Tag: genome-wide

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…

Welcome to another blog post! ‍ Reference genomes are essential benchmarks of a species’ genome that facilitate the accurate comparison of individual genomes and are crucial tools for identifying genetic variants and diagnosing rare diseases. Here, we will explore the evolution of the human reference genome, focusing on the transition…

Abstract CRISPR-based high-throughput genome-wide loss-of function screens are a valuable approach to functional genetics and strain engineering. The yeast Komagataella phaffii is a host of particular interest in the biopharmaceutical industry and as a metabolic engineering host for proteins and metabolites. Here, we design and validate a highly active 6-fold…

UV Radiation and Its Impact on Plant Genome Plants, as primary producers, rely on solar energy for photosynthesis, a vital process for their survival and growth. However, the UV component of solar radiation can impair genome stability in plants by creating DNA lesions known as UV photoproducts. These lesions hinder…

The Department of Biomedicine at Faculty of Health at Aarhus University invites applications for a position as Professor in the field of Medical Bioinformatics and Statistical Genetics as per 1 July 2024 or as soon as possible thereafter. The position is a time-limited full-time position for 5 years with extension…

The microbiota of the gut has an impact on bone mineral density (BMD) and osteoporosis, but the specific species involved and the underlying mechanisms remained largely unknown until now. A new study has found that Bacteroides vulgatus demonstrates a negative association with BMD, while serum valeric acid (VA) exhibits a…

At the end of 2023, the FDA approved Casgevy for sickle cell disease, its first approval for a therapeutic that used the genome editing tool clustered regulatory interspaced palindromic repeats (CRISPR) to specifically inactivate a human gene as a treatment for a genetic disease. While CRISPR-based gene therapies could potentially…

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein) genome editing enables precise, targeted genetic modification of plants. To date, the genomes of several crops, including rice, tomato, corn, wheat, soybean, barley, potato, sorghum, apple, grapefruit, and orange, have been edited using CRISPR-Cas-based genome editing technology. The CRISPR system cuts not…

Single nucleus RNA-seq reveals cell type heterogeneity in human SNpc We sampled SNpc from post-mortem human brains of 15 sporadic Parkinson’s disease (PD) patients and 14 Control individuals (see Supplementary Table 1 for full pathology reports). Using a 10X Genomics Chromium platform, we performed single nucleus RNA-seq (snRNA-seq) on more than…

Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…

Gladyshev, V. N. et al. Molecular damage in aging. Nat. Aging 1, 1096–1106 (2021). Article  PubMed  PubMed Central  Google Scholar  Sziráki, A., Tyshkovskiy, A. & Gladyshev, V. N. Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction. Aging Cell 17, e12738 (2018). Article  PubMed …

WATCH TIME: 3 minutes Welcome to this special edition of Neurology News Network. I’m Marco Meglio. Shortly after positive topline data from the phase 2 PARADIGM study of PrimeC was released, NeuroSense Therapeutics has announced that the FDA has confirmed its development plans for a phase 3 pivotal trial with…

Ethics and animal welfare statement All infectious work with RESTV, including sample inactivation, was performed in the Containment Level 4 laboratory (CL4) in accordance with the policies and protocols outlined by the Canadian Science Centre for Human and Animal Health Institutional Biosafety Committee. All animal work was performed in strict…

CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared…

Since the idea of genetic regulation was first postulated back in the 1950s, our scientific understanding of the transcriptome has deepened greatly.1 Looking into the transcriptome of cells and tissues has helped scientists to understand the biological processes that drive both health and disease; however, the complex and occasionally mysterious…

Russell PSS, Nagaraj S, Vengadavaradan A, Russell S, Mammen PM, Shankar SR, et al. Prevalence of intellectual disability in India: a meta-analysis. World J Clin Pediatr. 2022;11:206–14. Article  PubMed  PubMed Central  Google Scholar  Winnepenninckx B, Rooms L, Kooy RF. Mental retardation: a review of the genetic causes. Br J Dev…

Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…

Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar  Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…

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…

Kershaw, F. et al. The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice. Conserv. Sci. Pract. 4, e12635 (2022). Article  Google Scholar  Waits, L. P. & Paetkau, D. Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations…

