, Peter W.; Grosser, Stefanie. (2022) Genomic insights into the secondary aquatic transition of penguins. Nature Communications. volum 13 (1).
  Academic article
• de Ferran, Vera; Figueiró, Henrique Vieira; de Jesus Trindade, Fernanda; Smith, Oliver; Sinding, Mikkel Holger Strander; Trinca, Cristine S.; Lazzari, Gabriele Zenato; Veron, Géraldine; Vianna, Juliana A.; Barbanera, Filippo; Kliver, Sergei; Serdyukova, Natalia; Bulyonkova, Tatiana; Ryder, Oliver A.; Gilbert, Marcus Thomas Pius; Koepfli, Klaus-Peter; Eizirik, Eduardo. (2022) Phylogenomics of the world's otters. Current Biology. volum 32 (16).
  Academic article
• Field, Matt A.; Yadav, Sonu; Dudchenko, Olga; Esvaran, Meera; Rosen, Benjamin D.; Skvortsova, Ksenia; Edwards, Richard J.; Keilwagen, Jens; Cochran, Blake J.; Manandhar, Bikash; Bustamante, Sonia; Rasmussen, Jacob Agerbo; Melvin, Richard G.; Chernoff, Barry; Omer, Arina; Colaric, Zane; Chan, Eva K.F.; Minoche, Andre E.; Smith, Timothy P.L.. (2022) The Australian dingo is an early offshoot of modern breed dogs. Science Advances. volum 8 (16).
  Academic article
• Formenti, Giulio; Theissinger, Kathrin; Fernandes, Carlos; Bista, Iliana; Bombarely, Aureliano; Bleidorn, Christoph; Ciofi, Claudio; Crottini, Angelica; Godoy, José A.; Höglund, Jacob; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah Alice; Paez, Sadye; Palsbøll, Per J.; Pampoulie, Christophe; Ruiz-López, María J.; Svardal, Hannes; Theofanopoulou, Constantina. (2022) The era of reference genomes in conservation genomics. Trends in Ecology & Evolution. volum 37 (3).
  Academic literature review
• Gopalakrishnan, Shyam; Ebenesersdottir, S.Sunna; Lundstrøm, Inge K.C.; Turner-Walker, Gordon; Moore, Kristjan H.S.; Luisi, Pierre; Magaryan, Ashot; Martin, Michael David; Ellegaard, Martin Rene; Magnusson, Olafur T.; Sigurdsson, Asgeir; Snorradóttir, Steinunn; Magnúsdóttir, Droplaug N.; Laffoon, Jason E.; van Dorp, Lucy; Liu, Xiaodong; Moltke, Ida; Avila-Arcos, María C.; Schraiber, Joshua G.. (2022) The population genomic legacy of the second plague pandemic. Current Biology. volum 32.
  Academic article
• Jensen, Evelyn L.; Díez-del-Molino, David; Gilbert, Marcus Thomas Pius; Bertola, Laura D.; Borges, Filipa; Cubric-Curik, Vlatka; de Navascués, Miguel; Frandsen, Peter; Heuertz, Myriam; Hvilsom, Christina; Jiménez-Mena, Belén; Miettinen, Antti; Moest, Markus; Pečnerová, Patrícia; Barnes, Ian; Vernesi, Cristiano. (2022) Ancient and historical DNA in conservation policy. Trends in Ecology & Evolution. volum 37 (5).
  Academic literature review
• Koziol, Adam; Odriozola, Iñaki; Nyholm, Lasse; Leonard, Aoife; San José, Carlos; Pauperio, Joana; Ferreira, Clara; Hansen, Anders J.; Aizpurua, Ostaizka; Gilbert, Marcus Thomas Pius; Alberdi, Antton. (2022) Enriching captivity conditions with natural elements does not prevent the loss of wild-like gut microbiota but shapes its compositional variation in two small mammals. MicrobiologyOpen. volum 11 (5).
  Academic article
• Lewin, Harris A.; Richards, Stephen; Aiden, Erez Lieberman; Allende, Miguel L.; Archibald, John M.; Bálint, Miklós; Barker, Katharine B.; Baumgartner, Bridget; Belov, Katherine; Bertorelle, Giorgio; Blaxter, Mark L.; Cai, Jing; Caperello, Nicolette D.; Carlson, Keith; Castilla-Rubio, Juan Carlos; Chaw, Shu-Miaw; Chen, Lei; Childers, Anna K.; Coddington, Jonathan A.. (2022) The Earth BioGenome Project 2020: Starting the clock. Proceedings of the National Academy of Sciences of the United States of America. volum 119 (4).
  Academic literature review
• Lin, Jianqing; Duchêne, David; Carøe, Christian; Smith, Oliver; Ciucani, Marta Maria; Niemann, Jonas; Richmond, Douglas; Greenwood, Alex D.; MacPhee, Ross; Zhang, Guojie; Gopalakrishnan, Shyam; Gilbert, Marcus Thomas Pius. (2022) Probing the genomic limits of de-extinction in the Christmas Island rat. Current Biology. volum 32 (7).
  Academic article
• Møbjerg, Ask; Kodama, Miyako; Ramos-Madrigal, Jazmín; Neves, Ricardo A. Cardoso; Jørgensen, Aslak; Schiøtt, Morten; Gilbert, Marcus Thomas Pius; Møbjerg, Nadja. (2022) Corrigendum to “Extreme freeze-tolerance in cryophilic tardigrades relies on controlled ice formation but does not involve significant change in transcription” [Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 271 (2022), 111245] (Comparative Biochemistry and Physiology, Part A (2022) 271, (S1095643322001039), (10.1016/j.cbpa.2022.111245)). Comparative Biochemistry and Physiology A. volum 274.
  Errata
• Møbjerg, Ask; Kodama, Miyako; Ramos-Madrigal, Jazmín; Neves, Ricardo A. Cardoso; Jørgensen, Aslak; Schiøtt, Morten; Gilbert, Marcus Thomas Pius; Møbjerg, Nadja. (2022) Extreme freeze-tolerance in cryophilic tardigrades relies on controlled ice formation but does not involve significant change in transcription. Comparative Biochemistry and Physiology A. volum 271.
  Academic article
• Neves, Ricardo A. Cardoso; Møbjerg, Ask; Kodama, Miyako; Ramos-Madrigal, Jazmín; Gilbert, Marcus Thomas Pius; Møbjerg, Nadja. (2022) Corrigendum to “Differential expression profiling of heat stressed tardigrades reveals major shift in the transcriptome” [Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 267 (2022), 111169] (Comparative Biochemistry and Physiology, Part A (2022) 267, (S1095643322000277), (10.1016/j.cbpa.2022.111169)). Comparative Biochemistry and Physiology A. volum 274.
  Errata
• Neves, Ricardo A. Cardoso; Møbjerg, Ask; Kodama, Miyako; Ramos-Madrigal, Jazmín; Gilbert, Marcus Thomas Pius; Møbjerg, Nadja. (2022) Differential expression profiling of heat stressed tardigrades reveals major shift in the transcriptome. Comparative Biochemistry and Physiology A. volum 267.
  Academic article
• Patrono, Livia V.; Vrancken, Bram; Budt, Matthias; Düx, Ariane; Lequime, Sebastian; Boral, Sengül; Gilbert, Marcus Thomas Pius; Gogarten, Jan F.; Hoffmann, Luisa; Horst, David; Merkel, Kevin; Morens, David; Prepoint, Baptiste; Schlotterbeck, Jasmin; Schuenemann, Verena J.; Suchard, Marc A.; Taubenberger, Jeffery K.; Tenkhoff, Luisa; Urban, Christian. (2022) Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic. Nature Communications. volum 13.
  Academic article
• Rasmussen, Jacob Agerbo; Villumsen, Kasper Rømer; Ernst, Madeleine; Hansen, Martin; Forberg, Torunn; Gopalakrishnan, Shyam; Gilbert, Marcus Thomas Pius; Bojesen, Anders Miki; Kristiansen, Karstein; Limborg, Morten Tønsberg. (2022) A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss). Microbiome. volum 10.
  Academic article
• Sun, Xin; Ciucani, Marta Maria; Rasmussen, Jacob Agerbo; Gilbert, Marcus Thomas Pius; Sinding, Mikkel Holger Strander. (2022) Genomic evidence refutes the hypothesis that the Bornean banteng is a distinct species. BMC Ecology and Evolution. volum 22.
  Academic article
• Tous, Núria; Marcos, Sofia; Goodarzi Boroojeni, Farshad; Pérez de Rozas, Ana; Zentek, Jürgen; Estonba, Andone; Sandvang, Dorthe; Gilbert, Marcus Thomas Pius; Esteve-Garcia, Enric; Finn, Robert; Alberdi, Antton; Tarradas, Joan. (2022) Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics. Frontiers in Physiology. volum 13.
  Academic article

2021

• Agerbo Rasmussen, Jacob; Nielsen, Martin; Mak, Sarah Siu Tze; Döring, Johanna; Klincke, Franziska; Gopalakrishnan, Shyam; Dunn, Robert R.; Kauer, Randolf; Gilbert, Marcus Thomas Pius. (2021) eDNA-based biomonitoring at an experimental German vineyard to characterize how management regimes shape ecosystem diversity. Environmental DNA. volum 3 (1).
