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3,635 results on '"Gilbert A."'

1. IFITM proteins assist cellular uptake of diverse linked chemotypes

Author

Lou, Kevin, Wassarman, Douglas R, Yang, Tangpo, Paung, YiTing, Zhang, Ziyang, O'Loughlin, Thomas A, Moore, Megan K, Egan, Regina K, Greninger, Patricia, Benes, Cyril H, Seeliger, Markus A, Taunton, Jack, Gilbert, Luke A, and Shokat, Kevan M

Subjects
Biochemistry and Cell Biology, Medicinal and Biomolecular Chemistry, Chemical Sciences, Biological Sciences, Biotechnology, 5.1 Pharmaceuticals, General Science & Technology
Abstract

The search for cell-permeable drugs has conventionally focused on low-molecular weight (MW), nonpolar, rigid chemical structures. However, emerging therapeutic strategies break traditional drug design rules by employing flexibly linked chemical entities composed of more than one ligand. Using complementary genome-scale chemical-genetic approaches we identified an endogenous chemical uptake pathway involving interferon-induced transmembrane proteins (IFITMs) that modulates the cell permeability of a prototypical biopic inhibitor of MTOR (RapaLink-1, MW: 1784 g/mol). We devised additional linked inhibitors targeting BCR-ABL1 (DasatiLink-1, MW: 1518 g/mol) and EIF4A1 (BisRoc-1, MW: 1466 g/mol), uptake of which was facilitated by IFITMs. We also found that IFITMs moderately assisted some proteolysis-targeting chimeras and examined the physicochemical requirements for involvement of this uptake pathway.

Published
2022

2. Discovery of davemaoite, CaSiO3-perovskite, as a mineral from the lower mantle

Author

Tschauner, Oliver, Huang, Shichun, Yang, Shuying, Humayun, Munir, Liu, Wenjun, Gilbert Corder, Stephanie N, Bechtel, Hans A, Tischler, Jon, and Rossman, George R

Subjects
Earth Sciences, Geology, Geophysics, General Science & Technology
Abstract

Calcium silicate perovskite, CaSiO3, is arguably the most geochemically important phase in the lower mantle, because it concentrates elements that are incompatible in the upper mantle, including the heat-generating elements thorium and uranium, which have half-lives longer than the geologic history of Earth. We report CaSiO3-perovskite as an approved mineral (IMA2020-012a) with the name davemaoite. The natural specimen of davemaoite proves the existence of compositional heterogeneity within the lower mantle. Our observations indicate that davemaoite also hosts potassium in addition to uranium and thorium in its structure. Hence, the regional and global abundances of davemaoite influence the heat budget of the deep mantle, where the mineral is thermodynamically stable.

Published
2021

3. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Author

Hufford, Matthew B, Seetharam, Arun S, Woodhouse, Margaret R, Chougule, Kapeel M, Ou, Shujun, Liu, Jianing, Ricci, William A, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher I, Marand, Alexandre P, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K, Piri, Rebecca D, Wang, Na, Kim, Dong Won, Zeng, Yibing, O'Connor, Christine H, Li, Xianran, Gilbert, Amanda M, Baggs, Erin, Krasileva, Ksenia V, Portwood, John L, Cannon, Ethalinda KS, Andorf, Carson M, Manchanda, Nancy, Snodgrass, Samantha J, Hufnagel, David E, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L, Kudrna, David A, Llaca, Victor, Fengler, Kevin, Schmitz, Robert J, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I, Hirsch, Candice N, Ware, Doreen, and Dawe, R Kelly

Subjects
Genetics, Human Genome, Centromere, Chromosome Mapping, Chromosomes, Plant, DNA Methylation, Disease Resistance, Genes, Plant, Genetic Variation, Genome, Plant, Genotype, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Multifactorial Inheritance, Phenotype, Plant Diseases, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid, Sequence Analysis, DNA, Tetraploidy, Transcriptome, Whole Genome Sequencing, Zea mays, General Science & Technology
Abstract

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

Published
2021

4. Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

Author

Norman, Thomas M, Horlbeck, Max A, Replogle, Joseph M, Ge, Alex Y, Xu, Albert, Jost, Marco, Gilbert, Luke A, and Weissman, Jonathan S

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Cancer, Human Genome, Machine Learning and Artificial Intelligence, Genetics, Cancer Genomics, Biotechnology, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Apoptosis, CRISPR-Cas Systems, Calcium-Binding Proteins, Cell Cycle Checkpoints, Cell Line, Tumor, Epistasis, Genetic, Erythroid Cells, Erythropoiesis, Female, Gene Expression Profiling, Granulocytes, Humans, Microfilament Proteins, Proto-Oncogene Proteins c-cbl, Sequence Analysis, RNA, Single-Cell Analysis, Calponins, General Science & Technology
Abstract

