A5025825738- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Genetic diversity and population structure
- Machine Learning in Bioinformatics
- Traumatic Brain Injury Research
- Species Distribution and Climate Change
- Microbial Community Ecology and Physiology
- Chromosomal and Genetic Variations
- Probiotics and Fermented Foods
- Salivary Gland Disorders and Functions
- Bacteriophages and microbial interactions
- SARS-CoV-2 detection and testing
- Ecology and Vegetation Dynamics Studies
- Gene expression and cancer classification
- Plant Virus Research Studies
- Virology and Viral Diseases
- Glycosylation and Glycoproteins Research
- Bacterial Identification and Susceptibility Testing
- Bioinformatics and Genomic Networks
- Peripheral Nerve Disorders
- Frailty in Older Adults
- Scientific Computing and Data Management
- Liver Disease Diagnosis and Treatment
- Nutritional Studies and Diet
- Fetal and Pediatric Neurological Disorders
Rice University
2020-2024
University of Illinois Urbana-Champaign
2016-2021
With advances in sequencing technologies, there are now massive amounts of genomic data from across all life, leading to the possibility that a robust Tree Life can be constructed. However, "gene tree heterogeneity", which is when different regions evolve differently, common phenomenon multi-locus sets, and reduces accuracy standard methods for species estimation do not take this heterogeneity into account. New have been developed specifically address gene heterogeneity, proven converge true...
Estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, gene duplication and loss, horizontal transfer, that result in differ each other the phylogeny. Methods to estimate presence tree discord due sorting have been developed proved be statistically consistent when only every includes full set species. We establish statistical consistency certain coalescent-based estimation methods under some models taxon deletion genes. also evaluate...
Abstract Motivation Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, process identifying nucleotides across multiple which share a common ancestor, is used as input to numerous downstream comparative analysis methods. Parsnp one few alignment methods able scale current era genomic data; however, there been no major release since its initial 2014. Results To address this gap, we developed v2, significantly...
Abstract Motivation Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, process identifying nucleotides across multiple which share a common ancestor, is used as input to numerous downstream comparative analysis methods. Parsnp one few alignment methods able scale current era genomic data; however, there been no major release since its initial 2014. Results To address this gap, we developed v2, significantly...
Abstract 16S rRNA targeted amplicon sequencing is an established standard for elucidating microbial community composition. While high‐throughput short‐read can elicit only a portion of the gene due to their limited read length, third generation in its entirety and thus provide more precise taxonomic classification. Here, we present protocol generating full‐length sequences with Oxford Nanopore Technologies (ONT) profile Emu. We select Emu analyzing ONT as it leverages information from entire...
Concussions, both single and repetitive, cause brain body alterations in athletes during contact sports. The role of the brain-gut connection changes microbiota have not been well established after sports-related concussions or repetitive subconcussive impacts. We recruited 33 Division I Collegiate football players collected blood, stool, saliva samples at three time points throughout athletic season: mid-season, following last competitive game (post-season), a resting period off-season....
The estimation of multiple sequence alignments protein sequences is a basic step in many bioinformatics pipelines, including structure prediction, family identification, and phylogeny estimation. Statistical coestimation trees under stochastic models evolution has long been considered the most rigorous technique for estimating trees, but little known about accuracy such methods on biological benchmarks. We report results an extensive study evaluating popular alignment as well statistical...
Given a new biological sequence, detecting membership in known family is basic step many bioinformatics analyses, with applications to protein structure and function prediction metagenomic taxon identification abundance profiling, among others. Yet of sequences that are distantly related public databases or fragmentary remains one the more difficult analytical problems bioinformatics.
Abstract Wastewater surveillance of vaccine-preventable diseases may provide early warning outbreaks and identify areas to target for immunization. To advance wastewater monitoring measles, mumps, rubella viruses, we developed validated a multiplexed RT-ddPCR assay the detection their RNA. Because measles-mumps-rubella (MMR) vaccine is an attenuated live virus vaccine, also that distinguishes between wild-type strains measles in it using sample collected from facility with active outbreak....
