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1. Clonal driver neoantigen loss under EGFR TKI and immune selection pressures

Author

Al Bakir, Maise, Reading, James L., Gamble, Samuel, Rosenthal, Rachel, Uddin, Imran, Rowan, Andrew, Przewrocka, Joanna, Rogers, Amber, Wong, Yien Ning Sophia, Bentzen, Amalie K., Veeriah, Selvaraju, Ward, Sophia, Garnett, Aaron T., Kalavakur, Paula, Martínez-Ruiz, Carlos, Puttick, Clare, Huebner, Ariana, Cook, Daniel E., Moore, David A., Abbosh, Chris, Hiley, Crispin T., Naceur-Lombardelli, Cristina, Watkins, Thomas B. K., Petkovic, Marina, Schwarz, Roland F., Gálvez-Cancino, Felipe, Litchfield, Kevin, Meldgaard, Peter, Sorensen, Boe Sandahl, Madsen, Line Bille, Jäger, Dirk, Forster, Martin D., Arkenau, Tobias, Domingo-Vila, Clara, Tree, Timothy I. M., Kadivar, Mohammad, Hadrup, Sine Reker, Chain, Benny, Quezada, Sergio A., McGranahan, Nicholas, and Swanton, Charles more...

Published
2025
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2. 100 ancient genomes show repeated population turnovers in Neolithic Denmark

Author

Allentoft, Morten E, Sikora, Martin, Fischer, Anders, Sjögren, Karl-Göran, Ingason, Andrés, Macleod, Ruairidh, Rosengren, Anders, Schulz Paulsson, Bettina, Jørkov, Marie Louise Schjellerup, Novosolov, Maria, Stenderup, Jesper, Price, T Douglas, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Sørensen, Lasse, Nielsen, Poul Otto, Rasmussen, Peter, Jensen, Theis Zetner Trolle, Refoyo-Martínez, Alba, Irving-Pease, Evan K, Barrie, William, Pearson, Alice, Sousa da Mota, Bárbara, Demeter, Fabrice, Henriksen, Rasmus A, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Johannsen, Niels Nørkjær, Ramsøe, Abigail Daisy, Schork, Andrew Joseph, Ruter, Anthony, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, Brinch Petersen, Erik, Kannegaard, Esben, Hansen, Jesper, Buck Pedersen, Kristoffer, Pedersen, Lisbeth, Klassen, Lutz, Meldgaard, Morten, Johansen, Morten, Uldum, Otto Christian, Lotz, Per, Lysdahl, Per, Bangsgaard, Pernille, Petersen, Peter Vang, Maring, Rikke, Iversen, Rune, Wåhlin, Sidsel, Anker Sørensen, Søren, Andersen, Søren H, Jørgensen, Thomas, Lynnerup, Niels, Lawson, Daniel J, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Kjær, Kurt H, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Kristiansen, Kristian, and Willerslev, Eske more...

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Archaeology, Historical Studies, Anthropology, Humans, Denmark, Emigrants and Immigrants, Genomics, Genotype, Scandinavians and Nordic People, Human Migration, Genome, Human, History, Ancient, Pollen, Diet, Hunting, Farmers, Culture, Phenotype, Datasets as Topic, General Science & Technology
Abstract

Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use. more...

Published
2024

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6. Population genomics of post-glacial western Eurasia

Author

Allentoft, Morten E., Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise Schjellerup, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis Zetner Trolle, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar-García, Domingo C., Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Brinch Petersen, Erik, Kannegaard, Esben, Radina, Francesca, Eylem Yediay, Fulya, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, de Barros Damgaard, Peter, Vang Petersen, Peter, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske more...

