Methods (San Diego, Calif.)
Apr 13, 2019
Polyadenylation signals (PAS) are found in most protein-coding and some non-coding genes in eukaryotes. Their accurate recognition improves understanding gene regulation mechanisms and recognition of the 3'-end of transcribed gene regions where prema...
Methods (San Diego, Calif.)
Mar 26, 2019
Due to the large numbers of transcription factors (TFs) and cell types, querying binding profiles of all valid TF/cell type pairs is not experimentally feasible. To address this issue, we developed a convolutional-recurrent neural network model, call...
Methods (San Diego, Calif.)
Mar 22, 2019
Inverse Virtual Screening is a powerful technique in the early stage of drug discovery process. This technique can provide important clues for biologically active molecules, which is useful in the following researches of durg discovery. In this work,...
Methods (San Diego, Calif.)
Mar 21, 2019
Enhancer is a DNA sequence of a genome that controls transcription of downstream target genes. Enhancers are known to be associated with certain epigenetic signatures. Machine learning tools, such as CSI-ANN, ChromHMM, and RFECS, were developed for p...
Methods (San Diego, Calif.)
Mar 16, 2019
The human microbiome plays a number of critical roles, impacting almost every aspect of human health and well-being. Conditions in the microbiome have been linked to a number of significant diseases. Additionally, revolutions in sequencing technology...
Methods (San Diego, Calif.)
Mar 7, 2019
We present machine learning models of human genome three-dimensional structure that combine one dimensional (linear) sequence specificity, epigenomic information, and transcription factor binding profiles, with the polymer-based biophysical simulatio...
Methods (San Diego, Calif.)
Mar 7, 2019
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...
Methods (San Diego, Calif.)
Feb 27, 2019
The biomedical literature provides a rich source of knowledge such as protein-protein interactions (PPIs), drug-drug interactions (DDIs) and chemical-protein interactions (CPIs). Biomedical relation extraction aims to automatically extract biomedical...
Methods (San Diego, Calif.)
Aug 10, 2018
Due to the complex and intricate nature associated with their production, the acoustic-prosodic properties of a speech signal are modulated with a range of health related effects. There is an active and growing area of machine learning research in th...
Methods (San Diego, Calif.)
Jun 8, 2018
Mobile health (m-Health) has been repeatedly called the biggest technological breakthrough of our modern times. Similarly, the concept of big data in the context of healthcare is considered one of the transformative drivers for intelligent healthcare...