Tag: TRAIT

Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

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  Google Scholar  Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47,…

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Penetrance of Mendelian Disease Variants Ranges in Heterozygous Carriers

NEW YORK – Using genetic data from the UK Biobank, a team from Brigham and Women’s Hospital, the Broad Institute, Harvard Medical School, and the Massachusetts Institute of Technology has documented various levels of recessiveness for variants previously implicated in Mendelian conditions. “With increasing exome sequencing of population biobank cohorts,…

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Scientists Genetically Edited Regular Tomatoes To Improve Vitamin D Levels

Scientists have genetically edited tomatoes that are more nutritious in provitamin D3 — a precursor to vitamin D, and they’re as high as two whole eggs or a tablespoon full of tuna. Unsplash Also Read: Tomato Maestros At Heinz Mimicked Mars To Create Alien Ketchup They did so by disabling a…

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Tempo and drivers of plant diversification in the European mountain system

Hughes, C. E. & Atchinson, G. W. The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains. N. Phytol. 207, 275–282 (2015). Article  Google Scholar  Rahbek, C. et al. Humboldt’s enigma: what causes global patterns of mountain biodiversity? Science 365, 1108–1113 (2019). ADS  CAS  PubMed  Article  Google…

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Polygenic Risk Score Performance Improved With Expression-Related Rare Variant Insights

NEW YORK – A team from Stanford University and other centers in the US and China have demonstrated that polygenic risk scores (PRS) based on common variants can be bolstered by incorporating clues from rare variants linked to significant gene expression shifts, dubbed expression outliers. “As individual PRS estimates are…

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Single-cell eQTL models reveal dynamic T cell state dependence of disease loci – Nature – Alert Breaking News

Wei, K. et al. Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature 582, 259–264 (2020). ADS CAS PubMed PubMed Central Article Google Scholar  Cembrowski, M. S. & Menon, V. Continuous variation within cell types of the nervous system. Trends Neurosci. 41, 337–348 (2018). CAS PubMed Article Google Scholar  Maurano, M. T. et al. Systematic localization of…

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George Church on 4D Omics, Natural Computing, and the BioWeatherMap

By Allison Proffitt May 4, 2022 | George Church opened the 20th Anniversary Bio-IT World Conference & Expo last night, speaking virtually to a packed room at Boston’s Hynes Convention Center while many more attendees tuned in online.  Church, the Robert Winthrop Professor, Genetics, Harvard Medical School, spoke about both…

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Solved Need some help In C++, thanks!! /*Class

Need some help In C++, thanks!! /*Class Hierarchy Design a Class “Hierarchy” of 4 derived classes representing 4 generations of a family tree as follow:Grandparent -> Parent -> Child -> Grandchild Add a unique “trait” data member of type integer to EACH CLASS in the hierarchy: A, B, C, DNote…

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Data – com.andrewmccall.faker.Data

Data – com.andrewmccall.faker.Data trait Data extends AnyRef Abstract Value Members abstract def fetch(key: String, locale: Option[String] = None, defaultLocale: String = Faker.defaultLocale): Option[Entry] abstract def getKeys(): Iterable[String] Deprecated Value Members def finalize(): Unit Inherited from AnyRef Inherited from Any Read more here: Source link

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Researchers boost rice yield by overcoming tr

image: The mechanism of boosting rice yield by overcoming a trait trade-off beteen tiller number and panicle size view more  Credit: IGDB Crop breeding is largely constrained by tradeoffs among different agronomic traits. Since many of these tradeoffs are caused by gene pleiotropy, reducing gene pleiotropy may make it easier to…

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Endometriosis-related functional modules and hub genes

Introduction Endometriosis (EMS) is a chronic gynecological disease defined as implantation and periodic growth of the endometrial glands and stroma outside the uterine cavity, causing chronic pelvic pain, severe dysmenorrhea, and infertility in 10% reproductive-age women, among which the infertility rate is approximately 30–50%.1,2 Surgical excision is commonly used for…

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Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure

Cattle are among the largest populations of domesticated animals and used as food resources for humans; therefore, their phenotypes and genetic structure have been shaped by artificial selection for human needs and natural adaptation to environmental changes. The phenotypic selection causes genomic changes in breeding traits within breeds, resulting in…

