It is well known that DNA sequence contains a certain amount of transcription factors (TF) binding sites, and only part of them are identified through biological experiments. However, these experiments are expensive and time-consuming. To overcome th...
IEEE/ACM transactions on computational biology and bioinformatics
Aug 31, 2018
Gapped k-mers frequency vectors (gkm-fv) has been presented for extracting sequence features. Coupled with support vector machine (gkm-SVM), gkm-fvs have been used to achieve effective sequence-based predictions. However, the huge computation of a la...
Journal of computational biology : a journal of computational molecular cell biology
Aug 22, 2018
The identification of transcription factor binding sites (TFBSs) is a problem for which computational methods offer great hope. Thus far, the expectation maximization (EM) technique has been successfully utilized in finding TFBSs in DNA sequences, bu...
IEEE/ACM transactions on computational biology and bioinformatics
Aug 7, 2018
Although convolutional neural networks (CNN) have outperformed conventional methods in predicting the sequence specificities of protein-DNA binding in recent years, they do not take full advantage of the intrinsic weakly-supervised information of DNA...
Class labels are required for supervised learning but may be corrupted or missing in various applications. In binary classification, for example, when only a subset of positive instances is labeled whereas the remaining are unlabeled, positive-unlabe...
IEEE/ACM transactions on computational biology and bioinformatics
Mar 26, 2018
Although Deep learning algorithms have outperformed conventional methods in predicting the sequence specificities of DNA-protein binding, they lack to consider the dependencies among nucleotides and the diverse binding lengths for different transcrip...
Cancers that appear pathologically similar often respond differently to the same drug regimens. Methods to better match patients to drugs are in high demand. We demonstrate a promising approach to identify robust molecular markers for targeted treatm...
Comparative biochemistry and physiology. Part D, Genomics & proteomics
Nov 11, 2017
In order to understand the mechanisms underlying stress responses, meta-analysis of transcriptome is made to identify differentially expressed genes (DEGs) and their biological, molecular and cellular mechanisms in response to stressors. The present ...
Transcriptional enhancers regulate spatio-temporal gene expression. While genomic assays can identify putative enhancers en masse, assigning target genes is a complex challenge. We devised a machine learning approach, McEnhancer, which links target g...
Understanding the molecular machinery involved in transcriptional regulation is central to improving our knowledge of an organism's development, disease, and evolution. The building blocks of this complex molecular machinery are an organism's genomic...