  Academic article
• Alberdi, Antton; Andersen, Sandra B.; Limborg, Morten T.; Dunn, Robert R.; Gilbert, M. Thomas P.. (2021) Disentangling host–microbiota complexity through hologenomics. Nature reviews genetics.
  Academic literature review
• Alfano, Niccolò; Dayaram, Anisha; Axtner, Jan; Tsangaras, Kyriakos; Kampmann, Marie-Louise; Mohamed, Azlan; Wong, Seth T.; Gilbert, Marcus Thomas Pius; Wilting, Andreas; Greenwood, Alex D.. (2021) Non-invasive surveys of mammalian viruses using environmental DNA. Methods in Ecology and Evolution. volum 12 (10).
  Academic article
• Andrade, Pedro; Gazda, Małgorzata A.; Araújo, Pedro M.; Afonso, Sandra; Rasmussen, Jacob A.; Marques, Cristiana I.; Lopes, Ricardo J.; Gilbert, Marcus Thomas Pius; Carneiro, Miguel. (2021) Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates. PLoS Genetics. volum 17 (2).
  Academic article
• Azevedo-Silva, D.; Rasmussen, J.A.; Carneiro, M.; Gilbert, Marcus Thomas Pius; Azevedo, H.. (2021) Feasibility of applying shotgun metagenomic analyses to grapevine leaf, rhizosphere and soil microbiome characterisation. Australian journal of grape and wine research. volum 27 (4).
  Academic article
• Bergeron, Lucie A.; Besenbacher, Søren; Bakker, Jaco; Zheng, Jiao; Li, Panyi; Pacheco, George; Sinding, Mikkel-Holger S.; Kamilari, Maria; Gilbert, Marcus Thomas Pius; Schiedrup, Mikkel H.; Zhang, Guojie. (2021) The germline mutational process in rhesus macaque and its implications for phylogenetic dating. GigaScience. volum 10 (5).
  Academic article
• Bogaard, Amy; Allaby, Robin G.; Arbuckle, Benjamin; Bendrey, Robin; Crowley, Sarah; Cucchi, Thomas; Denham, Tim; Frantz, Laurent; Fuller, Dorian; Gilbert, Marcus Thomas Pius; Karlsson, Elinor K.; Manin, Aurélie; Marshall, Fiona; Mueller, Natalie; Peters, Joris; Stépanoff, Charles; Weide, Alexander; Larson, Greger. (2021) Reconsidering domestication from a process archaeology perspective. World archaeology. volum 53 (1).
  Academic article
• Cavill, Emily L.; Gopalakrishnan, Shyam; Puetz, Lara C.; Ribeiro, Ângela M.; Mak, Sarah S. T.; da Fonseca, Rute R.; Pacheco, George; Dunlop, Bronwyn; Accouche, Wilna; Shah, Nirmal; Zora, Anna; Calabrese, Licia; Genner, Martin; Jones, Gareth; Guo, Chunxue; Zhang, Guojie; Gilbert, Marcus Thomas Pius. (2021) Conservation genomics of the endangered Seychelles Magpie-Robin (Copsychus sechellarum): a unique insight into the history of a precious endemic bird. IBIS.
  Academic article
• Cavill, Emily; Liu, Shanlin; Zhou, Xin; Gilbert, Marcus Thomas Pius. (2021) To bee, or not to bee? One leg is the question. Molecular Ecology Resources.
  Academic article
• Ciucani, Marta M.; Jensen, Julie Kragmose; Sinding, Mikkel-Holger S.; Smith, Oliver; Lucenti, Saverio Bartolini; Rosengren, Erika; Rook, Lorenzo; Tuveri, Caterinella; Arca, Marisa; Cappellini, Enrico; Galaverni, Marco; Randi, Ettore; Guo, Chunxue; Zhang, Guojie; Sicheritz-Pontén, Thomas; Dalén, Love; Gilbert, Marcus Thomas Pius; Gopalakrishnan, Shyam. (2021) Evolutionary history of the extinct Sardinian dhole. Current Biology. volum 31 (24).
  Academic article
• Feng, Shaohong; Stiller, Josefin; Deng, Yuan; Armstrong, Joel; Fang, Qi; Reeve, Andrew Hart; Xie, Duo; Chen, Guangji; Guo, Chunxue; Faircloth, Brant C.; Petersen, Bent; Wang, Zongji; Zhou, Qi; Diekhans, Mark; Chen, Wanjun; Andreu-Sánchez, Sergio; Margaryan, Ashot; Howard, Jason Travis; Parent, Carole. (2021) Author Correction: Dense sampling of bird diversity increases power of comparative genomics (Nature, (2020), 587, 7833, (252-257), 10.1038/s41586-020-2873-9). Nature. volum 592 (7856).
  Errata
• Feuerborn, Tatiana R.; Carmagnini, Alberto; Losey, Robert J.; Nomokonova, Tatiana; Askeyev, Arthur; Askeyev, Igor; Askeyev, Oleg; Antipina, Ekaterina E.; Appelt, Martin; Bachura, Olga P.; Beglane, Fiona; Bradley, Daniel G.; Daly, Kevin G.; Gopalakrishnan, Shyam; Gregersen, Kristian Murphy; Guo, Chunxue; Gusev, Andrei V.; Jones, Carleton; Kosintsev, Pavel A.. (2021) Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal. Proceedings of the National Academy of Sciences of the United States of America. volum 118 (39).
  Academic article
• Fontsere, Claudia; Frandsen, Peter; Hernandez-Rodriguez, Jessica; Niemann, Jonas; Scharff-Olsen, Camilla Hjorth; Vallet, Dominique; Le Gouar, Pascaline; Ménard, Nelly; Navarro, Arcadi; Siegismund, Hans Redlef; Hvilsom, Christina; Gilbert, Marcus Thomas Pius; Kuhlwilm, Martin; Hughes, David; Marques-Bonet, Tomas. (2021) The genetic impact of an Ebola outbreak on a wild gorilla population. BMC Genomics. volum 22.
  Academic article
• Foote, Andrew; Gilbert, Marcus Thomas Pius; Gopalakrishnan, Shyam; Louis, Marie; Martin, Michael David; Morin, Phillip A.; Nykänen, Milaja; Scharff-Olsen, Camilla; Excoffier, Laurent. (2021) Evidence of long-term purging of mutation load in killer whale genomes. bioRxiv - the preprint server for biology.
  Academic article
• Foote, Andrew; Hooper, Rebecca; Alexander, Alana; Baird, Robin; Baker, Charles Scott; Ballance, Lisa; Barlow, Jay; Brownlow, Andrew; Collins, Tim; Constantine, Rochelle; Rosa, Luciano Dalla; Davison, Nicholas J.; Durban, John; Esteban, Ruth; Excoffier, Laurent; Martin, Sarah; Forney, Karin A.; Gerrodette, Tim; Gilbert, Marcus Thomas Pius. (2021) Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Molecular Ecology. volum 30 (23).
  Academic article
• Fromm, Bastian; Tarbier, Marcel; Smith, Oliver; Mármol-Sánchez, Emilio; Dalén, Love; Gilbert, Marcus Thomas Pius; Friedländer, Marc R.. (2021) Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene. RNA: A publication of the RNA Society. volum 27.
  Academic article
• Kirch, Melanie; Romundset, Anders; Gilbert, Marcus Thomas Pius; Jones, Felicity C.; Foote, Andrew. (2021) Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. Current Biology. volum 31.
  Academic article
• Liu, Chang; Gao, Jianbo; Cui, Xinxin; Li, Zhipeng; Chen, Lei; Yuan, Yuan; Zhang, Yaolei; Mei, Liangwei; Zhao, Lan; Cai, Dan; Hu, Mingliang; Zhou, Botong; Li, Zihe; Qin, Tao; Si, Huazhe; Li, Guangyu; Lin, Zeshan; Xu, Yicheng; Zhu, Chenglong. (2021) A towering genome: Experimentally validated adaptations to high blood pressure and extreme stature in the giraffe. Science Advances. volum 7 (12).
  Academic article
• Liu, Shanlin; Westbury, Michael V; Dussex, Nicolas; Mitchell, Kieren J.; Sinding, Mikkel-Holger S.; Heintzman, Peter D.; Duchêne, David A.; Kapp, Joshua D.; von Seth, Johanna; Heiniger, Holly; Sánchez-Barreiro, Fatima; Margaryan, Ashot; André-Olsen, Remi; De Cahsan, Binia; Meng, Guanliang; Yang, Chentao; Chen, Lei; van der Valk, Tom; Moodley, Yoshan. (2021) Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell. volum 184.
  Academic article
• Lynggaard, Christina; Oceguera-Figueroa, Alejandro; Kvist, Sebastian; Gilbert, Marcus Thomas Pius; Bohmann, Kristine. (2021) The potential of aquatic bloodfeeding and nonbloodfeeding leeches as a tool for iDNA characterisation. Molecular Ecology Resources.
  Academic article
• Margaryan, Ashot; Noer, Christina Lehmkuhl; Richter, Stine R.; Restrup, Marlene Elise; Bülow-Hansen, Julie Lee; Leerhøi, Frederik; Langkjær, Emilia Marie Rolander; Gopalakrishnan, Shyam; Carøe, Christian; Gilbert, Marcus Thomas Pius; Bohmann, Kristine. (2021) Mitochondrial genomes of Danish vertebrate species generated for the national DNA reference database, DNAmark. Environmental DNA. volum 3 (2).
