12 papers · ranked by Valyu relevance
Henri Schmidt, Benjamin J. Raphael
Reconstructing unobserved ancestral states of a phylogenetic tree provides insight into the history of evolving systems and is one of the fundamental problems in phylogenetics. For a fixed phylogenetic tree, the most parsimonious ancestral reconstruction – a solution to the small parsimony problem – can be efficiently…
Kexin Niu, Maxat Kulmanov, Robert Hoehndorf
Current machine learning methods for enzyme function prediction primarily treat proteins as independent entities, ignoring the metabolic context in which they operate. This reductionist approach often generates biologically implausible annotations that fail to satisfy stoichiometric or thermodynamic constraints. While…
Sanjana Tule, Gabriel Foley, Chongting Zhao, Michael Forbes + 1 more
Insertions and deletions (indels) influence the genetic code in fundamentally distinct ways from substitutions, significantly impacting gene product structure and function. Despite their influence, the evolutionary history of indels is often neglected in phylogenetic tree inference and ancestral sequence…
Charlotte Merzbacher, Oisin Mac Aodha, Diego A. Oyarzún
Recent advances in synthetic biology have enabled the construction of molecular circuits that operate across multiple scales of cellular organization, such as gene regulation, signalling pathways and cellular metabolism. Computational optimization can effectively aid the design process, but current methods are…
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…
Josh A. Taylor, Alain Rapaport, Denis Dochain
Polyhedral models of metabolic networks are computationally tractable and can predict some cellular functions. A longstanding challenge is incorporating metabolites without losing tractability. In this paper, we do so using a new second-order cone representation of the Michaelis-Menten kinetics. The resulting model…
Elena J. Forchielli, Taiyao Wang, Meghan Thommes, Ioannis Ch. Paschalidis + 1 more
Given an array of phenotypes (e.g., yield across strains and conditions), one can ask how to best choose subsets of conditions that are informative about the whole dataset, enabling efficient system identification and providing a basis vector in phenotype space. Here we introduce a mixed integer linear programming…
Ehsan Motamedian, Kristaps Berzins, Reinis Muiznieks, Egils Stalidzans
Finding the best knockout strategy for coupling biomass growth and production of a target metabolite using a metabolic model is a challenge in biotechnology. In this research, a three-step method named OptEnvelope is developed based on finding minimal active reactions for a target point in the feasible solution space…
Olesya Melnichenko, Venkat S. Malladi
In the field of genomics, bioinformatics pipelines play a crucial role in processing and analyzing vast biological datasets. These pipelines, consisting of interconnected tasks, can be optimized for efficiency and scalability by leveraging cloud platforms such as Microsoft Azure. The choice of compute resources…
Oğuz Mesüm, Ali Rana Atilgan, Burak Kocuk
Antibiotics Time Machine is an important problem to understand antibiotic resistance and how it can be reversed. Mathematically, it can be modelled as follows: Consider a set of genotypes, each of which contain a set of mutated and unmutated genes. Suppose that a set of growth rate measurements of each genotype under a…
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…