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Tag: Zenodo
Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout
FAO. The State of World Fisheries and Aquaculture 2022: Towards Blue Transformation (FAO, 2022). Google Scholar Hua, K. et al. The future of aquatic protein: Implications for protein sources in aquaculture diets. One Earth 3, 316–329 (2019). Article Google Scholar Hardy, R. W. Utilization of plant proteins in fish diets:…
Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships | BMC Genomics
Johnson DV, Al-Khayri JM, Jain SM. Introduction: Date Production Status and Prospects in Africa and the Americas. In: Al-Khayri J, Jain S, Johnson D, editors. Date Palm Genetic Resources and Utilization: Volume 1: Africa and the Americas. Springer Netherlands, Dordrecht; 2015. p. 1–18. doi.org/10.1007/978-94-017-9694-1_1 Gros-Balthazard M, Hazzouri KM, Flowers JM. Genomic…
Genetic architecture of cardiac dynamic flow volumes
Virani, S. S. et al. Heart disease and stroke statistics-2021 update: a report from the American Heart Association. Circulation 143, e254–e743 (2021). Article PubMed Google Scholar Nauffal, V. et al. Genetics of myocardial interstitial fibrosis in the human heart and association with disease. Nat. Genet. 55, 777–786 (2023). Article CAS …
Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)
Wang, P. et al. The genome evolution and domestication of tropical fruit mango. Genome Biol 21 (2020). Tang, C. et al. The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants 2 (2016). Bredeson, J. V. et al. Sequencing wild and cultivated cassava and related…
Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis
Centers for Disease Control and Prevention (U.S.). Antibiotic Resistance Threats in the United States, 2019. doi.org/10.15620/cdc:82532 (2019). Centers for Disease Control and Prevention. COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022. doi.org/10.15620/CDC:117915 (2022). Fricks-Lima, J. et al. Differences in biofilm formation and antimicrobial resistance of Pseudomonas aeruginosa isolated from…
Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability
Szekanecz, Z. et al. Autoinflammation and autoimmunity across rheumatic and musculoskeletal diseases. Nat. Rev. Rheumatol. 17, 585–595 (2021). Article CAS PubMed Google Scholar Rosenblum, M. D., Remedios, K. A. & Abbas, A. K. Mechanisms of human autoimmunity. J. Clin. Invest. 125, 2228–2233 (2015). Article PubMed PubMed Central Google Scholar Wang,…
Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings
Avsec, Ž. et al. Effective gene expression prediction from sequence by integrating long-range interactions. Nat. Methods 18, 1196–1203 (2021). Article CAS PubMed PubMed Central Google Scholar Avsec, Ž. et al. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nat. Genet. 53, 354–366 (2021). Article CAS PubMed PubMed Central Google…
Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century
Distributed cgMLST scheme and the species tree based on a global dataset of 70,000 Neisseria genomes To set up the new dcgMLST scheme, we established a global collection of genomic sequences for 69,994 Neisseria strains (Supplementary Data 1), consisting of 4411 assembled genomes from GenBank, 65,434 genomes assembled based on short…
Analyzing somatic mutations by single-cell whole-genome sequencing
Failla, G. The aging process and cancerogenesis. Ann. N. Y. Acad. Sci. 71, 1124–1140 (1958). Article CAS PubMed Google Scholar Szilard, L. On the nature of the aging process. Proc. Natl Acad. Sci. USA 45, 30–45 (1959). Article CAS PubMed PubMed Central Google Scholar Vijg, J. & Dong, X. Pathogenic…
Shotgun metagenomes from productive lakes in an urban region of Sweden
Williamson, C. E., Saros, J. E., Vincent, W. F. & Smol, J. P. Lakes and reservoirs as sentinels, integrators, and regulators of climate change. Limnology and Oceanography 54, 2273–2282, doi.org/10.4319/lo.2009.54.6_part_2.2273 (2009). Article ADS Google Scholar Cavicchioli, R. et al. 2019. Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews…
Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006). Article ADS CAS PubMed PubMed Central Google Scholar Gao, C. & Guo, L. Progress on microbial species diversity, community assembly and functional traits. Biodivers. Sci. 30, 22429 (2022)….