How cellular and organismal complexity emerges from combinatorial expression of genes is a central question in biology. High-content phenotyping approaches such as Perturb-seq (single-cell RNA-sequencing pooled CRISPR screens) present an opportunity for exploring such genetic interactions (GIs) at scale. Here, we present an analytical framework for interpreting high-dimensional landscapes of cell states (manifolds) constructed from transcriptional phenotypes. We applied this approach to Perturb-seq profiling of strong GIs mined from a growth-based, gain-of-function GI map. Exploration of this manifold enabled ordering of regulatory pathways, principled classification of GIs (e.g., identifying suppressors), and mechanistic elucidation of synergistic interactions, including an unexpected synergy between CBL and CNN1 driving erythroid differentiation. Finally, we applied recommender system machine learning to predict interactions, facilitating exploration of vastly larger GI manifolds.

Published
2019

5. Parallel adaptation of rabbit populations to myxoma virus.

Author

Alves, Joel, Carneiro, Miguel, Cheng, Jade, Lemos de Matos, Ana, Rahman, Masmudur, Loog, Liisa, Campos, Paula, Wales, Nathan, Eriksson, Anders, Manica, Andrea, Strive, Tanja, Graham, Stephen, Afonso, Sandra, Bell, Diana, Belmont, Laura, Day, Jonathan, Fuller, Susan, Marchandeau, Stéphane, Palmer, William, Queney, Guillaume, Surridge, Alison, Vieira, Filipe, McFadden, Grant, Gilbert, M, Esteves, Pedro, Ferrand, Nuno, Jiggins, Francis, and Nielsen, Rasmus

Subjects
Adaptation, Biological, Alleles, Animals, Australia, Evolution, Molecular, France, Gene Frequency, Genetic Variation, Immunity, Innate, Interferon alpha-2, Myxoma virus, Myxomatosis, Infectious, Polymorphism, Single Nucleotide, Population, Rabbits, United Kingdom
Abstract

In the 1950s the myxoma virus was released into European rabbit populations in Australia and Europe, decimating populations and resulting in the rapid evolution of resistance. We investigated the genetic basis of resistance by comparing the exomes of rabbits collected before and after the pandemic. We found a strong pattern of parallel evolution, with selection on standing genetic variation favoring the same alleles in Australia, France, and the United Kingdom. Many of these changes occurred in immunity-related genes, supporting a polygenic basis of resistance. We experimentally validated the role of several genes in viral replication and showed that selection acting on an interferon protein has increased the proteins antiviral effect.

Published
2019

7. A hydrated crystalline calcium carbonate phase: Calcium carbonate hemihydrate

Author

Zou, Zhaoyong, Habraken, Wouter JEM, Matveeva, Galina, Jensen, Anders CS, Bertinetti, Luca, Hood, Matthew A, Sun, Chang-Yu, Gilbert, Pupa UPA, Polishchuk, Iryna, Pokroy, Boaz, Mahamid, Julia, Politi, Yael, Weiner, Steve, Werner, Peter, Bette, Sebastian, Dinnebier, Robert, Kolb, Ute, Zolotoyabko, Emil, and Fratzl, Peter

Subjects
Earth Sciences, Built Environment and Design, Building, General Science & Technology
Abstract

As one of the most abundant materials in the world, calcium carbonate, CaCO3, is the main constituent of the skeletons and shells of various marine organisms. It is used in the cement industry and plays a crucial role in the global carbon cycle and formation of sedimentary rocks. For more than a century, only three polymorphs of pure CaCO3-calcite, aragonite, and vaterite-were known to exist at ambient conditions, as well as two hydrated crystal phases, monohydrocalcite (CaCO3·1H2O) and ikaite (CaCO3·6H2O). While investigating the role of magnesium ions in crystallization pathways of amorphous calcium carbonate, we unexpectedly discovered an unknown crystalline phase, hemihydrate CaCO3·½H2O, with monoclinic structure. This discovery may have important implications in biomineralization, geology, and industrial processes based on hydration of CaCO3.