  Academic article
• Niemann, Jonas; Gopalakrishnan, Shyam; Yamaguchi, Nobuyuki; Ramos-Madrigal, Jazmín; Wales, Nathan; Gilbert, Marcus Thomas Pius; Sinding, Mikkel-Holger S.. (2021) Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshū. iScience. volum 24.
  Academic article
• Pereira, Cátia Lúcio; Gilbert, Marcus Thomas Pius; Araújo, Miguel B.; Matias, Miguel Graça. (2021) Fine-tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches. Methods in Ecology and Evolution. volum 12 (12).
  Academic article
• Perri, Angela; Mitchell, Kieren J.; Mouton, Alice; Álvarez-Carretero, Sandra; Hulme-Beaman, Ardern; Haile, James; Jamieson, Alexandra; Meachen, Julie; Lin, Audrey T.; Schubert, Blaine W.; Ameen, Carly; Antipina, Ekaterina E.; Bover, Pere; Brace, Selina; Carmagnini, Alberto; Carøe, Christian; Samaniego Castruita, Jose A.; Chatters, James C.; Dobney, Keith. (2021) Dire wolves were the last of an ancient New World canid lineage. Nature. volum 591 (7848).
  Academic article
• Piñeiro, Rosalía; Hardy, Olivier J.; Tovar, Carolina; Gopalakrishnan, Shyam; Vieira, Filipe Garrett; Gilbert, Marcus Thomas Pius. (2021) Contrasting genetic signal of recolonization after rainforest fragmentation in African trees with different dispersal abilities. Proceedings of the National Academy of Sciences of the United States of America. volum 118 (27).
  Academic article
• Poliseno, Angelo; Altuna, Alvaro; Puetz, Lara; Mak, Sarah Siu Tze; Ríos, Pilar; Petroni, Emily; McFadden, Catherine S.; Sørensen, Martin V.; Gilbert, Marcus Thomas Pius. (2021) An integrated morphological-molecular approach reveals new insights on the systematics of the octocoral Telestula humilis (Thomson, 1927) (Octocorallia: Alcyonacea: Clavulariidae). Invertebrate systematics. volum 35 (3).
  Academic article
• Rasmussen, Jacob A.; Villumsen, Kasper Rømer; Duchêne, David; Puetz, Lara; Delmont, Tom; Sveier, Harald; von Gersdorff Jørgensen, Louise; Præbel, Kim; Martin, Michael David; Bojesen, Anders Miki; Gilbert, Marcus Thomas Pius; Kristiansen, Karsten; Limborg, Morten T.. (2021) Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts. Communications Biology. volum 4.
  Academic article
• Rhie, Arang; McCarthy, Shane A.; Fedrigo, Olivier; Damas, Joana; Formenti, Giulio; Koren, Sergey; Uiano-Silva, Marcela; Chow, William; Fungtammasan, Arkarachai; Kim, Juwan; Lee, Chul; Ko, Byung June; Chaisson, Mark; Gedman, Gregory L.; Cantin, Lindsey J.; Thibaud-Nissen, Francoise; Haggerty, Leanne; Bista, Iliana; Smith, Michelle. (2021) Towards complete and error-free genome assemblies of all vertebrate species. Nature. volum 592.
  Academic article
• Sánchez-Barreiro, Fátima; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; Westbury, Michael V.; de Manuel, Marc; Margaryan, Ashot; Ciucani, Marta M.; Vieira, Filipe G.; Patramanis, Yannis; Kalthoff, Daniela C.; Timmons, Zena; Sicheritz-Pontén, Thomas; Dalén, Love; Ryder, Oliver A.; Zhang, Guojie; Marquès-Bonet, Tomás; Moodley, Yoshan; Gilbert, Marcus Thomas Pius. (2021) Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). Molecular Ecology. volum 30 (23).
  Academic article
• Sinding, Mikkel-Holger S.; Ciucani, Marta M.; Ramos-Madrigal, Jazmín; Carmagnini, Alberto; Rasmussen, Jacob A.; Feng, Shaohong; Chen, Guangji; Vieira, Filipe G.; Mattiangeli, Valeria; Ganjoo, Rajinder K.; Larson, Greger; Sicheritz-Pontén, Thomas; Petersen, Bent; Frantz, Laurent A.F.; Gilbert, Marcus Thomas Pius; Bradley, Daniel G.. (2021) Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos. iScience. volum 24 (11).
  Academic article
• Sinding, Mikkel-Holger S.; Gopalakrishnan, Shyam; Raundrup, Katrine; Dalén, Love; Threlfall, Jonathan; Gilbert, Marcus Thomas Pius. (2021) The genome sequence of the grey wolf, Canis lupus Linnaeus 1758. Wellcome Open Research. volum 6.
  Academic article
• Sirén, Kimmo; Millard, Andrew; Petersen, Bent; Gilbert, Marcus Thomas Pius; Clokie, Martha R.J.; Sicheritz-Pontén, Thomas. (2021) Rapid discovery of novel prophages using biological feature engineering and machine learning. NAR Genomics and Bioinformatics. volum 3 (1).
  Academic article
• Stenøien, Hans K.; Sun, Xin; Martin, Michael David; Scharff-Olsen, Camilla Hjorth; Alonso, Germán Hernàndez; Martins, Nuno Filipe Gomes; Lanigan, Liam T; Ciucani, Marta M.; Sinding, Mikkel-Holger S.; Gopalakrishnan, Shyam; Gilbert, Marcus Thomas Pius. (2021) Genetisk opphav til den norsksvenske ulvestammen (Canis lupus lupus). 2021. NTNU Vitenskapsmuseet naturhistorisk rapport (11).
  Report
• von Seth, Johanna; Dussex, Nicolas; Díez-del-Molino, David; van der Valk, Tom; Kutschera, Verena E.; Kierczak, Marcin; Steiner, Cynthia C.; Liu, Shanlin; Gilbert, Marcus Thomas Pius; Sinding, Mikkel-Holger S.; Prost, Stefan; Guschanski, Katerina; Nathan, Senthilvel K. S. S.; Brace, Selina; Chan, Yvonne L.; Wheat, Christopher W.; Skoglund, Pontus; Ryder, Oliver A.; Goossens, Benoit. (2021) Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations. Nature Communications. volum 12.
  Academic article
• Westbury, Michael V; Barnett, Ross; Sandoval-Velasco, Marcela; Gower, Graham; Vieira, Filipe G.; de Manuel, Marc; Hansen, Anders J.; Yamaguchi, Nobuyuki; Werdelin, Lars; Marquès-Bonet, Tomás; Gilbert, Marcus Thomas Pius; Lorenzen, Eline D.. (2021) A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives. Open Research Europe. volum 2021 (1:25).
  Academic article

2020

• Alberdi, Antton; Razgour, Orly; Aizpurua, Ostaizka; Novella-Fernandez, Roberto; Aihartza, Joxerra; Budinski, Ivana; Garin, Inazio; Ibáñez, Carlos; Izagirre, Eñaut; Rebelo, Hugo; Russo, Danilo; Vlaschenko, Anton; Zhelyazkova, Violeta; Zrncic, Vida; Gilbert, Marcus Thomas Pius. (2020) DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats. Nature Communications. volum 11.
  Academic article
• Barnett, Ross; Westbury, Michael V; Sandoval-Velasco, Marcela; Vieira, Filipe G.; Jeon, Sungwon; Zazula, Grant; Martin, Michael David; Ho, Simon Y.W.; Mather, Niklas; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; de Manuel, Marc; Zepeda-Mendoza, Marie Lisandra; Antunes, Agostinho; Carmona Baez, Aldo; De Cahsan, Binia; Larson, Greger; O'Brien, Stephen J.; Eizirik, Eduardo. (2020) Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat, Homotherium latidens. Current Biology. volum 30 (24).
  Academic article
• Bohmann, Kristine; Mirarab, Siavash; Bafna, Vineet; Gilbert, Marcus Thomas Pius. (2020) Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification. Molecular Ecology. volum 29.
  Academic article
• Da Fonseca, Rute R.; Couto, Alvarina; Machado, Andre M; Brejova, Brona; Albertin, Carolin B; Silva, Filipe; Gardner, Paul; Baril, Tobias; Hayward, Alex; Campos, Alexandre; Ribeiro, Ângela M; Barrio-Hernandez, Inigo; Hoving, Henk-Jan; Tafur-Jimenez, Ricardo; Chu, Chong; Frazão, Barbara; Petersen, Bent; Peñaloza, Fernando; Musacchia, Francesco. (2020) A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience. volum 9 (1).
  Academic article
• de Manuel, Marc; Barnett, Ross; Sandoval-Velasco, Marcela; Yamaguchi, Nobuyuki; Vieira, Filipe G.; Lisandra Zepeda Mendoza, Zepeda; Liu, Shiping; Martin, Michael David; Sinding, Mikkel-Holger S.; Mak, Sarah Siu Tze; Carøe, Christian; Liu, Shanlin; Guo, Chunxue; Zheng, Jiao; Zazula, Grant; Baryshnikov, Gennady; Eizirik, Eduardo; Koepfli, Klaus-Peter; Johnson, Warren E.. (2020) The evolutionary history of extinct and living lions. Proceedings of the National Academy of Sciences of the United States of America. volum 117 (20).