When will RNA get its AlphaFold moment? | Nucleic Acids Research
Abstract The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches….
Read file with the DSSAT R package – rstudio
Good evening All,I am trying to read experimental file from my system using the DSSAT R package and I get the following error below: I don’t know if there is any expert here that can help me; Here is my reprex: # Load Required Packages library(DSSAT) #> When using the…
Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders
Kessler, R. C. et al. Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Arch. Gen. Psychiatry 62, 593–602 (2005). Article PubMed Google Scholar Kessler, R. C. et al. Prevalence, persistence, and sociodemographic correlates of DSM-IV disorders in the National Comorbidity Survey Replication Adolescent Supplement….
Characterization of intrinsic and effective fitness changes caused by temporarily fixed mutations in the SARS-CoV-2 spike E484 epitope and identification of an epistatic precondition for the evolution of E484A in variant Omicron | Virology Journal
Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021;593(7857):142–6. Article CAS PubMed PubMed Central Google Scholar Planas D, Bruel T, Grzelak L, Guivel-Benhassine F, Staropoli I, Porrot F, et al. Sensitivity of infectious SARS-CoV-2…
Temperate species underfill their tropical thermal potentials on land
Pecl, G. T. et al. Biodiversity redistribution under climate change: impacts on ecosystems and human well-being. Science 355, eaai9214 (2017). Article PubMed Google Scholar Chen, I. C., Hill, J. K., Ohlemüller, R., Roy, D. B. & Thomas, C. D. Rapid range shifts of species associated with high levels of climate…
Bacterial SNPs in the human gut microbiome associate with host BMI
Lynch, S. V. & Pedersen, O. The human intestinal microbiome in health and disease. N. Engl. J. Med. 375, 2369–2379 (2016). Article CAS PubMed Google Scholar Manichanh, C. et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55, 205–211 (2006). Article CAS PubMed …
Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species
Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, et al. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Arch Virol. 2021;166:2633–48. Article CAS PubMed Google Scholar Koonin EV, Dolja VV,…
Genomic signatures of convergent shifts to plunge-diving behavior in birds
Wyles, J. S., Kunkel, J. G. & Wilson, A. C. Birds, behavior, and anatomical evolution. Proc. Natl Acad. Sci. 80, 4394–4397 (1983). Article CAS PubMed PubMed Central Google Scholar Lapiedra, O., Sol, D., Carranza, S. & Beaulieu, J. M. Behavioural changes and the adaptive diversification of pigeons and doves. Proc….
Cellular plasticity of the bone marrow niche promotes hematopoietic stem cell regeneration
Ding, L., Saunders, T. L., Enikolopov, G. & Morrison, S. J. Endothelial and perivascular cells maintain haematopoietic stem cells. Nature 481, 457–462 (2012). Article CAS PubMed PubMed Central Google Scholar Ding, L. & Morrison, S. J. Haematopoietic stem cells and early lymphoid progenitors occupy distinct bone marrow niches. Nature 495,…
Disease-specific loss of microbial cross-feeding interactions in the human gut
Wang, T., Goyal, A., Dubinkina, V. & Maslov, S. Evidence for a multi-level trophic organization of the human gut microbiome. PLOS Comput. Biol. 15, e1007524 (2019). Article ADS PubMed PubMed Central Google Scholar Fischbach, M. A. & Sonnenburg, J. L. Eating for two: how metabolism establishes interspecies interactions in the…
Systematic differences in discovery of genetic effects on gene expression and complex traits
Claussnitzer, M. et al. A brief history of human disease genetics. Nature 577, 179–189 (2020). Article CAS PubMed PubMed Central Google Scholar Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012). Article CAS PubMed PubMed Central Google Scholar Gusev, A. et…
Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks
Compagno, L. J. V. Alternative life-history styles of cartilaginous fishes in time and space. Environ. Biol. Fishes 28, 33–75 (1990). Article Google Scholar Kriwet, J., Witzmann, F., Klug, S. & Heidtke, U. H. J. First direct evidence of a vertebrate three-level trophic chain in the fossil record. Proc. Biol. Sci….