Continue Reading Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure

Still doubts over embryo selection based on PGT for polygenic conditions

Advances in genomic technologies continue to expand the possibilities of PGT. In a preclinical research study recently published in Nature Medicine, scientists from Silicon Valley-based genetic testing companies have examined the potential of using PGT to predict complex polygenically inherited conditions in human embryos. While the authors present interesting data,…

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NCBI RefSeq representative and reference genomes precalculated in PhenDB

News PhenDB now contains in the “Browse” section the trait precalculations for the reference genomes and representative genomes in NCBI RefSeq. The trait prediction results can be filtered by user-specific criteria for minimal prediction confidence and minimal balanced accuracy. Three figures demonstrate the number of positive and negative predictions for…

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Polygenic Transcriptome Risk Scores for COPD Show Improved Cross-Ancestry Portability

NEW YORK — Polygenic transcriptome risk scores may be better at gauging chronic obstructive pulmonary disease susceptibility across human ancestry groups than polygenic risk scores, a new study has found. COPD affects about 16 million people in the US and is typically diagnosed through two measures of lung function: forced…

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Genomic Mate Selection version 0.2.0 from GitHub

Predict the usefulness of a cross. Multi-trait selection index mean and variance prediction based on parental haplotypes, a genetic map, and marker effects. Implement cross-validation procedures to estimate the accuracy predicting the performance (breeding value, total genetic value including dominance) of previously unobserved individuals as well as cross means and…

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Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals

Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands Aysu Okbay, Hyeokmoon Kweon & Philipp D. Koellinger Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia Yeda Wu, Julia Sidorenko, Jian Yang, Loic Yengo & Peter M. Visscher National Bureau of Economic Research, Cambridge, MA, USA Nancy Wang, Hariharan Jayashankar, Michael Bennett, Grant Goldman, Tamara Gjorgjieva, Steven…

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Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

Fricke, R., Eschmeyer, W. N. & van der Laan, R. (eds). Eschmeyer’s Catalog of Fishes: Genera, Species, Rererences. researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp. Electronic version, Accessed 15 October 2021. Nelson, J. S. Fishes of the World 4th edn, 372 (Wiley, 2006). Google Scholar  Chen, X. H., Lin, K. B. & Wang, X. W. Outbreaks…

Continue Reading Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

What are the PRLR-SLICK cattle?

Earlier this month, a type of short-haired cattle, called PRLR-SLICK, was added to a very short list of animals given a low-risk assessment by the FDA’s Center for Veterinary Medicine (CVM). What’s so special about these cattle is that they are the first intentional genomic alteration (IGA) in an animal…

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Less Sleep, Better Sleep | Genomeweb

Based on their genetics, some people don’t need as much sleep as others, which could also influence their risk for disease, the Atlanta Journal-Constitution writes. Researchers from the University of California, San Francisco, have been studying people who only need four to six hours of sleep, less than the commonly…

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Towards the Genetic Architecture of Complex Gene Expression Traits: Challenges and Prospects for eQTL Mapping in Humans

Review doi: 10.3390/genes13020235. Affiliations Expand Affiliation 1 Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, Korea. Free PMC article Item in Clipboard Review Chaeyoung Lee. Genes (Basel). 2022. Free PMC article Show details Display options Display options Format AbstractPubMedPMID doi: 10.3390/genes13020235. Affiliation 1 Department of…

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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,…

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eQTL mapping using allele-specific count data is computationally feasible, powerful, and provides individual-specific estimates of genetic effects

Using information from allele-specific gene expression (ASE) can improve the power to map gene expression quantitative trait loci (eQTLs). However, such practice has been limited, partly due to computational challenges and lack of clarification on the size of power gain or new findings besides improved power. We have developed geoP,…

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Cutting Edge Agriculture Gene Editing with Cas-CLOVER

Blog Agriculture Biotechnology Though CRISPR-Cas enabled targeted genome engineering across a vast array of organisms, the system features major disadvantages. Frequent off-target mutagenesis, licensing restrictions and non-ideal economic license terms have inhibited commercial crop-science product upscaling, and, in many cases, entirely disqualified CRISPR’s use by many commercial crop developers. Seeking…

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Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases

Cooper, G. S., Bynum, M. L. K. & Somers, E. C. Recent insights in the epidemiology of autoimmune diseases: improved prevalence estimates and understanding of clustering of diseases. J. Autoimmun. 33, 197–207 (2009). PubMed  PubMed Central  Google Scholar  El-Gabalawy, H., Guenther, L. C. & Bernstein, C. N. Epidemiology of immune-mediated…

