9 papers · ranked by Valyu relevance
Ghanshyam Chandra, Md Helal Hossen, Stephan Scholz, Alexander T Dilthey + 2 more
Affordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference genome is unreliable in highly polymorphic and repetitive regions, further…
Mercè Llabrés, Gabriel Valiente
Beside socio-economic issues, coronavirus pandemic COVID-19, the infectious disease caused by the newly discovered coronavirus SARS-CoV-2, has caused a deep impact in the scientific community, that has considerably increased its effort to discover the infection strategies of the new virus. Among the extensive and…
Richard Schuster, Jeffrey O. Hanson, Matt Strimas-Mackey, Joseph R. Bennett
The resources available for conserving biodiversity are limited, and so protected areas need to be established in places that will achieve objectives for minimal cost. Two of the main algorithms for solving systematic conservation planning problems are Simulated Annealing (SA) and Integer linear programming (ILP).…
Mengzhen Guo, Stefan Grünewald
We present Lpnet, a variant of the widely used Neighbor-net method that approximates pairwise distances between taxa by a circular phylogenetic network. We first apply standard methods to construct a binary phylogenetic tree and then use integer linear programming to compute an optimal circular orderings that agrees…
Vaibhav Rajan, Carl Kingsford, Xiuwei Zhang
The study of the evolutionary history of biological networks enables deep functional understanding of various bio-molecular processes. Network growth models, such as the Duplication-Mutation with Complementarity (DMC) model, provide a principled approach to characterizing the evolution of protein-protein interactions…
Conor F. Hayes, Andre R. Goncalves, Steven Magana-Zook, Jacob Pettit + 3 more
Designing effective antibody libraries is a challenging combinatorial search problem in computational biology. We propose a novel integer linear programming (ILP) method that explicitly controls diversity and affinity objectives when generating candidate libraries. Our approach formulates library design as a…
Salem Malikić, Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, Mohammad Haghir Ebrahimabadi + 1 more
Single-cell sequencing data has great potential in reconstructing the evolutionary history of tumors. Rapid advances in single-cell sequencing technology in the past decade were followed by the design of various computational methods for inferring trees of tumor evolution. Some of the earliest of these methods were…
Pouya Ahadi, Balabhaskar Balasundaram, Juan S. Borrero, Charles Chen
In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic…
Daniel Machado
Genome-scale metabolic modeling is a powerful framework for predicting metabolic phenotypes of any organism with an annotated genome. For two decades, this framework has been used for rational design of microbial cell factories. In the last decade, the range of applications has exploded, and new frontiers have emerged…