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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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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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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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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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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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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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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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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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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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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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PPalign: optimal alignment of Potts models representing proteins with direct coupling information
BackgroundTo assign structural and functional annotations to the ever increasing amount of sequenced proteins, the main approach relies on...
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Maximizing the economic benefit for cable yarding timber harvesting operations by spatially optimizing tree selection
The efficiency of forest logging operations can be strongly affected by the layout of the harvesting pattern, which is usually based on silvicultural...
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Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks
BackgroundThe concept of minimal cut sets (MCS) has become an important mathematical framework for analyzing and (re)designing metabolic networks....
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Harvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data
BackgroundSupervised learning from high-throughput sequencing data presents many challenges. For one, the curse of dimensionality often leads to...
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Optimal Location for Renewable Gas Production and Distribution Facilities: Resource Planning and Management
Renewable energy contributes to the energy portfolios of many countries. One form of renewable energy is syngas which is generated from bio-residues....
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Matchtigs: minimum plain text representation of k-mer sets
We propose a polynomial algorithm computing a minimum plain-text representation of k -mer sets, as well as an efficient near-minimum greedy heuristic....
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ESKEMAP: exact sketch-based read map**
BackgroundGiven a sequencing read, the broad goal of read map** is to find the location(s) in the reference genome that have a “similar sequence”....
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The distance and median problems in the single-cut-or-join model with single-gene duplications
Background.In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while...
