[HTML][HTML] Antioxidant response elements: Discovery, classes, regulation and potential applications
Exposure to antioxidants and xenobiotics triggers the expression of a myriad of genes
encoding antioxidant proteins, detoxifying enzymes, and xenobiotic transporters to offer …
encoding antioxidant proteins, detoxifying enzymes, and xenobiotic transporters to offer …
Machine learning: a powerful tool for gene function prediction in plants
Recent advances in sequencing and informatic technologies have led to a deluge of publicly
available genomic data. While it is now relatively easy to sequence, assemble, and identify …
available genomic data. While it is now relatively easy to sequence, assemble, and identify …
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Motivation Deciphering the language of non-coding DNA is one of the fundamental
problems in genome research. Gene regulatory code is highly complex due to the existence …
problems in genome research. Gene regulatory code is highly complex due to the existence …
A compendium of genetic regulatory effects across pig tissues
Abstract The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been
established to develop a public resource of genetic regulatory variants in livestock, which is …
established to develop a public resource of genetic regulatory variants in livestock, which is …
HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors
We present a major update of the HOCOMOCO collection that provides DNA binding
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …
[HTML][HTML] CiiiDER: A tool for predicting and analysing transcription factor binding sites
The availability of large amounts of high-throughput genomic, transcriptomic and
epigenomic data has provided opportunity to understand regulation of the cellular …
epigenomic data has provided opportunity to understand regulation of the cellular …
In silico methods for identification of potential active sites of therapeutic targets
J Liao, Q Wang, F Wu, Z Huang - Molecules, 2022 - mdpi.com
Target identification is an important step in drug discovery, and computer-aided drug target
identification methods are attracting more attention compared with traditional drug target …
identification methods are attracting more attention compared with traditional drug target …
A novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shape
Y Zhang, Z Wang, Y Zeng, Y Liu, S **ong… - Briefings in …, 2022 - academic.oup.com
The discovery of putative transcription factor binding sites (TFBSs) is important for
understanding the underlying binding mechanism and cellular functions. Recently, many …
understanding the underlying binding mechanism and cellular functions. Recently, many …
[HTML][HTML] Invited review: Good practices in genome-wide association studies to identify candidate sequence variants in dairy cattle
Genotype data from dairy cattle selection programs have greatly facilitated GWAS to identify
variants related to economic traits. Results can enhance the accuracy of genomic prediction …
variants related to economic traits. Results can enhance the accuracy of genomic prediction …
A review about transcription factor binding sites prediction based on deep learning
Y Zeng, M Gong, M Lin, D Gao, Y Zhang - Ieee Access, 2020 - ieeexplore.ieee.org
Transcription factors (TFs) recognize and bind to specific DNA sequences, thereby altering
the chromatin structure and regulating transcription. TFs aid in the formation of a guide …
the chromatin structure and regulating transcription. TFs aid in the formation of a guide …