2025

• Eriksen, Anne Marie Høier; Rodríguez, Juan Antonio; Seersholm, Frederik; Hollund, Hege Ingjerd; Gotfredsen, Anne Birgitte; Collins, Matthew James. (2025) Exploring DNA degradation in situ and in museum storage through genomics and metagenomics. Communications Biology
  Academic article
• Rogers, Alexander B.; Kale, Varsha; Baldi, Germana; Alberdi, Antton; Gilbert, Marcus Thomas Pius; Gupta, Dipayan. (2025) HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production. Database: The Journal of Biological Databases and Curation
  Academic article
• Aizpurua, Ostaizka; Botnen, Amanda Bolt; Eisenhofer, Raphael; Odriozola, Iñaki; Santos-Bay, Luisa; Bjørnsen, Mads Bjørn. (2025) Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide. Molecular Ecology
  Academic article
• Silver, Luke W.; Farquharson, Katherine A.; Peel, Emma; Gilbert, Marcus Thomas Pius; Belov, Katherine; Morales, Hernán E.. (2025) Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot. Molecular Ecology
  Academic article
• Duchêne, David A.; Chowdhury, Al-Aabid; Yang, Jingyi; Iglesias-Carrasco, Maider; Stiller, Josefin; Feng, Shaohong. (2025) Drivers of avian genomic change revealed by evolutionary rate decomposition. Nature
  Academic article
• Lobo, Diana; Morales, Hernán E.; Van Oosterhout, Cock; López-Bao, José Vicente; Silva, Pedro; Llaneza, Luis. (2025) Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes. Genome Research
  Academic article
• Muurmann, Asmus Toftkær; Eriksen, Niels Thomas; Jacobsen, Jacob Agerbo; Limborg, Morten T.; Tomberlin, Jeffery K.; Gilbert, Marcus Thomas Pius. (2025) Growth and metabolic performance of house fly and black soldier fly larvae differ across densities and waste-based growth substrates. Waste Management
  Academic article
• Ramos-Madrigal, Jazmín; Fritz, Gayle J.; Schroeder, Bryon; Smith, Bruce; Sánchez-Barreiro, Fátima; Carøe, Christian. (2025) The genomic origin of early maize in eastern North America. Cell
  Academic article

2024

• Stiller, Josefin; Feng, Shaohong; Chowdhury, Al-Aabid; Rivas-González, Iker; Duchêne, David A.; Fang, Qi. (2024) Complexity of avian evolution revealed by family-level genomes. Nature
  Academic article
• Rose, Jennifer; Gilbert, Marcus Thomas Pius; Outerbridge, Mark; Morales, Hernán E.. (2024) Evolutionary genomics analysis reveals a unique lineage of Megachile pruina found in an isolated population in Bermuda. Insect Conservation and Diversity
  Academic article
• Cavill, Emily L.; Morales, Hernán E.; Sun, Xin; Westbury, Michael V.; van Oosterhout, Cock; Accouche, Wilna. (2024) When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine. Evolutionary Applications
  Academic article
• Sun, Xin; Cavill, Emily Louisa; Margaryan, Ashot; Lin, Jianqing; Thingaard, Søren; Said, Tamrini A.. (2024) A Genomic Exploration of the Possible De-Extirpation of the Zanzibar Leopard. Molecular Ecology
  Academic article
• Bordenstein, Seth R.; Gilbert, Marcus Thomas Pius; Ginnan, Nichole; Malacrinò, Antonino; Martino, Maria Elena; Bahrndorf, Simon. (2024) The disciplinary matrix of holobiont biology. Uniting life’s seen and unseen realms guides a conceptual advance in research. Science
  Academic article
• Muurmann, Asmus Toftkær; Banovic, Marija; Gilbert, Marcus Thomas Pius; Sogari, Giovanni; Limborg, Morten Tønsberg; Sicheritz-Pontén, Thomas. (2024) Framework for valorizing waste- and by-products through insects and their microbiomes for food and feed. Food Research International
  Academic literature review
• Kothe, Caroline Isabel; Rasmussen, Jacob Agerbo; Mak, Sarah S.T.; Gilbert, Marcus Thomas Pius; Evans, Joshua. (2024) Exploring the microbial diversity of novel misos with metagenomics. Food Microbiology
  Academic article
• Dehasque, Marianne; Morales, Hernán E.; Díez-del-Molino, David; Pečnerová, Patrícia; Chacón-Duque, J. Camilo; Kanellidou, Foteini. (2024) Temporal dynamics of woolly mammoth genome erosion prior to extinction. Cell
  Academic article
• Sandoval-Velasco, Marcela; Dudchenko, Olga; Rodríguez, Juan Antonio; Pérez Estrada, Cynthia; Dehasque, Marianne; Fontsere, Claudia. (2024) Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell
  Academic article
• Odriozola, Iñaki; Rasmussen, Jacob A.; Gilbert, Marcus Thomas Pius; Limborg, Morten T.; Alberdi, Antton. (2024) A practical introduction to holo-omics. Cell Reports Methods
  Academic literature review
• Barnes, Christopher J.; Bünner, Maria Sophie; Ramírez-Flores, M. Rosario; Nielsen, Ida Broman; Ramos-Madrigal, Jazmin; Zharikova, Daria. (2024) The ancestral environment of teosinte populations shapes their root microbiome. Environmental Microbiome
  Academic article
• Barnes, Christopher James; Bahram, Mo; Nicolaisen, Mogens; Gilbert, Marcus Thomas Pius; Vestergård, Mette. (2024) Microbiome selection and evolution within wild and domesticated plants. Trends in Microbiology
  Academic literature review
• Brealey, Jaelle Caitlin; Kodama, Miyako; Agerbo Rasmussen, Jacob; Hansen, Søren B.; Santos-Bay, Luisa; Lecaudey, Laurene Alicia. (2024) Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon. mSystems
  Academic article
• Ellegaard, Martin Rene; Ebenesersdóttir, S. Sunna; Moore, Kristjan H.S.; Petersen, Anna Helena; Vågene, Åshild J.; Bieker, Vanessa Carina. (2024) Corroborating written history with ancient DNA: The case of the Well-man described in an Old Norse saga. iScience
  Academic article
• Rasmussen, Jacob A.; Bernhard, Annette; Lecaudey, Laurene Alicia; Kale, Varsha; Baldi, Germana; Myrmel, Lene Secher. (2024) A holo-omics analysis shows how sugar kelp can boost gut health in Atlantic salmon. Aquaculture
  Academic article
• Laine, Jan Tapio; Mak, Sarah S.T.; Martins, Nuno F.G.; Chen, Xihan; Gilbert, Marcus Thomas Pius; Jones, Felicity C.. (2024) Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation. Current Biology
  Academic article
• Kliver, Sergei; Kovacic, Iva; Mak, Sarah; Sinding, Mikkel-Holder S.; Stagegaard, Julia; Petersen, Bent. (2024) A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus). Journal of Heredity
  Academic article