  Academic literature review
• Drinkwater, Rosie; Jucker, Tommaso; Potter, Joshua H. T.; Swinfield, Tom; Coomes, D; Slade, Eleanor M.; Gilbert, Marcus Thomas Pius; Lewis, Owen T.; Bernard, Henry; Struebig, Matthew J.; Clare, Elizabeth; Rossiter, Stephen J.. (2020) Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats. Molecular Ecology.
  Academic article
• Eriksen, Anne Marie Høier; Matthiesen, Henning; Kontopoulos, Ioannis; Gregory, David John; Snoeck, Christophe; Zhang, Guojie; Collins, Matthew James; Gilbert, Marcus Thomas Pius. (2020) Rapid loss of endogenous DNA in pig bone buried in five different environments. Archaeometry. volum 62 (4).
  Academic literature review
• Eriksen, Anne Marie Høier; Nielsen, Tue Kjærgaard; Matthiesen, Henning; Carøe, Christian; Hansen, Lars Hestbjerg; Gregory, David John; Turner-Walker, Gordon; Collins, Matthew James; Gilbert, Marcus Thomas Pius. (2020) Bone biodeterioration—The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community. PLOS ONE. volum 15 (10).
  Academic article
• Eriksen, Anne Marie Høier; Rocha, Carolina; Puetz, Lara; Nielsen, Tue K.; Hansen, Lars H.; Gilbert, Marcus Thomas Pius. (2020) Releasing the microbes from old bones: the effect of different DNA extraction protocols on microbial community profiling. Science and Technology of Archaeological Research. volum 6 (1).
  Academic article
• Feng, Shaohong; Stiller, Josefin; Deng, Yuan; Armstrong, Joel; Fang, Qi; Reeve, Andrew Hart; Xie, Duo; Chen, Guangji; Guo, Chunxue; Faircloth, Brant C.; Petersen, Bent; Wang, Zongji; Zhou, Qi; Diekhans, Mark; Chen, Wanjun; Andreu-Sánchez, Sergio; Margaryan, Ashot; Howard, Jason Travis; Parent, Carole. (2020) Dense sampling of bird diversity increases power of comparative genomics. Nature. volum 587.
  Academic article
• Fordham, Damien A.; Jackson, Stephen T.; Brown, Stuart C.; Huntley, Brian; Brook, Barry W.; Dahl-Jensen, Dorthe; Gilbert, Marcus Thomas Pius; Otto-Bliesner, Bette L.; Svensson, Anders; Theodoridis, Spyros; Wilmshurst, Janet M.; Buettel, Jessie C.; Canteri, Elisabetta; McDowell, Matthew; Orlando, Ludovic; Pilowsky, Julia; Rahbek, Carsten; Nogués-Bravo, David. (2020) Using paleo-archives to safeguard biodiversity under climate change. Science. volum 369 (6507).
  Academic literature review
• Fotakis, Anna K.; Denham, Sean Dexter; Mackie, Meaghan; Orbegozo, Miren Iraeta; Mylopotamitaki, Dorothea; Gopalakrishnan, Shyam; Sicheritz-Pontén, Thomas; Olsen, Jesper V.; Cappellini, Enrico; Zhang, Guojie; Christophersen, Axel; Gilbert, Marcus Thomas Pius; Vågene, Åshild J.. (2020) Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. Philosophical Transactions of the Royal Society of London. Biological Sciences. volum 375 (1812).
  Academic article
• Frantz, Laurent A.F.; Haile, James; Lin, Audrey T.; Scheu, Amelie; Geörg, Christina; Benecke, Norbert; Alexander, Michelle; Linderholm, Anna; Mullin, Victoria E.; Daly, Kevin G.; Battista, Vincent M.; Price, Max; Gron, Kurt J.; Alexandri, Panoraia; Arbogast, Rose-Marie; Arbuckle, Benjamin; Bǎlǎşescu, Adrian; Barnettl, Ross; Bartosiewicz, Laszlo. (2020) Erratum: Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe (Proceedings of the National Academy of Sciences of the United States of America (2019) 116 (17231-17238) DOI: 10.1073/pnas.1901169116). Proceedings of the National Academy of Sciences of the United States of America. volum 117 (25).
  Errata
• Gelabert, Pere; Sandoval-Velasco, Marcela; Serres, Aitor; de Manuel, Marc; Renom, Pere; Margaryan, Ashot; Stiller, Josefin; De-Dios, Toni; Fang, Qi; Feng, Shaohong; Mañosa, Santi; Pacheco, George; Ferrando-Bernal, Manuel; Shi, Guolin; Hao, Fei; Chen, Xianqing; Petersen, Bent; Olsen, Remi-André; Navarro, Arcadi. (2020) Evolutionary history, genomic adaptation to toxic diet, and extinction of the Carolina parakeet. Current Biology. volum 30 (1).
  Academic article
• Lord, Edana; Dussex, Nicolas; Kierczak, Marcin; Díez-del-Molino, David; Ryder, Oliver A.; Stanton, David W. G.; Gilbert, Marcus Thomas Pius; Sánchez-Barreiro, Fatima; Zhang, Guojie; Sinding, Mikkel-Holger S.; Lorenzen, Eline D.; Willerslev, Eske; Protopov, Albert; Shidlovskiy, Fedor K.; Fedorov, Sergey; Bocherens, Hervé; Nathan, Senthilvel K.S.S.; Goossens, Benoit; Johannes, van der Plicht. (2020) Pre-extinction demographic stability and genomic signatures of adaptation in the woolly rhinoceros. Current Biology. volum 30 (19).
  Academic article
• Lynggaard, Christina; Yu, Douglas W.; Oliveira, Guilherme; Caldeira, Cecilio F.; Ramos, Silvio J.; Ellegaard, Martin; Gilbert, Marcus Thomas Pius; Gastauer, Markus; Bohmann, Kristine. (2020) DNA-Based Arthropod Diversity Assessment in Amazonian Iron Mine Lands Show Ecological Succession Towards Undisturbed Reference Sites. Frontiers in Ecology and Evolution. volum 8.
  Academic article
• Margaryan, Ashot; Lawson, Daniel J.; Sikora, Martin; Racimo, Fernando; Rasmussen, Simon; Moltke, Ida; Cassidy, Lara M.; Jørsboe, Emil; Ingason, Andres; Pedersen, Mikkel Winther; Korneliussen, Thorfinn; Wilhelmson, Helene; Bus, Magdalena M.; de Barros Damgaard, Peter; Martiniano, Rui; Renaud, Gabriel; Bhérer, Claude; Moreno-Mayar, J. Víctor; Fotakis, Anna K.. (2020) Population genomics of the Viking world. Nature. volum 585 (7825).
  Academic article
• Margaryan, Ashot; Sinding, Mikkel Holger Strander; Shanlin, Liu; Vieira, Filipe Garrett; Chan, Yvonne L.; Nathan, Senthilvel K.S.S.; Moodley, Yoshan; Bruford, Michael W.; Gilbert, Marcus Thomas Pius. (2020) Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros. Zoological Journal of the Linnean Society. volum 190 (1).
  Academic article
• Møller, Henrik Devitt; Ramos-Madrigal, Jazmín; Prada-Luengo, Iñigo; Gilbert, Marcus Thomas Pius; Regenberg, Birgitte. (2020) Near-Random Distribution of Chromosome-Derived Circular DNA in the Condensed Genome of Pigeons and the Larger, More Repeat-Rich Human Genome. Genome Biology and Evolution (GBE). volum 12 (2).
  Academic article
• Nyholm, Lasse; Koziol, Adam; Marcos, Sofia; Botnen, Amanda Bolt; Aizpurua, Ostaizka; Gopalakrishnan, Shyam; Limborg, Morten T.; Gilbert, Marcus Thomas Pius; Alberdi, Antton. (2020) Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research. iScience. volum 23.
  Academic literature review
• Pacheco, George; Van Grouw, Hein; Shapiro, Michael D.; Gilbert, Marcus Thomas Pius; Vieira, Filipe G.. (2020) Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds. Genome Biology and Evolution (GBE). volum 12 (3).
  Academic article
• Pan, Hailin; Cole, Theresa L; Bi, Xupeng; Fang, Miaoquan; Zhou, Chengran; Yang, Zhengtao; Ksepka, Daniel T; Hart, Tom; Bouzat, Juan L; Argilla, Lisa S; Bertelsen, Mads F; Boersma, P. Dee; Bost, Charles-Andre; Cherel, Yves; Dann, Peter; Fiddaman, Steven R; Howard, Pauline; Labuschagne, Kim; Mattern, Thomas. (2020) Erratum: High-coverage genomes to elucidate the evolution of penguins (GigaScience (2019) 8:9 (giz117) DOI: 10.1093/gigascience/giz117). GigaScience. volum 9 (3).
  Errata
• Ramos-Madrigal, Jazmín; Sinding, Mikkel Holger Strander; Carøe, Christian; Mak, Sarah Siu Tze; Niemann, Jonas; Samaniego Castruita, José A.; Fedorov, Sergey; Kandyba, Alexander; Germonpré, Mietje; Bocherens, Hervé; Feuerborn, Tatiana R.; Pitulko, Vladimir V.; Pavlova, Elena Y.; Nikolskiy, Pavel A.; Kasparov, Aleksei K.; Ivanova, Varvara V.; Larson, Greger; Frantz, Laurent A.F.; Willerslev, Eske. (2020) Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages. Current Biology. volum 31 (1).
