CysHis zinc finger (ZF) domains engineered to bind specific target sequences in the genome provide an effective strategy for programmable regulation of gene expression, with many potential therapeutic applications. However, the structurally intricate...
Cancer cells are formed when the associated, active genes fail to function the way they are meant to function. Multiple genes collectively control cell growth by activating a proper set of genes. Regulation of gene expression is controlled through th...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2022
Identification of transcription factor binding sites (TFBSs) is essential for revealing the rules of protein-DNA binding. Although some computational methods have been presented to predict TFBSs using epigenomic and sequence features, most of them ig...
Despite extensive efforts to generate and analyze reference genomes, genetic models to predict gene regulation and cell fate decisions are lacking for most species. Here, we generated whole-body single-cell transcriptomic landscapes of zebrafish, Dro...
In recent years, major advances have been made in various chromosome conformation capture technologies to further satisfy the needs of researchers for high-quality, high-resolution contact interactions. Discriminating the loops from genome-wide conta...
Determining transcriptional factor binding sites (TFBSs) is critical for understanding the molecular mechanisms regulating gene expression in different biological conditions. Biological assays designed to directly mapping TFBSs require large sample s...
A common goal in the convolutional neural network (CNN) modeling of genomic data is to discover specific sequence motifs. Post hoc analysis methods aid in this task but are dependent on parameters whose optimal values are unclear and applying the dis...
Mammalian genomes have multiple enhancers spanning an ultralong distance (>megabases) to modulate important genes, but it is unclear how these enhancers coordinate to achieve this task. We combine multiplexed CRISPRi screening with machine learning t...
Journal of bioinformatics and computational biology
Jul 25, 2022
The basic helix loop helix (bHLH) superfamily is a large and diverse protein family that plays a role in various vital functions in nearly all animals and plants. The bHLH proteins form one of the largest families of transcription factors found in pl...
Biochimica et biophysica acta. Gene regulatory mechanisms
Jun 8, 2022
Transcription factors directly bind to DNA and regulate the expression of the gene, causing epigenetic modification of the DNA. They often mediate epigenetic parameters of transcriptional and posttranscriptional mechanisms, and their expression activ...