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The Atlantic chub mackerel, Scomber colias Gmelin, 1789, is a medium-size pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotated the first high-quality draft genome assembly of S. colias, produced with PacBio HiFi long reads and Illumina Paired-End short reads. The estimated genome... Читать дальше...

Due to human error, sample swapping in large cohort studies with heterogeneous data types (e.g. mix of Oxford Nanopore, Pacific Bioscience, Illumina data, etc.) remains a common issue plaguing large-scale studies. At present, all sample swapping detection methods require costly and unnecessary (e.g. if data is only used for genome assembly) alignment, positional sorting, and indexing of the data in order to compare similarly. As studies include more samples and new sequencing data types, robust quality... Читать дальше...

Hepatic steatosis is the initial manifestation of abnormal liver functions and often leads to liver diseases such as non-alcoholic fatty liver disease in humans and fatty liver syndrome in animals. In this study, we conducted a comprehensive analysis of a large chicken population consisting of 705 adult hens by combining host genome resequencing, liver transcriptome, proteome, and metabolome analysis, as well as microbial 16S rRNA gene sequencing of each gut segment. The results showed the heritability... Читать дальше...

Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy, largely due to the paucity of reliable biomarkers for early detection and therapeutic targeting. Existing blood protein biomarkers for PDAC often suffer from replicability issues, arising from inherent limitations such as unmeasured confounding factors in conventional epidemiologic study designs. To circumvent these limitations, we use genetic instruments to identify proteins with genetically predicted levels to be associated with PDAC risk. Читать дальше...

With the advancement of long-read sequencing technologies and their more widespread use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also the need for measuring completeness and accuracy of such assemblies... Читать дальше...

Most available reference genomes lack the sequence map of sex-limited (such as Y and W) chromosomes, which make the assemblies incomplete and difficult to conduct further research on sex chromosomes. Recent advances in long reads sequencing and population sequencing raise the opportunity to assemble sex-limited chromosomes without the traditional complicated experimental efforts. We introduced the first computational method, Sorting long Reads of Y or other sex-limited chromosome (SRY), which achieved... Читать дальше...

The accurate identification of the functional elements in the bovine genome is a fundamental requirement for high quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalogue of transcript isoforms across bovine tissues.
A total number of 160,820 unique transcripts (50% protein-coding) representing 34,882 unique genes (60% protein-coding) were identified across tissues. Among them,... Читать дальше...

As biological data increases, we need additional infrastructure to share it and promote interoperability. While major effort has been put into sharing data, relatively less emphasis is placed on sharing metadata. Yet, sharing metadata is also important, and in some ways has a wider scope than sharing data itself.
Here, we present PEPhub, an approach to improve sharing and interoperability of biological metadata. PEPhub provides an API, natural language search, and user-friendly web-based sharing and editing of sample metadata tables. Читать дальше...

Phenome-wide association studies (PheWASs) have been conducted on Asian populations, including Koreans, but many were based on chip or exome genotyping data. Such studies have limitations regarding whole-genome-wide association analysis, making it crucial to have genome-to-phenome association information with the largest possible whole-genome and matched phenome data to conduct further population-genome studies and develop healthcare services based on population genomics.
Here, we present 4,157... Читать дальше...

Molecular Property Diagnostic Suite (MPDS) was conceived and developed as an open-source disease-specific web portal based on Galaxy. MPDSCOVID-19 was developed for COVID-19 as a one-stop solution for drug discovery research. Galaxy platforms enable the creation of customized workflows connecting various modules in the web server. The architecture of MPDSCOVID-19 effectively employs Galaxy v22.04 features, which are ported on CentOS 7.8 and Python 3.7. MPDSCOVID-19 provides significant updates and... Читать дальше...