Genome research biorxiv Most new Epidemiology papers also should be submitted to medRxiv, but if a paper contains no health-related information, authors may choose to submit it to another bioRxiv subject category (e. Yet this data stream has also created challenges for finding interoperable and extensible modes of analysis. Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia. CRISPR-based gene editors derived from microbes, while powerful, often show significant functional tradeoffs when ported into non-native environments, such as human cells. 2015) indicates a genome completeness of 91. However, the existing reference genome for pigs is incomplete, with thousands of segments and missing centromeres and telomeres, which limits our understanding of the important traits in these genomic regions. Jan 17, 2024 · The remarkable pace of genomic data generation focused on the physiology and ecology of microbes is rapidly transforming our understanding of life at the micron scale. To address this issue, we present a near complete genome assembly for Oct 24, 2019 · ↵ † Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia. We train Evo 2 with 7B and 40B parameters to have an unprecedented 1 million token context window with single-nucleotide resolution. Analyses of data from genome-wide association studies (GWAS) on unrelated individuals have shown that for human traits and disease, approximately one-third to two-thirds of Sep 9, 2024 · annotated. . 2 assembly was incomplete and unresolved Mar 1, 2023 · Amphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. 4% of 89 articles), followed by Genome Biology (39. Here, we newly developed a genome-free computational method to aid accurate transcriptome assembly, using the amphioxus as the example. Thus, Sep 24, 2024 · As genomic research continues to advance, sharing of genomic data and research outcomes has become increasingly important for fostering collaboration and accelerating scientific discovery. Mar 4, 2024 · Consensus guidelines for assessing eligibility of pathogenic DNA variants for antisense oligonucleotide treatments. This version of the manuscript has been revised to include updated Ensembl annotation of Sscrofa11. openRxiv is the organizational home of bioRxiv and medRxiv, platforms for sharing biomedical research manuscripts before journal peer review. 7% of 169 articles). Citation. The analysis of vertebrate single-copy orthologs via BUSCO (Simao et al. The Sscrofa10. WGS datasets were employed to construct the pan-genome and identify genomic variants, including single nucleotide polymorphisms (SNPs) and DNA insertion and deletion (InDels), within the genome. bioRxiv DOIs assigned prior to December 11, 2019, have a simple six-digit suffix, whereas those assigned after this date will also include the date stamp for the day of submission approval (see below). Addressing this Genome Biology publishes outstanding research in all areas of biology and biomedicine studied from a genomic and post-genomic perspective. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. 8%. However, there is a need for ongoing development to improve accessibility and affordability of the required data, increase the range of usable sample types, and reliably resolve the most challenging, repetitive GigaScience had the highest proportion of articles from preprints in 2018 (49. Via integrating ten next generation sequencing (NGS) transcriptome datasets and one third-generation sequencing (TGS) dataset, we Jul 5, 2019 · The domestic pig ( Sus scrofa ) is important both as a food source and as a biomedical model with high anatomical and immunological similarity to humans. Feb 21, 2025 · We introduce Evo 2, a biological foundation model trained on 9. RNA-seq and miRNA-seq datasets were used to Mar 25, 2019 · Heritability, the proportion of phenotypic variance explained by genetic factors, can be estimated from pedigree data [1][1], but such estimates are uninformative with respect to the underlying genetic architecture. Since then, inventories of genome-wide diversity have been generated at increasingly precise Nov 16, 2022 · To characterise the somatic alterations in colorectal cancer (CRC), we conducted whole-genome sequencing analysis of 2,023 tumours. The genome, annotation, and gene expression data are publicly accessible through a dedicated genome browser (https://glshark. Biofilm formation and cell aggregation under a high shear force depends on temperature and salt concentrations. While these drafts and the updates that followed effectively covered the euchromatic fraction of the genome, the heterochromatin and many other complex regions were left unfinished or erroneous. The draft reference genome (Sscrofa10. This paper presents a bidirectional framework for evaluating Dec 26, 2024 · Arabidopsis thaliana was the first plant for which a high-quality genome sequence became available. Here we investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the human genome and that transcription of the integrated sequences might account for PCR Nov 6, 2021 · The Cucurbitaceae contains multiple species of important food plants. 2) represented a purebred female pig from a commercial pork production breed (Duroc), and was established using older clone-based sequencing methods. 