  Academic article
• Sandoval-Velasco, Marcela; Rodriguez, Juan Antonio; Estrada, Cynthia Perez; Zhang, Guojie; Aiden, Erez Lieberman; Marti-Renom, Marc A.; Gilbert, Marcus Thomas Pius; Smith, Oliver. (2020) Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform. GigaScience. volum 9 (8).
  Academic article
• Sinding, Mikkel Holger Strander; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; de Manuel, Marc; Pitulko, Vladimir V.; Kuderna, Lukas; Feuerborn, Tatiana R.; Frantz, Laurent A.F.; Vieira, Filipe G.; Niemann, Jonas; Castruita, Jose A. Samaniego; Carøe, Christian; Andersen-Ranberg, Emilie; Jordan, Peter; Pavlova, Elena Y.; Nikolskiy, Pavel A.; Kasparov, Aleksei K.; Ivanova, Varvara V.; Willerslev, Eske. (2020) Arctic-adapted dogs emerged at the Pleistocene–Holocene transition. Science. volum 368 (6498).
  Academic article
• van Dorp, Lucy; Gelabert, Pere; Rieux, Adrien; De Manuel, Marc; De-Dios, Toni; Gopalakrishnan, Shyam; Carøe, Christian; Sandoval-Velasco, Marcela; Fregel, Rosa; Olalde, Iñigo; Escosa, Raül; Aranda, Carles; Huijben, Silvie; Mueller, Ivo; Marques-Bonet, Tomas; Balloux, Francois; Gilbert, Marcus Thomas Pius; Lalueza-Fox, Carles. (2020) Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Molecular Biology and Evolution (MBE). volum 37 (3).
  Academic article
• Vieira, Filipe Garrett; Castruita, Jose A. Samaniego; Gilbert, Marcus Thomas Pius. (2020) Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction. Ecology and Evolution. volum 10.
  Academic article

2019

• Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Hulme-Beaman, Ardern; Lebrasseur, Ophélie; Sinding, Mikkel Holger Strander; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; Bachmann, Lutz; Betts, Matthew; Britton, Kate; Darwent, John; Dietz, Rune; Fredholm, Merethe; Gopalakrishnan, Shyam; Goruinova, Olga I.; Grønnow, Bjarne. (2019) Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic. Proceedings of the Royal Society of London. Biological Sciences. volum 286:20291929 (1929).
  Academic article
• Loog, Liisa; Thalmann, Olaf; Sinding, Mikkel Holger Strander; Schuenemann, Verena J.; Perri, Angela; Germonpré, Mietje; Bocherens, Herve; Witt, Kelsey E.; Samaniego Castruita, José Alfredo; Velasco, Marcela Sandoval; Lundstrøm, Inge K.C.; Wales, Nathan; Sonet, Gontran; Frantz, Laurent; Schroeder, Hannes; Budd, Jane; Jimenez, Elodie-Laure; Fedorov, Sergey; Gasparyan, Boris. (2019) Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia. Molecular Ecology.
  Academic article
• Pan, Hailin; Cole, Theresa L.; Bi, Xupeng; Fang, Miaoquan; Zhou, Chengran; Yang, Zhengtao; Ksepka, Daniel T.; Hart, Tom; Bouzat, Juan L.; Argilla, Lisa S.; Bertelsen, Mads F.; Boersma, P. Dee; Bost, Charles-André; Cherel, Yves; Dann, Peter; Fiddaman, Steven R.; Howard, Pauline; Labuschagne, Kim; Mattern, Thomas. (2019) High-coverage genomes to elucidate the evolution of penguins. GigaScience. volum 8 (9).
  Academic article
• Rey-Iglesia, Alba; Gopalakrishan, Shyam; Carøe, Christian; Alquezar-Planas, David E.; Ahlmann Nielsen, Anne; Röder, Timo; Bruhn Pedersen, Lene; Næsborg-Nielsen, Christina; Sinding, Mikkel Holger Strander; Fredensborg Rath, Martin; Li, Zhipeng; Petersen, Bent; Gilbert, Marcus Thomas Pius; Bunce, Michael; Mourier, Tobias; Hansen, Anders Johannes. (2019) MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements. Molecular Ecology Resources. volum 19 (2).
  Academic article
• Alberdi, Antton; Gilbert, Marcus Thomas Pius. (2019) A guide to the application of Hill numbers to DNA-based diversity analyses. Molecular Ecology Resources. volum 19 (4).
  Academic literature review
• Alves, Joel M.; Carneiro, Miguel; Cheng, Jade Y.; de Matos, Ana Lemos; Rahman, Masmudur M.; Loog, Liisa; Campos, Paula F.; Wales, Nathan; Eriksson, Anders; Manica, Andrea; Strive, Tanja; Graham, Stephen C.; Afonso, Sandra; Bell, Diana J.; Belmont, Laura; Day, Jonathan P.; Fuller, Susan J.; Marchandeau, Stéphane; Palmer, William J.. (2019) Parallel adaptation of rabbit populations to myxoma virus. Science. volum 363 (6433).
  Academic article
• Cappellini, Enrico; Welker, Frido; Pandolfi, Luca; Ramos-Madrigal, Jazmín; Samodova, Diana; Rüther, Patrick L.; Fotakis, Anna K.; Lyon, David; Moreno-Mayar, J. Víctor; Bukhsianidze, Maia; Jersie-Christensen, Rosa Rakownikow; Mackie, Meaghan; Ginolhac, Aurélien; Ferring, Reid; Tappen, Martha; Palkopoulou, Eleftheria; Dickinson, Marc R.; Stafford, Jr., Thomas W.; Chan, Yvonne L.. (2019) Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature. volum 574 (7776).
  Academic article
• Chen, Lei; Qiu, Qiang; Jiang, Yu; Wang, Kun; Lin, Zeshan; Li, Zhipeng; Bibi, Faysal; Yang, Yongzhi; Wang, Jinhuan; Nie, Wenhui; Su, Weiting; Liu, Guichun; Li, Qiye; Fu, Weiwei; Pan, Xiangyu; Liu, Chang; Yang, Jie; Zhang, Chenzhou; Yin, Yuan. (2019) Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science. volum 364 (6446).
  Academic article
• De-Dios, Toni; van Dorp, Lucy; Gelabert, Pere; Carøe, Christian; Sandoval-Velasco, Marcela; Fregel, Rosa; Escosa, Raül; Aranda, Carles; Huijben, Silvie; Balloux, Francois; Gilbert, Marcus Thomas Pius; Lalueza-Fox, Carles. (2019) Genetic affinities of an eradicated european plasmodium falciparum strain. Microbial Genomics. volum 5 (9).
  Academic article
• Feng, Shaohong; Fang, Qi; Barnett, Ross; Li, Caí; Han, Sojung; Kuhlwilm, Martin; Zhou, Long; Pan, Hailin; Deng, Yuan; Chen, Guangji; Gamauf, Anita; Woog, Friederike; Prys-Jones, Robert; Marques-Bonet, Tomas; Gilbert, Marcus Thomas Pius; Zhang, Guojie. (2019) The Genomic Footprints of the Fall and Recovery of the Crested Ibis. Current Biology. volum 29 (2).
  Academic article
• Foote, Andrew D.; Martin, Michael David; Louis, Marie; Pacheco, George; Robertson, Kelly M.; Sinding, Mikkel-Holger; Amaral, Ana R.; Baird, Robin; Baker, Charles; Ballance, Lisa; Barlow, Jay; Brownlow, Andrew; Collins, Tim; Constantine, Rochelle; Dabin, Willy; Rosa, Luciano Dalla; Davison, Nicholas J.; Durban, John W.; Esteban, Ruth. (2019) Killer whale genomes reveal a complex history of recurrent admixture and vicariance. Molecular Ecology. volum 28 (14).
  Academic article
• Frantz, Laurent A.F.; Haile, James; Lin, Audrey T.; Scheu, Amelie; Geörg, Christina; Benecke, Norbert; Alexander, Michelle; Linderholm, Anna; Mullin, Victoria E.; Daly, Kevin G.; Battista, Vincent M.; Price, Max; Gron, Kurt J.; Alexandri, Panoraia; Arbogast, Rose-Marie; Arbuckle, Benjamin; Bӑlӑşescu, Adrian; Barnett, Ross; Bartosiewicz, László. (2019) Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe. Proceedings of the National Academy of Sciences of the United States of America. volum 116 (35).
  Academic article
• Jensen, Theis Zetner Trolle; Niemann, Jonas; Iversen, Katrine Højholt; Fotakis, Anna K.; Gopalakrishnan, Shyam; Vågene, Åshild J; Pedersen, Mikkel Winther; Sinding, Mikkel-Holger S.; Ellegaard, Martin R; Allentoft, Morten E.; Lanigan, Liam T; Taurozzi, Alberto J; Nielsen, Sofie Holtsmark; Dee, Michael W; Mortensen, Martin; Christensen, Mads C; Sørensen, Søren; Collins, Matthew J; Gilbert, Marcus Thomas Pius. (2019) A 5700 year-old human genome and oral microbiome from chewed birch pitch. Nature Communications. volum 10.
  Academic article
• Jones, Rhys; Velasco, Marcela Sandoval; Harris, Llinos G; Morgan, Sue; Temple, Mark; Ruddy, Michael C; Williams, Rhian; Perry, Michael D; Hitchings, Matt; Wilkinson, Thomas S; Humphrey, Thomas; Gilbert, Marcus Thomas Pius; Davies, Angharad P. (2019) Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies. Tuberculosis. volum 119.
