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index medicus (9) 9
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cellular potts model (2) 2
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aging (1) 1
agricultural and biological sciences (1) 1
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altitudes (1) 1
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amino acids (1) 1
angiogenesis; extracellular matrix; cellular potts model; branching growth; mmps (1) 1
animal behavior (1) 1
ants - classification (1) 1
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asia (1) 1
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1. Full Text Widespread Signals of Convergent Adaptation to High Altitude in Asia and America
by Foll, Matthieu and Gaggiotti, Oscar E and Daub, Josephine T and Vatsiou, Alexandra and Excoffier, Laurent
The American Journal of Human Genetics, ISSN 0002-9297, 10/2014, Volume 95, Issue 4, pp. 394 - 407
Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have... 
FALSE DISCOVERY RATE | POSITIVE SELECTION | SIGNATURES | GENETIC ADAPTATION | TIBETAN | GENETICS & HEREDITY | POPULATION-STRUCTURE | LOCI | SCAN | HYPOXIA | GENOMIC DIFFERENTIATION | Americas | Genetics, Population | Humans | Databases, Genetic | DNA Copy Number Variations - genetics | Gene Expression Profiling | Selection, Genetic - genetics | Biological Evolution | Hypoxia - genetics | Algorithms | Adaptation, Physiological - genetics | Asia | Computer Simulation | Bayes Theorem | Polymorphism, Single Nucleotide - genetics | Acclimatization - genetics | Genome, Human | Altitude | Genetic research | Hypoxia | Convergence (Biology) | Research | Human genetics | Quantitative Biology - Populations and Evolution
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2. Full Text Evidence for polygenic adaptation to pathogens in the human genome
by Daub, Josephine T and Hofer, Tamara and Cutivet, Emilie and Dupanloup, Isabelle and Quintana-Murci, Lluis and Robinson-Rechavi, Marc and Excoffier, Laurent
Molecular Biology and Evolution, ISSN 0737-4038, 07/2013, Volume 30, Issue 7, pp. 1544 - 1558
Most approaches aiming at finding genes involved in adaptive events have focused on the detection of outlier loci, which resulted in the discovery of... 
adaptation | polygenic selection | epistasis | pathway analysis | human evolution | VAV PROTEINS | GENE SET ENRICHMENT | BIOCHEMISTRY & MOLECULAR BIOLOGY | SWEEPS | IDENTIFICATION | IMMUNE | EVOLUTIONARY BIOLOGY | POPULATION DIFFERENTIATION | POSITIVE SELECTION | NATURAL-SELECTION | GENETICS & HEREDITY | DIVERSITY | SNP DATA | Models, Theoretical | Multifactorial Inheritance - genetics | Humans | Adaptation, Biological | Genotype | Linkage Disequilibrium | Selection, Genetic - genetics | Host-Pathogen Interactions - genetics | Metabolic Networks and Pathways | Epistasis, Genetic | Polymorphism, Single Nucleotide | Mutation | Genome, Human
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3. Full Text Patterns of positive selection in seven ant genomes
by Roux, Julien and Privman, Eyal and Moretti, Sébastien and Daub, Josephine T and Robinson-Rechavi, Marc and Keller, Laurent
Molecular Biology and Evolution, ISSN 0737-4038, 2014, Volume 31, Issue 7, pp. 1661 - 1685
The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific adaptations... 
Drosophila | lifespan | neurogenesis | metabolism | olfactory receptors | aging | immunity | Hymenoptera | comparative genomics | sociality | bees | TERM-MEMORY FORMATION | MITOCHONDRIAL GENOME | FREE-RADICAL PRODUCTION | LIFE-SPAN EXTENSION | BRANCH-SITE TEST | d(S) | GENETICS & HEREDITY | OXIDATIVE STRESS | GENE SET ENRICHMENT | BIOCHEMISTRY & MOLECULAR BIOLOGY | HONEY-BEE | d(N) | EVOLUTIONARY BIOLOGY | SEQUENCE ALIGNMENT | ADAPTIVE EVOLUTION | Multigene Family | Animals | Ants - genetics | Selection, Genetic | Databases, Genetic | Insect Proteins - genetics | Ants - classification | Genome, Insect | Phylogeny | Genes, Mitochondrial | Evolution, Molecular | Fast Tracks
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4. Full Text A Cell-Based Model of Extracellular-Matrix-Guided Endothelial Cell Migration During Angiogenesis
by Daub, Josephine and Merks, Roeland
Bulletin of Mathematical Biology, ISSN 0092-8240, 01/2013, Volume 75, Issue 8, pp. 1377 - 1399
htmlabstractAngiogenesis, the formation of new blood vessels sprouting from existing ones, occurs in several situations like wound healing, tissue remodeling... 