Published
2019

8. Toward unrestricted use of public genomic data

Author

Amann, Rudolf I, Baichoo, Shakuntala, Blencowe, Benjamin J, Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick SG, Colwell, Rita R, Daffonchio, Daniele G, Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C, Finn, Robert D, Fraser, Claire M, Gilbert, Jack A, Hallam, Steven J, Hugenholtz, Philip, Ioannidis, John PA, Jansson, Janet K, Kim, Jihyun F, Klenk, Hans-Peter, Klotz, Martin G, Knight, Rob, Konstantinidis, Konstantinos T, Kyrpides, Nikos C, Mason, Christopher E, McHardy, Alice C, Meyer, Folker, Ouzounis, Christos A, Patrinos, Aristides AN, Podar, Mircea, Pollard, Katherine S, Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J, Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D, Schriml, Lynn M, Setubal, João C, Sorek, Rotem, Stevens, Rick L, Tiedje, James M, Turjanski, Adrian, Tyson, Gene W, Ussery, David W, Weinstock, George M, White, Owen, Whitman, William B, and Xenarios, Ioannis

Subjects
Information and Computing Sciences, Law and Legal Studies, Library and Information Studies, Access to Information, Databases, Genetic, Genome, Human, Genomics, Humans, Information Dissemination, General Science & Technology
Abstract

Publication interests should not limit access to public data

Published
2019

9. Insulator-metal transition in dense fluid deuterium

Author

Celliers, Peter M, Millot, Marius, Brygoo, Stephanie, McWilliams, R. Stewart, Fratanduono, Dayne E, Rygg, J. Ryan, Goncharov, Alexander F, Loubeyre, Paul, Eggert, Jon H, Peterson, J. Luc, Meezan, Nathan B, Le Pape, Sebastien, Collins, Gilbert W, Jeanloz, Raymond, and Hemley, Russell J

Published
2018

10. Coherently aligned nanoparticles within a biogenic single crystal: A biological prestressing strategy

Author

Polishchuk, Iryna, Bracha, Avigail Aronhime, Bloch, Leonid, Levy, Davide, Kozachkevich, Stas, Etinger-Geller, Yael, Kauffmann, Yaron, Burghammer, Manfred, Giacobbe, Carlotta, Villanova, Julie, Hendler, Gordon, Sun, Chang-Yu, Giuffre, Anthony J, Marcus, Matthew A, Kundanati, Lakshminath, Zaslansky, Paul, Pugno, Nicola M, Gilbert, Pupa UPA, Katsman, Alex, and Pokroy, Boaz

Subjects
Engineering, Materials Engineering, Nanotechnology, Bioengineering, Animals, Biological Products, Calcium Carbonate, Crystallization, Echinodermata, Magnesium, Nanoparticles, Stress, Mechanical, General Science & Technology
Abstract

In contrast to synthetic materials, materials produced by organisms are formed in ambient conditions and with a limited selection of elements. Nevertheless, living organisms reveal elegant strategies for achieving specific functions, ranging from skeletal support to mastication, from sensors and defensive tools to optical function. Using state-of-the-art characterization techniques, we present a biostrategy for strengthening and toughening the otherwise brittle calcite optical lenses found in the brittlestar Ophiocoma wendtii This intriguing process uses coherent nanoprecipitates to induce compressive stresses on the host matrix, functionally resembling the Guinier-Preston zones known in classical metallurgy. We believe that these calcitic nanoparticles, being rich in magnesium, segregate during or just after transformation from amorphous to crystalline phase, similarly to segregation behavior from a supersaturated quenched alloy.

Published
2017

11. Ancient genomes from Iceland reveal the making of a human population

Author

Ebenesersdóttir, S. Sunna, Sandoval-Velasco, Marcela, Gunnarsdóttir, Ellen D., Jagadeesan, Anuradha, Guðmundsdóttir, Valdís B., Thordardóttir, Elísabet L., Einarsdóttir, Margrét S., Moore, Kristjan H. S., Sigurðsson, Ásgeir, Magnúsdóttir, Droplaug N., Jónsson, Hákon, Snorradóttir, Steinunn, Hovig, Eivind, Møller, Pål, Kockum, Ingrid, Olsson, Tomas, Alfredsson, Lars, Hansen, Thomas F., Werge, Thomas, Cavalleri, Gianpiero L., Gilbert, Edmund, Lalueza-Fox, Carles, W.Walser, Joe, Kristjánsdóttir, Steinunn, Gopalakrishnan, Shyam, Árnadóttir, Lilja, Magnússon, Ólafur Þ., Gilbert, M. Thomas P., Stefánsson, Kári, and Helgason, Agnar

Published
2018

12. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

Author

Liu, S John, Horlbeck, Max A, Cho, Seung Woo, Birk, Harjus S, Malatesta, Martina, He, Daniel, Attenello, Frank J, Villalta, Jacqueline E, Cho, Min Y, Chen, Yuwen, Mandegar, Mohammad A, Olvera, Michael P, Gilbert, Luke A, Conklin, Bruce R, Chang, Howard Y, Weissman, Jonathan S, and Lim, Daniel A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Stem Cell Research - Induced Pluripotent Stem Cell - Human, Stem Cell Research - Induced Pluripotent Stem Cell, Stem Cell Research, Human Genome, Biotechnology, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Generic health relevance, Cell Growth Processes, Cell Line, Clustered Regularly Interspaced Short Palindromic Repeats, Gene Knockdown Techniques, Gene Regulatory Networks, Genetic Loci, Genetic Testing, Genome, Human, Humans, Induced Pluripotent Stem Cells, Machine Learning, RNA Interference, RNA, Long Noncoding, Transcription, Genetic, Transcriptome, General Science & Technology
Abstract