  Academic article
• Kieler, Ida Nordang; Osto, Melania; Hugentobler, Leoni; Puetz, Lara; Gilbert, Marcus Thomas Pius; Hansen, Torben; Pedersen, Oluf; Reusch, Claudia E.; Zini, Eric; Lutz, Thomas A.; Bjørnvad, Charlotte Reinhard. (2019) Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria. Scientific Reports. volum 9.
  Academic article
• Knapp, Michael; Thomas, Jessica E; Haile, James; Prost, Stefan; Ho, Simon YW; Dussex, Nicolas; Cameron-Christie, Sophia; Kardailsky, Olga; Barnett, Ross; Bunce, Michael; Gilbert, Marcus Thomas Pius; Scofield, R Paul. (2019) Mitogenomic evidence of close relationships between New Zealand's extinct giant raptors and small-sized Australian sister-taxa. Molecular Phylogenetics and Evolution. volum 134.
  Academic article
• Lin, Zeshan; Chen, Lei; Chen, Xianqing; Zhong, Yingbin; Yang, Yue; Xia, Wenhao; Liu, Chang; Zhu, Wenbo; Wang, Han; Yan, Biyao; Yang, Yifeng; Liu, Xing; Kvie, Kjersti; Røed, Knut; Wang, Kun; Xiao, Wuhan; Wei, Haijun; Li, Guangyu; Heller, Rasmus. (2019) Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus). Science. volum 364 (6446).
  Academic article
• Nielsen, Martin; Gilbert, Marcus Thomas Pius; Pape, Thomas; Bohmann, Kristine. (2019) A simplified DNA extraction protocol for unsorted bulk arthropod samples that maintains exoskeletal integrity. Environmental DNA. volum 1 (2).
  Academic article
• Ramos-Madrigal, Jazmín; Runge, Anne Kathrine Wiborg; Bouby, Laurent; Lacombe, Thierry; Samaniego Castruita, José Alfredo; Adam-Blondon, Anne-Francoise; Figueiral, Isabel; Hallavant, Charlotte; Martinez-Zapater, Jose M; Schaal, Caroline; Topfer, Reinhard; Petersen, Bent; Sicheritz-Pontén, Thomas; This, Patrice; Bacilieri, Roberto; Gilbert, Marcus Thomas Pius; Wales, Nathan. (2019) Palaeogenomic insights into the origins of French grapevine diversity. Nature Plants. volum 5 (6).
  Academic article
• Ribeiro, Ângela M; Smit, Ben; Gilbert, Marcus Thomas Pius. (2019) 31° South: Dietary niche of an arid-zone endemic passerine. Environmental DNA. volum 1 (2).
  Academic article
• Ribeiro, Angela; Puetz, Lara; Pattinson, Nicholas B; Dalén, Love; Deng, Yuan; Zhang, Guojie; Da Fonseca, Rute R.; Smit, Ben; Gilbert, Marcus Thomas Pius. (2019) 31° South: The physiology of adaptation to arid conditions in a passerine bird. Molecular Ecology. volum 28 (16).
  Academic article
• Sarmashghi, Shahab; Bohmann, Kristine; Gilbert, Marcus Thomas Pius; Bafna, Vineet; Mirarab, Siavash. (2019) Skmer: assembly-free and alignment-free sample identification using genome skims. Genome Biology. volum 20.
  Academic article
• Sirén, Kimmo; Mak, Sarah Siu Tze; Fischer, Ulrich; Hansen, Lars Hestbjerg; Gilbert, Marcus Thomas Pius. (2019) Multi-omics and potential applications in wine production. Current Opinion in Biotechnology. volum 56.
  Academic article
• Sirén, Kimmo; Mak, Sarah Siu Tze; Melkonian, Chrats; Carøe, Christian; Swiegers, Jan Hendrik; Molenaar, Douwe; Fischer, Ulrich; Gilbert, Marcus Thomas Pius. (2019) Taxonomic and functional characterization of the microbial community during spontaneous in vitro fermentation of riesling must. Frontiers in Microbiology. volum 10.
  Academic article
• Smith, Oliver; Dunshea, Glenn; Sinding, Mikkel-Holger; Fedorov, Sergey; Germonpre, Mietje; Bocherens, Hervé; Gilbert, Marcus Thomas Pius. (2019) Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. PLoS Biology. volum 17 (7).
  Academic article
• Thomas, Jessica E.; Carvalho, Gary R.; Haile, James; Rawlence, Nicolas J.; Martin, Michael David; Ho, Simon Y.W.; Sigfússon, Arnór Þ.; Jósefsson, Vigfús A.; Frederiksen, Morten; Linnebjerg, Jannie F.; Castruita, Jose A. Samaniego; Niemann, Jonas; Sinding, Mikkel-Holger S.; Sandoval-Velasco, Marcela; Soares, André E.R.; Lacy, Robert; Barilaro, Christina; Best, Julia; Brandis, Dirk. (2019) Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. eLIFE. volum 8:e47509.
  Academic article
• Wales, Nathan; Akman, Melis; Watson, Ray H B; Sánchez Barreiro, Fatima; Smith, Bruce D; Gremillion, Kristen J; Gilbert, Marcus Thomas Pius; Blackman, Benjamin K. (2019) Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement. Evolutionary Applications. volum 12 (1).
  Academic article

2018

• Bro-Jørgensen, Maiken Hemme; Carøe, Christian; Vieira, Filipe G.; Nestor, Sofia; Hallström, Ann; Gregersen, Kristian M.; Etting, Vivian; Gilbert, Marcus Thomas Pius; Sinding, Mikkel Holger Strander. (2018) Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull. Journal of Archaeological Science. volum 99.
  Academic article
• Gopalakrishnan, Shyam; Sinding, Mikkel Holger Strander; Ramos-Madrigal, Jazmín; Niemann, Jonas; Samaniego Castruita, Jose A.; Vieira, Filipe G.; Carøe, Christian; Montero, Marc de Manuel; Kuderna, Lukas; Serres, Aitor; González-Basallote, Victor Manuel; Liu, Yan-Hu; Wang, Guo-Dong; Marques-Bonet, Tomas; Mirarab, Siavash; Fernandes, Carlos; Gaubert, Philippe; Koepfli, Klaus-Peter; Budd, Jane. (2018) Interspecific gene flow shaped the evolution of the genus Canis. Current Biology. volum 28 (21).
  Academic article
• Leathlobhair, Máire Ní; Perri, Angela R.; Irving-Pease, Evan K.; Witt, Kelsey E.; Linderholm, Anna; Haile, James; Lebrasseur, Ophelie; Ameen, Carly; Blick, Jeffrey; Boyko, Adam R.; Brace, Selina; Cortes, Yahaira Nunes; Crockford, Susan J.; Devault, Alison; Dimopoulos, Evangelos A.; Eldridge, Morley; Enk, Jacob; Gopalakrishnan, Shyam; Gori, Kevin. (2018) The evolutionary history of dogs in the Americas. Science. volum 361 (6397).
  Academic article
• Sinding, Mikkel Holger Strander; Gopalakrishnan, Shyam; Vieira, Filipe G.; Samaniego, Jose A; Raundrup, Katrine; Heide Jørgensen, Mads Peter; Meldgaard, Morten; Petersen, Bent; Sicheritz-Ponten, Thomas; Mikkelsen, Johan Brus; Marquard-Petersen, Ulf; Dietz, Rune; Sonne, Christian; Dalén, Love; Bachmann, Lutz; Wiig, Øystein; Hansen, Anders J.; Gilbert, Marcus Thomas Pius. (2018) Population genomics of grey wolves and wolf-like canids in North America. PLoS Genetics. volum 14:e1007745 (11).
  Academic article
• Aizpurua, Ostaizka; Budinski, Ivana; Georgiakakis, Panagiotis; Gopalakrishnan, Shyam; Ibañez, Carlos; Mata, Vanessa A.; Rebelo, Hugo; Russo, Danilo; Szodoray-Parádi, Farkas; Zhelyakzova, Violeta; Zrncic, Vida; Gilbert, Marcus Thomas Pius; Alberdi, Antton. (2018) Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding. Molecular Ecology. volum 27 (3).
  Academic article
• Alberdi, Antton; Aizpurua, Ostaizka; Bohmann, Kristine; Gopalakrishnan, Shyam; Lynggaard, Christina; Nielsen, Martin; Gilbert, Marcus Thomas Pius. (2018) Promises and pitfalls of using high-throughput sequencing for diet analysis. Molecular Ecology Resources. volum 19 (2).
  Academic literature review
• Alberdi, Antton; Aizpurua, Ostaizka; Gilbert, Marcus Thomas Pius; Bohmann, Kristine. (2018) Scrutinizing key steps for reliable metabarcoding of environmental samples. Methods in Ecology and Evolution. volum 9 (1).
  Academic article
• Barnett, Ross; Sinding, Mikkel Holger Strander; Vieira, Filipe G.; Mendoza, Marie Lisandra Zepeda; Bonnet, Matthieu; Araldi, Alessandro; Kienast, Ivonne; Zambarda, Alice; Yamaguchi, Nobuyuki; Henschel, Philipp; Gilbert, Marcus Thomas Pius. (2018) No longer locally extinct? Tracing the origins of a lion (Panthera leo) living in Gabon. Conservation Genetics. volum 19 (3).
