optimal transport

Improved assemblies and comparison of two ancient Yersinia pestis genomes

The paper improves the assembly of two ancient Yersinia pestis genomes using an optimization-based gap-filling method, resulting in highly supported assemblies with 95% ancient read coverage.

Efficient Breeding by Genomic Mating

This paper introduces genomic mating as an efficient breeding method using genome-wide markers and genetic algorithms, showing it outperforms truncation selection in improving breeding values for complex traits.

Optimal inventorying and monitoring of taxonomic, phylogenetic and functional diversity

The paper optimizes sampling protocols for inventorying and monitoring taxonomic, phylogenetic, and functional diversity across different ecosystems, showing cost-effective methods with minimal bias.

On the optimal response vigor and choice under variable motivational drives

This paper derives optimal choice and response vigor under variable motivational drives using an optimal control framework, showing constant response rates and explaining probability matching in multi-outcome environments.

Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

The paper introduces a method to identify active modules in multi-layer weighted gene co-expression networks using continuous optimization, validated on synthetic and real data with an R package.

JuPOETs: A Constrained Multiobjective Optimization Approach to Estimate Biochemical Model Ensembles in the Julia Programming Language

JuPOETs estimates biochemical model ensembles using constrained multiobjective optimization, achieving faster performance than Octave on test functions and providing parameter sets that balance conflicting training objectives.

Modeling Chromosome Maintenance as a Property of Cell Cycle in Saccharomyces cerevisiae

The paper uses linear programming to model chromosome maintenance in yeast, identifying gene interactions and temporal gene influence during the cell cycle.

Cerebrospinal Fluid and Interstitial Fluid Motion via the Glymphatic Pathway Modelled by Optimal Mass Transport

This study models glymphatic fluid flow in a live rat brain using optimal mass transport and diffusion equations to predict tracer concentrations.

Design and strain selection criteria for bacterial communication networks

The paper discusses challenges in designing bacterial communication networks using Escherichia coli and Geobacter sulfurreducens, and proposes optimization methods to balance energy production and biomass growth.

Synthesizing Combination Therapies for Evolutionary Dynamics of Disease for Nonlinear Pharmacodynamics

The paper extends a previous algorithm for designing combination therapies by modeling nonlinear pharmacodynamics using piecewise linear approximations and optimal controller synthesis for positive systems.