R for Ecological Data Analysis
This is an introduction to R designed for participants with no programming experience. It can be taught in 3/4 of a day (approximately 6 hours). The lesson starts with some basic information about syntax for the R programming language, the RStudio interface, and moves through to specific programming tasks, such…
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…
Challenges and opportunities in sharing microbiome data and analyses
Kyrpides, N. C., Eloe-Fadrosh, E. A. & Ivanova, N. N. Microbiome data science: understanding our microbial planet. Trends Microbiol. 24, 425–427 (2016). Article CAS PubMed Google Scholar Winkler, T. W. et al. Quality control and conduct of genome-wide association meta-analyses. Nat. Protoc. 9, 1192–1212 (2014). Article PubMed PubMed Central Google…
Comparing multiple RNASeq studies
Comparing multiple RNASeq studies 0 I am looking to perform a cumulative analysis of data from multiple RNASeq studies deposited online. Some of the studies uploaded the raw fastq files, but others only upload a post raw mapping counts table or normalized counts ex) zenodo.org/record/4114617 I do not have the…
Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning [PeerJ]
Introduction The rapid proliferation of high-throughput sequencing in metagenomics, combined with the advancement of scalable computational tools, has allowed scientists to digitally isolate tens of thousands of microbial genomes from large collections of metagenomic datasets (Nayfach et al., 2021). Although these genomes are only the tip of the iceberg of…
Research Breakthrough in Identifying Viral Escape Mutations for Improved Therapeutic Design
We are thrilled to announce a significant research milestone achieved by our team. Our latest study, published in the esteemed Briefings in Bioinformatics journal, represents a major advancement in the field of virology and computational biology. Abstract: Our research focuses on the coevolution of viruses with their hosts over millions…
Predictions for AlphaMissense | Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.8360242 Markdown [](https://doi.org/10.5281/zenodo.8360242) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.8360242.svg :target: doi.org/10.5281/zenodo.8360242 HTML <a href=”https://doi.org/10.5281/zenodo.8360242″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.8360242.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.8360242.svg Target URL doi.org/10.5281/zenodo.8360242 Read more here: Source link
Community-developed checklists for publishing images and image analyses
North, A. J. Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition. J. Cell Biol. 172, 9–18 (2006). Article CAS PubMed PubMed Central Google Scholar Brown, C. M. Fluorescence microscopy—avoiding the pitfalls. J. Cell Sci. 120, 1703–1705 (2007). Article CAS PubMed Google Scholar Senft, R. A. et…
The relationship between geographic range size and rates of species diversification
Darwin, C. On the origin of species by means of natural selection. (John Murray, 1859). Rosenzweig, M. L. Species diversity in space and time. (Cambridge University Press, 1995). Rosenzweig, M. L. Geographical speciation: on range size and the probability of isolate formation. in Proceedings of the Washington State University conference…
SC2EGSet: StarCraft II Esport Replay and Game-state Dataset
Reitman, J. G., Anderson-Coto, M. J., Wu, M., Lee, J. S. & Steinkuehler, C. Esports Research: A Literature Review. Games and Culture 15, 32–50, doi.org/10.1177/1555412019840892 (2020). Article Google Scholar Chiu, W., Fan, T. C. M., Nam, S.-B. & Sun, P.-H. Knowledge Mapping and Sustainable Development of eSports Research: A Bibliometric…
Panoramic analysis of coronaviruses carried by representative bat species in Southern China to better understand the coronavirus sphere
Bat sample collection From August 2016 to July 2021, a total of 13,064 oral and anal swabs were collected from bats in 14 provinces across China. Of these, 4755 samples were collected following the COVID-19 outbreak. Sampling sites covered the hotspots of bats carrying Alpha-CoV and Beta-CoV in China9,29(Supplementary Data 1…
Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409
Atanasov, A. G. et al. Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol. Adv. 33, 1582–1614 (2015). Article CAS PubMed PubMed Central Google Scholar Swamy, M. K. et al. Biotechnology of camptothecin production in Nothapodytes nimmoniana, Ophiorrhiza sp. and Camptotheca acuminata. Appl. Microbiol. Biotechnol. 105, 9089–9102…
Identification, sorting and profiling of functional killer cells via the capture of fluorescent target-cell lysate
Kagi, D., Ledermann, B., Burki, K., Zinkernagel, R. M. & Hengartner, H. Molecular mechanisms of lymphocyte-mediated cytotoxicity and their role in immunological protection and pathogenesis in vivo. Annu. Rev. Immunol. 14, 207–232 (1996). Article CAS PubMed Google Scholar Prager, I. & Watzl, C. Mechanisms of natural killer cell-mediated cellular cytotoxicity….