  Academic article
• Bohmann, Kristine; Gopalakrishnan, Shyam; Nielsen, Martin; Bay Nielsen, Luisa dos Santos; Jones, Gareth; Streicker, Daniel G.; Gilbert, Marcus Thomas Pius. (2018) Using DNA metabarcoding for simultaneous inference ofcommon vampire bat diet and population structure. Molecular Ecology Resources. volum 18 (5).
  Academic article
• Carøe, Christian; Gopalakrishnan, Shyam; Vinner, Lasse; Mak, Sarah S.T.; Sinding, Mikkel Holger Strander; Samaniego, Jose A; Wales, Nathan; Sicheritz-Pontén, Thomas; Gilbert, Marcus Thomas Pius. (2018) Singe-tube library preparation for degraded DNA. Methods in Ecology and Evolution. volum 9 (2).
  Academic article
• Drinkwater, Rosie; Schnell, Ida Bærholm; Bohmann, Kristine; Bernard, Henry; Veron, Géraldine; Clare, Elizabeth; Gilbert, Marcus Thomas Pius; Rossiter, Stephen J.. (2018) Using metabarcoding to compare the suitability of two blood‐feeding leech species for sampling mammalian diversity in North Borneo. Molecular Ecology Resources.
  Academic article
• Ebenesersdóttir, Sigríður Sunna; Sandoval-Velasco, Marcela; Gunnarsdóttir, Ellen D.; Jagadeesan, Anuradha; Guðmundsdóttir, Valdís B.; Thordardóttir, Elísabet L.; Einarsdóttir, Margrét S.; Moore, Kristjan H. S.; Sigurðsson, Ásgeir; Magnúsdóttir, Droplaug N.; Jónsson, Hákon; Snorradóttir, Steinunn; Hovig, Eivind; Møller, Pål; Kockum, Ingrid; Olsson, Tomas; Alfredsson, Lars; Hansen, Thomas F.; Werge, Thomas. (2018) Ancient genomes from Iceland reveal the making of a human population. Science. volum 360 (6392).
  Academic article
• Fietz, Katharina; Hintze, Christian O.R.; Skovrind, Mikkel; Nielsen, Tue Kjærgaard; Limborg, Morten; Krag, Marcus A.; Palsbøll, Per J.; Hansen, Lars Hestbjerg; Møller, Peter Rask; Gilbert, Marcus Thomas Pius. (2018) Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species. Microbiome. volum 6 (82).
  Academic article
• Holt, Carson; Campbell, Michael; Keays, David Anthony; Edelman, Nathaniel; Kapusta, Aurélie; Maclary, Emily; Domyan, Eric T.; Suh, Alexander; Warren, Wesley C.; Yandell, Mark; Gilbert, Marcus Thomas Pius; Shapiro, Michael D.. (2018) Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia). G3: Genes, Genomes, Genetics. volum 8 (5).
  Academic article
• Hooper, Rebecca; Brealey, Jaelle C.; van der Valk, Tom; Alberdi, Antton; Durban, John; Fearnbach, Holly; Robertson, Kelly M.; Baird, Robin; Hanson, M. Bradley; Wade, Paul; Gilbert, Marcus Thomas Pius; Morin, Phillip; Wolf, Jochen B.W.; Foote, Andrew D.; Guschanski, Katerina. (2018) Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. Molecular Ecology.
  Academic article
• Kistler, Logan; Maezumi, S. Yoshi; de Souza, Jonas Gregorio; Przelomska, Natalia A.S.; Costa, Flaviane Malaquias; Smith, Oliver; Loiselle, Hope; Ramos-Madrigal, Jazmín; Wales, Nathan; Ribeiro, Eduardo Rivail; Morrison, Ryan R.; Grimaldo, Claudia; Prous, Andre P.; Arriaza, Bernardo; Gilbert, Marcus Thomas Pius; de Oliveira Freitas, Fabio; Allaby, Robin G.. (2018) Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science. volum 362 (6420).
  Academic article
• Kodama, Miyako; Brinch-Pedersen, Henrik; Sharma, Shrikant; Holme, Inger B.; Joernsgaard, Bjarne; Dzhanfezova, Tsaneta; Amby, Daniel Buchvaldt; Vieira, Filipe G.; Liu, Shanlin; Gilbert, Marcus Thomas Pius. (2018) Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq. BMC Genomics. volum 19 (811).
  Academic article
• Lewin, Harris A.; Robinson, Gene E.; Kress, W. John; Baker, William J.; Coddington, Jonathan; Crandall, Keith A.; Durbin, Richard; Edwards, Scott V.; Forest, Félix; Gilbert, Marcus Thomas Pius; Goldstein, Melissa M.; Grigoriev, Igor V.; Hackett, Kevin J.; Haussler, David; Jarvis, Erich D.; Johnson, Warren E.; Patrinos, Aristides; Richards, Stephen; Castilla-Rubio, Juan Carlos. (2018) Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences of the United States of America. volum 115 (17).
  Academic literature review
• Limborg, Morten T.; Alberdi, Antton; Kodama, Miyako; Roggenbuck, Michael; Kristiansen, Karsten; Gilbert, Marcus Thomas Pius. (2018) Applied Hologenomics: Feasibility and Potential in Aquaculture. Trends in Biotechnology. volum 36 (3).
  Academic literature review
• Mak, Sarah Siu Tze; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger Strander; Kuderna, Lukas F.K.; Zhang, Wenwei; Fu, Shujin; Vieira, Filipe G.; Germonpré, Mietje; Bocherens, Hervé; Fedorov, Sergey; Petersen, Bent; Sicheritz-Pontén, Thomas; Marques-Bonet, Tomas; Zhang, Guojie; Jiang, Hui; Gilbert, Marcus Thomas Pius. (2018) Erratum: Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing (GigaScience (2017) 6:8 (1-13) DOI: 10.1093/gigascience/gix049). GigaScience. volum 7 (12).
  Errata
• Schnell, Ida Bærholm; Bohmann, Kristine; Schultze, Sebastian E.; Richter, Stine R.; Murray, Daíthí C.; Sinding, Mikkel-Holger; Bass, David; Cadle, John E.; Campbell, Mason; Dolch, Rainer; Edwards, David P.; Gray, Thomas N.E.; Hansen, Teis; Quang Hoa, Anh Nguyen; Lehmkuhl Noer, Christina; Heise-Pavlov, Sigrid; Pedersen, Adam F. Sander; Ramamonjisoa, Juliot Carl; Siddall, Mark. (2018) Debugging diversity–a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool. Molecular Ecology Resources. volum 18 (6).
  Academic article
• Teeling, E.; Vernes, S.; Davalos, L.M.; Ray, D.A.; Gilbert, Marcus Thomas Pius; Myers, E. (2018) Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species. Annual Review of Animal Biosciences. volum 6.
  Academic article
• Zepeda Mendoza, M. Lisandra; Roggenbuck, Michael; Manzano Vargas, Karla; Hestbjerg Hansen, Lars; Brunak, Søren; Gilbert, Marcus Thomas Pius; Sicheritz-Ponten, Thomas. (2018) Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging. Acta Veterinaria Scandinavica (AVS). volum 60.
  Academic article
• Zepeda Mendoza, M. Lisandra; Xiong, Zijun; Escalera-Zamudio, Marina; Runge, Anne Kathrine; Théze, Julien; Streicker, Daniel; Frank, Hannah K.; Loza-Rubio, Elizabeth; Liu, Shengmao; Ryder, Oliver A.; Samaniego Castruita, José Alfredo; Katzourakis, Aris; Pacheco, George; Taboada, Blanca; Löber, Ulrike; Pybus, Oliver G.; Li, Yang; Rojas-Anaya, Edith; Bohmann, Kristine. (2018) Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. Nature Ecology and Evolution. volum 2 (4).
  Academic article
• Zhou, Zhemin; Lundstrøm, Inge K. C.; Tran-Dien, Alicia; Duchêne, Sebastián; Alikhan, Nabil-Fareed; Sergeant, Martin J.; Langridge, Gemma; Fotakis, Anna K.; Nair, Satheesh; Stenøien, Hans K.; Suppersberger Hamre, Stian; Casjens, Sherwood; Christophersen, Axel; Quince, Christopher; Thomson, Nicholas R.; Weill, François-Xavier; Ho, Simon Y. W.; Gilbert, Marcus Thomas Pius; Achtman, Mark. (2018) Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia. Current Biology.
  Academic article

2017

• Bush, Alex; Sollmann, Rahel; Wilting, Andreas; Bohmann, Kristine; Cole, Beth; Balzter, Heiko; Martius, Christopher; Zlinszky, Andras; Calvignac-Spencer, Sébastien; Cobbold, Christina A.; Dawson, Terence P; Emerson, Brent C.; Ferrier, Simon; Gilbert, Marcus Thomas Pius; Herold, Martin; Jones, Laurence; Leendertz, Fabian H; Matthews, Louise; Millington, James D A. (2017) Connecting Earth observation to high-throughput biodiversity data. Nature Ecology and Evolution. volum 1 (7).
  Academic literature review
• Diez-del-Molino, DAvid; Sánchez-Barreiro, Fatima; Barnes, Ian; Gilbert, Marcus Thomas Pius; Dalén, Love. (2017) Quantifying temporal genomic erosion in endangered species. Trends in Ecology & Evolution. volum 33 (3).
