A5060210907- Environmental DNA in Biodiversity Studies
- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Species Distribution and Climate Change
- Identification and Quantification in Food
- Scientific Computing and Data Management
- Bat Biology and Ecology Studies
- Research Data Management Practices
- Physiological and biochemical adaptations
- Wildlife Ecology and Conservation
- Ecology and Vegetation Dynamics Studies
- Plant and animal studies
- Data Quality and Management
- Molecular Biology Techniques and Applications
- Evolution and Paleontology Studies
- Parallel Computing and Optimization Techniques
- Avian ecology and behavior
- High Altitude and Hypoxia
- Animal Ecology and Behavior Studies
- Metabolomics and Mass Spectrometry Studies
- Distributed and Parallel Computing Systems
- Natural Language Processing Techniques
- Modular Robots and Swarm Intelligence
- 3D IC and TSV technologies
- Gene expression and cancer classification
Stony Brook University
2015-2023
University of California, Davis
2020-2022
Wildlife Conservation Society
2020-2022
National University of Singapore
2022
University of California, Berkeley
2012-2014
Abstract Third‐generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long‐read sequences. This is not only advantageous for genome projects, but also amplicon‐based high‐throughput experiments, DNA barcoding. However, relatively high error rates associated with these technologies still pose challenges generating high‐quality consensus Here, we...
The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on conservation and health applications. However, the only currently available DNA sequencer, MinION by Oxford Nanopore Technologies, has high error rate compared standard laboratory-based sequencing platforms not been systematically validated for barcoding accuracy preserved non-invasively collected tissue samples. We tested whether various sample types, methods, our...
Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard genetics conventional Sanger sequencing; however, this gradually being replaced by high-throughput (HTS) approaches which can generate millions individual reads in a single experiment. HTS sequencing, now dominates molecular biology research, has already been demonstrated use number applications, including...
Current rates of global environmental and climate change pose potential challenges for migratory species that must cope with or adapt to new conditions different across broad spatial scales throughout their annual life cycle. North American hummingbirds may be especially sensitive changes in environment due extremely small body size, high metabolic rates, dependence on nectar as a main resource. We used occurrence information from the eBird citizen‐science database track movements five...
Climate change refugia, areas buffered from climate relative to their surroundings, are of increasing interest as natural resource managers seek prioritize adaptation actions. However, evidence that refugia buffer the effects anthropogenic is largely missing. Focusing on climate-sensitive Belding's ground squirrel (Urocitellus beldingi), we predicted highly connected Sierra Nevada meadows had warmed less or shown precipitation over last century would have greater population persistence,...
High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated extent to which biochemical pathways, genes, or sites were subject parallel molecular for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions high...
How traits affect speciation is a long-standing question in evolution. We investigate whether rates are affected by the themselves or of their evolution, hummingbirds, clade with great variation rates, morphology and ecological niches. Further, we test two opposing hypotheses, postulating that promoted trait conservatism or, alternatively, divergence. To address these questions, analyse morphological (body mass bill length) niche (temperature precipitation position breadth, mid-elevation),...
Irber et al., (2024). sourmash v4: A multitool to quickly search, compare, and analyze genomic metagenomic data sets. Journal of Open Source Software, 9(98), 6830, https://doi.org/10.21105/joss.06830
In the soft gripper design work, most of designs such as gripping width and finger actuator are purely based on experience, repeated trial-and-error. scenarios, designed actuators cannot achieve best/optimized grasping performance with a specific type. This optimized is important especially for food application, minor improvement capability will be helpful to increase success ratio, during high-speed pick place tasks. That motivates us develop optimization framework, focusing how an...
The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes Health without requiring owners move, reformat, or rehost those data. This is centered on catalog integrates detailed descriptions biomedical individual Programs' Coordination Centers (DCCs) into uniform metadata model can then be indexed and searched centralized portal. Crosscut Metadata Model (C2M2) supports wide variety...
We apply an integrative taxonomy approach to delimit species of ground squirrels in the genus Otospermophilus because diverse evolutionary histories organisms shape existence taxonomic characters. Previous studies mitochondrial DNA from this group recovered three divergent lineages within beecheyi separated into northern, central, and southern geographical populations, with atricapillus nested lineage O. beecheyi. To further evaluate boundaries complex, we collected additional genetic data...
The California vole, Microtus californicus, restricted to habitat patches where water is available nearly year-round, a remnant of the mesic history southern Great Basin and Mojave deserts eastern California. voles in this region model for species-edge population dynamics through periods climatic change. We sampled from examined variation mitochondrial cytb gene, three nuclear intron regions, across 12 microsatellite markers. Samples are allocated two clades: one associated with other...
Abstract Conserving biological diversity given ongoing environmental changes requires the knowledge of how organisms respond biologically to these changes; however, we rarely have this information. This data deficiency can be addressed with coordinated monitoring programs that provide field across temporal and spatial scales process‐based models, which a method for predicting species, in particular migrating species face different conditions their range, will climate change. We evaluate...
Populations along steep environmental gradients are subject to differentiating selection that can result in local adaptation, despite countervailing gene flow, and genetic drift. In montane systems, where species often restricted narrow ranges of elevation, it is unclear whether the strong enough influence functional differentiation subpopulations differing by a few hundred meters elevation. We used targeted capture 12 501 exons from across genome, including 271 genes previously implicated...
Abstract The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on conservation and health applications. However, the only currently available DNA sequencer, MinION by Oxford Nanopore Technologies, has high error rate compared standard laboratory-based sequencing platforms not been systematically validated for barcoding accuracy preserved non-invasively collected tissue samples. We tested whether various sample types,...
Species composition in high-alpine ecosystems is a useful indicator for monitoring climatic and environmental changes at the upper limits of habitable environments. We used DNA (eDNA) analysis to document breadth biodiversity present on Earth's highest mountain, Mt. Everest (8,849 m a.s.l.) Nepal's Khumbu region. In April-May 2019, we collected eDNA from ten ponds streams between 4,500 5,500 m. Using multiple sequencing bioinformatic approaches, identified taxa 36 phyla 187 potential orders...
High viral tolerance coupled with an extraordinary regulation of the immune response makes bats a great model to study host-pathogen evolution. Although many immune-related gene gains and losses have been previously reported in bats, important families such as antimicrobial peptides (AMPs) remain understudied. We built exhaustive bioinformatic pipeline targeting major defensins cathelicidins explore AMP diversity analyze their evolution distribution across six bat families. A combination...
Abstract The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables users to discover datasets from across the U.S. National Institutes Health without requiring owners move, reformat, or rehost those data. CFDE’s is centered on catalog ingests metadata individual Program’s Coordination Centers (DCCs) into uniform model can then be indexed and searched centralized portal. This Crosscut Metadata Model (C2M2) supports wide variety types terms used by...
Third generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long read sequences. This is not only advantageous for genome projects, but also amplicon-based high-throughput experiments, DNA barcoding. However, relatively high error rates associated with these technologies still pose challenges generating quality consensus Here we present NGSpeciesID,...
The Owens Valley vole (Microtus californicus vallicola) exists in populations fragmented by natural aridity, land cultivation, highways and canals, local urbanization. We used genetic analysis of six microsatellite DNA markers to investigate potential fragmentation, drift, geographic divergence three distributed on the northern, southern, central portions range. Our analyses found that have similar levels heterozygosity, no significant differences allelic richness, differentiation. With...