2023

• Hernández-Alonso, Germán; Ramos-Madrigal, Jazmín; van Grouw, Hein; Ciucani, MartaMaria; Cavill, Emily Louisa; Sinding, Mikkel-Holger S.. (2023) Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences. Molecular Biology and Evolution (MBE)
  Academic article
• Femerling, Georgette; van Oosterhout, Cock; Feng, Shaohong; Bristol, Rachel M.; Zhang, Guojie; Groombridge, Jim. (2023) Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction. Molecular Biology and Evolution (MBE)
  Academic article
• Pereira, Cátia Lúcio; Ersoy, Zeynep; Gilbert, Marcus Thomas Pius; Gravel, Dominique; Araújo, Miguel B.; Matias, Miguel Graça. (2023) Future-proofing environmental DNA and trait-based predictions of food webs. BioScience
  Academic article
• Ciucani, Marta Maria; Ramos-Madrigal, Jazmín; Hernández-Alonso, Germán; Carmagnini, Alberto; Aninta, Sabhrina Gita; Sun, Xin. (2023) The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs. iScience
  Academic article
• Germain, Ryan R.; Feng, Shaohong; Chen, Guangji; Graves, Gary R.; Tobias, Joseph A.; Rahbek, Carsten. (2023) Species-specific traits mediate avian demographic responses under past climate change. Nature Ecology and Evolution
  Academic article
• Díez-del-Molino, David; Dehasque, Marianne; Chacón-Duque, J. Camilo; Pečnerová, Patrícia; Tikhonov, Alexei; Protopopov, Albert. (2023) Genomics of adaptive evolution in the woolly mammoth. Current Biology
  Academic article
• Germain, Ryan R.; Feng, Shaohong; Buffan, Lucas; Carmona, Carlos P.; Chen, Guangii; Graves, Gary R.. (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 (PNAS)
  Academic article
• Aizpurua, Ostaizka; Blijleven, Kees; Trivedi, Urvish; Gilbert, Marcus Thomas Pius; Alberdi, Antton. (2023) Unravelling animal–microbiota evolution on a chip. Trends in Microbiology
  Academic literature review
• Sun, Xin; Liu, Yue-Chen; Tiunov, Mikhail P.; Gimranov, Dmitry O.; Zhuang, Yan; Han, Yu. (2023) Ancient DNA reveals genetic admixture in China during tiger evolution. Nature Ecology and Evolution
  Academic article
• Sandoval-Velasco, Marcela; Jagadeesan, Anuradha; Ramos-Madrigal, Jazmín; Ávila-Arcos, María C.; Fortes-Lima, Cesar A.; Watson, Judy. (2023) The ancestry and geographical origins of St Helena's liberated Africans. American Journal of Human Genetics
  Academic article
• Aizpurua, Ostaizka; Dunn, Robert R.; Hansen, Lars H.; Gilbert, Marcus Thomas Pius; Alberdi, Antton. (2023) Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Critical Reviews in Biotechnology
  Academic literature review
• Sánchez-Barreiro, Fátima; De Cahsan, Binia; Westbury, Michael V.; Sun, Xin; Margaryan, Ashot; Fontsere, Claudia. (2023) Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros. Molecular Biology and Evolution (MBE)
  Academic article
• Danabalan, Renita; Merkel, Kevin; Bærholm Schnell, Ida; Arandjelovic, Mimi; Boesch, Christophe; Brazzola, Gregory. (2023) Mammal mitogenomics from invertebrate-derived DNA. Environmental DNA
  Academic article
• Hansen, Søren B.; Bozzi, Davide; Mak, Sarah S.T.; Clausen, Cecilie G.; Nielsen, Tue K.; Kodama, Miyako. (2023) Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. Genomics
  Academic article
• Cohen, Pnina; Bacilieri, Roberto; Ramos-Madrigal, Jazmín; Privman, Eyal; Boaretto, Elisabetta; Weber, Audrey. (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 (PNAS)
  Academic article
• Rasmussen, Jacob A.; Kiilerich, Pia; Madhun, Abdullah Sami; Waagbø, Rune; Lock, Erik Jan Robert; Madsen, Lise. (2023) Co-diversification of an intestinal Mycoplasma and its salmonid host. The ISME Journal
  Academic article
• Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul Ragnar; Bleidorn, Christoph. (2023) How genomics can help biodiversity conservation. Trends in Genetics
  Academic literature review
• Hernández-Alonso, Germán; Ramos-Madrigal, Jazmín; Sun, Xin; Scharff-Olsen, Camilla Hjorth; Sinding, Mikkel Holger Strander; Martins, Nuno F.. (2023) Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing. Ecology and Evolution
  Academic article
• Skovrind, Mikkel; Pacheco, George; Christensen, Emil Aputsiaq Flindt; Gopalakrishnan, Shyam; Fietz, Katharina; Holm-Hansen, Tore Hejl. (2023) Uncovering neutral and adaptive genomic differentiation among European perch with brackish water and freshwater origin in the western Baltic Sea region. Fisheries Research
  Academic article
• Bergeron, Lucie A.; Besenbacher, Søren; Zheng, Jiao; Li, Panyi; Bertelsen, Mads Frost; Quintard, Benoit. (2023) Evolution of the germline mutation rate across vertebrates. Nature
  Academic article
• Rasmussen, Linett; Fontsere, Claudia; Soto-Calderón, Iván D.; Guillen, Rosamira; Savage, Anne; Hansen, Anders Johannes. (2023) Assessing the genetic composition of cotton-top tamarins (Saguinus oedipus) before sweeping anthropogenic impact. Molecular Ecology
  Academic article
• Hansen, Charles Christian Riis; Láruson, Áki Jarl; Rasmussen, Jacob Agerbo; Chimal Ballesteros, Jesus Adrian; Sinding, Mikkel Holger Strander; Hallgrimsson, Gunnar T.. (2023) Genomic diversity and differentiation between island and mainland populations of white-tailed eagles (Haliaeetus albicilla). Molecular Ecology
  Academic article
• Zhang, Pei; Zhu, Yuanzhen; Guo, Qunfei; Li, Ji; Zhan, Xiaoyu; Yu, Hao. (2023) On the origin and evolution of RNA editing in metazoans. Cell reports
  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
  Academic article
• Rodriguez-Varela, Ricardo; Moore, Kristjan H.S.; Ebenesersdottir, Sunna; Kilinc, Gulsah; Kjellström, Anna; Papmehl-Dufay, Ludvig. (2023) The genetic history of Scandinavia from the Roman Iron Age to the present. Cell
  Academic article