The human genome produces thousands of long noncoding RNAs (lncRNAs)-transcripts >200 nucleotides long that do not encode proteins. Although critical roles in normal biology and disease have been revealed for a subset of lncRNAs, the function of the vast majority remains untested. We developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in seven diverse cell lines, including six transformed cell lines and human induced pluripotent stem cells (iPSCs). Large-scale screening identified 499 lncRNA loci required for robust cellular growth, of which 89% showed growth-modifying function exclusively in one cell type. We further found that lncRNA knockdown can perturb complex transcriptional networks in a cell type-specific manner. These data underscore the functional importance and cell type specificity of many lncRNAs.

Published
2017

13. Cyber risk research impeded by disciplinary barriers

Author

Falco, Gregory, Eling, Martin, Jablanski, Danielle, Weber, Matthias, Miller, Virginia, Gordon, Lawrence A., Wang, Shaun Shuxun, Schmit, Joan, Thomas, Russell, Elvedi, Mauro, Maillart, Thomas, Donavan, Emy, Dejung, Simon, Durand, Eric, Nutter, Franklin, Scheffer, Uzi, Arazi, Gil, Ohana, Gilbert, and Lin, Herbert

Published
2019

14. A noninteracting low-mass black hole–giant star binary system

Author

Thompson, Todd A., Kochanek, Christopher S., Stanek, Krzysztof Z., Badenes, Carles, Post, Richard S., Jayasinghe, Tharindu, Latham, David W., Bieryla, Allyson, Esquerdo, Gilbert A., Berlind, Perry, Calkins, Michael L., Tayar, Jamie, Lindegren, Lennart, Johnson, Jennifer A., Holoien, Thomas W.-S., Auchettl, Katie, and Covey, Kevin

Published
2019

16. Biological adaptations in the Arctic cervid, the reindeer ( Rangifer tarandus )

Author

Lin, Zeshan, Chen, Lei, Chen, Xianqing, Zhong, Yingbin, Yang, Yue, Xia, Wenhao, Liu, Chang, Zhu, Wenbo, Wang, Han, Yan, Biyao, Yang, Yifeng, Liu, Xing, Kvie, Kjersti Sternang, Røed, Knut Håkon, Wang, Kun, Xiao, Wuhan, Wei, Haijun, Li, Guangyu, Heller, Rasmus, Gilbert, M. Thomas P., Qiu, Qiang, Wang, Wen, and Li, Zhipeng

Published
2019

17. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Author

Chen, Lei, Qiu, Qiang, Jiang, Yu, Wang, Kun, Lin, Zeshan, Li, Zhipeng, Bibi, Faysal, Yang, Yongzhi, Wang, Jinhuan, Nie, Wenhui, Su, Weiting, Liu, Guichun, Li, Qiye, Fu, Weiwei, Pan, Xiangyu, Liu, Chang, Yang, Jie, Zhang, Chenzhou, Yin, Yuan, Wang, Yu, Zhao, Yue, Zhang, Chen, Wang, Zhongkai, Qin, Yanli, Liu, Wei, Wang, Bao, Ren, Yandong, Zhang, Ru, Zeng, Yan, da Fonseca, Rute R., Wei, Bin, Li, Ran, Wan, Wenting, Zhao, Ruoping, Zhu, Wenbo, Wang, Yutao, Duan, Shengchang, Gao, Yun, Zhang, Yong E., Chen, Chunyan, Hvilsom, Christina, Epps, Clinton W., Chemnick, Leona G., Dong, Yang, Mirarab, Siavash, Siegismund, Hans Redlef, Ryder, Oliver A., Gilbert, M. Thomas P., Lewin, Harris A., Zhang, Guojie, Heller, Rasmus, and Wang, Wen

Published
2019

18. Response

Author

Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., K. Jansson, Janet, Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., C. McHardy, Alice, Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A. N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., and Xenarios, Ioannis

Published
2019

19. A unified initiative to harness Earth's microbiomes

Author

Alivisatos, A. P., Blaser, M. J., Brodie, E. L., Chun, M., Dangl, J. L., Donohue, T. J., Dorrestein, P. C., Gilbert, J. A., Green, J. L., Jansson, J. K., Knight, R., Maxon, M. E., McFall-Ngai, M. J., Miller, J. F., Pollard, K. S., Ruby, E. G., and Taha, S. A.

