Integrating a novel algorithm in assessing the impact of floods on the genetic diversity of a high commercial value fish (Cyprinidae: Spinibarbus sp.) in Lang Son province of Vietnam.

Floods, which occur when the amount of precipitation surpasses the capacity of an area to drain it adequately, have detrimental consequences on the survival and future generations of fishes. However, few works have reported the prediction of this natural phenomenon in a relation to certain fish species, especially in fast-flowing rivers. In the specific context of the northern mountainous provinces of Vietnam, where the Spinibarbus sp.

TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer.

Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications.

Investigating the antibacterial mechanism of extracts against methicillin-resistant via and analysis.

Methicillin-resistant (MRSA) is a critical pathogen responsible for a wide variety of serious infectious diseases in humans. The accelerated phenomena of drug tolerance, drug resistance, and dysbacteriosis provoked by antibiotic misuse are impeding the effectiveness of contemporary antibiotic therapies primarily used to treat this common worldwide pathogen. In this study, the antibacterial activity of 70% ethanol extract and multiple polar solvents of were measured against the clinical MRSA isolate.

Developmental chromatin programs determine oncogenic competence in melanoma.

Oncogenes only transform cells under certain cellular contexts, a phenomenon called oncogenic competence. Using a combination of a human pluripotent stem cell–derived cancer model along with zebrafish transgenesis, we demonstrate that the transforming ability of BRAF along with additional mutations depends on the intrinsic transcriptional program present in the cell of origin. In both systems, melanocytes are less responsive to mutations, whereas both neural crest and melanoblast populations are readily transformed.

Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.

RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(-) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples.

DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.

Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the effects of variants on CTCF/cohesin-mediated insulator loops. Application of DeepMILO on variants from whole-genome sequences of 1834 patients of twelve cancer types revealed 672 insulator loops disrupted in at least 10% of patients.

Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes.

Eukaryotic chromosomes are often composed of components organized into multiple scales, such as nucleosomes, chromatin fibers, topologically associated domains (TAD), chromosome compartments, and chromosome territories. Therefore, reconstructing detailed 3D models of chromosomes in high resolution is useful for advancing genome research. However, the task of constructing quality high-resolution 3D models is still challenging with existing methods.

GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure.

Motivation: Three-dimensional (3D) genome organization plays important functional roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal conformation capturing data and analyzing them are needed for the study of 3D genome organization.

Results: We built a comprehensive graphical tool (GenomeFlow) to facilitate the entire process of modeling and analysis of 3D genome organization.

3D genome structure modeling by Lorentzian objective function.

The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data.

Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing.

Background: Reconstructing three-dimensional structures of chromosomes is useful for visualizing their shapes in a cell and interpreting their function. In this work, we reconstruct chromosomal structures from Hi-C data by translating contact counts in Hi-C data into Euclidean distances between chromosomal regions and then satisfying these distances using a structure reconstruction method rigorously tested in the field of protein structure determination.

Results: We first evaluate the robustness of the overall reconstruction algorithm on noisy simulated data at various levels of noise by comparing with some of the state-of-the-art reconstruction methods.

MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data.

Motivation: The three-dimensional (3D) conformation of chromosomes and genomes play an important role in cellular processes such as gene regulation, DNA replication and genome methylation. Several methods have been developed to reconstruct 3D structures of individual chromosomes from chromosomal conformation capturing data such as Hi-C data. However, few methods can effectively reconstruct the 3D structures of an entire genome due to the difficulty of handling noisy and inconsistent inter-chromosomal contact data.

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.

Background: The entire collection of genetic information resides within the chromosomes, which themselves reside within almost every cell nucleus of eukaryotic organisms. Each individual chromosome is found to have its own preferred three-dimensional (3D) structure independent of the other chromosomes. The structure of each chromosome plays vital roles in controlling certain genome operations, including gene interaction and gene regulation.

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data.

Chromosomes are not positioned randomly within a nucleus, but instead, they adopt preferred spatial conformations to facilitate necessary long-range gene-gene interactions and regulations. Thus, obtaining the 3D shape of chromosomes of a genome is critical for understanding how the genome folds, functions and how its genes interact and are regulated. Here, we describe a method to reconstruct preferred 3D structures of individual chromosomes of the human genome from chromosomal contact data generated by the Hi-C chromosome conformation capturing technique.