Journal of computational biology : a journal of computational molecular cell biology
Jun 21, 2022
Codon optimization of a DNA sequence can significantly increase efficiency of protein expression, reducing the cost to manufacture biologic pharmaceuticals. Although directed methods based on such factors as codon usage bias and GC nucleotide content...
Journal of computational biology : a journal of computational molecular cell biology
Mar 23, 2022
We study the problem of binary agreement in a spiking neural network (SNN). We show that binary agreement on inputs can be achieved with of auxiliary neurons. Our simulation results suggest that agreement can be achieved in our network in time. We...
Journal of computational biology : a journal of computational molecular cell biology
Mar 11, 2022
Convolutional neural networks (CNNs), a class of deep learning models, have experienced recent success in modeling sensory cortices and retinal circuits through optimizing performance on machine learning tasks, otherwise known as task optimization. P...
Journal of computational biology : a journal of computational molecular cell biology
Jan 21, 2022
Template-based modeling (TBM), including homology modeling and protein threading, is one of the most reliable techniques for protein structure prediction. It predicts protein structure by building an alignment between the query sequence under predict...
Journal of computational biology : a journal of computational molecular cell biology
Jan 5, 2022
Deep neural networks (DNNs) have been recently proposed for quartet tree phylogeny estimation. Here, we present a study evaluating recently trained DNNs in comparison to a collection of standard phylogeny estimation methods on a heterogeneous collect...
Journal of computational biology : a journal of computational molecular cell biology
Jan 5, 2022
Non-negative matrix factorization (NMF) is a fundamental matrix decomposition technique that is used primarily for dimensionality reduction and is increasing in popularity in the biological domain. Although finding a unique NMF is generally not possi...
Journal of computational biology : a journal of computational molecular cell biology
Nov 29, 2021
Biomedical knowledge graphs are crucial to support data-intensive applications in the life sciences and health care. These graphs can be extended by generating a heterogeneous graph that contains both ontology terms and biomedical entities. However, ...