2022

• Bergström, Anders; Stanton, David W. G.; Taron, Ulrike H.; Frantz, Laurent; Sinding, Mikkel Holger Strander; Ersmark, Erik. (2022) Grey wolf genomic history reveals a dual ancestry of dogs. Nature
  Academic article
• Field, Matt A.; Yadav, Sonu; Dudchenko, Olga; Esvaran, Meera; Rosen, Benjamin D.; Skvortsova, Ksenia. (2022) The Australian dingo is an early offshoot of modern breed dogs. Science Advances
  Academic article
• Lin, Jianqing; Duchêne, David; Carøe, Christian; Smith, Oliver; Ciucani, Marta Maria; Niemann, Jonas. (2022) Probing the genomic limits of de-extinction in the Christmas Island rat. Current Biology
  Academic article
• Cerca, José; Petersen, Bent; Lazaro-Guevara, José Miguel; Rivera-Colón, Angel G.; Birkeland, Siri; Vizueta, Joel. (2022) The genomic basis of the plant island syndrome in Darwin’s giant daisies. Nature Communications
  Academic article
• de Ferran, Vera; Figueiró, Henrique Vieira; de Jesus Trindade, Fernanda; Smith, Oliver; Sinding, Mikkel Holger Strander; Trinca, Cristine S.. (2022) Phylogenomics of the world's otters. Current Biology
  Academic article
• Koziol, Adam; Odriozola, Iñaki; Nyholm, Lasse; Leonard, Aoife; San José, Carlos; Pauperio, Joana. (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
  Academic article
• Cole, Theresa L.; Zhou, Chengran; Fang, Miaoquan; Pan, Hailin; Ksepka, Daniel T.; Fiddaman, Steven R.. (2022) Genomic insights into the secondary aquatic transition of penguins. Nature Communications
  Academic article
• Patrono, Livia V.; Vrancken, Bram; Budt, Matthias; Düx, Ariane; Lequime, Sebastian; Boral, Sengül. (2022) Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic. Nature Communications
  Academic article
• Møbjerg, Ask; Kodama, Miyako; Ramos-Madrigal, Jazmín; Neves, Ricardo A. Cardoso; Jørgensen, Aslak; Schiøtt, Morten. (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
  Errata
• 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
  Errata
• Tous, Núria; Marcos, Sofia; Goodarzi Boroojeni, Farshad; Pérez de Rozas, Ana; Zentek, Jürgen; Estonba, Andone. (2022) Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics. Frontiers in Physiology
  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
  Academic article
• Formenti, Giulio; Theissinger, Kathrin; Fernandes, Carlos; Bista, Iliana; Bombarely, Aureliano; Bleidorn, Christoph. (2022) The era of reference genomes in conservation genomics. Trends in Ecology & Evolution
  Academic literature review
• Møbjerg, Ask; Kodama, Miyako; Ramos-Madrigal, Jazmín; Neves, Ricardo A. Cardoso; Jørgensen, Aslak; Schiøtt, Morten. (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
  Academic article
• Bieker, Vanessa Carina; Battlay, Paul; Petersen, Bent; Sun, Xin; Wilson, Jonathan; Brealey, Jaelle C.. (2022) Uncovering the genomic basis of an extraordinary plant invasion. Science Advances
  Academic article
• 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
  Academic article
• Rasmussen, Jacob Agerbo; Villumsen, Kasper Rømer; Ernst, Madeleine; Hansen, Martin; Forberg, Torunn; Gopalakrishnan, Shyam. (2022) A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss). Microbiome
  Academic article
• Jensen, Evelyn L.; Díez-del-Molino, David; Gilbert, Marcus Thomas Pius; Bertola, Laura D.; Borges, Filipa; Cubric-Curik, Vlatka. (2022) Ancient and historical DNA in conservation policy. Trends in Ecology & Evolution
  Academic literature review
• Lewin, Harris A.; Richards, Stephen; Aiden, Erez Lieberman; Allende, Miguel L.; Archibald, John M.; Bálint, Miklós. (2022) The Earth BioGenome Project 2020: Starting the clock. Proceedings of the National Academy of Sciences of the United States of America (PNAS)
  Academic literature review
• Gopalakrishnan, Shyam; Ebenesersdottir, S.Sunna; Lundstrøm, Inge K.C.; Turner-Walker, Gordon; Moore, Kristjan H.S.; Luisi, Pierre. (2022) The population genomic legacy of the second plague pandemic. Current Biology
  Academic article

