BACKGROUND: Determining protein-protein interactions and their binding affinity are important in understanding cellular biological processes, discovery and design of novel therapeutics, protein engineering, and mutagenesis studies. Due to the time an...
Assay interference compounds give rise to false-positives and cause substantial problems in medicinal chemistry. Nearly 500 compound classes have been designated as pan-assay interference compounds (PAINS), which typically occur as substructures in o...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 9, 2018
Protein tertiary structure prediction is an important open challenge in bioinformatics and requires effective methods to accurately evaluate the quality of protein 3-D models generated computationally. Many quality assessment (QA) methods have been p...
Alternative splicing (AS) is generally regulated by trans-splicing factors that specifically bind to cis-elements in pre-mRNAs. The human genome encodes ∼1,500 RNA binding proteins (RBPs) that potentially regulate AS, yet their functions remain large...
In predictive model development, gene expression data is associated with the unique challenge that the number of samples (n) is much smaller than the amount of features (p). This "n ≪ p" property has prevented classification of gene expression data f...
Long non-coding RNAs are involved in biological processes throughout the cell including the nucleus, chromatin and cytosol. However, most lncRNAs remain unannotated and functional annotation of lncRNAs is difficult due to their low conservation and t...
Precision or personalized cancer medicine is a clinical approach that strives to customize therapies based upon the genomic profiles of individual patient tumors. Machine learning (ML) is a computational method particularly suited to the establishmen...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 5, 2018
Epistasis learning, which is aimed at detecting associations between multiple Single Nucleotide Polymorphisms (SNPs) and complex diseases, has gained increasing attention in genome wide association studies. Although much work has been done on mapping...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 5, 2018
An important question in microbiology is whether treatment causes changes in gut flora, and whether it also affects metabolism. The reconstruction of causal relations purely from non-temporal observational data is challenging. We address the problem ...
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