Published
2015

20. Crystallization by particle attachment in synthetic, biogenic, and geologic environments

Author

De Yoreo, James J, Gilbert, Pupa UPA, Sommerdijk, Nico AJM, Penn, R Lee, Whitelam, Stephen, Joester, Derk, Zhang, Hengzhong, Rimer, Jeffrey D, Navrotsky, Alexandra, Banfield, Jillian F, Wallace, Adam F, Michel, F Marc, Meldrum, Fiona C, Cölfen, Helmut, and Dove, Patricia M

Subjects
Chemical Sciences, Physical Chemistry, Nanotechnology, Bioengineering, General Science & Technology
Abstract

Field and laboratory observations show that crystals commonly form by the addition and attachment of particles that range from multi-ion complexes to fully formed nanoparticles. The particles involved in these nonclassical pathways to crystallization are diverse, in contrast to classical models that consider only the addition of monomeric chemical species. We review progress toward understanding crystal growth by particle-attachment processes and show that multiple pathways result from the interplay of free-energy landscapes and reaction dynamics. Much remains unknown about the fundamental aspects, particularly the relationships between solution structure, interfacial forces, and particle motion. Developing a predictive description that connects molecular details to ensemble behavior will require revisiting long-standing interpretations of crystal formation in synthetic systems, biominerals, and patterns of mineralization in natural environments.

Published
2015

21. 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

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.

Published
2014

23. Multiproxy evidence highlights a complex evolutionary legacy of maize in South America

Author

Kistler, Logan, Maezumi, S. Yoshi, de Souza, Jonas Gregorio, Przelomska, Natalia A. S., Costa, Flaviane Malaquias, Smith, Oliver, Loiselle, Hope, Ramos-Madrigal, Jazmín, Wales, Nathan, Ribeiro, Eduardo Rivail, Morrison, Ryan R., Grimaldo, Claudia, Prous, Andre P., Arriaza, Bernardo, Gilbert, M. Thomas P., de Oliveira Freitas, Fabio, and Allaby, Robin G.

Published
2018

25. The evolutionary history of dogs in the Americas

Author

Leathlobhair, Máire Ní, Perri, Angela R., Irving-Pease, Evan K., Witt, Kelsey E., Linderholm, Anna, Haile, James, Lebrasseur, Ophelie, Ameen, Carly, Blick, Jeffrey, Boyko, Adam R., Brace, Selina, Cortes, Yahaira Nunes, Crockford, Susan J., Devault, Alison, Dimopoulos, Evangelos A., Eldridge, Morley, Enk, Jacob, Gopalakrishnan, Shyam, Gori, Kevin, Grimes, Vaughan, Guiry, Eric, Hansen, Anders J., Hulme-Beaman, Ardern, Johnson, John, Kitchen, Andrew, Kasparov, Aleksei K., Kwon, Young-Mi, Nikolskiy, Pavel A., Lope, Carlos Peraza, Manin, Aurélie, Martin, Terrance, Meyer, Michael, Myers, Kelsey Noack, Omura, Mark, Rouillard, Jean-Marie, Pavlova, Elena Y., Sciulli, Paul, Sinding, Mikkel-Holger S., Strakova, Andrea, Ivanova, Varvara V., Widga, Christopher, Willerslev, Eske, Pitulko, Vladimir V., Barnes, Ian, Gilbert, M. Thomas P., Dobney, Keith M., Malhi, Ripan S., Murchison, Elizabeth P., Larson, Greger, and Frantz, Laurent A. F.

Published
2018

27. Greenland sled dogs at risk of extinction

Author

Sills, Jennifer, Sonne, Christian, Langebæk, Rikke, Dietz, Rune, Andersen-Ranberg, Emilie, Houser, Geoff, Hansen, Anders J., Sinding, Mikkel-Holger S., Olsen, Morten Tange, Egevang, Carsten, Gilbert, M. Thomas P., and Meldgaard, Morten

Published
2018

28. Recent Asian origin of chytrid fungi causing global amphibian declines

Author

O’Hanlon, Simon J., Rieux, Adrien, Farrer, Rhys A., Rosa, Gonçalo M., Waldman, Bruce, Bataille, Arnaud, Kosch, Tiffany A., Murray, Kris A., Brankovics, Balázs, Fumagalli, Matteo, Martin, Michael D., Wales, Nathan, Alvarado-Rybak, Mario, Bates, Kieran A., Berger, Lee, Böll, Susanne, Brookes, Lola, Clare, Frances, Courtois, Elodie A., Cunningham, Andrew A., Doherty-Bone, Thomas M., Ghosh, Pria, Gower, David J., Hintz, William E., Höglund, Jacob, Jenkinson, Thomas S., Lin, Chun-Fu, Laurila, Anssi, Loyau, Adeline, Martel, An, Meurling, Sara, Miaud, Claude, Minting, Pete, Pasmans, Frank, Schmeller, Dirk S., Schmidt, Benedikt R., Shelton, Jennifer M. G., Skerratt, Lee F., Smith, Freya, Soto-Azat, Claudio, Spagnoletti, Matteo, Tessa, Giulia, Toledo, Luís Felipe, Valenzuela-Sánchez, Andrés, Verster, Ruhan, Vörös, Judit, Webb, Rebecca J., Wierzbicki, Claudia, Wombwell, Emma, Zamudio, Kelly R., Aanensen, David M., James, Timothy Y., Gilbert, M. Thomas P., Weldon, Ché, Bosch, Jaime, Balloux, François, Garner, Trenton W. J., and Fisher, Matthew C.