2021

• Aizpurua, Ostaizka; Nyholm, Lasse; Morris, Evie; Chaverri, Gloriana; Herrera Montalvo, L. Gerardo; Flores-Martinez, José Juan. (2021) The role of the gut microbiota in the dietary niche expansion of fishing bats. Animal Microbiome
  Academic article
• Niemann, Jonas; Gopalakrishnan, Shyam; Yamaguchi, Nobuyuki; Ramos-Madrigal, Jazmín; Wales, Nathan; Gilbert, Marcus Thomas Pius. (2021) Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshū. iScience
  Academic article
• Rasmussen, Jacob A.; Villumsen, Kasper Rømer; Duchêne, David; Puetz, Lara; Delmont, Tom; Sveier, Harald. (2021) Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts. Communications Biology
  Academic article
• Agerbo Rasmussen, Jacob; Nielsen, Martin; Mak, Sarah Siu Tze; Döring, Johanna; Klincke, Franziska; Gopalakrishnan, Shyam. (2021) eDNA-based biomonitoring at an experimental German vineyard to characterize how management regimes shape ecosystem diversity. Environmental DNA
  Academic article
• Liu, Shanlin; Westbury, Michael V; Dussex, Nicolas; Mitchell, Kieren J.; Sinding, Mikkel-Holger S.; Heintzman, Peter D.. (2021) Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell
  Academic article
• von Seth, Johanna; Dussex, Nicolas; Díez-del-Molino, David; van der Valk, Tom; Kutschera, Verena E.; Kierczak, Marcin. (2021) Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations. Nature Communications
  Academic article
• Liu, Chang; Gao, Jianbo; Cui, Xinxin; Li, Zhipeng; Chen, Lei; Yuan, Yuan. (2021) A towering genome: Experimentally validated adaptations to high blood pressure and extreme stature in the giraffe. Science Advances
  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
• 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
  Academic article
• Cavill, Emily L.; Gopalakrishnan, Shyam; Puetz, Lara C.; Ribeiro, Ângela M.; Mak, Sarah S. T.; da Fonseca, Rute R.. (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
• Foote, Andrew; Hooper, Rebecca; Alexander, Alana; Baird, Robin; Baker, Charles Scott; Ballance, Lisa. (2021) Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Molecular Ecology
  Academic article
• Andrade, Pedro; Gazda, Małgorzata A.; Araújo, Pedro M.; Afonso, Sandra; Rasmussen, Jacob A.; Marques, Cristiana I.. (2021) Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates. PLoS Genetics
  Academic article
• Perri, Angela; Mitchell, Kieren J.; Mouton, Alice; Álvarez-Carretero, Sandra; Hulme-Beaman, Ardern; Haile, James. (2021) Dire wolves were the last of an ancient New World canid lineage. Nature
  Academic article
• Ciucani, Marta M.; Jensen, Julie Kragmose; Sinding, Mikkel-Holger S.; Smith, Oliver; Lucenti, Saverio Bartolini; Rosengren, Erika. (2021) Evolutionary history of the extinct Sardinian dhole. Current Biology
  Academic article
• Sinding, Mikkel-Holger S.; Ciucani, Marta M.; Ramos-Madrigal, Jazmín; Carmagnini, Alberto; Rasmussen, Jacob A.; Feng, Shaohong. (2021) Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos. iScience
  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
• 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
  Academic article
• Poliseno, Angelo; Altuna, Alvaro; Puetz, Lara; Mak, Sarah Siu Tze; Ríos, Pilar; Petroni, Emily. (2021) An integrated morphological-molecular approach reveals new insights on the systematics of the octocoral Telestula humilis (Thomson, 1927) (Octocorallia: Alcyonacea: Clavulariidae). Invertebrate systematics
  Academic article
• Stenøien, Hans K.; Sun, Xin; Martin, Michael David; Scharff-Olsen, Camilla Hjorth; Alonso, Germán Hernàndez; Martins, Nuno Filipe Gomes. (2021) Genetisk opphav til den norsksvenske ulvestammen (Canis lupus lupus). NTNU Vitenskapsmuseet naturhistorisk rapport (11)
  Report
• Westbury, Michael V; Barnett, Ross; Sandoval-Velasco, Marcela; Gower, Graham; Vieira, Filipe G.; de Manuel, Marc. (2021) A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives. Open Research Europe
  Academic article
• Feuerborn, Tatiana R.; Carmagnini, Alberto; Losey, Robert J.; Nomokonova, Tatiana; Askeyev, Arthur; Askeyev, Igor. (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 (PNAS)
  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
  Academic article
• Fromm, Bastian; Tarbier, Marcel; Smith, Oliver; Mármol-Sánchez, Emilio; Dalén, Love; Gilbert, Marcus Thomas Pius. (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
  Academic article
• Sánchez-Barreiro, Fátima; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; Westbury, Michael V.; de Manuel, Marc; Margaryan, Ashot. (2021) Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). Molecular Ecology
  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 (PNAS)
  Academic article
• Alfano, Niccolò; Dayaram, Anisha; Axtner, Jan; Tsangaras, Kyriakos; Kampmann, Marie-Louise; Mohamed, Azlan. (2021) Non-invasive surveys of mammalian viruses using environmental DNA. Methods in Ecology and Evolution
  Academic article
• Rhie, Arang; McCarthy, Shane A.; Fedrigo, Olivier; Damas, Joana; Formenti, Giulio; Koren, Sergey. (2021) Towards complete and error-free genome assemblies of all vertebrate species. Nature
  Academic article
• Margaryan, Ashot; Noer, Christina Lehmkuhl; Richter, Stine R.; Restrup, Marlene Elise; Bülow-Hansen, Julie Lee; Leerhøi, Frederik. (2021) Mitochondrial genomes of Danish vertebrate species generated for the national DNA reference database, DNAmark. Environmental DNA
  Academic article
• Bogaard, Amy; Allaby, Robin G.; Arbuckle, Benjamin; Bendrey, Robin; Crowley, Sarah; Cucchi, Thomas. (2021) Reconsidering domestication from a process archaeology perspective. World archaeology
  Academic article
• Foote, Andrew; Gilbert, Marcus Thomas Pius; Gopalakrishnan, Shyam; Louis, Marie; Martin, Michael David; Morin, Phillip A.. (2021) Evidence of long-term purging of mutation load in killer whale genomes. bioRxiv
  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
• Fontsere, Claudia; Frandsen, Peter; Hernandez-Rodriguez, Jessica; Niemann, Jonas; Scharff-Olsen, Camilla Hjorth; Vallet, Dominique. (2021) The genetic impact of an Ebola outbreak on a wild gorilla population. BMC Genomics
  Academic article
• Bergeron, Lucie A.; Besenbacher, Søren; Bakker, Jaco; Zheng, Jiao; Li, Panyi; Pacheco, George. (2021) The germline mutational process in rhesus macaque and its implications for phylogenetic dating. GigaScience
  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
  Academic article
• Feng, Shaohong; Stiller, Josefin; Deng, Yuan; Armstrong, Joel; Fang, Qi; Reeve, Andrew Hart. (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
  Errata
• 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
  Academic article