Published
2024
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9. Generating stable molecules using imitation and reinforcement learning

Author

Meldgaard, Søren Ager, Köhler, Jonas, Mortensen, Henrik Lund, Christiansen, Mads-Peter V., Noé, Frank, and Hammer, Bjørk

Subjects
Physics - Chemical Physics, Computer Science - Machine Learning
Abstract

Chemical space is routinely explored by machine learning methods to discover interesting molecules, before time-consuming experimental synthesizing is attempted. However, these methods often rely on a graph representation, ignoring 3D information necessary for determining the stability of the molecules. We propose a reinforcement learning approach for generating molecules in cartesian coordinates allowing for quantum chemical prediction of the stability. To improve sample-efficiency we learn basic chemical rules from imitation learning on the GDB-11 database to create an initial model applicable for all stoichiometries. We then deploy multiple copies of the model conditioned on a specific stoichiometry in a reinforcement learning setting. The models correctly identify low energy molecules in the database and produce novel isomers not found in the training set. Finally, we apply the model to larger molecules to show how reinforcement learning further refines the imitation learning model in domains far from the training data. more...

Published
2021

10. Partitioned Graph Convolution Using Adversarial and Regression Networks for Road Travel Speed Prediction

Author

Kjær, Jakob Meldgaard, Kristensen, Lasse, and Christensen, Mads Alberg

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Discrete Mathematics, 68T05, I.2.6, G.2.2
Abstract

Access to quality travel time information for roads in a road network has become increasingly important with the rising demand for real-time travel time estimation for paths within road networks. In the context of the Danish road network (DRN) dataset used in this paper, the data coverage is sparse and skewed towards arterial roads, with a coverage of 23.88% across 850,980 road segments, which makes travel time estimation difficult. Existing solutions for graph-based data processing often neglect the size of the graph, which is an apparent problem for road networks with a large amount of connected road segments. To this end, we propose a framework for predicting road segment travel speed histograms for dataless edges, based on a latent representation generated by an adversarially regularized convolutional network. We apply a partitioning algorithm to divide the graph into dense subgraphs, and then train a model for each subgraph to predict speed histograms for the nodes. The framework achieves an accuracy of 71.5% intersection and 78.5% correlation on predicting travel speed histograms using the DRN dataset. Furthermore, experiments show that partitioning the dataset into clusters increases the performance of the framework. Specifically, partitioning the road network dataset into 100 clusters, with approximately 500 road segments in each cluster, achieves a better performance than when using 10 and 20 clusters., Comment: This thesis was completed 2020-06-12 and defended 2020-06-26 more...

Published
2021

11. Kaggle forecasting competitions: An overlooked learning opportunity

Author

Bojer, Casper Solheim and Meldgaard, Jens Peder

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning, Statistics - Applications
Abstract

Competitions play an invaluable role in the field of forecasting, as exemplified through the recent M4 competition. The competition received attention from both academics and practitioners and sparked discussions around the representativeness of the data for business forecasting. Several competitions featuring real-life business forecasting tasks on the Kaggle platform has, however, been largely ignored by the academic community. We believe the learnings from these competitions have much to offer to the forecasting community and provide a review of the results from six Kaggle competitions. We find that most of the Kaggle datasets are characterized by higher intermittence and entropy than the M-competitions and that global ensemble models tend to outperform local single models. Furthermore, we find the strong performance of gradient boosted decision trees, increasing success of neural networks for forecasting, and a variety of techniques for adapting machine learning models to the forecasting task. more...

Published
2020
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12. Atomistic Structure Learning Algorithm with surrogate energy model relaxation

Author

Mortensen, Henrik Lund, Meldgaard, Søren Ager, Bisbo, Malthe Kjær, Christiansen, Mads-Peter V., and Hammer, Bjørk

Subjects
Condensed Matter - Materials Science, Computer Science - Machine Learning, Physics - Chemical Physics, Physics - Computational Physics
Abstract

