A5020357256- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Genetic Mapping and Diversity in Plants and Animals
- Algorithms and Data Compression
- Evolution and Paleontology Studies
- Evolution and Genetic Dynamics
- Viral Infections and Outbreaks Research
- SARS-CoV-2 and COVID-19 Research
- Gene expression and cancer classification
- Plant Pathogens and Fungal Diseases
- Genetic and phenotypic traits in livestock
- Mycorrhizal Fungi and Plant Interactions
- Evolutionary Algorithms and Applications
- Vaccine Coverage and Hesitancy
- Bioinformatics and Genomic Networks
- Renal Diseases and Glomerulopathies
- Multiple Myeloma Research and Treatments
- Pregnancy and preeclampsia studies
- Morphological variations and asymmetry
- Mangiferin and Mango Extracts
- Acute Myeloid Leukemia Research
- Gene Regulatory Network Analysis
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- COVID-19 epidemiological studies
Temple University
2019-2025
Children's Mercy Hospital
2023
Abstract We introduce the 12th version of Molecular Evolutionary Genetics Analysis (MEGA12) software. This latest brings many significant improvements by reducing computational time needed for selecting optimal substitution models and conducting bootstrap tests on phylogenies using maximum likelihood (ML) methods. These are achieved implementing heuristics that minimize likely unnecessary computations. Analyses empirical simulated datasets show substantial savings these without compromising...
Global sequencing of genomes severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to reveal new genetic variants that are the key unraveling its early evolutionary history and tracking global spread over time. Here we present heretofore cryptic mutational spatiotemporal dynamics SARS-CoV-2 from an analysis thousands high-quality genomes. We report likely most recent common ancestor SARS-CoV-2, reconstructed through a novel application advancement computational methods...
Cases abound in which nearly identical traits have appeared distant species facing similar environments. These unmistakable examples of adaptive evolution offer opportunities to gain insight into their genetic origins and mechanisms through comparative analyses. Here, we present an approach build models that underlie the independent convergent using evolutionary sparse learning with paired contrast (ESL-PSC). We tested hypothesis common genes sites are involved two key traits: C4...
Phylogenomic analyses of long sequences, consisting many genes and genomic segments, reconstruct organismal relationships with high statistical confidence. But, inferred can be sensitive to excluding just a few sequences. Currently, there is no direct way identify fragile the associated individual gene sequences in species. Here, we introduce novel metrics for gene-species sequence concordance clade probability derived from evolutionary sparse learning models. We validated these using fungi,...
Cases abound in which nearly identical traits have appeared distant species facing similar environments. These unmistakable examples of adaptive evolution offer opportunities to gain insight into their genetic origins and mechanisms through comparative analyses. Here, we present a novel genomics approach build models that underlie the independent convergent using evolutionary sparse learning. We test hypothesis common genes sites are involved two key traits: C4 photosynthesis grasses...
Abstract We report the likely most recent common ancestor of SARS-CoV-2 – coronavirus that causes COVID-19. This progenitor genome was recovered through a novel application and advancement computational methods initially developed to reconstruct mutational history tumor cells in patient. The differs from earliest coronaviruses sampled China by three variants, implying none patients represent index case or gave rise all human infections. However, multiple infections USA harbored genetic...
We introduce a supervised machine learning approach with sparsity constraints for phylogenomics, referred to as evolutionary sparse (ESL). ESL builds models genomic loci-such genes, proteins, segments, and positions-as parameters. Using the Least Absolute Shrinkage Selection Operator, selects only most important loci explain given phylogenetic hypothesis or presence/absence of trait. do not directly involve conventional parameters such rates substitutions between nucleotides, rate variation...
A common practice in molecular systematics is to infer phylogeny and then scale it time by using a relaxed clock method calibrations. This sequential analysis ignores the effect of phylogenetic uncertainty on divergence estimates their confidence/credibility intervals. An alternative times jointly incorporate errors into dating. We compared performance these two alternatives reconstructing evolutionary timetrees computer-simulated empirical datasets. found joint analyses produce similar...
Abstract Success story of plant-based medicine had been overlooked during the advent modern pharmaceutical industry. Despite negligence multimillion-dollar drug industry, people entirely rely on medicinal plants in some part world. In this study, we have emphasized going back to those traditional practices figure out their underlying mechanism move forward phytochemical based development. We screened Medicinal Plant Database Bangladesh 1.0 (MPDB1.0) and on-going extension, MPDB2.0, that...
Felsenstein’s bootstrap resampling approach, applied in thousands of research articles, imposes a high computational burden for very long sequence alignments. We show that the bootstrapping collection little subsamples, coupled with median bagging subsample confidence limits, produces accurate phylogenetic relationships fraction time and memory. The bootstraps approach will enhance rigor, efficiency, parallelization big data phylogenomic analyses.
Background: The Coronavirus disease 2019 (COVID-19) pandemic is a public health threat. Equitable access to safe and effective vaccines critical end the COVID-19 pandemic. Promoting uptake of (particularly those against COVID-19) require understanding whether people are willing be vaccinated, reasons behind their decision. Objectives: This study aimed assess vaccine compliance factors associated with it among residents Kathmandu valley. Methods: A cross-sectional analytical was conducted...
Phylogenomic analyses of long sequences, consisting many genes and genomic segments, infer organismal relationships with high statistical confidence. But, these can be sensitive to excluding just a few sequences. Currently, there is no direct way identify fragile the associated individual gene sequences in species. Here, we introduce novel metrics for gene-species sequence concordance clade probability derived from evolutionary sparse learning models. We validated using fungi, plant, animal...
Abstract We introduce the 12th version of Molecular Evolutionary Genetics Analysis ( MEGA ) software. This latest brings many significant improvements by reducing computational time needed for selecting optimal substitution models and conducting bootstrap tests on phylogenies using maximum likelihood (ML) methods. These are achieved implementing heuristics that minimize likely unnecessary computations. Analyses empirical simulated datasets show substantial savings these without compromising...
The selection of the optimal substitution model molecular evolution imposes a high computational burden for long sequence alignments in phylogenomics. We discovered that analysis multiple tiny subsamples site patterns from full alignment recovers correct when sites subsample are upsampled to match total number alignment. costs maximum-likelihood analyses reduced by orders magnitude subsample-upsample (SU) approach because contains only small fraction all patterns. present an adaptive...
Abstract An individual's chronological age does not always correspond to the health of different tissues in their body, especially cases disease. Therefore, estimating and contrasting physiological with an may be a useful tool diagnose disease its progression. In this study, we present novel metrics quantify loss phylogenetic diversity hematopoietic stem cells (HSCs), which are precursors most blood cell types associated many blood-related diseases. These showed excellent correspondence...
A bstract We introduce a supervised machine learning approach with sparsity constraints for phylogenomics, referred to as evolutionary sparse (ESL). ESL builds models genomic loci—such genes, proteins, segments, and positions—as parameters. Using the Least Absolute Shrinkage Selection Operator (LASSO), selects only most important loci explain given phylogenetic hypothesis or presence/absence of trait. does not directly model conventional parameters such rates substitutions between...