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Accurate computational identification of promoters remains a challenge as these key DNA regulatory regions have variable structures composed of functional motifs that provide gene specific initiation of transcription. In this paper we…
Computational identification of promoters is notoriously difficult as human genes often have unique promoter sequences that provide regulation of transcription and interaction with transcription initiation complex. While there are many…
Promoter is a short region of DNA which is responsible for initiating transcription of specific genes. Development of computational tools for automatic identification of promoters is in high demand. According to the difference of functions,…
Transcription factors are proteins that regulate the expression of genes by binding to specific genomic regions known as Transcription Factor Binding Sites (TFBSs), typically located in the promoter regions of those genes. Accurate…
Deep-predictive-coding networks (DPCNs) are hierarchical, generative models. They rely on feed-forward and feed-back connections to modulate latent feature representations of stimuli in a dynamic and context-sensitive manner. A crucial…
Purpose: This study aimed to enhance protein sequence classification using natural language processing (NLP) techniques while addressing the impact of sequence similarity on model performance. We compared various machine learning and deep…
Background: In organisms' genomes, promoters are short DNA sequences on the upstream of structural genes, with the function of controlling genes' transcription. Promoters can be roughly divided into two classes: constitutive promoters and…
Gene-regulatory enhancers have been identified by many lines of evidence, including evolutionary conservation, regulatory protein binding, chromatin modifications, and DNA sequence motifs. To integrate these different approaches, we…
Background: In addition to known protein-coding genes, large amount of apparently non-coding sequence are conserved between the human and mouse genomes. It seems reasonable to assume that these conserved regions are more likely to contain…
In the genome biology research, regulatory genome modeling is an important topic for many regulatory downstream tasks, such as promoter classification, transaction factor binding sites prediction. The core problem is to model how regulatory…
Locating the promoter region in DNA sequences is of paramount importance in the field of bioinformatics. This is a problem widely studied in the literature, however, not yet fully resolved. Some researchers have presented remarkable results…
Evolutionary computation methods have been successfully applied to neural networks since two decades ago, while those methods cannot scale well to the modern deep neural networks due to the complicated architectures and large quantities of…
Convolutional Neural Networks (CNNs) have gained a significant attraction in the recent years due to their increasing real-world applications. Their performance is highly dependent to the network structure and the selected optimization…
We study the impact of neural networks in text classification. Our focus is on training deep neural networks with proper weight initialization and greedy layer-wise pretraining. Results are compared with 1-layer neural networks and Support…
Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promoters and initiate transcription. Finding the exact location of these binding sites (aka motifs) is important in a variety…
This study proposes a novel biologically-motivated learning method for deep convolutional neural networks (CNNs). The combination of CNNs and back propagation (BP) learning is the most powerful method in recent machine learning regimes.…
Gene enhancers control when and where genes switch on, yet their sequence diversity and tissue specificity make them hard to pinpoint in colorectal cancer. We take a sequence-only route and fine-tune DNABERT-2, a transformer genomic…
Big Data works perfectly along with Deep learning to extract knowledge from a huge amount of data. However, this processing could take a lot of training time. Genomics is a Big Data science with high dimensionality. It relies on deep…
The deep Convolutional Neural Network (CNN) is the state-of-the-art solution for large-scale visual recognition. Following basic principles such as increasing the depth and constructing highway connections, researchers have manually…
It is important to study on genes affecting to growing environment of main crops. Especially the recognition problem of promoter region, which is the problem to predict whether DNA sequences contain promoter regions or not, is prior to find…