5 days ago · Recent advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals, plants and other eukaryotes. Here we present the complete genomic sequence of this strain Dec 1, 2021 · Over the past few decades, the emergence of high-throughput sequencing technology has revolutionized biomedical research, and the continuous development of different methods has generated vast amounts of omics data, providing comprehensive information for all kinds of genomic studies, ranging from general genomics to specialized subfields. From our own experience, a single microbe often has multiple versions of its genome architecture, functional gene AbstractThe SARS-CoV-2 genome occupies a unique place in infection biology -- it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability. We provide the most detailed high-resolution map to date of somatic mutations in CRC, and demonstrate associations with clinicopathological features, in particular location in the large bowel. Its low transgenic efficiency is the major bottleneck in functional genome research and genome editing-based breeding. 1 (2023) * and the journal is ranked 3rd among research journals in the Genetics and Heredity category, and 2nd among research journals in the Biotechnology and Applied Microbiology category by Thomson Reuters. We train Evo 2 with 7B and 40B Jul 9, 2019 · The zebra mussel, Dreissena polymorpha , continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Here, with the help of genes that Preprints deposited in bioRxiv can be cited using their digital object identifier (DOI). Jan 22, 2019 · Escherichia coli C forms more robust biofilms than the other laboratory strains. May 30, 2020 · It is a long-term challenge to undertake reliable transcriptomic research under different circumstances of genome availability. Oct 15, 2024 · Pigs are crucial sources of meat and protein, valuable animal models, and potential donors for xenotransplantation. The publication of the first reference genome sequence almost 25 years ago was already accompanied by genome-wide data on sequence polymorphisms in another accession, or naturally occurring strain. Current publicly available LD block maps are based on sparse recombination maps and are only available for GRCh37 (hg19) and prior genome assemblies. g. Despite its remarkable longevity and lifestyle, there have been no genomic studies on this species. Artificial intelligence (AI) enabled design provides a powerful alternative with potential to bypass Apr 24, 2023 · A map of approximately independent linkage disequilibrium (LD) blocks has many uses in statistical genetics. Feb 22, 2025 · The Greenland shark ( Somniosus microcephalus ) is known for its slow metabolism and deep-sea habitat. Watermelon is one of the most important fruit species of Cucurbitaceae, and it is a model horticulture crops. We generated LD blocks in GRCh38 coordinates for African (AFR), East Asian (EAS), European (EUR) and South Asian (SAS) ancestry May 27, 2021 · In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. Preprints deposited in bioRxiv can be cited using their digital object identifier (DOI). The current impact factor is 10. However, such data sharing must be balanced with the need to protect the privacy of individuals whose genetic information is being utilized. Despite these impacts, there are few genomic resources for Dreissena or related bivalves, with nearly 450 million years of divergence between zebra mussels and its closest sequenced Apr 22, 2024 · Gene editing has the potential to solve fundamental challenges in agriculture, biotechnology, and human health. 1 and to report annotation of a further eleven short read pig genome assemblies (summarised in a new supplementary table). 3 trillion DNA base pairs from a highly curated genomic atlas spanning all domains of life. It is considered the longest-lived vertebrate on Earth, with an estimated lifespan of 392±120 years. de/). It is the last of five E. , Genetics or Microbiology). We refined the mutational processes and signatures acting in colorectal Dec 13, 2020 · Prolonged SARS-CoV-2 RNA shedding and recurrence of PCR-positive tests have been widely reported in patients after recovery, yet these patients most commonly are non-infectious[1][1]–[14][2]. leibniz-fli. New papers that report results of Clinical Trials must now be submitted to medRxiv. They have many unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex determination, and in some lineages even the Jun 3, 2017 · We report a genome-wide association meta-analysis of 20,183 ADHD cases and 35,191 controls that identifies variants surpassing genome-wide significance in 12 independent loci, revealing new and important information on the underlying biology of ADHD. Mar 24, 2025 · Provided here is a study of large language models (LLMs) and retrieval augmented generation (RAG) frameworks in air-gapped environments for genome research on small grain crops. Here, we report the first, chromosome-level assembly of the Greenland shark genome, which . But most of them are difficult to be genetically transformed. Incorporating all years in which bioRxiv preprints have been published (2014–2018), these are also the three top journals. We developed two main applications: (1) a RAG-based system for contextual analysis of scientific literature, collecting over 5,000 PDFs on wheat pathogens, and (2) a GFF3 file analysis tool called Genoma that enables Mar 10, 2024 · whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS). 9% of 183 articles) and Genome Research (36. hmo bywhx vhhg mxplhc kvir udtf eqmovas yymta jdjzpd fpjstzx fvas oes iey uirudm jqqb