  Academic article
• Fortes-Lima, Cesar; Gessain, Antoine; Ruiz-Linares, Andres; Bortolini, Maria; Migot-Nabias, Florence; Bellis, Gil; Moreno-Mayar, J. Victor; Restrepo, Berta Nelly; Rojas, Winston; Avendaño-Tamayo, Efren; Bedoya, Gabriel; Orlando, Ludovic; Salas, Antonio; Helgason, Agnar; Gilbert, Marcus Thomas Pius; Sikora, Martin; Schroeder, Hannes; Dugoujon, Jean-Michel. (2017) Genome-wide ancestry and demographic history of African-descendant Maroon communities from French Guiana and Suriname. American Journal of Human Genetics. volum 101 (5).
  Academic article
• Gilbert, Marcus Thomas Pius. (2017) Documenting DNA in the dust. Molecular Ecology. volum 26 (4).
  Short communication
• Gopalakrishnan, Shyam; Samaniego Castruita, José Alfredo; Sinding, Mikkel Holger Strander; Kuderna, Lukas FK; Räikkönen, Jannikke; Petersen, Bent; Sicheritz-Ponten, Thomas; Larson, Greger; Orlando, Ludovic; Marques-Bonet, Tomas; Hansen, Anders J.; Dalén, Love; Gilbert, Marcus Thomas Pius. (2017) The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics. BMC Genomics. volum 18.
  Academic article
• Grealy, Alicia; Phillips, Matthew; Miller, Gifford; Gilbert, Marcus Thomas Pius; Rouillard, Jean-Marie; Lambert, David; Bunce, Michael; Haile, James. (2017) Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Molecular Phylogenetics and Evolution. volum 109.
  Academic article
• Liu, Yan-Hu; Wang, Lu; Xu, Tao; Guo, Xiaomin; Li, Yang; Yin, Ting-Ting; Yang, He-Chuan; Hu, Yang; Adeola, Adeniyi C.; Sanke, Oscar J.; Otecko, Newton O.; Wang, Meng; Ma, Yaping; Charles, Olaogun S.; Sinding, Mikkel Holger Strander; Gopalakrishnan, Shyam; Samaniego, José Alfredo; Hansen, Anders J.; Fernandes, Carlos. (2017) Whole-genome sequencing of African dogs provides insights into adaptations against tropical parasites. Molecular Biology and Evolution (MBE). volum 35 (2).
  Academic article
• Mak, Sarah S.T.; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger Strander; Kuderna, Lukas FK; Zhang, Wenwei; Fu, Shujin; Vieira, Filipe G.; Germonpre, Mietje; Bocherens, Hervé; Fedorov, Sergey; Petersen, Bent; Sicheritz-Pontén, Thomas; Marques-Bonet, Tomas; Zhang, Guojie; Jiang, Hui; Gilbert, Marcus Thomas Pius. (2017) Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. GigaScience. volum 6 (8).
  Academic article
• Murray, Gemma G.R.; Soares, André E.R.; Novak, Ben J.; Schaefer, Nathan K.; Cahill, James A.; Baker, Allan J.; Demboski, John R.; Doll, Andrew; Da Fonseca, Rute R.; Fulton, Tara L.; Gilbert, Marcus Thomas Pius; Heintzman, Peter D.; Letts, Brandon; McIntosh, George; O'Connell, Brendan L.; Peck, Mark; Pipes, Marie-Lorraine; Rice, Edward S.; Santos, Kathryn M.. (2017) Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science. volum 358 (6365).
  Academic article
• Paijmans, Johanna L. A.; Barnett, Ross; Gilbert, Marcus Thomas Pius; Zepeda-Mendoza, Marie Lisandra; Reumer, Jelle WF; de Vos, John; Zazula, Grant; Nagel, Doris; Baryshnikov, Gennady F; Leonard, Jennifer A; Rohland, Nadin; Westbury, Michael V; Barlow, Axel; Hofreiter, Michael. (2017) Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics. Current Biology. volum 27 (21).
  Academic article
• Salleh, Faezah Mohd; Ramos-Madrigal, Jazmín; Peñaloza, Fernando; Liu, Shanlin; Sinding, Mikkel Holger Strander; Patel, Riddhi P.; Martins, Renata; Lenz, Dorina; Fickel, Jörns; Roos, Christian; Shamsir, Mohd Shahir; Azman, Mohammad Shahfiz; Lim, Burton K.; Rossiter, Stephen J.; Wilting, Andreas; Gilbert, Marcus Thomas Pius. (2017) An expanded mammal mitogenome dataset from Southeast asia. GigaScience. volum 6 (8).
  Academic article
• Sánchez Barreiro, Fatima; Vieira, Filipe G.; Martin, Michael D.; Haile, James; Gilbert, Marcus Thomas Pius; Wales, Nathan. (2017) Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes. Molecular Ecology Resources. volum 17 (2).
  Academic article
• Sandoval-Velasco, Marcela; Lundstrøm, Inge K. C.; Wales, Nathan; Ávila-Arcos, María C; Schroeder, Hannes; Gilbert, Marcus Thomas Pius. (2017) Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples. Science and Technology of Archaeological Research. volum 3 (1).
  Academic article
• Seki, Ryohei; Li, Caí; Fang, Qi; Hayashi, Shinichi; Egawa, Shiro; Hu, Jiang; Xu, Luohao; Pan, Hailin; Kondo, Mao; Sato, Tomohiko; Matsubara, Haruka; Kamiyama, Namiko; Kitajima, Keiichi; Saito, Daisuke; Liu, Yang; Gilbert, Marcus Thomas Pius; Zhou, Qi; Xu, Xing; Shiroishi, Toshihiko. (2017) Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. Nature Communications. volum 8 (14229).
  Academic article
• Sinding, Mikkel Holger Strander; Gilbert, Marcus Thomas Pius. (2017) Correction: The draft genome of extinct European aurochs and its implications for de-extinction(Open Quaternary, 2,7, 10.5334/oq.25). Open Quaternary. volum 3.
  Errata
• Tanner, Alastair R; Fuchs, Dirk; Winkelmann, Inger E; Gilbert, Marcus Thomas Pius; Pankey, M Sabrina; Ribeiro, Angela; Kocot, Kevin M.; Halanych, Kenneth M; Oakley, Todd H; Da Fonseca, Rute R.; Pisani, Davide; Vinther, Jakob. (2017) Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic marine revolution. Proceedings of the Royal Society of London. Biological Sciences. volum 284 (1850).
  Academic article
• Thomas, Jessica E; Carvalho, Gary R.; Haile, James; Martin, Michael David; Castruita, Jose A. Samaniego; Niemann, Jonas; Sinding, Mikkel Holger Strander; Sandoval-Velasco, Marcela; Rawlence, Nicolas J.; Fuller, Errol; Fjeldså, Jon; Hofreiter, Michael; Stewart, John R; Gilbert, Marcus Thomas Pius; Knapp, Michael. (2017) An ‛Aukward’ tale: a genetic approach to discover the whereabouts of the last Great Auks. Genes. volum 8 (6).
  Academic article

2016

• Alberdi, Antton; Aizpurua, Ostaizka; Bohmann, Kristine; Zepeda-Mendoza, Marie Lisandra; Gilbert, Marcus Thomas Pius. (2016) Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation?. Trends in Ecology & Evolution. volum 31 (9).
  Academic literature review
• Gelabert, Pere; Sandoval-Velasco, Marcela; Olalde, Iñigo; Fregel, Rosa; Rieux, Adrien; Escosa, Raül; Aranda, Carles; Paaijmans, Krijn; Mueller, Ivo; Gilbert, Marcus Thomas Pius; Lalueza-Fox, Carles. (2016) Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year-old slides from the Ebro Delta in Spain. Proceedings of the National Academy of Sciences of the United States of America. volum 113 (41).
  Academic article
• Martin, Michael D; Olsen, Morten T; Samaniego, Jose; Zimmer, Elizabeth A; Gilbert, Marcus Thomas Pius. (2016) The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.). Ecology and Evolution. volum 6 (11).
  Academic article
• Ramos-Madrigal, Jazmín; Smith, Bruce D; Moreno-Mayar, J Víctor; Gopalakrishnan, Shyam; Ross-Ibarra, Jeffrey; Gilbert, Marcus Thomas Pius; Wales, Nathan. (2016) Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication. Current Biology. volum 26 (23).
  Academic article
• Richmond, Douglas J.; Sinding, Mikkel Holger Strander; Gilbert, Marcus Thomas Pius. (2016) The potential and pitfalls of de-extinction. Zoologica Scripta. volum 45.
  Academic literature review
• Sinding, Mikkel Holger Strander; Gilbert, Marcus Thomas Pius. (2016) The draft genome of extinct european aurochs and its implications for de-extinction. Open Quaternary. volum 2.
  Academic article
• Wales, Nathan; Ramos Madrigal, Jazmín; Cappellini, Enrico; Carmona Baez, Aldo; Samaniego Castruita, José Alfredo; Romero-Navarro, J. Alberto; Carøe, Christian; Ávila-Arcos, María C; Peñaloza, Fernando; Moreno-Mayar, J. Victor; Gasparyan, Boris; Zardaryan, Diana; Bagoyan, Tamara; Smith, Alexia; Pinhasi, Ron; Bosi, Giovanna; Fiorentino, Girolamo; Grasso, Anna Maria; Celant, Alessandra. (2016) The limits and potential of paleogenomic techniques for reconstructing grapevine domestication. Journal of Archaeological Science. volum 72.
  Academic article