Loss of ASH2L prevents cell proliferation We have studied the molecular and cellular consequences of Ash2l loss in mouse embryo fibroblasts (MEFs) with floxed Ash2l alleles and an inducible Cre-ER recombinase (iMEF-Ash2lfl/fl-Cre-ER). While the knockout of Ash2l was rapid, the downstream effects, including the decrease in promoter-associated H3K4me3, altered gene…

Waters JK, Reznik SI. Update on management of squamous cell esophageal cancer. Curr Oncol Rep. 2022;24:375–85. Article  PubMed  Google Scholar  Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185…

Normalization and Genome-Wide Comparisons with Chipseq 0 Hi all, and apologies if this has been asked before. I have chipseq data (technical and biological replicates for 2 groups) and want to test whether my experimental group has a genome-wide increase in methylation compared to controls. Under the hypothesis, this group…

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….

Wang, A. L. & Wang, C. C. Viruses of the protozoa. Annu. Rev. Microbiol. 45, 251–263 (1991). Article  CAS  PubMed  Google Scholar  Banik, G., Stark, D., Rashid, H. & Ellis, J. Recent advances in molecular biology of parasitic viruses. Infect. Disord. – Drug Targets 14, 155–167 (2015). Article  Google Scholar …

Introduction Skin cutaneous melanoma (SKCM), as one of the most aggressive types of cancer due to its elevated degree of heterogeneity, has gained increasing attention during the past few decades.1 Also known as “the cancer that rises with the sun”,2 melanoma originates from cancerous melanocytes due to molecular or genetic…

Whole-genome sequencing (WGS) analysis of early and advanced adenocarcinomas Whole-genome short read and long read sequencing datasets of 76 lung cancer specimens were analyzed. The datasets included newly generated data for 48 early small-sized lung adenocarcinoma cases (collectively called “Early-Ad” hereafter). These cases included 26 AIS (9 and 17 cases…

iISC-BOs exhibit a CpG methylation signature that closely resembles ISC-BOs Genomic DNA was extracted from MEFs, iISC-BOs, and ISC-BOs, and high-resolution methylome analysis was performed using the PBAT method (Fig. 1A). The genome-wide methylation states of cytosine-containing sequences such as CpG, CHH, and CHG were compared among the samples. The data…

image:  LoGoFunc identifies harmful (left) and harmless (right) genetic variations in the Vasopressin V2 receptor protein using a structure predicted by AlphaFold2. This helps explain how genetic changes affect proteins. view more  Credit: Stein et al., Genome Medicine New York, NY [December 14, 2023]—In a novel study, researchers from the…

Or the full title: ‘The future of GWAS in drug discovery and biobank design: are tools like isGWAS the solution to a pressing problem?’ Zhana (from Optima Partners) will be talking about their work on isGWAS: While genome-wide association studies (GWAS) have proven a powerful tool for human geneticists, there…

HOUSTON ― The University of Texas MD Anderson Cancer Center’s Research Highlights showcases the latest breakthroughs in cancer care, research and prevention. These advances are made possible through seamless collaboration between MD Anderson’s world-leading clinicians and scientists, bringing discoveries from the lab to the clinic and back. Recent developments at…

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…

Dynamic mRNA signatures in the early phase of epileptogenesis after Pilocarpine-induced SE To decipher transcriptional changes early after pilocarpine-induced SE in the hippocampal CA1 subfield, we compared mRNA expression profiles of pilocarpine-induced SE animals and non-SE controls in hippocampal CA1 at five different time points, i.e. 6, 12, 24, 36…

published on 2023-12-12T21:06:52Z 💚 [PDF] FREE Omic Association Studies with R and Bioconductor by Juan R. González,Alejandro Cáceres Its work: [ACCESS] Omic Association Studies with R and Bioconductor by Juan R. González,Alejandro Cáceres EBOOK EPUB KINDLE PDF 📣 topstarsmedia.blogspot.gr/3X2aIXGuX1/1138340561 Omic Association Studies with R and Bioconductor by Juan R. González,Alejandro…

Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article  ADS  CAS  PubMed  Google Scholar  Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Srivastava, M….