Multiplexed transcriptomic profiling of the fate of human CAR T cells in vivo via genetic barcoding with shielded small nucleotides
Wagner, A., Regev, A. & Yosef, N. Revealing the vectors of cellular identity with single-cell genomics. Nat. Biotechnol. 34, 1145–1160 (2016). Article CAS PubMed PubMed Central Google Scholar Gehring, J., Hwee Park, J., Chen, S., Thomson, M. & Pachter, L. Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular…
scrnaseq: Introduction
Introduction nf-core/scrnaseq is a bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data. This is a community effort in building a pipeline capable to support: Alevin-Fry + AlevinQC STARSolo Kallisto + BUStools Cellranger UniverSC Documentation The nf-core/scrnaseq pipeline comes with documentation about the pipeline usage, parameters and output….
Modeling tissue co-regulation estimates tissue-specific contributions to disease
Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020). Article CAS PubMed Google Scholar Ongen, H. et al. Estimating the causal tissues for complex traits and diseases. Nat. Genet. 49, 1676–1683 (2017). Article CAS PubMed Google Scholar …
Isothermal self-assembly of multicomponent and evolutive DNA nanostructures
Isothermal self-assembly of user-defined DNA origamis in a magnesium-free NaCl buffer. (a), An origami mix (M13 scaffold plus a 40× excess of desired staples) can spontaneously self-assemble at constant temperature into the target equilibrium shape (for example, a triangle) in TANa buffer. (b), AFM observation of the isothermal origami formation…
Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer
Espedido, B. A., Partridge, S. R. & Iredell, J. R. bla(IMP-4) in different genetic contexts in Enterobacteriaceae isolates from Australia. Antimicrob. Agents Chemother. 52, 2984–2987 (2008). Article CAS PubMed PubMed Central Google Scholar Kizny Gordon, A. et al. Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated…
Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis
. 2023 Feb 21;47(2):158-163. doi: 10.55730/1300-0152.2650. eCollection 2023. Affiliations Expand Affiliations 1 Faculty of Engineering and Natural Sciences, Sabancı University, İstanbul, Turkey. 2 TÜBİTAK Research Institute for Fundamental Sciences, Gebze, Turkey. Item in Clipboard Ümit Akköse et al. Turk J Biol. 2023. Show details Display options Display options Format AbstractPubMedPMID ….
pyGROMODS: a Python package for the generation of input files for molecular dynamic simulation with GROMACS
The pyGROMODS, an easy-to-use cross-platform python-based package, with a graphical user interface, for the generation of molecular dynamic (MD) input files and running MD simulation (MDS) of proteins, peptides, and protein-ligand complex using GROMACS, is here presented. Four routes, with underlining Python scripts, are implemented in pyGROMODS for the generation…
Low to high energy electron interactions with AlCl
L.G. Christophorou (ed.), Electron Molecule Interactions and Their Applications (Academic Press, Cambridge, 1984) Google Scholar L.G. Christophorou, J.K. Olthoff, Fundamental Electron Interactions with Plasma Processing Gases (Springer, New York, 2004) Book Google Scholar Y. Al-Douri, Metal Oxide Powder Technologies Fundamentals. Processing Methods and Applications (Elsevier, London, 2020) Google Scholar I….
