The Bioinformatic Applications of Hi-C and Linked Reads.

Long-range sequencing grants insight into additional genetic information beyond what can be accessed by both short reads and modern long-read technology. Several new sequencing technologies, such as "Hi-C" and "Linked Reads", produce long-range datasets for high-throughput and high-resolution genome analyses, which are rapidly advancing the field of genome assembly, genome scaffolding, and more comprehensive variant identification. In this review, we focused on five major long-range sequencing technologies: high-throughput chromosome conformation capture (Hi-C), 10X Genomics Linked Reads, haplotagging, transposase enzyme linked long-read sequencing (TELL-seq), and single- tube long fragment read (stLFR).

Image2Flow: A proof-of-concept hybrid image and graph convolutional neural network for rapid patient-specific pulmonary artery segmentation and CFD flow field calculation from 3D cardiac MRI data.

Computational fluid dynamics (CFD) can be used for non-invasive evaluation of hemodynamics. However, its routine use is limited by labor-intensive manual segmentation, CFD mesh creation, and time-consuming simulation. This study aims to train a deep learning model to both generate patient-specific volume-meshes of the pulmonary artery from 3D cardiac MRI data and directly estimate CFD flow fields.

Identifying the best PCR enzyme for library amplification in NGS.

PCR amplification is a necessary step in many next-generation sequencing (NGS) library preparation methods [1, 2]. Whilst many PCR enzymes are developed to amplify single targets efficiently, accurately and with specificity, few are developed to meet the challenges imposed by NGS PCR, namely unbiased amplification of a wide range of different sizes and GC content. As a result PCR amplification during NGS library prep often results in bias toward GC neutral and smaller fragments.

Haplotype-specific assembly of shattered chromosomes in esophageal adenocarcinomas.

The epigenetic landscape of cancer is regulated by many factors, but primarily it derives from the underlying genome sequence. Chromothripsis is a catastrophic localized genome shattering event that drives, and often initiates, cancer evolution. We characterized five esophageal adenocarcinoma organoids with chromothripsis using long-read sequencing and transcriptome and epigenome profiling.

A Deep Learning Pipeline for Assessing Ventricular Volumes from a Cardiac MRI Registry of Patients with Single Ventricle Physiology.

Purpose To develop an end-to-end deep learning (DL) pipeline for automated ventricular segmentation of cardiac MRI data from a multicenter registry of patients with Fontan circulation (Fontan Outcomes Registry Using CMR Examinations [FORCE]). Materials and Methods This retrospective study used 250 cardiac MRI examinations (November 2007-December 2022) from 13 institutions for training, validation, and testing. The pipeline contained three DL models: a classifier to identify short-axis cine stacks and two U-Net 3+ models for image cropping and segmentation.

Inferring gene regulatory networks using transcriptional profiles as dynamical attractors.

Genetic regulatory networks (GRNs) regulate the flow of genetic information from the genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the phenotypic characteristics of cells. Numerous methods exist for profiling mRNA transcript levels and identifying protein-DNA binding interactions at the genome-wide scale. These enable researchers to determine the structure and output of transcriptional regulatory networks, but uncovering the complete structure and regulatory logic of GRNs remains a challenge.

NCTC3000: a century of bacterial strain collecting leads to a rich genomic data resource.

The National Collection of Type Cultures (NCTC) was founded on 1 January 1920 in order to fulfil a recognized need for a centralized repository for bacterial and fungal strains within the UK. It is among the longest-established collections of its kind anywhere in the world and today holds approximately 6000 type and reference bacterial strains - many of medical, scientific and veterinary importance - available to academic, health, food and veterinary institutions worldwide. Recently, a collaboration between NCTC, Pacific Biosciences and the Wellcome Sanger Institute established the NCTC3000 project to long-read sequence and assemble the genomes of up to 3000 NCTC strains.

Shape-driven deep neural networks for fast acquisition of aortic 3D pressure and velocity flow fields.

Computational fluid dynamics (CFD) can be used to simulate vascular haemodynamics and analyse potential treatment options. CFD has shown to be beneficial in improving patient outcomes. However, the implementation of CFD for routine clinical use is yet to be realised.

The evolution of two transmissible cancers in Tasmanian devils.

Tasmanian devils have spawned two transmissible cancer lineages, named devil facial tumor 1 (DFT1) and devil facial tumor 2 (DFT2). We investigated the genetic diversity and evolution of these clones by analyzing 78 DFT1 and 41 DFT2 genomes relative to a newly assembled, chromosome-level reference. Time-resolved phylogenetic trees reveal that DFT1 first emerged in 1986 (1982 to 1989) and DFT2 in 2011 (2009 to 2012).

Rising abuse of veterinary drugs.

There has been a significant increase in veterinary drugs found on toxicology screens and postmortem analyses, especially in the Northeast region of the US. This article details the effects and treatment of two common culprits: xylazine and tiletamine-zolazepam.

The genome sequence of the European water vole, Linnaeus 1758.

We present a genome assembly from an individual male (the European water vole; Chordata; Mammalia; Rodentia; Cricetidae). The genome sequence is 2.30 gigabases in span.

The complete genome sequence of (Tyzzer 1929), a common gut parasite of chickens.

We present a genome assembly from a clonal population of Houghton parasites (Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The genome sequence is 53.25 megabases in span.

The genome sequence of the Norway rat, Berkenhout 1769.

We present a genome assembly from an individual male (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span.

Plant diversity and community composition in managed humid coastal dune slacks in NW England.

Humid coastal dune slacks are an endangered habitat in Northwestern Europe. In the UK, dune slacks are currently classified as being in 'unfavourable' condition, with projected decrease in England of up to 30% by 2036. Studies in mainland Europe suggest that regional factors (e.

The genome sequence of the European turtle dove, Linnaeus 1758.

We present a genome assembly from an individual female (the European turtle dove; Chordata; Aves; Columbidae). The genome sequence is 1.18 gigabases in span.

A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.).

Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology.

Reducing Contrast Agent Dose in Cardiovascular MR Angiography with Deep Learning.

Background: Contrast-enhanced magnetic resonance angiography (MRA) is used to assess various cardiovascular conditions. However, gadolinium-based contrast agents (GBCAs) carry a risk of dose-related adverse effects.

Purpose: To develop a deep learning method to reduce GBCA dose by 80%.

Transcriptional Circuits Regulating Developmental Processes in .

is a commensal member of the human microbiota that colonizes multiple niches in the body including the skin, oral cavity, and gastrointestinal and genitourinary tracts of healthy individuals. It is also the most common human fungal pathogen isolated from patients in clinical settings. can cause a number of superficial and invasive infections, especially in immunocompromised individuals.

The genome sequence of the eastern grey squirrel, Gmelin, 1788.

We present a genome assembly from an individual male (the eastern grey squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.82 gigabases in span.

Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm.

Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants and has become a key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Here, we report using PacBio long-read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome for the MHco3(ISE).