The recently proposed Atomistic Structure Learning Algorithm (ASLA) builds on neural network enabled image recognition and reinforcement learning. It enables fully autonomous structure determination when used in combination with a first-principles total energy calculator, e.g. a density functional theory (DFT) program. To save on the computational requirements, ASLA utilizes the DFT program in a single-point mode, i.e. without allowing for relaxation of the structural candidates according to the force information at the DFT level. In this work, we augment ASLA to establish a surrogate energy model concurrently with its structure search. This enables approximative but computationally cheap relaxation of the structural candidates before the single-point energy evaluation with the computationally expensive DFT program. We demonstrate a significantly increased performance of ASLA for building benzene while utilizing a surrogate energy landscape. Further we apply this model-enhanced ASLA in a thorough investigation of the c(4x8) phase of the Ag(111) surface oxide. ASLA successfully identifies a surface reconstruction which has previously only been guessed on the basis of scanning tunnelling microscopy images. more...

Published
2020
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18. Publisher Correction: Population genomics of post-glacial western Eurasia

Author

Allentoft, Morten E., Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise Schjellerup, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis Zetner Trolle, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar-García, Domingo C., Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Brinch Petersen, Erik, Kannegaard, Esben, Radina, Francesca, Eylem Yediay, Fulya, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, de Barros Damgaard, Peter, Vang Petersen, Peter, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske more...

Published
2024
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19. Atomistic structure learning

Author

Jørgensen, Mathias S., Mortensen, Henrik L., Meldgaard, Søren A., Kolsbjerg, Esben L., Jacobsen, Thomas L., Sørensen, Knud H., and Hammer, Bjørk

Subjects
Condensed Matter - Materials Science, Computer Science - Machine Learning, Physics - Chemical Physics, Statistics - Machine Learning
Abstract

One endeavour of modern physical chemistry is to use bottom-up approaches to design materials and drugs with desired properties. Here we introduce an atomistic structure learning algorithm (ASLA) that utilizes a convolutional neural network to build 2D compounds and layered structures atom by atom. The algorithm takes no prior data or knowledge on atomic interactions but inquires a first-principles quantum mechanical program for physical properties. Using reinforcement learning, the algorithm accumulates knowledge of chemical compound space for a given number and type of atoms and stores this in the neural network, ultimately learning the blueprint for the optimal structural arrangement of the atoms for a given target property. ASLA is demonstrated to work on diverse problems, including grain boundaries in graphene sheets, organic compound formation and a surface oxide structure. This approach to structure prediction is a first step toward direct manipulation of atoms with artificially intelligent first principles computer codes. more...

Published
2019
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21. Machine learning enhanced global optimization by clustering local environments to enable bundled atomic energies

Author

Meldgaard, Søren A., Kolsbjerg, Esben L., and Hammer, Bjørk

Subjects
Physics - Computational Physics
Abstract

We show how to speed up global optimization of molecular structures using machine learning methods. To represent the molecular structures we introduce the auto-bag feature vector that combines: i) a local feature vector for each atom, ii) an unsupervised clustering of such feature vectors for many atoms across several structures, and iii) a count for a given structure of how many times each cluster is represented. During subsequent global optimization searches, accumulated structure-energy relations of relaxed structural candidates are used to assign local energies to each atom using supervised learning. Specifically, the local energies follow from assigning energies to each cluster of local feature vectors and demanding the sum of local energies to amount to the structural energies in the least squares sense. The usefulness of the method is demonstrated in basin hopping searches for 19-atom structures described by single- or double-well Lennard- Jones type potentials and for 24-atom carbon structures described by density functional theory (DFT). In all cases, utilizing the local energy information derived on-the-fly enhances the rate at which the global minimum energy structure is found. more...