Smaller Australian raptors have greater urban tolerance
Grimm, N. B. et al. Global change and the ecology of cities. Science 319, 756–760. doi.org/10.1126/science.1150195 (2008). Article ADS CAS PubMed Google Scholar Aronson, M. F. J. et al. Hierarchical filters determine community assembly of urban species pools. Ecology 97, 2952–2963. doi.org/10.1002/ecy.1535 (2016). Article PubMed Google Scholar Shochat, E. et…
nf-core/sarek
Introduction Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses. It’s built using Nextflow, a…
nf-core/marsseq
Introduction nf-core/marsseq is a bioinformatics single-cell preprocessing pipeline for MARS-seq v2.0 experiments. MARS-seq is a plate-based technique that can be combined with FACS in order to study rare populations of cells. On top of the pre-existing pipeline, we have developed an RNA velocity workflow that can be used to study…
Assembly of functional diversity in an oceanic island flora
Carlquist, S. The biota of long-distance dispersal. II. Loss of dispersibility in Pacific Compositae. Evolution (N. Y.) 20, 30–48 (1966). Google Scholar Darwin, C. On the Origin of Species (Murray, 1859). Zizka, A. et al. The evolution of insular woodiness. Proc. Natl Acad. Sci. USA 119, e2208629119 (2022). Article CAS …
G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions
Jiang, C. & Pugh, B. F. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 10, 161–172 (2009). Article CAS PubMed PubMed Central Google Scholar Fenouil, R. et al. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res. 22, 2399–2408…
A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination
Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542 (2017). Article CAS PubMed Google Scholar Almeida, A. et al. A new genomic blueprint of the human gut microbiota. Nature 568, 499–504 (2019). Article CAS PubMed PubMed Central Google…
LDhat lookup table
LDhat lookup table 0 Hi everyone, I am new to the field and I am trying to understand what is the best way to compute a lookup table for LDhat for 135 individuals (n = 270). I see that there are pre-computed lookup tables that I can use but none…
Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence
Begier, E. et al. Epidemiology of invasive Escherichia coli infection and antibiotic resistance status among patients treated in US hospitals: 2009-2016. Clin. Infect. Dis. Publ. Infect. Dis. Soc. Am. 73, 565–574 (2021). Article CAS Google Scholar Bélanger, L. et al. Escherichia coli from animal reservoirs as a potential source of…
Cross-ancestry genome-wide association meta-analyses of hippocampal and subfield volumes
Scoville, W. B. & Milner, B. Loss of recent memory after bilateral hippocampal lesions. J. Neurol. Neurosurg. Psychiatry 20, 11–21 (1957). Article CAS PubMed PubMed Central Google Scholar Morris, R. G., Garrud, P., Rawlins, J. N. & O’Keefe, J. Place navigation impaired in rats with hippocampal lesions. Nature 297, 681–683…
codingsoo/nlp2rest: v0.7 | Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.8035090 Markdown [](https://doi.org/10.5281/zenodo.8035090) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.8035090.svg :target: doi.org/10.5281/zenodo.8035090 HTML <a href=”https://doi.org/10.5281/zenodo.8035090″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.8035090.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.8035090.svg Target URL doi.org/10.5281/zenodo.8035090 Read more here: Source link
Class B1 GPCR activation by an intracellular agonist
Expression and purification of human PTH1R The plasmid encoding human PTH1R (GenBank identifier: U17418.1; residues 27–491) was constructed and purified as previously reported17. The construct was expressed in HEK293 GnTI (N-acetylglucosaminyltransferase I-negative) cells (American Type Culture Collection, CRL-3022) using the BacMam system (Thermo Fisher Scientific), and the cells were grown…
The Biostar Herald for Monday, June 05, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes
Johnson, W. E. Endogenous retroviruses in the genomics era. Annu. Rev. Virol. 2, 135–159 (2015). Article CAS PubMed Google Scholar Johnson, W. E. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat. Rev. Microbiol. 17, 355–370 (2019). Article CAS PubMed Google Scholar Johnson, W. E. Endless forms most viral. PLoS…
Baraminic Analysis of Crocodylia Based on Mitochondrial DNA Similarity
Introduction The reptilian order Crocodylia is comprised of alligators, caimans, crocodiles, and gharials. These animals live in North and South America, Africa, India, Southeast Asia, and northern Australia. Crocodylia includes the families Alligatoridae, Crocodylidae, and Gavialidae. The latter two families belong to the clade Longirostres, since they…
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains
Kiu, R. & Hall, L. J. An update on the human and animal enteric pathogen Clostridium perfringens. Emerg. Microbes Infect. 7, 141 (2018). Article PubMed PubMed Central Google Scholar Li, J., Paredes-Sabja, D., Sarker, M. R. & McClane, B. A. Clostridium perfringens sporulation and sporulation-associated toxin production. Microbiol. Spectr. doi.org/10.1128/microbiolspec.TBS-0022-2015…
Selective control of parasitic nematodes using bioactivated nematicides
Tilman, D., Balzer, C., Hill, J. & Befort, B. L. Global food demand and the sustainable intensification of agriculture. Proc. Natl Acad. Sci. USA 108, 20260–20264 (2011). Article ADS CAS PubMed PubMed Central Google Scholar Hunter, M. C., Smith, R. G., Schipanski, M. E., Atwood, L. W. & Mortensen, D….
