Understanding the governing principles behind organisms' metabolism and growth
underpins their effective deployment as bioproduction chassis. A central objective of …

Motivation Deep neural network (DNN) algorithms were utilized in predicting various
biomedical phenotypes recently, and demonstrated very good prediction performances …

Motivation Understanding the mechanisms and structural mappings between molecules and
pathway classes are critical for design of reaction predictors for synthesizing new molecules …

Food-drug interactions (FDIs) arise when nutritional dietary consumption regulates
biochemical mechanisms involved in drug metabolism. This study proposes FDMine, a …

Transcription factor binding sites (TFBS) and RNA-binding proteins (RBP) plays a key role in
gene regulation, transcription, RNA editing. Identifying and locating these potential sites is …

Abstract Two-dimensional (2D) chemical fingerprints are widely used as binary features for
the quantification of structural similarity of chemical compounds, which is an important step …

Abstract Motivation The Anatomical Therapeutic Chemical (ATC) system is an official
classification system established by the World Health Organization for medicines. Correctly …

Group contribution (GC) methods are conventionally used in thermodynamics analysis of
metabolic pathways to estimate the standard Gibbs energy change (Δ r G′ o) of enzymatic …

Recently, metabolic pathway design has attracted considerable attention and become an
increasingly important area in metabolic engineering. Manual or computational methods …

The fundamental laws of thermodynamics determine the feasibility of all natural processes
including metabolism. Although several algorithms have been developed to predict the most …