Published
2018
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22. Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic

Author

Ameen, Carly, Feuerborn, Tatiana R, Brown, Sarah K, Linderholm, Anna, Hulme-Beaman, Ardern, Lebrasseur, Ophélie, Sinding, Mikkel-Holger S, Lounsberry, Zachary T, Lin, Audrey T, Appelt, Martin, Bachmann, Lutz, Betts, Matthew, Britton, Kate, Darwent, John, Dietz, Rune, Fredholm, Merete, Gopalakrishnan, Shyam, Goriunova, Olga I, Grønnow, Bjarne, Haile, James, Hallsson, Jón Hallsteinn, Harrison, Ramona, Heide-Jørgensen, Mads Peter, Knecht, Rick, Losey, Robert J, Masson-MacLean, Edouard, McGovern, Thomas H, McManus-Fry, Ellen, Meldgaard, Morten, Midtdal, Åslaug, Moss, Madonna L, Nikitin, Iurii G, Nomokonova, Tatiana, Pálsdóttir, Albína Hulda, Perri, Angela, Popov, Aleksandr N, Rankin, Lisa, Reuther, Joshua D, Sablin, Mikhail, Schmidt, Anne Lisbeth, Shirar, Scott, Smiarowski, Konrad, Sonne, Christian, Stiner, Mary C, Vasyukov, Mitya, West, Catherine F, Ween, Gro Birgit, Wennerberg, Sanne Eline, Wiig, Øystein, Woollett, James, Dalén, Love, Hansen, Anders J, Gilbert, M Thomas P, Sacks, Benjamin N, Frantz, Laurent, Larson, Greger, Dobney, Keith, Darwent, Christyann M, and Evin, Allowen more...

Subjects
Biological Sciences, Genetics, Alaska, Animal Distribution, Animals, Archaeology, Arctic Regions, Canada, DNA, Ancient, DNA, Mitochondrial, Dogs, Genome, Mitochondrial, Greenland, Human Migration, Phenotype, archaeology, geometric morphometrics, ancient DNA, migration, Canis lupus familiaris, circumpolar, Agricultural and Veterinary Sciences, Medical and Health Sciences, Agricultural, veterinary and food sciences, Biological sciences, Environmental sciences
Abstract

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP. more...

Published
2019

23. The population history of northeastern Siberia since the Pleistocene

Author

Sikora, Martin, Pitulko, Vladimir V, Sousa, Vitor C, Allentoft, Morten E, Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A, Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V, Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y, Chasnyk, Vyacheslav G, Nikolskiy, Pavel A, Gromov, Andrei V, Khartanovich, Valeriy I, Moiseyev, Vyacheslav, Grebenyuk, Pavel S, Fedorchenko, Alexander Yu, Lebedintsev, Alexander I, Slobodin, Sergey B, Malyarchuk, Boris A, Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U, Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S, Sjögren, Karl-Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J, Excoffier, Laurent, and Willerslev, Eske more...

Subjects
Asia, DNA, Ancient, Europe, Gene Pool, Genome, Human, Haplotypes, History, 15th Century, History, Ancient, History, Medieval, Human Migration, Humans, Indians, North American, Male, Siberia, General Science & Technology
Abstract

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas. more...

Published
2019

24. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk

Author

Thomas, Jessica E, Carvalho, Gary R, Haile, James, Rawlence, Nicolas J, Martin, Michael D, Ho, Simon YW, 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 ER, Lacy, Robert, Barilaro, Christina, Best, Juila, Brandis, Dirk, Cavallo, Chiara, Elorza, Mikelo, Garrett, Kimball L, Groot, Maaike, Johansson, Friederike, Lifjeld, Jan T, Nilson, Göran, Serjeanston, Dale, Sweet, Paul, Fuller, Errol, Hufthammer, Anne Karin, Meldgaard, Morten, Fjeldså, Jon, Shapiro, Beth, Hofreiter, Michael, Stewart, John R, Gilbert, M Thomas P, and Knapp, Michael more...

Subjects
Biological Sciences, Ecology, Genetics, Life on Land, Animals, Charadriiformes, DNA, Ancient, DNA, Mitochondrial, Extinction, Biological, Genetic Variation, Genome, Mitochondrial, Humans, Phylogeny, Population Dynamics, 19th century extinction, ancient DNA, evolutionary biology, genetics, genomics, hunting, paleogenetics, seabird exploitation, Biochemistry and Cell Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation. more...

Published
2019

28. Prepregnancy and Gestational Interventions to Prevent Childhood Obesity

Author

Kampmann, Ulla, Suder, Louise Birk, Nygaard, Malene, Geiker, Nina Rica Wium, Nielsen, Henriette Svarre, Almstrup, Kristian, Bruun, Jens Meldgaard, Magkos, Faidon, Ovesen, Per, and Catalano, Patrick

Abstract

Childhood obesity is a significant global health issue with complex and multifactorial origins, often beginning before conception and influenced by both maternal and paternal health. The increased prevalence of prepregnancy obesity and gestational diabetes mellitus in women of reproductive age contributes to a heightened risk of metabolic dysfunction in offspring. Current clinical practices often implement lifestyle interventions after the first trimester and have limited success, implying that they miss a critical window for effective metabolic adjustments. This review examines the limitations of lifestyle interventions during pregnancy in improving perinatal outcomes and highlights the importance of initiating such interventions before conception to positively impact parental health and fetal development. A re-evaluation of strategies is needed to enhance the metabolic health of prospective parents as a preventive measure against childhood obesity. more...

Published
2025
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31. Clinical impact of clonal hematopoiesis in patients with lymphoma undergoing ASCT: a national population-based cohort study

Author

Husby, Simon, Favero, Francesco, Nielsen, Christian, Sørensen, Betina S., Bæch, John, Grell, Kathrine, Hansen, Jakob W., Rodriguez-Gonzalez, Francisco G., Haastrup, Eva K., Fischer-Nielsen, Anne, Andersen, Pernille, Arboe, Bente, Sækmose, Susanne G., Hansen, Per B., Christiansen, Ilse, Clasen-Linde, Erik, Meldgaard, Lene, Ebbesen, Lene H., Segel, Erik K., Josefsson, Pär, Thorsgaard, Michael, El-Galaly, Tarec C., Brown, Peter, Weischenfeldt, Joachim, Larsen, Thomas S., and Grønbæk, Kirsten more...

Published
2020
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34. The genetic prehistory of the New World Arctic

Author

Raghavan, Maanasa, DeGiorgio, Michael, Albrechtsen, Anders, Moltke, Ida, Skoglund, Pontus, Korneliussen, Thorfinn S, Grønnow, Bjarne, Appelt, Martin, Gulløv, Hans Christian, Friesen, T Max, Fitzhugh, William, Malmström, Helena, Rasmussen, Simon, Olsen, Jesper, Melchior, Linea, Fuller, Benjamin T, Fahrni, Simon M, Stafford, Thomas, Grimes, Vaughan, Renouf, MA Priscilla, Cybulski, Jerome, Lynnerup, Niels, Lahr, Marta Mirazon, Britton, Kate, Knecht, Rick, Arneborg, Jette, Metspalu, Mait, Cornejo, Omar E, Malaspinas, Anna-Sapfo, Wang, Yong, Rasmussen, Morten, Raghavan, Vibha, Hansen, Thomas VO, Khusnutdinova, Elza, Pierre, Tracey, Dneprovsky, Kirill, Andreasen, Claus, Lange, Hans, Hayes, M Geoffrey, Coltrain, Joan, Spitsyn, Victor A, Götherström, Anders, Orlando, Ludovic, Kivisild, Toomas, Villems, Richard, Crawford, Michael H, Nielsen, Finn C, Dissing, Jørgen, Heinemeier, Jan, Meldgaard, Morten, Bustamante, Carlos, O'Rourke, Dennis H, Jakobsson, Mattias, Gilbert, M Thomas P, Nielsen, Rasmus, and Willerslev, Eske more...

Subjects
Genetics, Alaska, Arctic Regions, Base Sequence, Bone and Bones, Canada, DNA, Mitochondrial, Genome, Human, Greenland, Hair, History, Ancient, Human Migration, Humans, Inuit, Molecular Sequence Data, Siberia, Survivors, Tooth, General Science & Technology
Abstract

The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago. more...

Published
2014

35. Growth differentiation factor 15 (GDF15) levels are associated with malnutrition in acutely admitted older adults.

Author

Nielsen, Rikke Lundsgaard, Bornæs, Olivia, Iversen, Esben, Strejby Christensen, Louise Westberg, Kallemose, Thomas, Jawad, Baker, Rasmussen, Henrik Højgaard, Munk, Tina, Lund, Trine Meldgaard, Andersen, Ove, Houlind, Morten Baltzer, Leegaard Andersen, Aino, and Tavenier, Juliette more...

Abstract

The aging process is often accompanied by high risk of malnutrition and elevated levels of growth differentiation factor 15 (GDF15). GDF15 is an increasingly recognized biomarker for regulation of metabolism, but few studies have investigated the connection between GDF15 and malnutrition in older age and how it relates to other features of aging such as decreased appetite and physical function. Therefore, we investigated the associations between GDF15 levels and nutritional status, appetite, and physical function in acutely admitted older adults. Plasma GDF15 levels were measured using immunoassays in 302 older adults (≥65 years) admitted to the emergency department (ED). Nutritional status was evaluated with the Mini Nutritional Assessment Short-Form (MNA®-SF), appetite was evaluated with the Simplified Nutritional Appetite Questionnaire (SNAQ), and physical function was evaluated with handgrip strength (HGS), 30-s chair stand test (30s-RSS), and gait speed (GS). Associations between GDF15 and each outcome was determined by logistic regression adjusted for age, sex, and C-reactive protein (CRP). Each doubling in plasma GDF15 level was associated with an adjusted odds ratio (OR) (95% confidence interval) of 1.59 (1.10–2.29, P = 0.01) for risk of malnutrition compared to normal nutrition and 1.19 (0.85–1.69, P = 0.3)) for malnutrition compared to risk of malnutrition. Each doubling in GDF15 was associated with an adjusted OR of 1.63 (1.21–2.23)) for having poor appetite, 1.46 (1.07–1.99) for having low HGS, 1.74 (1.23–2.51) for having low 30s-RSS, and 1.99 (1.39–2.94) for having low GS. Among older adults admitted to the ED, higher GDF15 levels were significantly associated with malnutrition, poor appetite, and low physical function independent of age, sex, and CRP. [ABSTRACT FROM AUTHOR] more...

Published
2024
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36. Prevalence and clinical association of gene mutations through multiplex mutation testing in patients with NSCLC: results from the ETOP Lungscape Project

Author

Kerr, K.M., Dafni, U., Schulze, K., Thunnissen, E., Bubendorf, L., Hager, H., Finn, S., Biernat, W., Vliegen, L., Losa, J.H., Marchetti, A., Cheney, R., Warth, A., Speel, E.-J., Blackhall, F., Monkhorst, K., Jantus Lewintre, E., Tischler, V., Clark, C., Bertran-Alamillo, J., Meldgaard, P., Gately, K., Wrona, A., Vandenberghe, P., Felip, E., De Luca, G., Savic, S., Muley, T., Smit, E.F., Dingemans, A.-M.C., Priest, L., Baas, P., Camps, C., Weder, W., Polydoropoulou, V., Geiger, T.R., Kammler, R., Sumiyoshi, T., Molina, M.A., Shames, D.S., Stahel, R.A., and Peters, S. more...

Published
2018
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41. Long-term changes in eating-related problems and quality of life in children with overweight and obesity attending a 10-week lifestyle camp.

