A5001432390- Genetic diversity and population structure
- Animal Behavior and Reproduction
- Plant and animal studies
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Wildlife Ecology and Conservation
- Genetic and phenotypic traits in livestock
- Species Distribution and Climate Change
- Physiological and biochemical adaptations
- Rural development and sustainability
- Bat Biology and Ecology Studies
- Genetic Mapping and Diversity in Plants and Animals
- Avian ecology and behavior
- Bird parasitology and diseases
- Cultural Heritage Management and Preservation
- Plant Ecology and Taxonomy Studies
- Machine Learning and Data Classification
- Rangeland and Wildlife Management
- Gene Regulatory Network Analysis
- Botany, Ecology, and Taxonomy Studies
- Advanced biosensing and bioanalysis techniques
- Machine Learning in Bioinformatics
- Urbanization and City Planning
- Animal Vocal Communication and Behavior
- Animal Ecology and Behavior Studies
University of Montana
2015-2023
United States Geological Survey
2021-2022
Southwest Biological Science Center
2021-2022
Astrogeology Science Center
2021-2022
Arizona State University
2019-2020
Northwestern University
2020
Illumina (United States)
2015-2016
Icahn School of Medicine at Mount Sinai
2015-2016
University of Wyoming
2013-2015
Therapeutics Clinical Research
2015
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present significant update to one of the tools in this domain called Enrichr. Enrichr currently contains large collection diverse set libraries available and download. In total, 180 184 annotated from 102 libraries. New features have been added including ability submit fuzzy sets, upload BED files, improved application programming interface visualization results as clustergrams....
Snowshoe hares (Lepus americanus) maintain seasonal camouflage by molting to a white winter coat, but some remain brown during the in regions with low snow cover. We show that cis-regulatory variation controlling expression of Agouti gene underlies this adaptive polymorphism. Genetic at clustered coat color across multiple hare and jackrabbit species, revealing history recurrent interspecific flow. Brown coats snowshoe likely originated from an introgressed black-tailed allele has swept high...
Gene expression data are accumulating exponentially in public repositories. Reanalysis and integration of themed collections from these studies may provide new insights, but requires further human curation. Here we report a crowdsourcing project to annotate reanalyse large number gene profiles Expression Omnibus (GEO). Through massive open online course on Coursera, over 70 participants 25 countries identify 2,460 single-gene perturbation signatures, 839 disease versus normal 906 drug...
Abstract The spatial structure of the environment (e.g. configuration habitat patches) may play an important role in determining strength local adaptation. However, previous studies heterogeneity and adaptation have largely been limited to simple landscapes, which poorly represent multiscale common nature. Here, we use simulations pursue two goals: (i) explore how landscape heterogeneity, dispersal ability selection affect adaptation, (ii) evaluate performance several genotype–environment...
Since its introduction, landscape genomics has developed quickly with the increasing availability of both molecular and topo-climatic data. The current challenges field mainly involve processing large numbers models disentangling selection from demography. Several methods address latter, either by estimating a neutral model population structure or inferring simultaneously environmental demographic effects. Here we present Sam$\beta$ada, an integrated approach to study signatures local...
Uncovering the genetic basis of adaptation hinges on ability to detect loci under selection. However, population genomics outlier approaches selected may be inappropriate for clinal populations or those with unclear structure because they require that individuals clustered into populations. An alternate approach, landscape genomics, uses individual-based selection and reveal potential environmental drivers We tested four methods a simulated determine their effectiveness at identifying locus...
Evolutionary adaptation to extreme environments often requires coordinated changes in multiple intersecting physiological pathways, but how such multi-trait occurs remains unresolved. Transcription factors, which regulate the expression of many genes and can simultaneously alter phenotypes, may be common targets selection if benefits induced outweigh costs negative pleiotropic effects. We combined complimentary population genetic analyses experiments North American deer mice (Peromyscus...
Adaptation is central to population persistence in the face of environmental change, yet we seldom precisely understand origin and spread adaptive variation natural populations. Snowshoe hares (Lepus americanus) along Pacific Northwest coast have evolved brown winter camouflage through positive selection on recessive at Agouti pigmentation gene introgressed from black-tailed jackrabbits californicus). Here, combine new published whole-genome exome sequences with targeted genotyping...
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts introgression have seldom been evaluated in phylogenetic context a radiation. Hares (Lepus) represent widespread mammalian radiation 32 extant species characterized by striking ecological adaptations recurrent admixture. To understand relevance introgressive hybridization during diversification Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 hares (1-4 individuals per...
