Institution
Pompeu Fabra University
Education•Barcelona, Spain•
About: Pompeu Fabra University is a education organization based out in Barcelona, Spain. It is known for research contribution in the topics: Population & Gene. The organization has 8093 authors who have published 23570 publications receiving 858431 citations. The organization is also known as: Universitat Pompeu Fabra & UPF.
Topics: Population, Gene, European union, Genome, Context (language use)
Papers published on a yearly basis
Papers
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University of Copenhagen1, University of California, Santa Cruz2, University of Bern3, Swiss Institute of Bioinformatics4, Technical University of Denmark5, University College London6, Joint Genome Institute7, Uppsala University8, King Saud University9, University College Dublin10, University of Louisville11, University of Kentucky12, University of Potsdam13, Pompeu Fabra University14, University of California, Berkeley15
TL;DR: In this article, the authors sequenced two ancient horse genomes from Taymyr, Russia (at 7.4 and 24.3fold coverage) and compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleistocene.
Abstract: The domestication of the horse ∼5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski’s horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the “cost of domestication” hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.
258 citations
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Erasmus University Medical Center1, University of Porto2, University of Western Australia3, Stockholm County Council4, Paris Descartes University5, Maastricht University6, French Institute of Health and Medical Research7, National and Kapodistrian University of Athens8, University Medical Center Groningen9, University of Valencia10, University of Southampton11, Liverpool School of Tropical Medicine12, Université de Sherbrooke13, Norwegian Institute of Public Health14, University of Bologna15, University of Crete16, University Hospital Southampton NHS Foundation Trust17, Ludwig Maximilian University of Munich18, Nofer Institute of Occupational Medicine19, University of California20, Harvard University21, University of Illinois at Chicago22, National Institutes of Health23, Wageningen University and Research Centre24, University of Turku25, Helmholtz Centre for Environmental Research - UFZ26, Jagiellonian University Medical College27, Åbo Akademi University28, Harokopio University29, University College Dublin30, University of Calgary31, Boston Children's Hospital32, University of Copenhagen33, University College Cork34, VU University Medical Center35, University of Helsinki36, University of Turin37, Radboud University Nijmegen38, University of Trieste39, University of Bergen40, Slovak Medical University41, Utrecht University42, Pompeu Fabra University43, Bradford Royal Infirmary44, University of Bristol45
TL;DR: In this paper, the separate and combined associations of maternal pre-pregnancy body mass index (BMI) and gestational weight gain with the risks of pregnancy complications and their population impact were assessed.
258 citations
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01 Dec 2008TL;DR: An answer ranking engine for non-factoid questions built using a large online community-generated question-answer collection (Yahoo! Answers) is described and it is demonstrated that using them in combination leads to considerable improvements in accuracy.
Abstract: This work describes an answer ranking engine for non-factoid questions built using a large online community-generated question-answer collection (Yahoo! Answers). We show how such collections may be used to effectively set up large supervised learning experiments. Furthermore we investigate a wide range of feature types, some exploiting NLP processors, and demonstrate that using them in combination leads to considerable improvements in accuracy.
258 citations
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TL;DR: The SMC^2 algorithm proposed in this paper is a sequential Monte Carlo algorithm, defined in the theta-dimension, which propagates and resamples many particle filters in the x-dimension.
Abstract: We consider the generic problem of performing sequential Bayesian inference in a state-space model with observation process y, state process x and fixed parameter theta. An idealized approach would be to apply the iterated batch importance sampling (IBIS) algorithm of Chopin (2002). This is a sequential Monte Carlo algorithm in the theta-dimension, that samples values of theta, reweights iteratively these values using the likelihood increments p(y_t|y_1:t-1, theta), and rejuvenates the theta-particles through a resampling step and a MCMC update step. In state-space models these likelihood increments are intractable in most cases, but they may be unbiasedly estimated by a particle filter in the x-dimension, for any fixed theta. This motivates the SMC^2 algorithm proposed in this article: a sequential Monte Carlo algorithm, defined in the theta-dimension, which propagates and resamples many particle filters in the x-dimension. The filters in the x-dimension are an example of the random weight particle filter as in Fearnhead et al. (2010). On the other hand, the particle Markov chain Monte Carlo (PMCMC) framework developed in Andrieu et al. (2010) allows us to design appropriate MCMC rejuvenation steps. Thus, the theta-particles target the correct posterior distribution at each iteration t, despite the intractability of the likelihood increments. We explore the applicability of our algorithm in both sequential and non-sequential applications and consider various degrees of freedom, as for example increasing dynamically the number of x-particles. We contrast our approach to various competing methods, both conceptually and empirically through a detailed simulation study, included here and in a supplement, and based on particularly challenging examples.
258 citations
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Karolinska Institutet1, European Bioinformatics Institute2, St. Vincent's Institute of Medical Research3, Catalan Institution for Research and Advanced Studies4, Max Planck Society5, Fluidigm Corporation6, Stanford University7, Max Delbrück Center for Molecular Medicine8, Charité9, Broad Institute10, Howard Hughes Medical Institute11, Massachusetts Institute of Technology12, Ludwig Maximilian University of Munich13, University of Tsukuba14, Pompeu Fabra University15, German Cancer Research Center16
TL;DR: In this paper, a multicenter study comparing 13 commonly used scRNA-seq and single-nucleus RNA-seq protocols applied to a heterogeneous reference sample resource was conducted.
Abstract: Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands of cells and are being used to compile cell atlases of tissues, organs and organisms. However, the protocols differ substantially with respect to their RNA capture efficiency, bias, scale and costs, and their relative advantages for different applications are unclear. In the present study, we generated benchmark datasets to systematically evaluate protocols in terms of their power to comprehensively describe cell types and states. We performed a multicenter study comparing 13 commonly used scRNA-seq and single-nucleus RNA-seq protocols applied to a heterogeneous reference sample resource. Comparative analysis revealed marked differences in protocol performance. The protocols differed in library complexity and their ability to detect cell-type markers, impacting their predictive value and suitability for integration into reference cell atlases. These results provide guidance both for individual researchers and for consortium projects such as the Human Cell Atlas.
257 citations
Authors
Showing all 8248 results
Name | H-index | Papers | Citations |
---|---|---|---|
Andrei Shleifer | 171 | 514 | 271880 |
Paul Elliott | 153 | 773 | 103839 |
Bert Brunekreef | 124 | 806 | 81938 |
Philippe Aghion | 122 | 507 | 73438 |
Anjana Rao | 118 | 337 | 61395 |
Jordi Sunyer | 115 | 798 | 57211 |
Kenneth J. Arrow | 113 | 411 | 111221 |
Xavier Estivill | 110 | 673 | 59568 |
Roderic Guigó | 108 | 304 | 106914 |
Mark J. Nieuwenhuijsen | 107 | 647 | 49080 |
Jordi Alonso | 107 | 523 | 64058 |
Alfonso Valencia | 106 | 542 | 55192 |
Luis Serrano | 105 | 452 | 42515 |
Vadim N. Gladyshev | 102 | 490 | 34148 |
Josep M. Antó | 100 | 493 | 38663 |