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The Information Age needs a new data storage powerhouse. With an expanded molecular alphabet and a 21st century twist, DNA may just fit the bill. — ScienceDaily

Imagine Bach’s “Cello Suite No. 1” played on a strand of DNA. This scenario is not as impossible as it seems. Too small to withstand a rhythmic strum or sliding bowstring, DNA is a powerhouse for storing audio files and all kinds of other media. “DNA is nature’s original data…

Continue Reading The Information Age needs a new data storage powerhouse. With an expanded molecular alphabet and a 21st century twist, DNA may just fit the bill. — ScienceDaily

Katia Feve – Academia.edu

Katia Feve – Academia.edu Academia.edu no longer supports Internet Explorer. To browse Academia.edu and the wider internet faster and more securely, please take a few seconds to upgrade your browser. Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our…

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Deep learning and genomics: predicting gene expression from DNA sequence

The human genome is enormously complex. Before the first draft of the genome was completed in 2003, there was an optimism that knowing its sequence could smoothly translate into cures and treatments for various diseases. Unfortunately, the scientific community quickly discovered that having the DNA sequence is still many steps…

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Trait Data Representation – CraftTweaker Documentation

A Trait data representation represents a Tinkers’ Construct Trait’s Data and is ItemBound.You can get such an object from an existing Trait object by supplying an IItemStack to the getData method. It might be required for you to import the class if you encounter any issues (like casting an Array),…

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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…

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Postdoctoral Fellow – Plant Genomics & Bioinformatics – Fort Collins

Working Title Postdoctoral Fellow – Plant Genomics & Bioinformatics Position Location Fort Collins, CO Research Professional Position Yes Posting Number 202101543AP Position Type Admin Professional/ Research Professional Classification Title Postdoctoral Fellows Number of Vacancies Work Hours/Week 40 Proposed Annual Salary Range $50,000-$59,000. Salary is commensurate with experience and qualifications. Employee…

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Genetic strategies reverse pesticide resistance

Nature Communications i>In a new empirical study published in, a gene drive designed to bias heredity, called an allelic drive, was applied without pesticide treatment to create natural-level insects that were balanced with pesticide susceptibility. Population that has been shown to be recoverable. Credits: Bier Lab, University of California, San…

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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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Genetic diversity and selection in Puerto Rican horses

Horses have been considered one of our most prized possessions, used for travel, work, food, and pleasure for at least five and a half millennia17,18,19,20. Nevertheless, the ancestry of various horse breeds and their characteristic traits remains unclear21. In this paper, we describe the patterns and the origins of genetic…

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Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

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Dominant expression of multiple drug resistance after in vitro X-irradiation exposure in intraspecific Chinese hamster ovary hybrid cells | Health & Environmental Research Online (HERO)

BACKGROUND: Exposure of Chinese hamster ovary (CHO) cells to fractionated x irradiation in vitro has led to expression of a distinctive multiple-drug-resistant phenotype. This phenotype is characterized by overexpression of P-glycoprotein without an increase in P-glycoprotein messenger RNA or gene amplification; increased glutathione S-transferase (GST) activity; and resistance to vincristine,…

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17q12-21 risk-variants influence cord blood immune regulation and multitrigger-wheeze

Background: Childhood wheeze represents a first symptom of asthma. Early identification of children at risk for wheeze related to 17q12-21 variants and their underlying immunological mechanisms remain unknown. We aimed to assess the influence of 17q12-21 variants and mRNA-expression at birth on development of wheeze. Methods: Children were classified as…

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Towards the biogeography of prokaryotic genes

1. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015). PubMed  Google Scholar  2. Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019). CAS  PubMed  PubMed Central  Google Scholar  3. Mohammad,…

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Diverse Ancestry GWAS Yields More Accurate Heart Disease Risk Scores

Big genomic data visualization. DNA test, genom map. Graphic concept for your design A multi-ancestry genome-wide association study (GWAS),  led by scientists from the Global Lipids Genetics Consortium (GLGC) recently analyzed genomic data from nearly 1.65 million individuals to narrow down the number of genomic variants strongly associated with blood…

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Director of Bioinformatics Research Job Opening in Hudson, FL at M2GEN