2020

• Pan, Hailin; Cole, Theresa L; Bi, Xupeng; Fang, Miaoquan; Zhou, Chengran; Yang, Zhengtao. (2020) Erratum: High-coverage genomes to elucidate the evolution of penguins (GigaScience (2019) 8:9 (giz117) DOI: 10.1093/gigascience/giz117). GigaScience
  Errata
• Frantz, Laurent A.F.; Haile, James; Lin, Audrey T.; Scheu, Amelie; Geörg, Christina; Benecke, Norbert. (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 (PNAS)
  Errata
• Margaryan, Ashot; Sinding, Mikkel Holger Strander; Shanlin, Liu; Vieira, Filipe Garrett; Chan, Yvonne L.; Nathan, Senthilvel K.S.S.. (2020) Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros. Zoological Journal of the Linnean Society
  Academic article
• Sandoval-Velasco, Marcela; Rodriguez, Juan Antonio; Estrada, Cynthia Perez; Zhang, Guojie; Aiden, Erez Lieberman; Marti-Renom, Marc A.. (2020) Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform. GigaScience
  Academic article
• Eriksen, Anne Marie Høier; Matthiesen, Henning; Kontopoulos, Ioannis; Gregory, David John; Snoeck, Christophe; Zhang, Guojie. (2020) Rapid loss of endogenous DNA in pig bone buried in five different environments. Archaeometry
  Academic literature review
• Drinkwater, Rosie; Jucker, Tommaso; Potter, Joshua H. T.; Swinfield, Tom; Coomes, D; Slade, Eleanor M.. (2020) Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats. Molecular Ecology
  Academic article
• Barnett, Ross; Westbury, Michael V; Sandoval-Velasco, Marcela; Vieira, Filipe G.; Jeon, Sungwon; Zazula, Grant. (2020) Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat, Homotherium latidens. Current Biology
  Academic article
• Fordham, Damien A.; Jackson, Stephen T.; Brown, Stuart C.; Huntley, Brian; Brook, Barry W.; Dahl-Jensen, Dorthe. (2020) Using paleo-archives to safeguard biodiversity under climate change. Science
  Academic literature review
• Da Fonseca, Rute R.; Couto, Alvarina; Machado, Andre M; Brejova, Brona; Albertin, Carolin B; Silva, Filipe. (2020) A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience
  Academic article
• Sinding, Mikkel Holger Strander; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; de Manuel, Marc; Pitulko, Vladimir V.; Kuderna, Lukas. (2020) Arctic-adapted dogs emerged at the Pleistocene–Holocene transition. Science
  Academic article
• Lord, Edana; Dussex, Nicolas; Kierczak, Marcin; Díez-del-Molino, David; Ryder, Oliver A.; Stanton, David W. G.. (2020) Pre-extinction demographic stability and genomic signatures of adaptation in the woolly rhinoceros. Current Biology
  Academic article
• de Manuel, Marc; Barnett, Ross; Sandoval-Velasco, Marcela; Yamaguchi, Nobuyuki; Vieira, Filipe G.; Lisandra Zepeda Mendoza, Zepeda. (2020) The evolutionary history of extinct and living lions. Proceedings of the National Academy of Sciences of the United States of America (PNAS)
  Academic literature review
• Alberdi, Antton; Razgour, Orly; Aizpurua, Ostaizka; Novella-Fernandez, Roberto; Aihartza, Joxerra; Budinski, Ivana. (2020) DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats. Nature Communications
  Academic article
• van Dorp, Lucy; Gelabert, Pere; Rieux, Adrien; De Manuel, Marc; De-Dios, Toni; Gopalakrishnan, Shyam. (2020) Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Molecular Biology and Evolution (MBE)
  Academic article
• Fotakis, Anna K.; Denham, Sean Dexter; Mackie, Meaghan; Orbegozo, Miren Iraeta; Mylopotamitaki, Dorothea; Gopalakrishnan, Shyam. (2020) Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. Philosophical Transactions of the Royal Society of London. Biological Sciences
  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)
  Academic article
• Margaryan, Ashot; Lawson, Daniel J.; Sikora, Martin; Racimo, Fernando; Rasmussen, Simon; Moltke, Ida. (2020) Population genomics of the Viking world. Nature
  Academic article
• Feng, Shaohong; Stiller, Josefin; Deng, Yuan; Armstrong, Joel; Fang, Qi; Reeve, Andrew Hart. (2020) Dense sampling of bird diversity increases power of comparative genomics. Nature
  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
  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
  Academic article
• Gelabert, Pere; Sandoval-Velasco, Marcela; Serres, Aitor; de Manuel, Marc; Renom, Pere; Margaryan, Ashot. (2020) Evolutionary history, genomic adaptation to toxic diet, and extinction of the Carolina parakeet. Current Biology
  Academic article
• Nyholm, Lasse; Koziol, Adam; Marcos, Sofia; Botnen, Amanda Bolt; Aizpurua, Ostaizka; Gopalakrishnan, Shyam. (2020) Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research. iScience
  Academic literature review
• Eriksen, Anne Marie Høier; Nielsen, Tue Kjærgaard; Matthiesen, Henning; Carøe, Christian; Hansen, Lars Hestbjerg; Gregory, David John. (2020) Bone biodeterioration—The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community. PLOS ONE
  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
  Academic article
• Lynggaard, Christina; Yu, Douglas W.; Oliveira, Guilherme; Caldeira, Cecilio F.; Ramos, Silvio J.; Ellegaard, Martin. (2020) DNA-Based Arthropod Diversity Assessment in Amazonian Iron Mine Lands Show Ecological Succession Towards Undisturbed Reference Sites. Frontiers in Ecology and Evolution
  Academic article
• 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)
  Academic article
• Ramos-Madrigal, Jazmín; Sinding, Mikkel Holger Strander; Carøe, Christian; Mak, Sarah Siu Tze; Niemann, Jonas; Samaniego Castruita, José A.. (2020) Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages. Current Biology
  Academic article

