The three-dimensional genome organization influences diverse nuclear processes. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks, random forest, and gradient boosting to predict cohesin-mediated chromatin interaction strength between any two loci in the genome. The predictions of ChIPr correlate well with ChIA-PET data in four cell lines.
View Article and Find Full Text PDF, often referred to as the 'roundworm', provides a powerful model for studying cell autonomous and cell-cell interactions through the direct observation of embryonic development . By leveraging the precisely mapped cell lineage at single cell resolution, we are able to study at a systems level how early embryonic cells communicate across morphogenetic domains for the coordinated processes of gene expressions and collective cellular behaviors that regulate tissue morphogenesis. In this study, we developed a computational framework for the exploration of the morphogenetic domain cell signaling networks that may regulate gastrulation and embryonic organogenesis.
View Article and Find Full Text PDFBackground: Core promoter controls transcription initiation. However, little is known for core promoter diversity in the human genome and its relationship with diseases. We hypothesized that as a functional important component in the genome, the core promoter in the human genome could be under evolutionary selection, as reflected by its highly diversification in order to adjust gene expression for better adaptation to the different environment.
View Article and Find Full Text PDFBackground: Pathogenic variation in and () is one of the most frequent genetic predispositions for hereditary breast cancer. The identification of the variant carriers plays an important role in prevention and treatment of cancer. Despite a population size of 1.
View Article and Find Full Text PDFPurpose: DNA mismatch repair (MMR) genes play important roles in maintaining genome stability. Mutations in MMR genes disrupt their mismatch repair function, cause genome instability and lead to increased risk of cancer in the mutation carriers as represented by Lynch Syndrome. Studies have identified a large number of MMR variants, mostly in the Caucasian population, whereas data from non-Caucasian populations remain poorly illustrated.
View Article and Find Full Text PDFBRCA1 and BRCA2 play essential roles in maintaining the genome stability. Pathogenic germline mutations in these two genes disrupt their function, lead to genome instability and increase the risk of developing breast and ovarian cancers. BRCA mutations have been extensively screened in Caucasian populations, and the resulting information are used globally as the standard reference in clinical diagnosis, treatment and prevention of BRCA-related cancers.
View Article and Find Full Text PDFWe report the draft genome of Brevundimonas diminuta strain XGC1, isolated from a tuberculosis-infected patient in Gujarat, India. This study also reveals that the B. diminuta XGC1 strain has acquired mutation to confer resistance to quinolone drugs.
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