A5038934812- Genomics and Phylogenetic Studies
- Evolution and Paleontology Studies
- Genetic diversity and population structure
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Metabolomics and Mass Spectrometry Studies
- Antimicrobial Resistance in Staphylococcus
- Gut microbiota and health
- Plant and animal studies
- Cell Image Analysis Techniques
- Morphological variations and asymmetry
- Bacterial biofilms and quorum sensing
- Statistical Methods and Inference
- Machine Learning in Bioinformatics
- Genetic Associations and Epidemiology
- Bacterial Genetics and Biotechnology
- Genetic Mapping and Diversity in Plants and Animals
- Genetics, Bioinformatics, and Biomedical Research
- Wildlife Ecology and Conservation
- Microbial Community Ecology and Physiology
- Advanced Causal Inference Techniques
- Data Analysis with R
- Plant Parasitism and Resistance
- Animal Vocal Communication and Behavior
- Sparse and Compressive Sensing Techniques
Wisconsin Institutes for Discovery
2020-2025
University of Wisconsin–Madison
2015-2025
Plant (United States)
2022
Emory University
2018-2021
Yale University
2017
Duke University
2017
Universidad Nacional Autónoma de México
2017
University of Connecticut
2017
Iowa State University
2017
University of California, Los Angeles
2017
Phylogenetic networks are necessary to represent the tree of life expanded by edges events such as horizontal gene transfers, hybridizations or flow. Not all species follow paradigm vertical inheritance their genetic material. While a great deal research has flourished into inference phylogenetic trees, statistical methods infer still limited and under development. The main disadvantage existing is lack scalability. Here, we present method from multi-locus data in pseudolikelihood framework....
PhyloNetworks is a Julia package for the inference, manipulation, visualization, and use of phylogenetic networks in an interactive environment. Inference done with maximum pseudolikelihood from gene trees or multi-locus sequences (SNaQ), possible bootstrap analysis. first software providing tools to summarize set (from posterior sample) measures tree edge support, hybrid node support. Networks can be used comparative analysis continuous traits, estimate ancestral states do regression. The...
Delimitation of species based exclusively on genetic data has been advocated despite a critical knowledge gap: how might such approaches fail because they rely alone, and would their accuracy be improved by using multiple types. We provide here the requisite framework for addressing these key questions. Because both phenotypic molecular can analyzed in common Bayesian with our program iBPP, we compare delimited taxa alone versus when integrated data. also evaluate integration improve...
Coalescent-based methods are now broadly used to infer evolutionary relationships between groups of organisms under the assumption that incomplete lineage sorting (ILS) is only source gene tree discordance. Many these known consistently estimate species when all their assumptions met. Nonetheless, little work has been done test robustness such violations assumptions. Here, we study performance two most efficient coalescent-based methods, ASTRAL and NJst, in presence flow. Gene flow violates...
The goal of phylogenetic comparative methods (PCMs) is to study the distribution quantitative traits among related species. observed are often seen as result a Brownian Motion (BM) along branches tree. Reticulation events such hybridization, gene flow or horizontal transfer, can substantially affect species' traits, but not modeled by Phylogenetic networks have been designed represent reticulate evolution. As they become available for downstream analyses, new models trait evolution needed,...
Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring may be hindered by complexities homology determination in taxa. We use simulations to show that phasing alleles from allopolyploid individuals improve network inference under multispecies coalescent obtaining true with fewer loci compared haplotype consensus...
Abstract Motivation Scientists world-wide are putting together massive efforts to understand how the biodiversity that we see on Earth evolved from single-cell organisms at origin of life and this diversification process is represented through Tree Life. Low sampling rates high heterogeneity in rate evolution across sites lineages produce a phenomenon denoted “long branch attraction” (LBA) which long nonsister estimated be sisters regardless their true evolutionary relationship. LBA has been...
Staphylococcus aureus is a widespread, hospital- and community-acquired pathogen, many strains of which are antibiotic resistant. It causes diverse diseases, ranging from local to systemic infection, affects both the skin internal organs, including heart, lungs, bones, brain.
To protect tropical forest biodiversity, we need to be able detect it reliably, cheaply, and at scale. Automated detection of sound producing animals from passively recorded soundscapes via machine-learning approaches is a promising technique towards this goal, but constrained by the necessity large training data sets. Using in Borneo Convolutional Neural Network model (CNN), investigate i) minimum viable set size for accurate prediction call types ('sonotypes'), ii) extent which...
High-dimensional mixed-effects models are an increasingly important form of regression in which the number covariates rivals or exceeds samples, collected groups clusters. The penalized likelihood approach to fitting these relies on a coordinate descent algorithm that lacks guarantees convergence global optimum. Here, we empirically study behavior this simulated and real examples three types data common modern biology: transcriptome, genome-wide association, microbiome data. Our simulations...