cellular Potts model | Angiogenesis | extracellular matrix | Branching growth | Life Sciences, general | Mathematical and Computational Biology | Cellular Potts model | MMPs | Extracellular matrix | Mathematics | Cell Biology | FIBROBLAST | VASCULOGENESIS | VEGF | DIFFERENTIAL ADHESION | PROLIFERATION | TUMOR-INDUCED ANGIOGENESIS | IN-VITRO | GROWTH | BIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | CLINICAL-IMPLICATIONS | CAPILLARY FORMATION | Animals | Models, Cardiovascular | Extracellular Matrix - physiology | Humans | Neovascularization, Pathologic | Mathematical Concepts | Systems Biology | Vascular Endothelial Growth Factor A - physiology | Endothelial Cells - physiology | Neovascularization, Physiologic | Cell Movement | Models | Tumors | Endothelium | Original
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5. Widespread Signals of Convergent Adaptation to High Altitude in Asia and America
by Matthieu Foll and Oscar E Gaggiotti and Josephine T Daub and Alexandra Vatsiou and Laurent Excoffier
American Journal of Human Genetics, ISSN 0002-9297, 10/2014, Volume 95, Issue 4, p. 394
  Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have... 
Evolutionary biology | Genomics | Biogeography | Altitudes | Bayesian analysis | Population genetics
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6. Full Text Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit
by Daub, Josephine T and Merks, Roeland M. H
Methods in Molecular Biology, ISSN 1064-3745, 2015, Volume 1214, pp. 67 - 127
Computational modeling has become a widely used tool for unraveling the mechanisms of higher level cooperative cell behavior during vascular morphogenesis.... 
Parameter study | Angiogenesis | Glazier-Graner-Hogeweg model | Cell-based model | Quantification | Cellular Potts model | Agent-based modeling | Tissue Simulation Toolkit | Cellular potts model | Glazier-graner-hogeweg model | Morphogenesis | Blood Vessels - growth & development | Models, Biological | Computer Simulation | Extracellular Matrix - metabolism | Software | Vascular Endothelial Growth Factor A - metabolism | Blood Vessels - physiology | Blood Vessels - cytology | Neovascularization, Physiologic
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7. Full Text Detection of convergent genome-wide signals of adaptation to tropical forests in humans
by Amorim, Carlos Eduardo G and Daub, Josephine T and Salzano, Francisco M and Foll, Matthieu and Excoffier, Laurent
PLoS ONE, ISSN 1932-6203, 04/2015, Volume 10, Issue 4, p. e0121557
Tropical forests are believed to be very harsh environments for human life. It is unclear whether human beings would have ever subsisted in those environments... 
EPITHELIAL CHEMOKINE MEC/CCL28 | GENETIC-STRUCTURE | EVOLUTION | AFRICAN RAIN-FORESTS | MULTIDISCIPLINARY SCIENCES | POPULATIONS | LOCI | DIVERSITY | SELECTION | ASSOCIATION | HISTORY | Genome-Wide Association Study | Adaptation, Physiological - genetics | Humans | Female | Male | Polymorphism, Single Nucleotide | Genome, Human | Rainforest | Genomics | Physiological aspects | Evolution | Genomes | Forests and forestry | Genetic transcription | Comparative analysis | Adaptations | Forests | Populations | Laboratories | Positive selection | Biological evolution | Thermoregulation | Single-nucleotide polymorphism | Tropical forests | DNA-directed RNA polymerase | Population genetics | Convergence | Genotype & phenotype | Food selection | Lipid metabolism | Bioinformatics | Adaptation | Immune system | Data processing | Ecology | Metabolism | Ribonucleic acid--RNA | Studies | Polymerase | Harsh environments | Mutation | Transcription initiation | Bayesian analysis | Evolution & development | Chemokines | Cancer | RNA | Ribonucleic acid
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8. Patterns of Positive Selection in Seven Ant Genomes
by Julien Roux and Eyal Privman and Sébastien Moretti and Josephine T Daub and Marc Robinson-Rechavi and Laurent Keller
Molecular Biology and Evolution, ISSN 0737-4038, 07/2014, Volume 31, Issue 7, p. 1661
  The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific... 