PrecisionLife’s Dr Sayoni Das, a computational biologist who leads the research and development of bioinformatics pipelines that generate biological insights from PrecisionLife’s core technology and support drug discovery programmes, details a new study. Using combinatorial analysis, genetic variants associated with long COVID have been identified and, furthermore, it has been…

Problem Description: I am facing an issue while running a Genome-Wide Association Study (GWAS) using PLINK. Despite specifying the phenotype file and confirming the presence of the phenotype column (‘ChildPhenotype’), I consistently receive the error message: “0 individuals have non-missing phenotypes.” I have ensured that the values in the specified…

Annesley SJ, Fisher PR (2019) Mitochondria in health and disease. Cells 8(7). doi.org/10.3390/cells8070680 Cannino G, Ferruggia E, Luparello C, Rinaldi AM (2009) Cadmium and mitochondria. Mitochondrion 9(6):377–384. doi.org/10.1016/j.mito.2009.08.009 Article  CAS  PubMed  Google Scholar  Bonora M, Missiroli S, Perrone M, Fiorica F, Pinton P, Giorgi C (2021) Mitochondrial control of genomic…

Enhancers control gene expression and play crucial roles in development and homeostasis1–3. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here, we combine deep learning and transfer learning to design tissue-specific enhancers for five tissues in the Drosophila melanogaster embryo – the central nervous…

–Must See– Northumbria University Research Fellowship Research Fellow in Health and Life Sciences Northumbria University, Newcastle City Campus, United Kingdom ABOUT THE ROLE We are seeking to appoint a highly committed, motivated, and creative scientist to join the Northumbria University bioinformatics research group. The research will develop new data science…

Flemming, H.-C. & Wuertz, S. Bacteria and archaea on earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019). Article  CAS  PubMed  Google Scholar  Flemming, H.-C., Neu, T. R. & Wozniak, D. J. The EPS matrix: The “house of biofilm cells”. J. Bacteriol. 189, 7945–7947 (2007). Article  CAS …

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article  PubMed  Google Scholar  Giaquinto AN, Sung H, Miller KD, Kramer JL, Newman LA,…

Understanding how genes are regulated Our DNA code provides the “blueprint” for life, enabling our cellular machinery to produce proteins that carry out essential molecular functions. While each cell possesses the same DNA code, the regulation of specific genes within that cell contribute to its unique function. Genes need to…

Identification of the AP2/ERF transcription factors in lettuce genome To identify AP2/ERF family genes in lettuce, we queried the lettuce genomic protein database (version 8) using the Pfam model (PF00847) of the AP2 domain. This search led us to discover 223 genes that showed a significant match with the AP2…

Lichtenstein P, Yip BH, Bjork C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet. 2009;373(9659):234–9. Article  PubMed  Google Scholar  Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R,…

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

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 …

1. Introduction Allergies affect millions of people worldwide and are characterized by an excessive type 2 immune response to normally harmless substances, generally known as antigens or allergens, specifically [1,2]. Consequently, this response leads to the development of various allergic symptoms, including asthma, allergic rhinitis, and atopic dermatitis. In the…

In a collaborative effort co-led by teams from Vanderbilt University Medical Center (VUMC) and the University of Michigan, a comprehensive study that integrates multiple analytic approaches has linked a regulatory gene network and functional defects in insulin-producing pancreatic beta cells to Type 2 diabetes. The study, published in the journal…

Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS  PubMed  PubMed Central  Google Scholar  Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…

Benjamin, E. J. et al. Heart disease and stroke statistics-2019 update: A report from the American Heart Association. Circulation 139, e56–e528 (2019). Article  PubMed  Google Scholar  Yusuf, S. et al. Effect of potentially modifiable risk factors associated with myocardial infarction in 52 countries (the INTERHEART study): Case-control study. Lancet 364,…

1. Carlson ER, Schlieve T. Salivary gland malignancies. Oral Maxillofac Surg Clin North Am 2019; 31: 125-144. 2. Seethala RR. Salivary gland tumors: current concepts and controversies. Surg Pathol Clin 2017; 10: 155-176. 3. Bradley PJ, McGurk M. Incidence of salivary gland neoplasms in a defined UK population….

