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New imputation methodologies for genotype-by-environment data: an extensive study of properties of estimators
The site regression model (SREG) is utilized by plant breeders for analyzing multi-environment trials (MET) to examine the relationships among test...
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Analyzing postprandial metabolomics data using multiway models: a simulation study
BackgroundAnalysis of time-resolved postprandial metabolomics data can improve the understanding of metabolic mechanisms, potentially revealing...
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Molecular Dynamics Simulation Methods to Study Structural Dynamics of Proteins
Molecular dynamics (MD) simulation is a computational technique for understanding the physical motions of atomic and molecular particles. In this...
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Tower yarder powertrain performance simulation analysis: electrification study
Radical changes are necessary to address challenges related to global warming and pollution. Ever-tightening emission standards for combustion...
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Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods
BackgroundComputational cell type deconvolution enables the estimation of cell type abundance from bulk tissues and is important for understanding...
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How much can farmers pay for weeding robots? A Monte Carlo simulation study
This paper investigates the Maximum Acquisition Values (MAVs) of weeding robots and their determinants in both organic and conventional sugar beet...
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Molecular Dynamics Simulation to Study Protein Conformation and Ligand Interaction
The field of molecular dynamics (MD) simulations has become indispensable today to studying the conformational flexibility and dynamics of proteins...
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Bioinformatics in Pathway Identification, Design, Modelling, and Simulation
Bioinformatics plays a crucial contribution in the study of complex biological systems, particularly in the areas of pathway identification, design,...
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Estimation of carbon footprint and sources of emissions of an extensive alpaca production system
A cradle-to-farm gate life cycle assessment was conducted following international standards (ISO 14040, 2006) to estimate sources of greenhouse gas...
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Structural Evolution and Stability Simulation of Wetland Ecological Network: A Case Study of Wuhan City, China
The stability of the wetland ecological network (WEN) is affected by the population gathering and rapid urbanization in metropolises. The...
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Dimensionality of genomic information and its impact on genome-wide associations and variant selection for genomic prediction: a simulation study
BackgroundIdentifying true positive variants in genome-wide associations (GWA) depends on several factors, including the number of genotyped...
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Cytomulate: accurate and efficient simulation of CyTOF data
Recently, many analysis tools have been devised to offer insights into data generated via cytometry by time-of-flight (CyTOF). However, objective...
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Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei
BackgroundThe “Assay for Transposase Accessible Chromatin sequencing” (ATAC-seq) is an efficient and easy to implement protocol to measure chromatin...
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Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework
Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing...
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Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme
In protein simulation or structure refinement based on values of observable quantities measured in (aqueous) solution, solvent (water) molecules may...
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SViMULATE: a computer program facilitating interactive, multi-mode simulation of analytical ultracentrifugation data
The ability to simulate sedimentation velocity (SV) analytical ultracentrifugation (AUC) experiments has proved to be a valuable tool for research...
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Fuel treatment effectiveness at the landscape scale: a systematic review of simulation studies comparing treatment scenarios in North America
BackgroundThe risk of destructive wildfire on fire-prone landscapes with excessive fuel buildup has prompted the use of fuel reduction treatments to...
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Effects of Stimulus Sequences on Brain-Computer Interfaces Using Code-Modulated Visual Evoked Potentials: An Offline Simulation
Brain-computer interfaces (BCIs) translate brain activity into computer commands opening a novel non-muscular channel for communication and control....
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Proposal and extensive test of a calibration protocol for crop phenology models
A major effect of environment on crops is through crop phenology, and therefore, the capacity to predict phenology for new environments is important....
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Molecular Dynamics Simulation of the Conformational Mobility of the Lipid-Binding Site in the Apolipoprotein E Isoforms ε2, ε3, and ε4
AbstractNeurodegenerative disorders, particularly Alzheimer’s disease, have become a major global healthcare issue. Despite extensive research, the...