Director of Bioinformatics Research Location:  Remote Status:  Full-time ExemptReports to:  VP Bioinformatics & BiostatisticsDirect Reports:  Build and lead a team consisting of bioinformatics research scientists that support internal business development client engagements, as well as, external academic partner research projects and biopharma sponsored bioinformatics services Who we are M2GEN is…

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Genetic architecture modulates diet-induced hepatic mRNA and miRNA expression profiles in Diversity Outbred mice

Genetic approaches in model organisms have consistently demonstrated that molecular traits such as gene expression are under genetic regulation, similar to clinical traits. The resulting expression quantitative trait loci (eQTL) have revolutionized our understanding of genetic regulation and identified numerous candidate genes for clinically relevant traits. More recently, these analyses…

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An exercise-regulated noncoding RNA counteracts muscle aging

Credit: CC0 public domain In a collaborative effort between EPFL, NTNU Norway, and CBMR Danish laboratories, researchers investigated the molecular effects of exercise on non-coding RNA genes in skeletal muscle. Scientific translation medicine.. In this study, they discovered the long non-coding RNA “CYTOR” and investigated its role in rodent, worm,…

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RNAging: An exercise-regulated noncoding RNA

Skeletal muscle displays remarkable plasticity upon exercise, but is at the same time one of our organs that is most affected by aging. Skeletal muscle aging is characterized by estimated yearly losses of ~1% muscle mass and ~3% muscle strength in the elderly, resulting in an accumulated net loss of…

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Are there some methods can be used to do association analysis in a very small size group?

Are there some methods can be used to do association analysis in a very small size group? 0 Sorry that I’m not native English speaker, so maybe I did not make myself clear somewhere. If so, please forgive me and welcome to ask. we foung a new trait in our…

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Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 CAS  PubMed  PubMed Central  Article  Google Scholar  Alexander DH, Shringarpure SS, Novembre J, Lange K (2015) Admixture 1.3 software manual. UCLA Hum Genet Softw Distrib, Los Angeles Google Scholar  Angert AL, Bontrager…

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GitHub – sdellicour/sars-cov-2_liege

This repo gathers all the input files and scripts related to our study entitled “Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020” (Bollen et al. submitted): R scripts to prepare, analyse, and visualise the phylogeographic analyses performed in this study, Geographic Information…

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Why may BOLT-LMM and SAIGE (quantitative, linear-mixed model) yield different results when ran on the absolutely the same dataset?

As a validation experiment, I have run the same GWAS of a quantitative phenotype derived from the UKBiobank, alongside the genomic data from the UKBiobank, once using the program BOLT-LMM and once using SAIGE linear mixed model (with selected quantitative trait tag). I wanted to see if the results would…

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Accelerating genetic analysis of Alzheimer’s disease

Whether you’re picking stocks or managing a professional sports franchise, investing in data analysis is critical to success in today’s world. Alzheimer’s disease and related dementias research is no different! Since I joined NIA two years ago, I’ve been proud to apply my previous experience in the genomics of infectious…

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Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange

Significance A great challenge for humanity is feeding its growing population while minimizing ecosystem damage and climate change. Here, we uncover the global benefits arising from the introduction of one wild species accession to peanut-breeding programs decades ago. This work emphasizes the importance of biodiversity to crop improvement: peanut cultivars…

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GWAS Power Calculation for Quantitative Trait

GWAS Power Calculation for Quantitative Trait 0 Hi All, I’m fairly new to computational genetics and I am planning on conducting a GWAS of general cognitive ability. I’m planning on using summary statistics so the data are already collected. I am struggling with post-hoc power calculations for a quantitative trait….

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The taxonomy of two uncultivated fungal mammalian pathogens is revealed through phylogeny and population genetic analyses

After 90 years of taxonomic uncertainties, using phenotypic, phylogenetic, and population genetics analyses, the two uncultivated fungi causing skin disease in humans and dolphins, long known as Lacazia loboi8, are now placed as separate species within the genus Paracoccidioides. Early studies using phenotypic or phylogenetic data alone erroneously placed these two…

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A Mouse Model of Mitochondrial Disease Reveals Germline Selection Against Severe mtDNA Mutations

The interesting recent Report, “A mouse model of mitochondrial disease reveals germline selection against severe mtDNA mutations” by W. Fan et al. (15 February 2008, p. 958) provides convincing evidence that mitochondrial mutations with severe effects are eliminated from the female germ line by selection within the ovary. We agree…

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S.T.E.M. Students Discuss Their Summer Research and Internship Experiences

Kayla Bertholf Science and Environment Editor   Sobika Thapa ‘23, Computer Science What was your summer experience/internship called? I interned as an user interface design (UI/UX) intern for a software company in Nepal. Give a summary of your experience. During my internship, I participated in user research and interaction studies,…

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GWAS with phenotype adjusted for covariate (age, sex, PC, batch, centre) using PLINK or external linear model and take residual?

