BACKGROUND: The ability to predict which pairs of amino acid residues in a protein are in contact with each other offers many advantages for various areas of research that focus on proteins. For example, contact prediction can be used to reduce the c...
Systems biology requires not only genome-scale data but also methods to integrate these data into interpretable models. Previously, we developed approaches that organize omics data into a structured hierarchy of cellular components and pathways, call...
Protein-peptide interactions play an important role in major cellular processes, and are associated with several human diseases. To understand and potentially regulate these cellular function and diseases it is important to know the molecular details...
Measuring conditional relatedness between a pair of genes is a fundamental technique and still a significant challenge in computational biology. Such relatedness can be assessed by gene expression similarities while suffering high false discovery rat...
The ability to predict local structural features of a protein from the primary sequence is of paramount importance for unraveling its function in absence of experimental structural information. Two main factors affect the utility of potential predict...
IEEE/ACM transactions on computational biology and bioinformatics
Mar 7, 2019
Antimicrobial peptides are short amino acid sequences that may be antibacterial, antifungal, and antiviral. Most machine learning methodologies applied to identifying antibacterial peptides have developed feature vectors of identical lengths for each...
Integration of multi-omics in cardiovascular diseases (CVDs) presents high potentials for translational discoveries. By analyzing abundance levels of heterogeneous molecules over time, we may uncover biological interactions and networks that were pre...
Journal of chemical information and modeling
Mar 6, 2019
Predicting the outcome of biological assays based on high-throughput imaging data is a highly promising task in drug discovery since it can tremendously increase hit rates and suggest novel chemical scaffolds. However, end-to-end learning with convol...
Journal of molecular graphics & modelling
Mar 5, 2019
BACKGROUND: The activation of follicle stimulating hormone receptor (FSHR) by FSH and the consequent downstream signaling activities are crucial for reproductive health. The role of FSHR in tumor progression as well as osteoporosis advancement has al...
The amino acid sequence of a protein encodes the blueprint of its native structure. To predict the corresponding structural fold from the protein's sequence is one of most challenging problems in computational biology. In this work, we introduce DEST...
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