The effects of host quantitative genetic architecture on the gut microbiota composition of Chinook salmon (Oncorhynchus tshawytscha)
Anderson MJ (2001) A new method for non‐parametric multivariate analysis of variance. Austral Ecol 26(1):32–46 Google Scholar Anderson MJ (2004) PERMDISP: a FORTRAN computer program for permutational analysis of multivariate dispersions (for any two-factor ANOVA design) using permutation tests. Department of Statistics, University of Auckland, New Zealand, 24. Aykanat T,…
Activation of the urotensin-II receptor by remdesivir induces cardiomyocyte dysfunction
Study design The overall goal of this study was to explore the molecular mechanisms of remdesivir-related cardiotoxicity in anti-COVID-19 therapy. We first performed the GPCR screening using major anti-COVID-19 drugs as ligands (n = 3 per GPCR). We validated the results of GPCR screening by concentration-response analysis and determined the EC50 and…
CRAN – Package ggplot2.utils
ggplot2.utils: Selected Utilities Extending ‘ggplot2’ Selected utilities, in particular ‘geoms’ and ‘stats’ functions, extending the ‘ggplot2’ package. Note that this package does not define the functions itself, but instead imports them from a collection of other packages and then exports them. These functions are tested as well to make sure…
Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments
Dekker, J. & Mirny, L. The 3D genome as moderator of chromosomal communication. Cell 164, 1110–1121 (2016). Article CAS PubMed PubMed Central Google Scholar Oudelaar, A. M. et al. The relationship between genome structure and function. Nat. Rev. Genet. 22, 154–168 (2021). Article CAS PubMed Google Scholar Lieberman-Aiden, E. et…
IL-6 and cfDNA monitoring throughout COVID-19 hospitalization are accurate markers of its outcomes | Respiratory Research
Tay MZ, Poh CM, Rénia L, et al. The trinity of COVID-19: immunity, inflammation and intervention. Nat Rev Immunol. 2020;20(6):363–74. Article CAS PubMed PubMed Central Google Scholar Akter F, Araf Y, Hosen MJ. Corticosteroids for COVID-19: worth it or not? Mol Biol Rep. 2021. doi.org/10.1007/s11033-021-06793-0. Article PubMed PubMed Central Google…
PascalX: a python library for GWAS gene and pathway enrichment tests
doi: 10.1093/bioinformatics/btad296. Online ahead of print. Affiliations Expand Affiliations 1 Department of Computational Biology, University of Lausanne, Switzerland. 2 Swiss Institute of Bioinformatics, Lausanne, Switzerland. 3 Dept. of Integrative Biomedical Sciences, University of Cape Town, South Africa. Item in Clipboard Daniel Krefl et al. Bioinformatics. 2023. Show details Display options Display…
Quantifying bias introduced by sample collection in relative and absolute microbiome measurements
Song, S. J. et al. Preservation methods differ in fecal microbiome stability, affecting suitability for field studies. mSystems 1, e00021–16 (2016). Article PubMed PubMed Central Google Scholar Lauber, C. L., Zhou, N., Gordon, J. I., Knight, R. & Fierer, N. Effect of storage conditions on the assessment of bacterial community…
The evolution of non-small cell lung cancer metastases in TRACERx
The TRACERx 421 cohort The TRACERx study (clinicaltrials.gov/ct2/show/NCT01888601) is a prospective observational cohort study that aims to transform our understanding of NSCLC, the design of which has been approved by an independent research ethics committee (13/LO/1546). Informed consent for entry into the TRACERx study was mandatory and obtained from every…
Mutation-induced infections of phage-plasmids | Nature Communications
Media The minimal marine media, MBL media, was used for serial dilution growth of Tritonibacter mobilis A3R06. It contained 10 mM NH4Cl, 10 mM Na2HPO4, 1 mM Na2SO4, 50 mM HEPES buffer (pH 8.2), NaCl (20 g/liter), MgCl2*6H2O (3 g/l), CaCl2*2H2O (0.15 g/l), and KCl (0.5 g/l). Glucose was added as the only carbon source at a…
Phenoscape – Email Format & Email Checker
What does Phenoscape do? Try the Phenoscape Knowledgebase . Your feedback is welcome! The objective is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Similar to how Google, IBM Watson, and others have enabled…
PBMC CITE-seq reference | Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.7779017 Markdown [](https://doi.org/10.5281/zenodo.7779017) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.7779017.svg :target: doi.org/10.5281/zenodo.7779017 HTML <a href=”https://doi.org/10.5281/zenodo.7779017″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.7779017.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.7779017.svg Target URL doi.org/10.5281/zenodo.7779017 Read more here: Source link
Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition
. 2023 Mar 22;18(3):e0282428. doi: 10.1371/journal.pone.0282428. eCollection 2023. Sarah K Highlander 1 , Jason M Wood 2 , John D Gillece 1 3 , Megan Folkerts 1 , Viacheslav Fofanov 3 4 , Tara Furstenau 3 , Nitin K Singh 2 , Lisa Guan 2 , Arman Seuylemezian 2 , James N Benardini 2 , David M Engelthaler …
nf-core/isoseq: Simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing
doi: 10.1093/bioinformatics/btad150. Online ahead of print. Affiliations Expand Affiliations 1 The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG. 2 Wobble Genomics, University of Edinburgh, Edinburgh, EH25 9RG. Item in Clipboard Sébastien Guizard et al. Bioinformatics. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/bioinformatics/btad150. Online ahead…
Thymidine nucleotide metabolism controls human telomere length
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A new pandemic origin report is stirring controversy. Here are key takeaways | Science
Last week, journalists rushed to report on previously undisclosed genetic evidence that mammals sold at the Huanan Seafood Wholesale Market in Wuhan, China—possibly raccoon dogs—might have sparked the COVID-19 pandemic. But to the chagrin of the researchers who conveyed their findings confidentially to a World Health Organization (WHO) advisory group…
konradjk/loftee: v.1.0.4 on GRCh38 | Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.7745710 Markdown [](https://doi.org/10.5281/zenodo.7745710) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.7745710.svg :target: doi.org/10.5281/zenodo.7745710 HTML <a href=”https://doi.org/10.5281/zenodo.7745710″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.7745710.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.7745710.svg Target URL doi.org/10.5281/zenodo.7745710 Read more here: Source link
Exporting structured data like RO-Crate or BioComputeObjects
Galaxy has over the last month gained a powerful and extensible exporting framework. Two export formats have alreaady been added to Galaxy: Every format can be downloaded directly, or written to pluggable Galaxy file sources (Dropbox, Google Drive, FTP, S3 …). The feature described here will be part of the…
Interpersonal variability of the human gut virome confounds disease signal detection in IBD
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Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N2O cycling
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Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm
Gupta, A., Rico-Medina, A. & Cano-Delgado, A. I. The physiology of plant responses to drought. Science 368, 266–269 (2020). Article CAS PubMed Google Scholar Hu, H. & Xiong, L. Genetic engineering and breeding of drought-resistant crops. Annu Rev. Plant Biol. 65, 715–741 (2014). Article CAS PubMed Google Scholar Ashraf, M….
Whole-genome CRISPRa screening identified LRRC15 as a novel SARS-CoV-2 spike-binding protein.