ABSTRACT 16S rRNA based analysis is the established standard for elucidating microbial community composition. While short read analyses are largely confined to genus-level resolution at best since only a portion of gene sequenced, full-length sequences have potential provide species-level accuracy. However, existing taxonomic identification algorithms not optimized increased length and error rate long-read data. Here we present Emu, novel approach that employs an expectation-maximization...
Multiple sequence alignment is an important task in bioinformatics, and alignments of large datasets containing hundreds or thousands sequences are increasingly interest. While many methods exist, the most accurate likely to be based on stochastic models where evolve down a tree with substitutions, insertions, deletions. some have been developed estimate under these models, only Bayesian method BAli-Phy has able run even moderately datasets, 100 so sequences. A technique extend enable could...
Characterizing metagenomes via kmer-based, database-dependent taxonomic classification has yielded key insights into underlying microbiome dynamics. However, novel approaches are needed to track community dynamics and genomic flux within metagenomes, particularly in response perturbations. We describe KOMB, a method for tracking genome level microbiomes. KOMB utilizes K-core decomposition identify Structural variations (SVs), specifically, population-level Copy Number Variation (CNV)...
Wastewater surveillance of vaccine-preventable diseases may provide early warning outbreaks and identify areas to target for immunization. To advance wastewater monitoring measles, mumps, rubella viruses, we developed validated a multiplexed RT-ddPCR assay the detection their RNA. Because measles-mumps-rubella (MMR) vaccine is an attenuated live virus vaccine, also that distinguishes between wild-type strains measles in it using sample collected from facility with active outbreak. We...
Interactions among microbes within microbial communities have been shown to play crucial roles in human health. In spite of recent progress, low-level knowledge bacteria driving interactions microbiomes remains unknown, limiting our ability fully decipher and control communities.We present a novel approach for identifying species microbiomes. Bakdrive infers ecological networks given metagenomic sequencing samples identifies minimum sets driver (MDS) using theory. has three key innovations...
With recent advances in sequencing technology it has become affordable and practical to sequence genomes very high depth-of-coverage, allowing researchers discover low-frequency variants the genome. However, due errors is an active area of research develop algorithms that can separate noise from true variants. LoFreq a state art algorithm for variant detection but relatively long runtime compared other tools. In addition this, interface running parallel could be simplified, multithreading as...
ABSTRACT The COVID-19 pandemic forever underscored the need for biosurveillance platforms capable of rapid detection previously unseen pathogens. Oxford Nanopore Technology (ONT) couples long-read sequencing with in-field capability, opening door to real-time, biosurveillance. Though a promising technology, streaming assignment accurate functional and taxonomic labels nanopore reads remains challenging given: (i) individual can span multiple genes, (ii) may contain truncated pseudogenes,...
The COVID-19 pandemic forever underscored the need for bio-surveillance platforms capable of rapidly detecting emerging pathogens. Oxford Nanopore Technology (ONT) couples long-read sequencing with in-field capability, opening door to real-time, biosurveillance. Though a promising technology, streaming assignment accurate functional and taxonomic labels nanopore reads remains challenging given: (i) individual can span multiple genes, (ii) may contain truncated genes pseudogenes, (iii) error...
Species tree estimation from multi-locus datasets is statistically challenging for multiple reasons, including gene heterogeneity across the genome due to incomplete lineage sorting (ILS). methods have been developed that operate by estimating trees and then using those estimate species tree. Several of these (e.g., ASTRAL, ASTRID, NJst) are provably consistent under multi-species coalescent (MSC) model, provided estimated correctly, there no missing data. Recently, Nute et al. (BMC Genomics...
The advent of long-read sequencing microbiomes necessitates the development new taxonomic profilers tailored to shotgun metagenomic datasets. Here, we introduce Lemur and Magnet, a pair tools optimized for lightweight accurate profiling is marker-gene-based method that leverages an EM algorithm reduce false positive calls while preserving true positives; Magnet whole-genome read mapping based provides detailed presence absence bacterial genomes. We demonstrate can run in minutes hours on...