Abstract Motivation: Identification of differentially expressed genes is an important step in extracting knowledge from gene expression profiling studies. The raw data microarray and other high-throughput technologies deposited into the Gene Expression Omnibus (GEO) served as Simple Format Text (SOFT) files. However, to extract analyze GEO requires significant computational skills. Results: Here we introduce GEO2Enrichr, a browser extension for sets analyzing those with Enrichr, independent...
The genetic basis of adaptive traits has rarely been used to predict future vulnerability populations climate change. We show that light versus dark seasonal pelage in white-tailed jackrabbits (Lepus townsendii) tracks snow cover and is primarily determined by variation at endothelin receptor type B (EDNRB), corin serine peptidase (CORIN), agouti signaling protein (ASIP). Winter color was associated with deeply divergent alleles these genes, reflecting selection on both ancestral...
Environmental heterogeneity largely dictates the spatial distributions of parasites and therefore susceptibility to infection host populations. We surveyed avian malaria infections in Rufous-collared sparrows (Zonotrichia capensis) across replicated altitudinal latitudinal transects along western slope Peruvian Andes assess geographic patterns prevalence. found prevalence peaked at midelevations all 3 (x̄ ≈ 2,733 m), with highest overall observed northern transect. low levels malarial...
Determining how different populations adapt to similar environments is fundamental understanding the limits of adaptation under changing environments. Snowshoe hares (Lepus americanus) typically molt into white winter coats remain camouflaged against snow. In some warmer climates, have evolved brown camouflage-an that may spread in response climate change. We used extensive range-wide genomic data (1) resolve broad patterns population structure and gene flow (2) investigate factors shaping...
When species are continuously distributed across environmental gradients, the relative strength of selection and gene flow shape spatial patterns genetic variation, potentially leading to variable levels differentiation loci. Determining whether adaptive variation tends be structured differently than neutral along gradients is an open important question in evolutionary genetics. We performed exome-wide population genomic analysis on deer mice sampled elevational gradient nearly 4,000 m...
Understanding the links between genetic variation and fitness in natural populations is a central goal of evolutionary genetics. This monumental task spans fields classical molecular genetics, population biochemistry, physiology, developmental biology, ecology. Advances to our toolkits are facilitating integrative approaches across these traditionally separate fields, providing more complete picture genotype-phenotype map non-model systems. Here, we summarize research presented at first...
Despite its efficacy, the use of morphine for treatment chronic pain remains limited because rapid development tolerance, dependence and ultimately addiction. These undesired effects are thought to be alterations in synaptic transmission neuroplasticity within reward circuitry including striatum. In this study we used subcellular fractionation quantitative proteomics combined with computational approaches investigate morphine-induced protein profile changes at striatal postsynaptic density....
Abstract Organismal traits often represent the outcome of opposing selection pressures. Although social or sexual can cause evolution that constrain function survival (e.g. ornamental feathers), it is unclear how strength and direction respond to ecological shifts increase severity constraint. For example, reduced body size might evolve by natural enhance flight performance in migratory birds, but favouring large may provide a countervailing force. Tracheal elongation potential these...
Abstract Aim Evolutionary radiations are central to the origin and maintenance of biodiversity, yet we rarely understand how they jointly shaped by demography ecological opportunity. Astragalus is largest plant genus in world disproportionately comprised rare species restricted narrow geographic regions. Here, explored demographic mechanisms underlying patterns diversification a threatened complex endemic small desert region western United States. Location Southeast Utah, USA. Methods We...
This is a case report of the occurrence cerebral diplopia with right-side superior homonymous quadrantanopia in young woman after chiropractic neck manipulation. Magnetic resonance imaging confirmed an infarct left inferior V2/V3 (extrastriate) cortex. The characteristics are illustrated patient's drawings, and persisting abnormalities perception described area initial field defter static (computed) visual testing yielded normal results.
Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power this approach lies in its reduction the dimensionality statistical problem and incorporation biological interpretation by construction. Many approaches to have been proposed, but benchmarking their performance setting real data is difficult due lack a gold standard. In previously published work we proposed geometrical expression...
Abstract The environment shapes host–parasite interactions, but how environmental variation affects the diversity and composition of parasite‐defense genes hosts is unresolved. In vertebrates, highly variable major histocompatibility complex ( MHC ) gene family plays an essential role in adaptive immune system by recognizing pathogen infection initiating cellular response. Investigating ‐parasite associations across heterogeneous landscapes may elucidate spatially fluctuating selection...