The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data mo...
BACKGROUND: The analysis and interpretation of data generated from patient-derived clinical samples relies on access to high-quality bioinformatics resources. These are maintained and updated by expert curators extracting knowledge from unstructured ...
Human genome contains ca. 20,000 protein-coding genes that could be translated into millions of unique protein species (proteoforms). Proteoforms coded by a single gene often have different functions, which implies different protein partners. By inte...
Self-Interacting Proteins (SIPs), whose two or more copies can interact with each other, have significant roles in cellular functions and evolution of Protein Interaction Networks (PINs). Knowing whether a protein can act on itself is important to un...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2020
Identifying residue-residue contacts in protein-protein interactions or complex is crucial for understanding protein and cell functions. DCA (direct-coupling analysis) methods shed some light on this, but they need many sequence homologs to yield acc...
MOTIVATION: Computationally predicting disease genes helps scientists optimize the in-depth experimental validation and accelerates the identification of real disease-associated genes. Modern high-throughput technologies have generated a vast amount ...
Protein-protein interactions (PPIs) are important for the study of protein functions and pathways involved in different biological processes, as well as for understanding the cause and progression of diseases. Several high-throughput experimental tec...
Prioritization of cancer-related genes from gene expression profiles and proteomic data is vital to improve the targeted therapies research. Although computational approaches have been complementing high-throughput biological experiments on the under...
Journal of bioinformatics and computational biology
Jun 1, 2019
Deep learning technologies are permeating every field from image and speech recognition to computational and systems biology. However, the application of convolutional neural networks (CCNs) to "omics" data poses some difficulties, such as the proces...
N 6-methyladenosine (m6A) is the most prevalent post-transcriptional modification in eukaryotes, and plays a pivotal role in various biological processes, such as splicing, RNA degradation and RNA-protein interaction. We report here a prediction fram...