GWAS with phenotype adjusted for covariate (age, sex, PC, batch, centre) using PLINK or external linear model and take residual? 0 Hi everyone, I am conducting GWAS analysis using PLINK but I wonder should I use PLINK to adjust the phenotype for fix effect (age, sex, PC, batch, centre) or…

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Improving tomato production and size to help growers increase their yield

Florida growers produced 606 million pounds of fresh-market tomatoes last year, which brought in $463 million in revenue. But with competition from places like Mexico, farmers are always looking for an edge – to grow more and bigger fruit. That’s why University of Florida scientist Tong Geon Lee spends countless…

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How to estimate polygenic risk score (PRSs) using the scoring files from PGSCatalog for one individual?

How to estimate polygenic risk score (PRSs) using the scoring files from PGSCatalog for one individual? 2 Hi all, I have an annotated vcf file for one individual which I want to estimate his polygenic risk score (PRS) for a certain trait, using the scoring files from the PGSCatalog. The…

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Bacterial endosymbionts protect beneficial soil fungus from nematode attack

A healthy soil nourishes plants and animals, purifies water and air, and promotes sustainable agriculture. Characteristic for highly complex and competitive soil ecosystems are the frequent and direct interactions between all soil-dwelling microorganisms, animals, and plants (1, 2), all of which need to be provided with minerals and carbon sources….

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Weird PCA plot based on WGCNA results

Weird PCA plot based on WGCNA results 0 Dear all, I used WGCNA to find the associated gene modules with the different subtypes of a given cancer as trait. I obtained multiple modules associated with some of the cancer subtypes as shown in . Next, I plotted PCA to visualize…

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is…

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Expanding the diagnosis for Xia-Gibbs Syndrome

Xia-Gibbs Syndrome (XGS) is a rare genetic disorder that results in severe developmental delay, sleep apnea, delayed speech and upper body weakness. Image courtesy of the National Human Genome Research Institute In 2014, a team led by Dr. Richard Gibbs, director of the Human Genome Sequencing Center and Wofford Cain Chair and…

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Satellite DNA-mediated diversification of a sex-ratio meiotic drive gene family in Drosophila

1. Sandler, L. & Novitski, E. Meiotic drive as an evolutionary force. Am. Nat. 91, 105–110 (1957). Article  Google Scholar  2. Lindholm, A. K. et al. The ecology and evolutionary dynamics of meiotic drive. Trends Ecol. Evol. 31, 315–326 (2016). Article  PubMed  Google Scholar  3. Lyttle, T. W. Segregation distorters….

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Joining the DNA dots to improve dairy breeding worldwide

Scientists from Agriculture Victoria, in collaboration with the University of Melbourne, have developed a world-first customised single nucleotide polymorphism chip designed with the latest known genes that affect dairy cattle traits. The work involves the customisation of a small piece of plastic — an SNP chip — with 50,000 small…

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Precision Oncology – Data Scientist – Principal Scientist, Immuno-Oncology Bioinformatics at Sanofi

  Position Overview: We seek an experienced computational biologist / data scientist to identify and advance new immuno-oncology therapies for solid tumors and hematological malignancies. In this hands-on role, you will work as an integral part of project teams to identify targets, advance programs, and develop and test actionable biomarker strategies for…

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NAPB Puts a Focus on Breaking Down Barriers

The National Association of Plant Breeders 2021 virtual meeting highlighted the need to reach out and form new collaborations to advance plant breeding for the 21st century. Fabian Leon was born in Bakersfield, Calif., where his parents were migrant farm workers. He grew up in Nicholasville, Kentucky, where his chance at…

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New Techniques and Complex Models

CRISPR systems that rely on inactivated Cas enzymes—that is, dead Cas (dCas) enzymes—never looked more alive. They harness the targeting power associated with CRISPR—but not the double-strand cuts. As such, they give researchers new ways to interrogate and manipulate gene function. Possibilities include CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa)…

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Could gene editing be the solution to food shortage?

