Patrick Abbot
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View article: Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci
Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci Open
Currently, there is no comprehensive framework to evaluate the evolutionary forces acting on genomic regions associated with human complex traits and contextualize the relationship between evolution and molecular function. Here, we develop…
View article: Accounting for diverse evolutionary forces reveals the mosaic nature of selection on genomic regions associated with human preterm birth
Accounting for diverse evolutionary forces reveals the mosaic nature of selection on genomic regions associated with human preterm birth Open
Human pregnancy requires the coordinated function of multiple tissues in both mother and fetus and has evolved in concert with major human adaptations. As a result, pregnancy-associated phenotypes and related disorders are genetically comp…
View article: Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues
Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues Open
Evolutionary changes in enhancers are widely associated with variation in human traits and diseases. However, studies comprehensively quantifying levels of selection on enhancers at multiple evolutionary periods during recent human evoluti…
View article: Supplemental Material for Moon et al., 2019
Supplemental Material for Moon et al., 2019 Open
This repository contains supplementary figures, supplementary tables, and supplementary files associated with the G3 publication entitled "Signatures of recent positive selection in enhancers\nacross 41 human tissues"
View article: Signatures of recent positive selection in enhancers across 41 human tissues
Signatures of recent positive selection in enhancers across 41 human tissues Open
Evolutionary changes in enhancers are widely associated with variation in human traits and diseases. However, studies comprehensively quantifying levels of selection on enhancers at multiple evolutionary time points during recent human evo…
View article: Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication
Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication Open
The genetic contributors to variation in mammalian reproductive traits remain largely unknown. We took advantage of the domestic dog, a powerful model system, to test for associations between genome-wide variants and four reproductive trai…
View article: Maintaining Biological Cultures and Measuring Gene Expression in <em>Aphis nerii</em>: A Non-model System for Plant-insect Interactions
Maintaining Biological Cultures and Measuring Gene Expression in <em>Aphis nerii</em>: A Non-model System for Plant-insect Interactions Open
Aphids are excellent experimental models for a variety of biological questions ranging from the evolution of symbioses and the development of polyphenisms to questions surrounding insect's interactions with their host plants. Genomic resou…
View article: integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth Open
Background The integration of high-quality, genome-wide analyses offers a robust approach to elucidating genetic factors involved in complex human diseases. Even though several methods exist to integrate heterogeneous omics data, most biol…
View article: Adaptive Divergence in a Defense Symbiosis Driven from the Top Down
Adaptive Divergence in a Defense Symbiosis Driven from the Top Down Open
Most studies of adaptive radiation in animals focus on resource competition as the primary driver of trait divergence. The roles of other ecological interactions in shaping divergent phenotypes during such radiations have received less att…
View article: Insect adaptations toward plant toxins in milkweed–herbivores systems – a review
Insect adaptations toward plant toxins in milkweed–herbivores systems – a review Open
Studies of plant defenses and insect herbivores have been important in the development of our understanding of coevolution and specialization. Milkweed–herbivore systems have been a model for studying plant secondary chemistry defense evol…
View article: Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology
Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology Open
Sialic acids are nine carbon sugars ubiquitously found on the surfaces of vertebrate cells and are involved in various immune response-related processes. In humans, at least 58 genes spanning diverse functions, from biosynthesis and activa…
View article: Additional file 11: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
Additional file 11: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth Open
Raw data for manual overlap based on significance dichotomization. All 18,727 genes identified as significant in at least 1 study and overlap across the entire data set. (XLSX 769 kb)
View article: Additional file 2: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
Additional file 2: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth Open
All results from iR-none. All desirability scores across all variables in all studies as well as overall desirabilities and normalized overall desirabilities are presented. (XLSX 3762 kb)
View article: Additional file 3: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
Additional file 3: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth Open
All results from iR-num. All desirability scores across all variables in all studies as well as overall desirabilities and normalized overall desirabilities are presented. (XLSX 1988 kb)
View article: Additional file 1: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
Additional file 1: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth Open
Results of meta-analysis to identify studies for integration. We outline the 10 studies meeting all inclusion criteria for integrative analysis. Furthermore, we list the other 44 studies that we identified through our literature search but…
View article: Additional file 7: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
Additional file 7: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth Open
All results from iR-per. All desirability scores across all variables in all studies as well as overall desirabilities and normalized overall desirabilities are presented. (XLSX 3512 kb)
View article: Additional file 13: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
Additional file 13: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth Open
GO-Slim gene set enrichment results. The PANTHER output for gene set functional enrichment is provided, including 37 statistically enriched biological pathways. (XLSX 13 kb)
View article: Additional file 14: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
Additional file 14: of integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth Open
All results without including the Zhang 2017 data set [30]. All desirability scores across all variables in all studies as well as overall desirabilities and normalized overall desirabilities are presented. (XLSX 2908 kb)
View article: What is a placental mammal anyway?
What is a placental mammal anyway? Open
Many developmental functions in marsupials and eutherian mammals are accomplished by different tissues, but similar genes.
View article: Examination of signatures of recent positive selection on genes involved in human sialic acid biology
Examination of signatures of recent positive selection on genes involved in human sialic acid biology Open
Sialic acids are nine carbon sugars ubiquitously found on the surfaces of vertebrate cells and are involved in various immune response-related processes. In humans, at least 58 genes spanning diverse functions, from biosynthesis and activa…