Insects | Animal behavior | Genes | Amino acids | Genomes | Neurogenesis
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9. Full Text 267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation
by Dopazo, Joaquín and Amadoz, Alicia and Bleda, Marta and Garcia-Alonso, Luz and Alemán, Alejandro and García-García, Francisco and Rodriguez, Juan A and Daub, Josephine T and Muntané, Gerard and Rueda, Antonio and Vela-Boza, Alicia and López-Domingo, Francisco J and Florido, Javier P and Arce, Pablo and Ruiz-Ferrer, Macarena and Méndez-Vidal, Cristina and Arnold, Todd E and Spleiss, Olivia and Alvarez-Tejado, Miguel and Navarro, Arcadi and Bhattacharya, Shomi S and Borrego, Salud and Santoyo-López, Javier and Antiñolo, Guillermo
Molecular Biology and Evolution, ISSN 0737-4038, 05/2016, Volume 33, Issue 5, pp. 1205 - 1218
Recent results from large-scale genomic projects suggest that allele frequencies, which are highly relevant for medical purposes, differ considerably across... 
pharmacogenomic variants | exome sequencing | population variability | disease variants | Genetic Predisposition to Disease | Disease - genetics | Gene Frequency | Humans | Pharmacogenomic Testing | Polymorphism, Genetic | Exome | Genetic Variation | Drug Resistance - genetics | Genetics, Population - methods | Spain - epidemiology | Internet | Databases, Nucleic Acid | Pharmacogenomic variants | Farmacogenòmica | Disease variants | Population variability | Exome sequencing | Discoveries
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10. Evidence for Polygenic Adaptation to Pathogens in the Human Genome
by Josephine T Daub and Tamara Hofer and Emilie Cutivet and Isabelle Dupanloup and Lluis Quintana-Murci and Marc Robinson-Rechavi and Laurent Excoffier
Molecular Biology and Evolution, ISSN 0737-4038, 07/2013, Volume 30, Issue 7, p. 1544
  Most approaches aiming at finding genes involved in adaptive events have focused on the detection of outlier loci, which resulted in the discovery of... 
Genotype & phenotype | Genes | Bacteria | Genomes | Mutation
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11. Full Text Inference of Evolutionary Forces Acting on Human Biological Pathways
by Daub, Josephine T and Daub, Josephine T and Dupanloup, Isabelle and Dupanloup, Isabelle and Robinson-Rechavi, Marc and Robinson-Rechavi, Marc and Excoffier, Laurent and Excoffier, Laurent
Genome biology and evolution, ISSN 1759-6653, 06/2015, Volume 7, Issue 6, pp. 1546 - 1558
Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past... 
McDonald–Kreitman test | polygenic selection | McDonald-Kreitman test | pathway analysis | human evolution | RECOMBINATION | ADAPTIVE PROTEIN EVOLUTION | SIGNATURES | MOLECULAR EVOLUTION | POPULATION-SIZE | EVOLUTIONARY BIOLOGY | POLYMORPHISMS | ADAPTATION | GENES | GENETICS & HEREDITY | SELECTIVE SWEEPS | DELETERIOUS MUTATIONS | Data Interpretation, Statistical | Metabolic Networks and Pathways - genetics | Demography | Genes | Genomics | Humans | Selection, Genetic | Signal Transduction - genetics | African Continental Ancestry Group - genetics | Gene Regulatory Networks | Multifactorial Inheritance | Evolution, Molecular
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12. Detection of Convergent Genome-Wide Signals of Adaptation to Tropical Forests in Humans: e0121557
by Amorim, Carlos EduardoG and Daub, Josephine T and Salzano, Francisco M and Foll, Matthieu and Excoffier, Laurent
PLoS ONE, 04/2015, Volume 10, Issue 4
Tropical forests are believed to be very harsh environments for human life. It is unclear whether human beings would have ever subsisted in those environments... 
Journal Article
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13. Full Text Detecting gene subnetworks under selection in biological pathways
by Gouy, Alexandre and Daub, Joséphine T and Excoffier, Laurent
Nucleic Acids Research, ISSN 0305-1048, 09/2017, Volume 45, Issue 16, pp. e149 - e149
Advances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from... 
HIGH-ALTITUDE ADAPTATION | EVOLUTION | SET ENRICHMENT ANALYSIS | POSITIVE SELECTION | TIBETAN | BIOCHEMISTRY & MOLECULAR BIOLOGY | NATURAL-SELECTION | QUANTITATIVE TRAIT LOCUS | STABILIZING SELECTION | NETWORKS | POLYGENIC TRAITS | Computational Biology - methods | Metabolic Networks and Pathways - genetics | Adaptation, Physiological - genetics | Humans | Selection, Genetic | Signal Transduction - genetics | Software | Gene Regulatory Networks | Altitude | Methods Online
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14. Full Text Patterns of positive selection in seven ant genomes
by Roux, Julien and Privman, Eyal and Moretti, Sebastien and Daub, Josephine T and Robinson-Rechavi, Marc and Keller, Laurent
11/2013
The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific adaptations... 
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