GMO tomato. [Courtesy: iStockphoto] The ageless debate on genetically modified organisms (GMOs) is getting a new twist as scientists make fresh discoveries. Experts from the International Institute of Tropical Agriculture (IITA) are now keen to extinguish a lingering assumption that genetic modification, and gene editing, are more or less the…

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Molecular Biologist, Crop Genetics

Chat message has been posted [Job Posting ID: BASFJP00012179]Regarding: Molecular Biologist, Crop GeneticsGo to SourceChat with: BASF Corporation (BASF), All SuppliersInama, JenniferBASF08/17/2021 08:54 AMHM will be sending Teams details directly to the candidates. Please reach out to make sure those details are received.—-Chat message has been posted [Job Posting ID:…

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normality assumption for GWAS QT

normality assumption for GWAS QT 0 Hi Planning to perform GWAS on quantitative trait using linear reg in plink. From my basic knowledge of statistics, i know that the assumption of normality (residuals) should be only approximately true. But i have seen so many papers on GWAS transforming the data…

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Regarding finding hub genes using WGCNA

Regarding finding hub genes using WGCNA 1 Dear all, I have got the gene expression microarray dataset (about 17000 genes) of about 400 cancer samples with different cancer subtypes. I considered subtypes as traits (binary traits) and used WGCNA to find the possible modules associated with traits and to identify…

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Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

1. Thompson, J. N. & Pellmyr, O. Evolution of oviposition behavior and host preference in Lepidoptera. Annu. Rev. Entomol. 36, 65–89 (1991). Article  Google Scholar  2. Bowers, M. D. Iridoid glycosides and host-plant specificity in larvae of the buckeye butterfly, Junonia coenia (Nymphalidae). J. Chem. Ecol. 10, 1567–1577 (1984). CAS …

Continue Reading Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

WGCNA (TRAIT DATA)

WGCNA (TRAIT DATA) 0 I had already obtained a group of significant proteins after performing analysis on data obtained from LC-MS. I would like to perform network analysis on selected proteins using WGCNA package in R. Network analysis using WGCNA:- Removed outlier samples and Genes. Identified softpower (Beta) for singed…

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GWASpower calculation

GWASpower calculation 0 Dear All, Sorry , sounds like a stupid question but been struggling with this for a while. I am trying to do post-hoc power calculation for my GWAS using GWASpower software for quantitative trait (i know many don’t prefer post-hoc power calculation, but reviewer asked me despite…

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Snp and a disease in the family : promethease

I hope any of this is of use to you: www.ncbi.nlm.nih.gov/snp/rs121434448?horizontal_tab=true#frequency_tab There is only one publication associated with this area and it is linked on that site – but here is the full version: academic.oup.com/hmg/article/7/11/1671/2355991 & CORRECTION: academic.oup.com/hmg/article/7/12/1987/581729 It’s rather unfortunate that there have been no more recent studies into…

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WGCNA significant genes

Hi, I am using WGCNA to construct a network and find significant genes for a trait of interest. After making the network, I chose a module based on the pvalue and correlation value. Then I calculated gene significance values for all genes in that module. trait_x <- as.data.frame(datTraits[, “trait_x”, drop…

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Controlling Banana Xanthomonas Wilt Disease in East Africa

© Olena Danileiko Experts Leena Tripathi, Jaindra Nath Tripathi and Richard Goodman, provide a compelling analysis of controlling Banana Xanthomonas Wilt Disease in East Africa By way of an introduction, banana (Musa spp.) is one of the most common fruits worldwide. However, it is an important staple crop in the…

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Python fast way to get ONLY MAIN metadata for GSE ? (not walking through thousands underlying GSM-samples : slow or even endless)

  Not Python but using EntrezDirect you can get: $ esearch -db bioproject -query “GSE118723” | esummary | xtract -pattern DocumentSummary -element Project_Description Quantification of gene expression levels at the single cell level has revealed that gene expression can vary substantially even across a population of homogeneous cells. However, it…

Continue Reading Python fast way to get ONLY MAIN metadata for GSE ? (not walking through thousands underlying GSM-samples : slow or even endless)

Mixed model analysis using lme4

Mixed model analysis using lme4 0 Hi all, I am a novice in using mixed models. I am not sure how to set up the fixed and random effects in mixed model. Your expertise would be much appreciated. My experimental set up is as follows: Three years of experiment (Experiment),…

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