Published
2018

30. Drilling to Gabbro in Intact Ocean Crust

Author

Wilson, Douglas S., Alt, Jeffrey C., Banerjee, Neil R., Umino, Susumu, Miyashita, Sumio, Acton, Gary D., Anma, Ryo, Barr, Samantha R., Belghoul, Akram, Carlut, Julie, Christie, David M., Coggon, Rosalind M., Cooper, Kari M., Cordier, Carole, Crispini, Laura, Durand, Sedelia Rodriguez, Einaudi, Florence, Galli, Laura, Gao, Yongjun, Geldmacher, Jörg, Gilbert, Lisa A., Hayman, Nicholas W., Herrero-Bervera, Emilio, Hirano, Nobuo, Holter, Sara, Ingle, Stephanie, Jiang, Shijun, Kalberkamp, Ulrich, Kerneklian, Marcie, Koepke, Jürgen, Laverne, Christine, Maclennan, John, Morgan, Sally, Neo, Natsuki, Nichols, Holly J., Park, Sung-Hyun, Reichow, Marc K., Sakuyama, Tetsuya, Sano, Takashi, Sandwell, Rachel, Scheibner, Birgit, Smith-Duque, Chris E., Swift, Stephen A., Tartarotti, Paola, Tikku, Anahita A., Tominaga, Masako, Veloso, Eugenio A., Yamasaki, Toru, Yamazaki, Shusaku, and Ziegler, Christa

Published
2006

31. Sequence Variants in SLITRK1 Are Associated with Tourette's Syndrome

Author

Abelson, Jesse F., Kwan, Kenneth Y., O'Roak, Brian J., Baek, Danielle Y., Stillman, Althea A., Morgan, Thomas M., Mathews, Carol A., Pauls, David L., Rašin, Mladen-Roko, Gunel, Murat, Davis, Nicole R., Ercan-Sencicek, A. Gulhan, Guez, Danielle H., Spertus, John A., Leckman, James F., Dure, Leon S., Kurlan, Roger, Singer, Harvey S., Gilbert, Donald L., Farhi, Anita, Louvi, Angeliki, Lifton, Richard P., Šestan, Nenad, and State, Matthew W.

Published
2005

33. Composition and Dynamics of Plasma in Saturn's Magnetosphere

Author

Young, D. T., Blanc, M., Burch, J. L., Bolton, S., Coates, A. J., Crary, F. J., Goldstein, R., Grande, M., Hill, T. W., Johnson, R. E., Baragiola, R. A., Kelha, V., McComas, D. J., Mursula, K., Sittler, E. C., Svenes, K. R., Szegö, K., Tanskanen, P., Thomsen, M. F., Bakshi, S., Barraclough, B. L., Bebesi, Z., Delapp, D., Dunlop, M. W., Gosling, J. T., Furman, J. D., Gilbert, L. K., Glenn, D., Holmlund, C., Lewis, G. R., Linder, D. R., Maurice, S., McAndrews, H. J., Narheim, B. T., Pallier, E., Reisenfeld, D., Rymer, A. M., Smith, H. T., Tokar, R. L., Vilppola, J., and Zinsmeyer, C.

Published
2005

34. Declining oxygen in the global ocean and coastal waters

Author

Breitburg, Denise, Levin, Lisa A., Oschlies, Andreas, Grégoire, Marilaure, Chavez, Francisco P., Conley, Daniel J., Garçon, Véronique, Gilbert, Denis, Gutiérrez, Dimitri, Isensee, Kirsten, Jacinto, Gil S., Limburg, Karin E., Montes, Ivonne, Naqvi, S. W. A., Pitcher, Grant C., Rabalais, Nancy N., Roman, Michael R., Rose, Kenneth A., Seibel, Brad A., Telszewski, Maciej, Yasuhara, Moriaki, and Zhang, Jing