A recent study published in Nature demonstrates the potential of genomic sequencing in exploring non-coding regions of the genome. Until now, the focus has primarily been on coding regions that make up a small percentage of the genome. However, researchers have recognized the importance of non-coding regions in complex human…

In a recent study published in Nature, researchers in the United  States aggregated and processed 76,156 human genomes to construct a genomic constraint map named “genomic non-coding constraint of haploinsufficient variation” (Gnocchi) for the whole genome. They found that non-coding constrained regions in the genome were rich in known regulatory…

In this study, genome-wide methylation profiles of 128 blood samples were examined. Two blood DNA methylation profiles from 64 individuals were obtained using the Illumina EPIC850k array. Two blood DNA methylation profiles were generated from samples collected in 2007 and 2021, respectively. All samples passed the SeSAMe quality control. A…

Sample collection A total of nine species of marine fish were collected across three different sampling days (September 7th, 9th, and 12th 2022) under IACUC Animal Use Protocol S12219 (Supplementary Data 1). Six species were collected using a speargun donated by a local fisher. Fish were transported back to shore, euthanized,…

American Diabetes A. Economic costs of Diabetes in the U.S. in 2017. Diabetes Care. 2018;41(5):917–28. Article  Google Scholar  Linssen PBC, Veugen MGJ, Henry RMA, van der Kallen CJH, Kroon AA, Schram MT, Brunner-La Rocca HP, Stehouwer CDA. Associations of (pre)Diabetes with right ventricular and atrial structure and function: the Maastricht…

A joint effort involving research teams from Vanderbilt University Medical Center (VUMC) and the University of Michigan has linked the activities of a regulatory gene network and functional defects in insulin-producing pancreatic beta cells to type 2 diabetes. Details of the study are published in a Nature paper titled, “Genetic…

The history of using genes as a tool to treat humans goes back nearly five decades, marking a pivotal moment in medical science.  In 1972, the concept of gene therapy was first considered as a form of treatment. This groundbreaking idea was introduced in a paper titled “Gene therapy for…

The need for targeted drugsCRISPR/Cas9 in drug discoveryPrecision medicine and personalized therapiesFuture prospects and conclusionsReferences Further reading  Clustered regular interspaced short palindromic repeat/CRISPR-associated 9 (CRISPR/Cas9) is a gene-editing technology that has revolutionized biomedical research since its original publication in 2012. The two primary components involved in CRISPR/Cas9 include a guide ribonucleic…

Diener HC, Hankey GJ (2020) Primary and secondary Prevention of ischemic Stroke and Cerebral Hemorrhage: JACC Focus Seminar. J Am Coll Cardiol 75(15):1804–1818 Article  PubMed  Google Scholar  Dou Z, Yu Q, Wang G, Wu S, Reis C, Ruan W, Yan F, Chen G (2020) Circular RNA expression profiles alter significantly…

Astrid Böhne1, Zeynep Oğuzhan1, Ioannis Chrysostomakis1, Simon Vitt2, Denis Meuthen2,3, Sebastian Martin1, Sandra Kukowka1 and Timo Thünken2 1Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn, Germany; 2Bonn Institute of Organismic Biology (BIOB), Department of Animal Biodiversity, University of Bonn, 53121 Bonn, Germany; 3Evolutionary Biology,…

ABOUT THE ROLE We are seeking to appoint a highly committed, motivated, and creative scientist to join the Northumbria University bioinformatics research group. The research will develop new data science methods that leverage the large amounts of public data from UKBiobank, dbGAP, and internal Whole Sequence data and use state-of-the-art…

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…

Base editing is bringing the next breakthrough in cell and gene therapy, explains Michelle Fraser. Cell and gene therapies (CGTs) hold the promise to transform medicine for patients globally. These therapies work by correcting DNA to treat a genetic disease, or by modifying cells from the immune system to specifically…

Software support For command-line users: BGEN support has been implemented in several software packages, click on the links below for more information. For R users: The rbgen package can be used to load data directly into R. For python users: A number of python solutions have been developed, see e.g….

Introduction to the T-test in Bioinformatics: The t-test is a statistical method used to determine if there is a significant difference between the means of two groups. This is particularly crucial in bioinformatics for analyzing gene expression data. Types of T-tests: – One-Sample T-test: Compares the mean of a single…

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….

Burstein, H. J. Systemic therapy for estrogen receptor-positive, HER2-negative breast cancer. N. