Tag: TRAIT

Understanding the Role of Rare Genetic Variants Recent research on the UK Biobank cohort, a large-scale genetic data set, has shed light on the significant role of rare genetic variants (RVs) in complex trait heritability. The study confirms that these RVs account for a substantial portion of the complex trait…

I’ve got an AST structure for IR, and another for Data. Each of these consist of mostly the same types nodes, but each have some nodes which only belong in them. In general IR can contain logical operations like IfThenElse or function application, while Data has to be simpler records….

PRSice and R lm() show different association analysis output (coefficient, SE and P) 0 Hey, I am struggling to understand Why am I getting different association analysis output (coefficient, SE and P) between PRSice and lm() function in R. Not only the values, even the direction of association is different….

A novel STR panel for human protein-coding genes To explore STR mutations in CRC, we first annotated STRs in the introns, exons, and promoter sequence of all protein-coding genes in the GRCh38 reference genome (“Methods”). We discarded STR loci for which genotyping was expected to be inaccurate due to genomic…

README: Trait-based mechanistic approach highlights global patterns and losses of herbivore biomass functional diversity Purpose of data: the dataset contains species trait data used for creation of Herbivore Functional Types and density data used for calculating empirical-derived biomass. Authors: F Berzaghi*, D Zhu, J Alroy, P Ciais. *contact author: fabe@unitus.it…

What evidence suggests that a gene in the mtDNA is causing this disorder? Males are more often affected but do not pass on the trait. Males and females are both affected and both likely to pass on the trait. The disorder exhibits a high degree of penetrance from generation to…

Project Ten: eQTL, GWAS, and SARS-CoV2 We’ll use this last project to learn a bit more about SARS-CoV-2, and about approaches used by population geneticists to investigate aspects of its pathogenicity and transmission among humans. You’ll be introduced to the concept of eQTLs (expression quantitative trait loci) and how they…

Sugarcane, a crucial worldwide food and bioenergy crop, accounts for approximately 80% of the world’s sugar production, with its largest cultivation in Brazil and India. As the 5th largest crop by production value and acreage, it presents unique breeding challenges due to its complex polyploid genome, derived from interspecific hybridization….

Genome assembly and annotation The DNA sequencing data (1119.58 Gb, average 110× coverage) of the A. konjac sample were obtained using the Illumina Hiseq 2500 sequencer. A summary of the sequence data used for the assembly is presented in Table S1. The estimated genome size is 4,512,012,462 bp using 19-mer frequency distribution based…

Do the plant species with the greatest intraspecific trait variation have the highest abundance?5 answersPlant species with the greatest intraspecific trait variation do not necessarily have the highest abundance. In a study of understorey plants in a Polish mixed temperate forest, it was found that abundances of non-dominant species significantly…

Almeida OAC, Moreira GCM, Rezende FM et al (2019) Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics 20:1–20. doi.org/10.1186/s12864-019-5811-1 Article  Google Scholar  Alshawi A, Essa A, Al-Bayatti S, Hanotte O (2019) Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and…

In the dynamic panorama of technological advancement, the fusion of machine learning paradigms with the realm of software development has taken center stage. The burgeoning complexity of contemporary software necessitates a paradigm shift, and this metamorphosis is aptly facilitated by the integration of sophisticated machine-learning tools. These tools, endowed with…

By 2049, our global population will reach ~9 billion people. Pests, diseases and adverse environmental conditions are impacting crops across the globe, compounding the issue of feeding a growing population. Traditional breeding techniques have enabled scientists and farmers to develop many varieties of plants and livestock tailored for specific agricultural…

Ornamental plants, valued for their varied morphological characteristics, are increasingly used in urban greening initiatives such as rooftop greening. But this application presents challenges like limited soil depth and no irrigation, requiring plants such as the Phedimus species, known for their resilience to these conditions. Current research focuses on understanding the genetic…

To investigate potential functional SNPs in APOBEC3 genes involved in COVID-19 severity, we evaluated the COVID-19 association signals around 7 APOBEB3 genes, comprising APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H, in the two COVID-19 hospitalization GWASs with European and African ancestries (HGI-B2-EUR and HGI-B2-AFR, respectively). Around these 7 APOBEC3…

Cao, C. et al. Power analysis of transcriptome-wide association study: Implications for practical protocol choice. PLoS Genet. 17(2), e1009405 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  De Camargo, G. M. F. et al. Prospecting major genes in dairy buffaloes. BMC Genomics 16, 1–14 (2015). Article  Google Scholar  El-Halawany, N….

This package allows you to integrate the specification validation into the flow of tests. Installation NoteThis package is mostly intended to be used as part of an API test suite. Via Composer: composer require –dev r3bzya/openapi-specification-testing Usage You can use \R3bzya\OpenApiTesting\Concerns\HasSpecificationAssertion or \R3bzya\OpenApiTesting\Concerns\ValidateOpenApiSpecification just add one of them into your…

Available data: Associations Studies Full summary statistics LocusZoom Download Associations Download files Include background traits data Associations Variant and risk allele P-value P-value annotation RAF OR Beta CI Mapped gene Reported trait Trait(s) Background trait(s) Study accession First Author PubMed ID Location Variant and risk allele P-value P-value annotation RAF…

Albrecht, A. & Kandji, S. T. Carbon sequestration in tropical agroforestry systems. Agric. Ecosyst. Environ. 1–3, 15–27 (2003). Article  Google Scholar  Nair, P. K. R. Agroforestry systems and environmental quality: Introduction. J. Environ. Qual. 40, 784–790 (2011). Article  CAS  PubMed  Google Scholar  Schroth, G. & McNeely, J. A. Biodiversity conservation,…

Abstract When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in…

Sign up for CNN’s Wonder Theory science newsletter. Explore the universe with news on fascinating discoveries, scientific advancements and more. CNN  —  Early risers may have inherited genetic variants from Neanderthals that increased their odds of being morning rather than evening people, new research has found. While the human body clock…

TAMPA, Fla. — The FDA recently approved two different gene therapies to treat sickle cell disease, and many doctors and patients living with the painful disease say this is a long time coming. What You Need To Know The two newly approved gene therapies each use a different method According to the FDA, in…

Hersbach, H. et al. ERA5 hourly data on single levels from 1940 to present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS). In Copernicus Climate Change Service (C3S) Climate Data Store (CDS) (2023). doi.org/10.24381/cds.adbb2d47. Constable, A. J. et al. Cross-chapter paper 6: Polar regions. In Climate Change 2022: Impacts,…

McGill, B. J., Enquist, B. J., Weiher, E. & Westoby, M. Rebuilding community ecology from functional traits. Trends Ecol. Evol. 21, 178–185 (2006). Article  PubMed  Google Scholar  Diaz, S. et al. The global spectrum of plant form and function: enhanced species-level trait dataset. Sci. Data 9, 755 (2022). Article  PubMed …

What are the challenges and opportunities in using phylogenomics to study spiders?5 answersPhylogenomics has provided valuable insights into the study of spiders, but it also presents challenges and opportunities. One challenge is the low capture efficiency of available UCE probe sets for spider phylogenomics, which are not optimized for certain…

INTERVAL RNA-seq Portal | eQTL Gene ID Gene Type Range Lead RsID qVal Z-score Independent eQTL signals Rank Variant RsID Variant PosID AF Dist Beta (joint) P-val (joint) Nominal eQTL summary statistics Variant RsID Variant PosID AF Beta P-val Z-score PheWAS for lead variant (OpenTargets) Trait Author PMID Beta P-val…

Background: Expression quantitative trait locus (eQTL) analysis has emerged as an important tool in elucidating the link between genetic variants and gene expression, thereby bridging the gap between risk SNPs and associated diseases. We recently identified and validated a specific case where the methylation of a CpG site influences the…

Kansas State University researchers have reported a breakthrough in developing wheat-based foods that contain lower amounts of gluten, a discovery that may lessen the adverse effects for those with celiac or other autoimmune diseases. Scientists from K-State’s Wheat Genetics Resource Center and the USDA’s Agricultural Research Service — in partnership with Kansas Wheat — successfully used…

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 …

How to DNA sequence a yeast?3 answersDNA sequencing of yeast can be done using various methods. One protocol involves preparing yeast DNA by digesting the cell wall and lysing the resulting spheroplasts with SDS. This method yields several micrograms of yeast DNA that can be cleaved by restriction enzymes and…

Abstract Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map…

On December 8, 2023 the U.S. Food and Drug Administration (FDA) approved Casgevy and Lyfgenia, both cell-based gene therapies for the treatment of sickle cell disease in patients 12 and older. Further, Casgevy is the first approved treatment utilizing CRISPR, an innovative gene editing technology that was the basis of the…

Regulatory authorities have given the green light to two innovative gene therapies designed to combat sickle cell disease, offering a glimmer of hope for individuals grappling with this excruciating inherited blood disorder, primarily affecting Black communities in the United States. Revolutionizing sickle cell treatment: The FDA’s historic Decision The Food…

Weighted gene co-expression network analysis GSE131329 has comprehensive clinical data, and WGCNA was carried out with this expression profile. WGCNA is a systems biology method for characterizing gene association patterns between different samples, used to identify highly synergistic sets of genes and to screen for candidate biomarker genes or therapeutic…

For centuries, horse breeders have chosen to mate specific sires and dams based on information in pedigrees and traits that they find desirable within them. The goal of pedigree analyses, and the resulting breeding pair selection, is production of successful offspring through the propagation of beneficial genes. Although this has…

Regulators on Friday approved two new gene therapies for sickle cell disease that doctors hope can cure the painful, inherited blood disorder that afflicts mostly Black people in the U.S. The Food and Drug Administration said the one-time treatments can be used for patients 12 and older with severe forms…

Genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) mapping use conceptually similar ideas to identify genetic variants contributing to complex trait and gene expression variation, respectively. Despite the proven role of gene expression in mediating biological functions, the observed level of colocalization between GWAS hits and eQTLs shows…

Lo YMD, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CWG, et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997;350:485–7. Article  CAS  PubMed  Google Scholar  Warsof SL, Larion S, Abuhamad AZ. Overview of the impact of noninvasive prenatal testing on diagnostic procedures. Prenat Diagn. 2015;35:972–9….

Transcribed image text: An RFLP that is linked to the stubby toe trait is depicted below. PCR primers (the arrows depicted below) amplify the DNA sequence with the RFLP. The dominant, wildtype allele is linked to the DNA sequence that is missing the restriction site while the recessive, mutant allele…

Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…

Translating Alzheimer’s disease-associated polymorphisms into functional candidates: a survey of IGAP genes and SNPs. Publication ,  Journal Article Katsumata, Y; Nelson, PT; Estus, S; Alzheimer’s Disease Neuroimaging Initiative (ADNI), ; Fardo, DW Published in: Neurobiol Aging The International Genomics of Alzheimer’s Project (IGAP) is a consortium for characterizing the genetic landscape…

Dear Nachiket- Sorry for the slow reply. I think this strange behavior results from the fact that your data violate the assumption of the Brownian motion model. Basically, you are modeling a discrete character with a model for continuous data. Because you have huge areas of your tree with the…

Tsudzuki, M. Mutations of Japanese quail (Coturnix japonica) and recent advances of molecular genetics for this species. J. Poult. Sci. 45, 159–179 (2008). CAS  Google Scholar  Recoquillay, J. et al. A medium density genetic map and QTL for behavioral and production traits in Japanese quail. BMC Genom. 16, 10 (2015)….

Inspiration from Circular barplot with R and ggplot2 — the R Graph Gallery (r-graph-gallery.com) I will show you how to create this barplot step by step. Bar charts are a popular way to visualize data, but customizing them in R often requires complex code. This leaves many R users with…

Out along Europe’s western fringe, Ireland occupies a unique geographical and cultural space, where the continent ends and the vast ocean begins. Separated from Britain by as little as 12 miles (19 km), Ireland’s island history has been inextricably linked to that of its larger fellow island nation throughout the…

The following questions are based on the following paper: Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS. Nat Commun. 2018; 9:1512. (PMID: 29666371) (i) How is a cis-expression quantitative trait locus (cis-eQTL) defined? (ii) What experimental technique for detecting chromosomal interactions was applied…

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,…

We conducted a three-stage genome-wide analysis of PUD and its subtypes. An overview of the workflow is provided in Fig. 1 and Supplementary Fig. 1. PUD cases in the east Asian populations were obtained by combining individuals with any of the two major PUD subtypes (DU and GU), which were…

Abstract The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe’s only intergovernmental life sciences organisation. This…

Barnett R. Schistosomiasis. (1474–547X (Electronic)). Steinmann P, Keiser J, Bos R, Tanner M, Utzinger J. Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk. Lancet Infect Dis. 2006;6(7):411–25. Article  PubMed  Google Scholar  Uthailak N, Adisakwattana P, Thiangtrongjit T, Limpanont Y, Chusongsang P, Chusongsang Y, et…

Title: The Maternal Imprint: Deciphering the Physical Traits Passed Down from Mother to Child The intricate dance of genetics determines the unique tapestry of traits that each individual carries. While both parents contribute to the genetic makeup of their offspring, certain physical characteristics are more prominently inherited from the mother….

Picture this: Almost 6,000 years ago, a girl walks along Lolland’s south coast and spits a piece of birch tar into the reeds. It didn’t taste great, but it helped to soothe her tooth ache. Fast forward 6,000 years, Danish archaeologists working on the Fehmarnbelt project stumble across the piece…

Globally, the prevalence of obesity has increased, which has had severe detrimental effects on physical health in recent years. Several hypotheses explain the causes of obesity. The change in people’s eating habits is one significant reason, with high-fat diets (HFD) being of particular concern. Research has indicated that the gut…

DNA Markers: nuclear DNA SNPs, mtDNA, SNPs, DNA sequences, microsatellites Popular neutral markers: Mitochondrial gene sequences (COI: animal), SNPs (single nucleotide polymorphisms), nuclear sequence (RUBISCO, rDNA: plants) (show SNP heteros have 2 lower peaks), genome resequencing, microsatellites (STR) Microsatellites: tandem repeats of 10-30 copies of 2-4 base pairs (diff in…

WHETHER in forests or in captivity, animals are not free from diseases. However, generally speaking forest animals are least vulnerable to genetic disorders. A pragmatic response to that generalisation could be, “we don’t know if forest animals have fewer or more genetic disorders than humans because we don’t have enough…

Diversity of the RCA cluster and genome characteristics The phylogenomic analysis yielded three major clades within the RCA cluster (Fig. 1) Genomes of the three clades were relatively distinct with appr. < 70% average nucleotide identity (ANI), resulting in the proposal of three genera, the known genus Planktomarina, and two new genera without…

Natali_Mis Gene editing, also known as genome editing, is a method where the DNA of an organism is modified using biotechnological techniques. It allows scientists to add, remove, or alter genetic material at particular locations in the genome. This 2-part series will cover the basics of CRISPR-Cas9 (see below) in…

Method selection We reviewed the published literature through February 2020 to identify methods that met the following criteria: i. Descriptively categorized as (a) annotation-based; (b) pleiotropy-based; or (c) eQTL-based. ii. Utilized GWAS summary statistics, as opposed to individual-level genotype data. iii. Implemented using freely-available software or packages. iv. Provided either…

README: Native herbivore browsing alters plant physical and chemical traits in a eucalypt forest understory Dataset contains six excel files containing raw data used for calculations of trait values for nine species in an open eucalypt understorey under two herbivory treatments. Data is also used to calculate community weighted means…

Grill, G. et al. Mapping the world’s free-flowing rivers. Nature 569, 215–221. doi.org/10.1038/s41586-019-1111-9 (2019). Article  ADS  CAS  PubMed  Google Scholar  Díaz, S. et al. Pervasive human-driven decline of life on Earth points to the need for transformative change. Science 366, 6471. doi.org/10.1126/science.aax3100 (2019). Article  CAS  Google Scholar  Vörösmarty, C. J….

README: Wood trait preferences of Neotropical xylophagous beetles doi.org/10.5061/dryad.tb2rbp07j This rearing project examines the community composition of wood-boring beetles (family: Cerambycidae) in Panama. We reared cerambycids from freshly cut trees on a 1 ha headland on the W bank of the Panama Canal (9º07’N, 79º45’W, Prov. de Colon, approximately 20…

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article  ADS  CAS  PubMed  Google Scholar  Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….

In the field of genetics, the concept of tandem repeats has been both scientifically fascinating, experimentally challenging, and motivating for technology development. As DNA sequencing technologies and analysis tools have evolved, scientists are now able to reveal the secrets hidden within these repetitive sequences, shedding light on their significance in…

Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. Biological identifications through DNA barcodes. Proc Biol Sci 270, 313–321 (2003). Article  CAS  PubMed  PubMed Central  Google Scholar  Huang, X., Ci, X., Conran, J. G. & Li, J. Application of DNA barcodes in Asian tropical trees –…

Dinkler L, Bryant-Waugh R. Assessment of avoidant restrictive food intake disorder, pica and rumination disorder: interview and questionnaire measures. Curr Opin Psychiatry. 2021;34(6):532–42. Article  Google Scholar  American Psychiatric Association. Diagnostic and Statistical Manual of Mental Disorders (5th ed.). Arlington, VA: American Psychiatric Publishing; 2013. Thomas JJ, Lawson EA, Micali N, Misra…

Inclusion and ethics statement We included researchers from the iPSYCH biobank and the PGC, who played a role in study design. This research was not restricted or prohibited in the setting of any of the included researchers. All studies were approved by local instituational research boards and ethics review committees….

Krause, J. & Ruxton, G. D. Living in Groups (Oxford Univ. Press, 2002). Réale, D., Reader, S. M., Sol, D., McDougall, P. T. & Dingemanse, N. J. Integrating animal temperament within ecology and evolution. Biol. Rev. 82, 291–318 (2007). Article  PubMed  Google Scholar  Gartland, L. A., Firth, J. A., Laskowski,…

Phenotype imputation increases effective sample size We focused on the deepest available measure of MDD in UK Biobank11, LifetimeMDD, which we derived by applying clinical diagnostic criteria in silico to MDD symptom data from the Patient Health Questionnaire 9 (PHQ9) and the Composite International Diagnostic Interview Short Form (CIDI-SF) in…

GMO Corn Market – DataM Intelligence GMO Corn Market Size The Global GMO Corn Market reached US$ 260.1 billion in 2022 and is expected to reach US$ 384.2 billion by 2030 and is expected to grow with a CAGR of 5.0% during the forecast period 2023-2030. The adoption of gene…

White Cloud, a female albino bison, lived with the National Buffalo Museum herd in Jamestown, North Dakota, until her death in 2016 at the age of 20. Researchers at Texas A&M University’s School of Veterinary Medicine and Biomedical Sciences recently the discovered the gene responsible for albinism in bison. Photo…

In a global first, the British medical regulator has given the green light to a gene therapy aiming to cure two untreatable blood disorders – sickle cell disease (SCD) and beta-thalassemia. The treatment for sickle cell disease and beta-thalassemia is the first to be licensed using the gene-editing tool Crispr,…

Biological trait analysis (BTA) is a valuable tool for evaluating changes in community diversity and its link to ecosystem processes as well as environmental and anthropogenic perturbations. Trait-based analytical techniques like BTA rely on standardised datasets of species traits. However, there are currently only a limited number of datasets available…

Claramunt, S., Derryberry, E. P., Brumfield, R. T. & Remsen, J. V. Ecological Opportunity and Diversification in a Continental Radiation of Birds: Climbing Adaptations and Cladogenesis in the Furnariidae. Am. Naturalist 179, 649–666 (2012). Article  Google Scholar  Derryberry, E. P. et al. Lineage diversification and morphological evolution in a large-scale…

Plant Genomics Market | 360iResearch The “Plant Genomics Market by Objective (DNA Extraction & Purification, DNA/RNA Sequencing, Gene Expression Profiling), Type (Genetic Engineering, Molecular Engineering), Trait, Crops – Global Forecast 2023-2030” report has been added to 360iResearch.com‘s offering. The Global Plant Genomics Market to grow from USD 9.37 billion in…

R comp.score The function empirically estimate the variance of the score functions. The variance-covariance matrix consists of two parts: the additive part and the part for the individual-specific environmental effect. Other reasonable decompositions are possible. This program has the following improvement over “score.r”: 1. It works with selected nuclear families…

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)….

Phenotypeca, a biotech business from Nottingham, UK, has been working with the Bill & Melinda Gates Foundation to produce albumin for low and middle-income countries (LMICs), offering a catalyst for making life-saving vaccines affordable globally. Global vaccine production faces several challenges. Limited availability and the high costs associated with recombinant…

DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment 0 @724e8e11 Last seen 3 hours ago Australia Hi everyone, first time poster. I have resorted to this because I can’t seem to find substantive answers to my question (or don’t exactly fit my question), nor…

CEN/CEN4 CRISPR-Cas9 gene editing for fast maturity in diverse Actinidia spp. Credit: Horticulture Research While major advances have been made through speed breeding and other technologies, woody perennial fruit tree species have lagged behind. Among these is the kiwifruit (Actinidia chinensis), a crucial fresh fruit crop, which has limited genetic…

Clumping with r2=0 and 250kb radius in plink 1 Hi, I am doing clumping with the follow command: plink \ –bfile ${myfilename} \ –keep all_hg38_EUR.ids \ –clump ${trait}_tmp2.txt \ –clump-snp-field SNP \ –clump-field P \ –allow-extra-chr \ –memory 30000 \ –clump-p1 5e-8 \ –clump-r2 0 \ –clump-kb 250 \ –out…

Tutorial:Where to Get Genotyping Data/GWAS Data 0 First of all, it is important to understand that genotyping data and GWAS data are central to eQTL studies. These two types of data provide the foundational genetic information needed to understand how variations in gene expression contribute to complex traits and diseases….

Abstract Transcriptome-wide association studies (TWAS) have investigated the role of genetically regulated transcriptional activity in the etiologies of breast and ovarian cancer. However, methods performed to date have only considered regulatory effects of risk associated SNPs thought to act in cis on a nearby target gene. With growing evidence for…

A database in the Gene Set Enrichment Analysis (GSEA; www.gsea-msigdb.org/gsea/msigdb/index.jsp) platform10,11 was used to identify 134 GLN metabolism-associated genes. Weighted gene co-expression network analysis (WGCNA) and module screening GLN-associated gene sets were investigated using WGCNA. The results demonstrated that when the weighted value was 24 (Fig. 1A), scale independence was greater…

Scientists from Argentina’s National Institute of Agricultural Technology (INTA) are on the brink of releasing Latin America’s first genetically edited potato. Their focus has been on deactivating the gene responsible for enzymatic browning, a trait causing potatoes to darken after cutting, peeling, or during harvesting. Enzymatic browning negatively impacts flavor,…

DOI: 10.18129/B9.bioc.dreamlet   Cohort-scale differential expression analysis of single cell data using linear (mixed) models Bioconductor version: Release (3.18) Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of…

The 2024 South Australian Crop Sowing Guide, which aims to help South Australian grain growers determine the best crop variety for their situation, has been published. 11 November 2023, AU: Every year GRDC collaborates with the South Australian Grain Industry Trust and the South Australian Research and Development Institute of Primary Industries and Regions…

TTHealthWatch is a weekly podcast from Texas Tech. In it, Elizabeth Tracey, director of electronic media for Johns Hopkins Medicine in Baltimore, and Rick Lange, MD, president of the Texas Tech University Health Sciences Center in El Paso, look at the top medical stories of the week. This week’s topics…

Every day millions of farmers grapple with challenging climate conditions on low incomes. A project led by Kansas State seeks to support farmers in Kansas and across the world, Climate Resilient Cereals Innovational Lab director Jagger Harvey said. The United States Agency for International Development is funding K-State and five…

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….

Aizawa M, Yoshimaru H, Saito H, Katsuki T, Kawahara T, Kitamura K et al. (2009) Range‐wide genetic structure in a north‐east Asian spruce (Picea jezoensis) determined using nuclear microsatellite markers. J Biogeogr 36(5):996–1007 Article  Google Scholar  Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated…

This dataset corresponds to the original/raw trait data set used in the article It takes a village to grow a tree: most tree species benefit from dissimilar neighbors.  The data set include 7 columns: (1) species (sp), (2) genus, (3) trait, (4) standardized trait value (StdValue), (5) trait unit (traitUnit),…

The intersection of technology and agriculture has ushered in a new era of cultivation, where the once clandestine world of cannabis farming is now at the forefront of horticultural innovation.  This is particularly evident in the development of exotic weed strains that blend art, science, and technology in ways previously…

README: Trait data for common garden Primula elatior Dataset DOI: doi.org/10.5061/dryad.3j9kd51r8 Description of the data and file structure The dataset provides comprehensive trait data for Primula elatior, focusing on the impacts of climate change and habitat fragmentation. It includes field-based herkogamy data from 60 populations as well as greenhouse-based common…

The world of agriculture is constantly evolving, with new technologies continuously shaping the way we understand and interact with plants. One such advancement is the development of high-throughput plant phenotypic collection technology, which has revolutionized the field of plant phenomics. Through this technology, scientists are able to gather vast amounts…

Graphical abstract. Credit: Nucleic Acids Research (2023). DOI: 10.1093/nar/gkad975 Plant images contain a wealth of information that reflects key phenotypic characteristics such as color, shape, growth, and health status of plants. High-throughput plant phenotypic collection technology has been widely applied in plant phenomics, generating numerous images and image-based traits (i-traits)…

Identification of CH cases from WGS in ISL and UKB We used WGS from 45,510 Icelanders and 130,709 British ancestry participants from the UKB17,18. Average sequencing depth was 33× for UKB and 38× for ISL. Participants with prior diagnoses of hematological disorders or grossly abnormal hematology measurements on entry were…

07 November 2023 Ireland, along with other countries, had tried hill sheep breed improvement in the past, but ultimately it failed for several reasons. These include: a lack of market for parentage recorded rams; no short-term…

Chase, M. W. et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016). Article  Google Scholar  Jones, M. G. et al. Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot….

Im getting following error while running jupyterhub command C:\Users\admin>jupyterhub [I 2023-11-06 22:58:37.910 JupyterHub app:2859] Running JupyterHub version 4.0.2 [I 2023-11-06 22:58:37.910 JupyterHub app:2889] Using Authenticator: jupyterhub.auth.PAMAuthenticator-4.0.2 [I 2023-11-06 22:58:37.910 JupyterHub app:2889] Using Spawner: jupyterhub.spawner.SimpleLocalProcessSpawner-4.0.2 [I 2023-11-06 22:58:37.910 JupyterHub app:2889] Using Proxy: jupyterhub.proxy.ConfigurableHTTPProxy-4.0.2 [I 2023-11-06 22:58:37.910 JupyterHub app:1664] Loading cookie_secret from…

McGraw, J. B. & Caswell, H. Estimation of individual fitness from life-history data. Am. Naturalist 147, 47–64 (1996). Article  Google Scholar  Price, T. & Schluter, D. On the low heritability of life‐history traits. Evolution 45, 853–861 (1991). Article  PubMed  Google Scholar  Nylin, S. & Gotthard, K. Plasticity in life-history traits….