Published
2018

36. Natural selection shaped the rise and fall of passenger pigeon genomic diversity

Author

Murray, Gemma G. R., Soares, André E. R., Novak, Ben J., Schaefer, Nathan K., Cahill, James A., Baker, Allan J., Demboski, John R., Doll, Andrew, Da Fonseca, Rute R., Fulton, Tara L., Gilbert, M. Thomas P., Heintzman, Peter D., Letts, Brandon, McIntosh, George, O’Connell, Brendan L., Peck, Mark, Pipes, Marie-Lorraine, Rice, Edward S., Santos, Kathryn M., Sohrweide, A. Gregory, Vohr, Samuel H., Corbett-Detig, Russell B., Green, Richard E., and Shapiro, Beth

Published
2017

37. Reducing antimicrobial use in food animals

Author

Van Boeckel, Thomas P., Glennon, Emma E., Chen, Dora, Gilbert, Marius, Robinson, Timothy P., Grenfell, Bryan T, Levin, Simon A., Bonhoeffer, Sebastian, and Laxminarayan, Ramanan

Published
2017

39. DNA: A Programmable Force Sensor

Author

Albrecht, Christian, Blank, Kerstin, Lalic-Mülthaler, Mio, Hirler, Siegfried, Mai, Thao, Gilbert, Ilka, Schiffmann, Susanne, Bayer, Tom, Clausen-Schaumann, Hauke, and Gaub, Hermann E.

Published
2003

42. The Sequence of the Human Genome

Author

Venter, J. Craig, Adams, Mark D., Myers, Eugene W., Li, Peter W., Mural, Richard J., Sutton, Granger G., Smith, Hamilton O., Yandell, Mark, Evans, Cheryl A., Holt, Robert A., Gocayne, Jeannine D., Amanatides, Peter, Ballew, Richard M., Huson, Daniel H., Wortman, Jennifer Russo, Zhang, Qing, Kodira, Chinnappa D., Zheng, Xiangqun H., Chen, Lin, Skupski, Marian, Subramanian, Gangadharan, Thomas, Paul D., Zhang, Jinghui, Nelson, Catherine, Broder, Samuel, Clark, Andrew G., Nadeau, Joe, McKusick, Victor A., Zinder, Norton, Levine, Arnold J., Roberts, Richard J., Simon, Mel, Slayman, Carolyn, Hunkapiller, Michael, Bolanos, Randall, Delcher, Arthur, Dew, Ian, Fasulo, Daniel, Flanigan, Michael, Florea, Liliana, Halpern, Aaron, Hannenhalli, Sridhar, Kravitz, Saul, Levy, Samuel, Mobarry, Clark, Reinert, Knut, Remington, Karin, Abu-Threideh, Jane, Beasley, Ellen, Biddick, Kendra, Bonazzi, Vivien, Brandon, Rhonda, Cargill, Michele, Chandramouliswaran, Ishwar, Charlab, Rosane, Chaturvedi, Kabir, Deng, Zuoming, Di Francesco, Valentina, Dunn, Patrick, Eilbeck, Karen, Evangelista, Carlos, Gabrielian, Andrei E., Gan, Weiniu, Ge, Wangmao, Gong, Fangcheng, Gu, Zhiping, Guan, Ping, Heiman, Thomas J., Higgins, Maureen E., Ji, Rui-Ru, Ke, Zhaoxi, Ketchum, Karen A., Lai, Zhongwu, Lei, Yiding, Li, Zhenya, Li, Jiayin, Liang, Yong, Lin, Xiaoying, Lu, Fu, Merkulov, Gennady V., Milshina, Natalia, Moore, Helen M., Naik, Ashwinikumar K, Narayan, Vaibhav A., Neelam, Beena, Nusskern, Deborah, Rusch, Douglas B., Salzberg, Steven, Shao, Wei, Shue, Bixiong, Sun, Jingtao, Wang, Zhen Yuan, Wang, Aihui, Wang, Xin, Wang, Jian, Wei, Ming-Hui, Wides, Ron, Xiao, Chunlin, Yan, Chunhua, Yao, Alison, Ye, Jane, Zhan, Ming, Zhang, Weiqing, Zhang, Hongyu, Zhao, Qi, Zheng, Liansheng, Zhong, Fei, Zhong, Wenyan, Zhu, Shiaoping C., Zhao, Shaying, Gilbert, Dennis, Baumhueter, Suzanna, Spier, Gene, Carter, Christine, Cravchik, Anibal, Woodage, Trevor, Ali, Feroze, An, Huijin, Awe, Aderonke, Baldwin, Danita, Baden, Holly, Barnstead, Mary, Barrow, Ian, Beeson, Karen, Busam, Dana, Carver, Amy, Cheng, Ming Lai, Curry, Liz, Danaher, Steve, Davenport, Lionel, Desilets, Raymond, Dietz, Susanne, Dodson, Kristina, Doup, Lisa, Ferriera, Steven, Garg, Neha, Gluecksmann, Andres, Hart, Brit, Haynes, Jason, Haynes, Charles, Heiner, Cheryl, Hladun, Suzanne, Hostin, Damon, Houck, Jarrett, Howland, Timothy, Ibegwam, Chinyere, Johnson, Jeffery, Kalush, Francis, Kline, Lesley, Koduru, Shashi, Love, Amy, Mann, Felecia, May, David, McCawley, Steven, Mclntosh, Tina, McMullen, Ivy, Moy, Mee, Moy, Linda, Murphy, Brian, Nelson, Keith, Pfannkoch, Cynthia, Pratts, Eric, Puri, Vinita, Qureshi, Hina, Reardon, Matthew, Rodriguez, Robert, Rogers, Yu-Hui, Romblad, Deanna, Ruhfel, Bob, Scott, Richard, Sitter, Cynthia, Smallwood, Michelle, Stewart, Erin, Strong, Renee, Suh, Ellen, Thomas, Reginald, Tint, Tse, Sukyee, Vech, Claire, Wang, Gary, Wetter, Jeremy, Williams, Sherita, Williams, Monica, Windsor, Sandra, Winn-Deen, Emily, Wolfe, Keriellen, Zaveri, Jayshree, Zaveri, Karena, Abril, Josep F., Guigó, Roderic, Campbell, Michael J., Sjolander, Kimmen V., Karlak, Brian, Kejariwal, Anish, Mi, Huaiyu, Lazareva, Betty, Hatton, Thomas, Narechania, Apurva, Diemer, Karen, Muruganujan, Anushya, Guo, Nan, Sato, Shinji, Bafna, Vineet, Istrail, Sorin, Lippert, Ross, Schwartz, Russell, Walenz, Brian, Yooseph, Shibu, Allen, David, Basu, Anand, Baxendale, James, Blick, Louis, Caminha, Marcelo, Carnes-Stine, John, Caulk, Parris, Chiang, Yen-Hui, Coyne, My, Dahlke, Carl, Mays, Anne Deslattes, Dombroski, Maria, Donnelly, Michael, Ely, Dale, Esparham, Shiva, Fosler, Carl, Gire, Harold, Glanowski, Stephen, Glasser, Kenneth, Glodek, Anna, Gorokhov, Mark, Graham, Ken, Gropman, Barry, Harris, Michael, Heil, Jeremy, Henderson, Scott, Hoover, Jeffrey, Jennings, Donald, Jordan, Catherine, Jordan, James, Kasha, John, Kagan, Leonid, Kraft, Cheryl, Levitsky, Alexander, Lewis, Mark, Liu, Xiangjun, Lopez, John, Ma, Daniel, Majoros, William, McDaniel, Joe, Murphy, Sean, Newman, Matthew, Nguyen, Trung, Nguyen, Ngoc, Nodell, Marc, Pan, Sue, Peck, Jim, Peterson, Marshall, Rowe, William, Sanders, Robert, Scott, John, Simpson, Michael, Smith, Thomas, Sprague, Arlan, Stockwell, Timothy, Turner, Russell, Venter, Eli, Wang, Mei, Wen, Meiyuan, Wu, David, Wu, Mitchell, Xia, Ashley, Zandieh, Ali, and Zhu, Xiaohong