(A) Schematic of CRISPRa screen used to identify regulators of SARS-CoV-2 spike binding. (B) Ranking of all genes in screen 1 by log2 fold change (LFC) calculated using MAGeCK and plotted using MAGeCKFlute. See also S1 Table. (C) Gene enrichment analysis of screen 1 performed using MAGeCK. Horizontal dotted line…
Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga
Koonin, E. V. & Dolja, V. V. Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol. Mol. Biol. Rev. 78, 278–303 (2014). Article CAS Google Scholar Pritham, E. J., Putliwala, T. & Feschotte, C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and…
Comprehensive 100-bp resolution genome-wide epigenomic profiling data for the hg38 human reference genome
doi: 10.1016/j.dib.2022.108827. eCollection 2023 Feb. Affiliations Expand Affiliations 1 Graduate program in Neuroscience, Emory University, United States. 2 Department of Computer Science, Emory University, United States. 3 Department of Biostatistics and Bioinformatics, Emory University, United States. Item in Clipboard Ronnie Y Li et al. Data Brief. 2022. Show details Display options…
A multi-omics integrative network map of maize
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Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria
Miyakawa, T., Matsuzawa, H., Matsuhashi, M. & Sugino, Y. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112, 950–958 (1972). Article CAS PubMed PubMed Central Google Scholar Ayala, J. A., Garrido, T., De Pedro,…
Population-level variation in enhancer expression identifies disease mechanisms in the human brain
Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed Central Article CAS Google Scholar Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS PubMed PubMed Central …
Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation
Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018). CAS PubMed PubMed Central Google Scholar Yizhak, K. et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 364, eaaw0726 (2019). CAS PubMed PubMed Central Google Scholar Yokoyama, A….
Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data
Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS PubMed PubMed Central Article Google Scholar Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020)….
Tempo and drivers of plant diversification in the European mountain system
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ZC2 RNAseq | Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.6412442 Markdown [](https://doi.org/10.5281/zenodo.6412442) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg :target: doi.org/10.5281/zenodo.6412442 HTML <a href=”https://doi.org/10.5281/zenodo.6412442″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg Target URL doi.org/10.5281/zenodo.6412442 Read more here: Source link
AxelRosendahlHuber/Genotoxin_assay: Archiving code and data: Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.6424654 Markdown [](https://doi.org/10.5281/zenodo.6424654) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg :target: doi.org/10.5281/zenodo.6424654 HTML <a href=”https://doi.org/10.5281/zenodo.6424654″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg Target URL doi.org/10.5281/zenodo.6424654 Read more here: Source link
Accurate assembly of multi-end RNA-seq data with Scallop2
Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010). Article Google Scholar Guttman, M. et al. Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28,…
Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages
Díaz, S. et al. Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES, 2019). Fisher, R. A. The correlation between relatives on the supposition of Mendelian inheritance. Earth Environ. Sci. Trans. R. Soc. Edinb. 52,…
Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM
Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…
Xena TCGA TARGET TCGx RNAseq Data
Zenodo DOI Badge DOI 10.5281/zenodo.6323594 Markdown [](https://doi.org/10.5281/zenodo.6323594) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg :target: doi.org/10.5281/zenodo.6323594 HTML <a href=”https://doi.org/10.5281/zenodo.6323594″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg Target URL doi.org/10.5281/zenodo.6323594 Read more here: Source link
METASnake: a Snakemake workflow to facilitate…
Introduction As sequencing technology has become cheaper and more readily accessible, the need for the increased computational capacity to process these data has become apparent. In particular, high-throughput sequencing has been particularly useful when applied to the field of metagenomics. Substantial effort has been devoted to developing software and computational…
Accelerating minimap2 for long-read sequencing applications on modern CPUs
Chaisson, M. J. et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat. Commun. 10, 1–16 (2019). Article Google Scholar Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 1–19 (2016). Article Google Scholar Beyter, D. et al. Long-read sequencing of…
Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits
1. Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). CAS PubMed PubMed Central Google Scholar 2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed…
Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence
Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….
scikit-survival | Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.5831584 Markdown [](https://doi.org/10.5281/zenodo.5831584) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg :target: doi.org/10.5281/zenodo.5831584 HTML <a href=”https://doi.org/10.5281/zenodo.5831584″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg Target URL doi.org/10.5281/zenodo.5831584 Read more here: Source link