Author

Jakobsen, Dorthe Dalstrup, Järvholm, Kajsa, Brader, Lea, and Bruun, Jens Meldgaard

Subjects
WEIGHT loss, SELF-evaluation, BULIMIA, BEHAVIOR modification, QUESTIONNAIRES, PROBABILITY theory, LONELINESS, DESCRIPTIVE statistics, RELATIVE medical risk, CHI-squared test, HYPERPHAGIA, HEALTH behavior, QUALITY of life, CHILDHOOD obesity, HEALTH promotion, CONFIDENCE intervals, PATIENT aftercare, SOCIAL problems, CHILDREN
Abstract

Eating-related problems (e.g., binge eating (BE)) and impaired quality of life (QoL) is more prevalent in children with overweight and obesity. This study aimed to investigate changes in self-reported overeating (OE), BE, and QoL in children with overweight or obesity attending multicomponent 10-week lifestyle camps with a 52-weeks follow-up. Additionally, the study sought to investigate whether self-reported OE/BE before camp was associated with changes in QoL. Children aged 7 to 14-years could attend camp if they had overweight/obesity, were lonely, unhappy, or had social or family-related problems. In this study only children with overweight and obesity were included (n:185). OE, BE, and QoL were measured using self-reported questionnaires. In total, 38 % of the children reported regular BE at baseline. Regular OE, occasional BE, and occasional OE was reported by 14 %, 13 %, and 11 %, respectively, while 24 % reported no eating-related problems. The relative risk of experiencing eating-related problems decreased at 10-weeks compared to baseline. Additionally, the probability of regular OE (RR 0.12 (95 % CI 0.04;0.38) (X2 = 8.44, p = 0.004)) and regular BE (RR 0.01 (95 % CI 0.00;0.11) (X2 = 9.91, p = 0.002)) remained lower at 52-weeks relative to baseline. All QoL dimensions improved after camp, and the presence of self-reported OE and regular BE at baseline was significantly associated with lower QoL at baseline, 10 and 52-weeks. Children self-reporting OE and BE may be a particular vulnerable group that needs more support from camp staff and healthcare professionals to improve QoL. clinicaltrials.gov with ID: NCT04522921 [ABSTRACT FROM AUTHOR] more...

Published
2024
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48. Risk and Timing of Venous Thromboembolism After Surgery for Lung Cancer: A Nationwide Cohort Study.

Author

Mørkved, Amalie Lambert, Søgaard, Mette, Skjøth, Flemming, Ording, Anne Gulbech, Jensen, Martin, Larsen, Torben Bjerregaard, Jakobsen, Erik, Højen, Anette Arbjerg, Noble, Simon, Meldgaard, Peter, Petersen, Rene Horsleben, and Christensen, Thomas Decker more...

Abstract

Venous thromboembolism (VTE) is a potentially preventable serious complication in patients with lung cancer undergoing thoracic operation. We examined the risk and timing of VTE after surgery for primary non-small cell lung cancer (NSCLC). All patients undergoing operation for NSCLC in Denmark between 2003 and 2021 were identified in the Danish Lung Cancer Registry. VTE events in the year after operation were assessed by stage, patient characteristics, and surgical procedure. We identified 13,197 patients who underwent operation for NSCLC in 2003 to 2021 (mean age, 67.6 years; 50% female); 10,524 (79.7%) had stage I-II NSCLC, and 2673 (20.3%) had stage III-IV. During 1-year follow-up, there were 335 VTE events, yielding a rate of 2.87 events/100 person-years and an absolute risk of 3.3% (95% CI, 2.3-4.0). VTE risk increased with advancing cancer stage (1.8% for stage I vs 3.9% for stage IV) but varied little by pathologic type, sex, and comorbidity level. Bilobectomy was associated with highest VTE risk (4.8%; 95% CI, 3.2-6.9), followed by pneumonectomy (3.5%; 95% CI, 2.3-5.0). The hazard of VTE was highest during the first 3 months after operation, after which it declined. For stage IV cancer, hazards increased again after 6 months. At 1 year, all-cause death was 12.6% (95% CI, 12.0%-13.1%). VTE developed in 3.3% of patients undergoing operation for NSCLC, most commonly within 3 months postoperatively. Prolonged thromboprophylaxis could be considered, particularly in those with advanced cancer stage and undergoing extended resections. [Display omitted] [ABSTRACT FROM AUTHOR] more...

Published
2024
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