2019

• Ribeiro, Ângela M; Smit, Ben; Gilbert, Marcus Thomas Pius. (2019) 31° South: Dietary niche of an arid-zone endemic passerine. Environmental DNA
  Academic article
• Wales, Nathan; Akman, Melis; Watson, Ray H B; Sánchez Barreiro, Fatima; Smith, Bruce D; Gremillion, Kristen J. (2019) Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement. Evolutionary Applications
  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
  Academic article
• Jensen, Theis Zetner Trolle; Niemann, Jonas; Iversen, Katrine Højholt; Fotakis, Anna K.; Gopalakrishnan, Shyam; Vågene, Åshild J. (2019) A 5700 year-old human genome and oral microbiome from chewed birch pitch. Nature Communications
  Academic article
• Frantz, Laurent A.F.; Haile, James; Lin, Audrey T.; Scheu, Amelie; Geörg, Christina; Benecke, Norbert. (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 (PNAS)
  Academic article
• Pan, Hailin; Cole, Theresa L.; Bi, Xupeng; Fang, Miaoquan; Zhou, Chengran; Yang, Zhengtao. (2019) High-coverage genomes to elucidate the evolution of penguins. GigaScience
  Academic article
• Chen, Lei; Qiu, Qiang; Jiang, Yu; Wang, Kun; Lin, Zeshan; Li, Zhipeng. (2019) Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science
  Academic article
• Thomas, Jessica E.; Carvalho, Gary R.; Haile, James; Rawlence, Nicolas J.; Martin, Michael David; Ho, Simon Y.W.. (2019) Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. eLIFE
  Academic article
• Rey-Iglesia, Alba; Gopalakrishan, Shyam; Carøe, Christian; Alquezar-Planas, David E.; Ahlmann Nielsen, Anne; Röder, Timo. (2019) MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements. Molecular Ecology Resources
  Academic article
• Kieler, Ida Nordang; Osto, Melania; Hugentobler, Leoni; Puetz, Lara; Gilbert, Marcus Thomas Pius; Hansen, Torben. (2019) Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria. Scientific Reports
  Academic article
• Knapp, Michael; Thomas, Jessica E; Haile, James; Prost, Stefan; Ho, Simon YW; Dussex, Nicolas. (2019) Mitogenomic evidence of close relationships between New Zealand's extinct giant raptors and small-sized Australian sister-taxa. Molecular Phylogenetics and Evolution
  Academic article
• Alves, Joel M.; Carneiro, Miguel; Cheng, Jade Y.; de Matos, Ana Lemos; Rahman, Masmudur M.; Loog, Liisa. (2019) Parallel adaptation of rabbit populations to myxoma virus. Science
  Academic article
• De-Dios, Toni; van Dorp, Lucy; Gelabert, Pere; Carøe, Christian; Sandoval-Velasco, Marcela; Fregel, Rosa. (2019) Genetic affinities of an eradicated european plasmodium falciparum strain. Microbial Genomics
  Academic article
• Foote, Andrew D.; Martin, Michael David; Louis, Marie; Pacheco, George; Robertson, Kelly M.; Sinding, Mikkel-Holger. (2019) Killer whale genomes reveal a complex history of recurrent admixture and vicariance. Molecular Ecology
  Academic article
• Lin, Zeshan; Chen, Lei; Chen, Xianqing; Zhong, Yingbin; Yang, Yue; Xia, Wenhao. (2019) Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus). Science
  Academic article
• Smith, Oliver; Dunshea, Glenn; Sinding, Mikkel-Holger; Fedorov, Sergey; Germonpre, Mietje; Bocherens, Hervé. (2019) Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. PLoS Biology
  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
  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
  Academic literature review
• Cappellini, Enrico; Welker, Frido; Pandolfi, Luca; Ramos-Madrigal, Jazmín; Samodova, Diana; Rüther, Patrick L.. (2019) Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature
  Academic article
• Jones, Rhys; Velasco, Marcela Sandoval; Harris, Llinos G; Morgan, Sue; Temple, Mark; Ruddy, Michael C. (2019) Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies. Tuberculosis
  Academic article
• Feng, Shaohong; Fang, Qi; Barnett, Ross; Li, Caí; Han, Sojung; Kuhlwilm, Martin. (2019) The Genomic Footprints of the Fall and Recovery of the Crested Ibis. Current Biology
  Academic article
• Loog, Liisa; Thalmann, Olaf; Sinding, Mikkel Holger Strander; Schuenemann, Verena J.; Perri, Angela; Germonpré, Mietje. (2019) Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia. Molecular Ecology
  Academic article
• Ramos-Madrigal, Jazmín; Runge, Anne Kathrine Wiborg; Bouby, Laurent; Lacombe, Thierry; Samaniego Castruita, José Alfredo; Adam-Blondon, Anne-Francoise. (2019) Palaeogenomic insights into the origins of French grapevine diversity. Nature Plants
  Academic article
• Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Hulme-Beaman, Ardern; Lebrasseur, Ophélie. (2019) Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic. Proceedings of the Royal Society of London. Biological Sciences
  Academic article
• Sirén, Kimmo; Mak, Sarah Siu Tze; Melkonian, Chrats; Carøe, Christian; Swiegers, Jan Hendrik; Molenaar, Douwe. (2019) Taxonomic and functional characterization of the microbial community during spontaneous in vitro fermentation of riesling must. Frontiers in Microbiology
  Academic article
• Ribeiro, Angela; Puetz, Lara; Pattinson, Nicholas B; Dalén, Love; Deng, Yuan; Zhang, Guojie. (2019) 31° South: The physiology of adaptation to arid conditions in a passerine bird. Molecular Ecology
  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
  Academic article