Published
2001

45. Rise and Fall of the Beringian Steppe Bison

Author

Shapiro, Beth, Drummond, Alexei J, Rambaut, Andrew, Wilson, Michael C, Matheus, Paul E, Sher, Andrei V, Pybus, Oliver G, Gilbert, M Thomas P, Barnes, Ian, Binladen, Jonas, Willerslev, Eske, Hansen, Anders J, Baryshnikov, Gennady F, Burns, James A, Davydov, Sergei, Driver, Jonathan C, Froese, Duane G, Harington, C Richard, Keddie, Grant, Kosintsev, Pavel, Kunz, Michael L, Martin, Larry D, Stephenson, Robert O, Storer, John, Tedford, Richard, Zimov, Sergei, and Cooper, Alan

Subjects
Genetics, Alaska, Animals, Bayes Theorem, Bison, Canada, China, Climate, DNA, Mitochondrial, Environment, Fossils, Genetic Variation, Genetics, Population, Human Activities, Humans, North America, Phylogeny, Population Dynamics, Sequence Analysis, DNA, Time, General Science & Technology
Abstract

The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later.

Published
2004

50. Estimating the Age of the Common Ancestor of Men from the ZFY Intron

Author

Fu, Yun-Xin, Li, Wen-Hsiung, Donnelly, Peter, Tavaré, Simon, Balding, David J., Griffith, Robert C., Weiss, Gunter, von Haeseler, Arndt, Rogers, Jeffrey, Samollow, Paul B., Comuzzie, Anthony G., Dorit, Robert L., Akashi, Hiroshi, and Gilbert, Walter

Published
1996

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