IEEE journal of biomedical and health informatics
Jul 30, 2019
Metabolic reprogramming is a hallmark of cancer. In cancer cells, transcription factors (TFs) govern metabolic reprogramming through abnormally increasing or decreasing the transcription rate of metabolic enzymes, which provides cancer cells growth a...
BACKGROUND: Identification of functional non-coding variants and their mechanistic interpretation is a major challenge of modern genomics, especially for precision medicine. Transcription factor (TF) binding profiles and epigenomic landscapes in refe...
BACKGROUND: Visualization tools for deep learning models typically focus on discovering key input features without considering how such low level features are combined in intermediate layers to make decisions. Moreover, many of these methods examine ...
International journal of molecular sciences
Jul 12, 2019
Transcription factor binding sites (TFBSs) play an important role in gene expression regulation. Many computational methods for TFBS prediction need sufficient labeled data. However, many transcription factors (TFs) lack labeled data in cell types. W...
BACKGROUND: Transcription factors (TFs) play important roles in the regulation of gene expression. They can activate or block transcription of downstream genes in a manner of binding to specific genomic sequences. Therefore, motif discovery of these ...
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...
IEEE/ACM transactions on computational biology and bioinformatics
Jan 10, 2019
Most proposed methods for TF-binding site (TFBS) predictions only use low order dependencies for predictions due to the lack of efficient methods to extract higher order dependencies. In this work, we first propose a novel method to extract higher or...
AJR. American journal of roentgenology
Jan 2, 2019
OBJECTIVE: The purpose of this study is to evaluate the potential value of machine learning (ML)-based high-dimensional quantitative CT texture analysis in predicting the mutation status of the gene encoding the protein polybromo-1 (PBRM1) in patient...
BACKGROUND: Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solving protein-DNA complex struc...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 21, 2018
Transcription factors (TFs) are the major components of human gene regulation. In particular, they bind onto specific DNA sequences and regulate neighborhood genes in different tissues at different developmental stages. Non-synonymous single nucleoti...