2018

• Mak, Sarah Siu Tze; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger Strander. (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
  Errata
• Kodama, Miyako; Brinch-Pedersen, Henrik; Sharma, Shrikant; Holme, Inger B.; Joernsgaard, Bjarne; Dzhanfezova, Tsaneta. (2018) Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq. BMC Genomics
  Academic article
• Drinkwater, Rosie; Schnell, Ida Bærholm; Bohmann, Kristine; Bernard, Henry; Veron, Géraldine; Clare, Elizabeth. (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
• Schnell, Ida Bærholm; Bohmann, Kristine; Schultze, Sebastian E.; Richter, Stine R.; Murray, Daíthí C.; Sinding, Mikkel-Holger. (2018) Debugging diversity–a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool. Molecular Ecology Resources
  Academic article
• Zepeda Mendoza, M. Lisandra; Xiong, Zijun; Escalera-Zamudio, Marina; Runge, Anne Kathrine; Théze, Julien; Streicker, Daniel. (2018) Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. Nature Ecology and Evolution
  Academic article
• 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
  Academic literature review
• Kistler, Logan; Maezumi, S. Yoshi; de Souza, Jonas Gregorio; Przelomska, Natalia A.S.; Costa, Flaviane Malaquias; Smith, Oliver. (2018) Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science
  Academic article
• Zhou, Zhemin; Lundstrøm, Inge K. C.; Tran-Dien, Alicia; Duchêne, Sebastián; Alikhan, Nabil-Fareed; Sergeant, Martin J.. (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
• Gopalakrishnan, Shyam; Sinding, Mikkel Holger Strander; Ramos-Madrigal, Jazmín; Niemann, Jonas; Samaniego Castruita, Jose A.; Vieira, Filipe G.. (2018) Interspecific gene flow shaped the evolution of the genus Canis. Current Biology
  Academic article
• Sinding, Mikkel Holger Strander; Gopalakrishnan, Shyam; Vieira, Filipe G.; Samaniego, Jose A; Raundrup, Katrine; Heide Jørgensen, Mads Peter. (2018) Population genomics of grey wolves and wolf-like canids in North America . PLoS Genetics
  Academic article
• Bro-Jørgensen, Maiken Hemme; Carøe, Christian; Vieira, Filipe G.; Nestor, Sofia; Hallström, Ann; Gregersen, Kristian M.. (2018) Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull. Journal of Archaeological Science
  Academic article
• Holt, Carson; Campbell, Michael; Keays, David Anthony; Edelman, Nathaniel; Kapusta, Aurélie; Maclary, Emily. (2018) Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia). G3: Genes, Genomes, Genetics
  Academic article
• Bohmann, Kristine; Gopalakrishnan, Shyam; Nielsen, Martin; Bay Nielsen, Luisa dos Santos; Jones, Gareth; Streicker, Daniel G.. (2018) Using DNA metabarcoding for simultaneous inference ofcommon vampire bat diet and population structure. Molecular Ecology Resources
  Academic article
• Fietz, Katharina; Hintze, Christian O.R.; Skovrind, Mikkel; Nielsen, Tue Kjærgaard; Limborg, Morten; Krag, Marcus A.. (2018) Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species. Microbiome
  Academic article
• Alberdi, Antton; Aizpurua, Ostaizka; Bohmann, Kristine; Gopalakrishnan, Shyam; Lynggaard, Christina; Nielsen, Martin. (2018) Promises and pitfalls of using high-throughput sequencing for diet analysis. Molecular Ecology Resources
  Academic literature review
• Zepeda Mendoza, M. Lisandra; Roggenbuck, Michael; Manzano Vargas, Karla; Hestbjerg Hansen, Lars; Brunak, Søren; Gilbert, Marcus Thomas Pius. (2018) Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging. Acta Veterinaria Scandinavica (AVS)
  Academic article
• Hooper, Rebecca; Brealey, Jaelle C.; van der Valk, Tom; Alberdi, Antton; Durban, John; Fearnbach, Holly. (2018) Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. Molecular Ecology
  Academic article
• Barnett, Ross; Sinding, Mikkel Holger Strander; Vieira, Filipe G.; Mendoza, Marie Lisandra Zepeda; Bonnet, Matthieu; Araldi, Alessandro. (2018) No longer locally extinct? Tracing the origins of a lion (Panthera leo) living in Gabon. Conservation Genetics
  Academic article
• 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
  Academic article
• Carøe, Christian; Gopalakrishnan, Shyam; Vinner, Lasse; Mak, Sarah S.T.; Sinding, Mikkel Holger Strander; Samaniego, Jose A. (2018) Singe-tube library preparation for degraded DNA. Methods in Ecology and Evolution
  Academic article
• Leathlobhair, Máire Ní; Perri, Angela R.; Irving-Pease, Evan K.; Witt, Kelsey E.; Linderholm, Anna; Haile, James. (2018) The evolutionary history of dogs in the Americas. Science
  Academic article
• Ebenesersdóttir, Sigríður Sunna; Sandoval-Velasco, Marcela; Gunnarsdóttir, Ellen D.; Jagadeesan, Anuradha; Guðmundsdóttir, Valdís B.; Thordardóttir, Elísabet L.. (2018) Ancient genomes from Iceland reveal the making of a human population. Science
  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
  Academic article
• Aizpurua, Ostaizka; Budinski, Ivana; Georgiakakis, Panagiotis; Gopalakrishnan, Shyam; Ibañez, Carlos; Mata, Vanessa A.. (2018) Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding. Molecular Ecology
  Academic article
• Lewin, Harris A.; Robinson, Gene E.; Kress, W. John; Baker, William J.; Coddington, Jonathan; Crandall, Keith A.. (2018) Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences of the United States of America (PNAS)
  Academic literature review

