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Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
BackgroundThe alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a...
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Integer programming for selecting set of informative markers in paternity inference
BackgroundParentage information is fundamental to various life sciences. Recent advances in sequencing technologies have made it possible to...
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Generalized Linear Models
In the generalized linear model (GLM) (which is not highly general) y = Xβ + ϵ, the response variables are normally distributed, with constant...
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ELIMINATOR: essentiality analysis using multisystem networks and integer programming
A gene is considered as essential when it is indispensable for cells to grow and replicate in a certain environment. However, gene essentiality is...
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Generalized Linear Mixed Models for Proportions and Percentages
In this chapter, we will review generalized linear mixed models (GLMMs) whose response can be either a proportion or a percentage. For proportion and...
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A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming
Analysis of chemical graphs is becoming a major research topic in computational molecular biology due to its potential applications to drug design....
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Using mixed integer programming and airborne laser scanning to generate forest management units
Airborne laser scanning (ALS) has been widely applied to estimate tree and forest attributes, but it can also drive the segmentation of forest areas....
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LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences
BackgroundThe function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the...
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Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations
The interpretation of complex biological datasets requires the identification of representative variables that describe the data without critical...
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Optimal Production and Dispatch of Renewable Natural Gas, Electricity, and Fertilizer in Municipal-Scale Anaerobic Digestion Supply Chains
Global energy consumption is increasing, and there is a growing demand for renewable energy systems that replace fossil fuels with clean...
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MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
BackgroundIn this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and...
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Heuristic shortest hyperpaths in cell signaling hypergraphs
BackgroundCell signaling pathways, which are a series of reactions that start at receptors and end at transcription factors, are basic to systems...
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Global exact optimisations for chloroplast structural haplotype scaffolding
BackgroundScaffolding is an intermediate stage of fragment assembly. It consists in orienting and ordering the contigs obtained by the assembly of...
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Site reduction in redundant ecosystem sampling schemes
Data collection for fresh-water regions of The Ecosystem Health Monitoring Program (EHMP), in southeast Queensland, Australia, involves the sampling...
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Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections
Minimal Cut Sets (MCSs) identify sets of reactions which, when removed from a metabolic network, disable certain cellular functions. The traditional...
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Optimization of Harvesting Priority of Sugarcane Farms by the Generalized Assignment Problem
Mathematical modeling is a suitable method for solving agricultural production planning problems due to the restriction of resources available. In...
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Deep learning methods improve linear B-cell epitope prediction
BackgroundB-cell epitopes play important roles in vaccine design, clinical diagnosis, and antibody production. Although some models have been...
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Visualization of Oligonucleotide-Based Probes Along Pseudochromosomes Using RIdeogram, KaryoploteR, and Circlize (Circos)
Fluorescence in situ hybridization (FISH) using oligonucleotide-based probes is an innovative modification of classic FISH techniques, enabling...
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Development of performance and learning rate evaluation models in robot-assisted surgery using electroencephalography and eye-tracking
The existing performance evaluation methods in robot-assisted surgery (RAS) are mainly subjective, costly, and affected by shortcomings such as the...
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Biodiesel Supply Chain Optimization Modeled with Geographical Information System (GIS) and Mixed-Integer Linear Programming (MILP) for the Northern Great Plains Region
Drought-tolerant, industrial oilseeds such as Camelina sativa (camelina) grown on marginal land are being considered as feedstock alternatives to...