Abstract Background and Aims Resolving the phylogeny of hornworts is critical in understanding evolution key morphological characters that are unique to group, including pyrenoid. Extensive phylogenomic analyses have revealed unexpected complexities placement Leiosporoceros, previously identified sister taxon other hornworts. We explore role incomplete lineage sorting (ILS) ancient reticulation resolving interrelationships comprehending diversification evolutionary processes within Methods...
Constructing reliable microbiome co-occurrence networks and identifying disease-associated taxa remain major challenges in research due to variability introduced by different inference algorithms. To overcome these limitations, we present CMIMN, a novel R package that uses Bayesian network framework based on conditional mutual information infer robust microbial interaction networks. further enhance reliability, construct consensus integrating results from CMIMN three widely used...
This special collection includes topics related to the development of novel methods for reconstructing phylogenetic networks from different mathematical, statistical, and computational approaches that highlight challenges network reconstruction needs contemporary genomic data. In addition, broadcasts diverse applications on a wide variety organisms across Tree Life.
Abstract Gene flow is increasingly recognized as an important macroevolutionary process. The many mechanisms that contribute to gene (e.g. introgression, hybridization, lateral transfer) uniquely affect the diversification of dynamics species, making it be able account for these idiosyncrasies when constructing phylogenetic models. Existing phylogenetic‐network simulators macroevolution are limited in ways they model flow. We present SiPhyNetwork , R package simulating networks under a...
In Bayesian Network Regression models, networks are considered the predictors of continuous responses. These models have been successfully used in brain research to identify regions that associated with specific human traits, yet their potential elucidate microbial drivers biological phenotypes for microbiome remains unknown. particular, challenging due high dimension and sparsity compared networks. Furthermore, unlike connectome research, it is usually expected presence microbes has an...
Background The delta-toxin (δ-toxin) of Staphylococcus aureus is the only hemolysin shown to cause mast cell degranulation and linked atopic dermatitis, a chronic inflammatory skin disease. We sought characterize variation in δ-toxin production across S. strains identify genetic loci potentially associated with differences between strains. Methods A set 124 was genome-sequenced levels stationary phase supernatants determined by high performance liquid chromatography (HPLC). SNPs kmers were...
Vancomycin-intermediate Staphylococcus aureus (VISA) typically arises through accumulation of chromosomal mutations that alter cell-wall thickness and global regulatory pathways. Genome-based prediction VISA requires understanding whether strain background influences patterns mutation lead to resistance. We used an iterative method experimentally evolve three important methicillin-resistant S. (MRSA) backgrounds-(CC1, CC5 CC8 (USA300)) generate a library 120 laboratory selected isolates. At...
Premise of the Study The species boundaries wild and cultivated potatoes are controversial, with most taxonomic problems in potato clade. We here provide first in‐depth phylogenetic study clade to explore possible causes these problems. Methods examined 131 diploid accessions, using 12 nuclear orthologs, producing an aligned data set 14,072 DNA characters, 2171 which parsimony‐informative. analyzed produce phylogenies perform concordance analysis goodness‐of‐fit tests. Key Results There is...
When grown on agar surfaces, microbes can produce distinct multicellular spatial structures called colonies, which contain characteristic sizes, shapes, edges, textures, and degrees of opacity color. For over one hundred years, researchers have used these morphology cues to classify bacteria guide more targeted treatment pathogens. Advances in genome sequencing technology revolutionized our ability bacterial isolates while genomic methods are the ascendancy, morphological characterization...
This paper studies the following question: where should an adversary place outlier of a given magnitude in order to maximize error subspace estimated by PCA? We give exact location this worst possible outlier, and expression maximum error. Equivalently, we determine information-theoretic bounds on how much can tilt its direction. turn provides universal (worst-case) for PCA under arbitrary noisy settings. Our results also have several implications adaptive PCA, online rank-one updates....
A microbial network is a mathematical representation of community where nodes represent microbes and edges interactions.It well-recognized that are among the main drivers biological phenotypes in soil, plants, animals alike, thus, their study has vast implications for plant human health.In particular, recognizing microbial, environmental, agricultural factors drive soil crucial to comprehend processes connected health, identify global practices sustainable agriculture, as well predict...
The abundance of gene flow in the Tree Life challenges notion that evolution can be represented with a fully bifurcating process which cannot capture important biological realities like hybridization, introgression, or horizontal transfer. Coalescent-based network methods are increasingly popular, yet not scalable for big data, because they need to perform heuristic search space networks as well numerical optimization NP-hard. Here, we introduce novel method reconstruct phylogenetic based on...
Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to patterns genetic heritability that are unexpected under traditional, bifurcating models species trees. This phenomenon has led development methods infer these varied hybridization events, both reconstruct networks directly, well summary predict individual from a subset taxa. However, lack empirical comparisons between – especially those pertaining large with scenarios hinders their practical use....
Abstract Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring may be hindered by complexities homology determination in taxa. We use simulations to show that phasing alleles from allopolyploid individuals improve network inference under multispecies coalescent obtaining true with fewer loci compared haplotype...