Search · four archives
Search · four archives
12 papers · ranked by Valyu relevance
Sergio Garcia, Cong Trinh
A large space of chemicals with broad industrial and consumer applications could be synthesized by engineered microbial biocatalysts. However, the current strain optimization process is prohibitively laborious and costly to produce one target chemical and often requires new engineering efforts to produce new molecules.…
Nicola Hallmann, Catalina Guerra-Cornejo, Karl Burgess, Charlotte Merzbacher + 1 more
The optimization of culture media is critical for improving the efficiency and cost of cellular production systems. Traditional approaches often rely on extensive experimental trials or statistical methods, which can be both costly and time-consuming. Here, we present gsMOBO, a computational approach for media design…
Paul Bello, Pedro Gallardo, Lorena Pradenas, Jacques A. Ferland + 1 more
Childhood obesity is an undeniable reality and has shown a rapid growth in many countries. Obesity at an early age not only increases the risks of chronic diseases but also produces a problem for the whole healthcare system. One way to alleviate this problem is to provide each patient with an appropriate menu that can…
David Bassen, Michael Vilkhovoy, Mason Minot, Jonathan T Butcher + 1 more
Ensemble modeling is a well established approach for obtaining robust predictions and for simulating course grained population behavior in deterministic mathematical models. In this study, we present a multiobjective based technique to estimate model ensembles, the Pareto Optimal Ensemble Technique in the Julia…
Otto I. Pulkkinen, Prson Gautam, Ville Mustonen, Tero Aittokallio
Combinatorial therapies are required to treat patients with advanced cancers that have become resistant to monotherapies through rewiring of redundant pathways. Due to a massive number of potential drug combinations, there is a need for systematic approaches to identify safe and effective combinations for each patient…
Lu Hong, Tanja Kortemme
With recent methodological advances in the field of computational protein design, in particular those based on deep learning, there is an increasing need for frameworks that allow for coherent, direct integration of different models and objective functions into the generative design process. Here we demonstrate how…
Sergio Garcia, Cong T. Trinh
Diversity of cellular metabolism can be harnessed to produce a large space of molecules. However, development of optimal strains with high product titers, rates, and yields required for industrial production is laborious and expensive. To accelerate the strain engineering process, we have recently introduced a modular…
Rohan Chandraghatgi, Hai-Feng Ji, Gail L. Rosen, Bahrad A. Sokhansanj
Recent advances in computational methods provide the promise of dramatically accelerating drug discovery. While math-ematical modeling and machine learning have become vital in predicting drug-target interactions and properties, there is untapped potential in computational drug discovery due to the vast and complex…
Marc Griesemer, Ali Navid
Multi-objective Optimization (MO) is an important tool for quantitative examination of the trade-offs faced by biological organisms. Using genome-scale constraint-based models of metabolism (GSMs), Multi-Objective Flux Analysis (MOFA) allows MO analyses of trade-offs among key biological tasks. The leading software…
Álvaro Rubio-Largo, Miguel A. Vega-Rodríguez
The alignment among three or more nucleotides/amino-acids sequences at the same time is known as Multiple Sequence Alignment (MSA), an NP-hard optimization problem. The time complexity of finding an optimal alignment raises exponentially when the number of sequences to align increases. In this work, we deal with a…
Babita K. Verma, Ahmad A. Mannan, Fuzhong Zhang, Diego A. Oyarzún
Recent progress in synthetic biology allows the construction of dynamic control circuits for metabolic engineering. This technology promises to overcome many challenges encountered in traditional pathway engineering, thanks to their ability to self-regulate gene expression in response to bioreactor perturbations. The…
Adithya Sagar, Rachel LeCover, Christine Shoemaker, Jeffrey Varner
Mathematical modeling is a powerful tool to analyze, and ultimately design biochemical networks. However, the estimation of the parameters that appear in biochemical models is a significant challenge. Parameter estimation typically involves expensive function evaluations and noisy data, making it difficult to quickly…