2017

• 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
  Errata
• Murray, Gemma G.R.; Soares, André E.R.; Novak, Ben J.; Schaefer, Nathan K.; Cahill, James A.; Baker, Allan J.. (2017) Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science
  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
  Academic article
• Thomas, Jessica E; Carvalho, Gary R.; Haile, James; Martin, Michael David; Castruita, Jose A. Samaniego; Niemann, Jonas. (2017) An ‛Aukward’ tale: a genetic approach to discover the whereabouts of the last Great Auks. Genes
  Academic article
• Seki, Ryohei; Li, Caí; Fang, Qi; Hayashi, Shinichi; Egawa, Shiro; Hu, Jiang. (2017) Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. Nature Communications
  Academic article
• Grealy, Alicia; Phillips, Matthew; Miller, Gifford; Gilbert, Marcus Thomas Pius; Rouillard, Jean-Marie; Lambert, David. (2017) Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Molecular Phylogenetics and Evolution
  Academic article
• Bush, Alex; Sollmann, Rahel; Wilting, Andreas; Bohmann, Kristine; Cole, Beth; Balzter, Heiko. (2017) Connecting Earth observation to high-throughput biodiversity data. Nature Ecology and Evolution
  Academic literature review
• Paijmans, Johanna L. A.; Barnett, Ross; Gilbert, Marcus Thomas Pius; Zepeda-Mendoza, Marie Lisandra; Reumer, Jelle WF; de Vos, John. (2017) Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics. Current Biology
  Academic article
• Fortes-Lima, Cesar; Gessain, Antoine; Ruiz-Linares, Andres; Bortolini, Maria; Migot-Nabias, Florence; Bellis, Gil. (2017) Genome-wide ancestry and demographic history of African-descendant Maroon communities from French Guiana and Suriname. American Journal of Human Genetics
  Academic article
• Gilbert, Marcus Thomas Pius. (2017) Documenting DNA in the dust. Molecular Ecology
  Short communication
• Mak, Sarah S.T.; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger Strander. (2017) Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. GigaScience
  Academic article
• Salleh, Faezah Mohd; Ramos-Madrigal, Jazmín; Peñaloza, Fernando; Liu, Shanlin; Sinding, Mikkel Holger Strander; Patel, Riddhi P.. (2017) An expanded mammal mitogenome dataset from Southeast asia. GigaScience
  Academic article
• Liu, Yan-Hu; Wang, Lu; Xu, Tao; Guo, Xiaomin; Li, Yang; Yin, Ting-Ting. (2017) Whole-genome sequencing of African dogs provides insights into adaptations against tropical parasites. Molecular Biology and Evolution (MBE)
  Academic article
• 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
  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
  Academic article
• Gopalakrishnan, Shyam; Samaniego Castruita, José Alfredo; Sinding, Mikkel Holger Strander; Kuderna, Lukas FK; Räikkönen, Jannikke; Petersen, Bent. (2017) The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics. BMC Genomics
  Academic article
• Tanner, Alastair R; Fuchs, Dirk; Winkelmann, Inger E; Gilbert, Marcus Thomas Pius; Pankey, M Sabrina; Ribeiro, Angela. (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
  Academic article

2016

• Sinding, Mikkel Holger Strander; Gilbert, Marcus Thomas Pius. (2016) The draft genome of extinct european aurochs and its implications for de-extinction. Open Quaternary
  Academic article
• 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
  Academic literature review
• Richmond, Douglas J.; Sinding, Mikkel Holger Strander; Gilbert, Marcus Thomas Pius. (2016) The potential and pitfalls of de-extinction. Zoologica Scripta
  Academic literature review
• Wales, Nathan; Ramos Madrigal, Jazmín; Cappellini, Enrico; Carmona Baez, Aldo; Samaniego Castruita, José Alfredo; Romero-Navarro, J. Alberto. (2016) The limits and potential of paleogenomic techniques for reconstructing grapevine domestication. Journal of Archaeological Science
  Academic article
• Gelabert, Pere; Sandoval-Velasco, Marcela; Olalde, Iñigo; Fregel, Rosa; Rieux, Adrien; Escosa, Raül. (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 (PNAS)
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• Ramos-Madrigal, Jazmín; Smith, Bruce D; Moreno-Mayar, J Víctor; Gopalakrishnan, Shyam; Ross-Ibarra, Jeffrey; Gilbert, Marcus Thomas Pius. (2016) Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication. Current Biology
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• 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
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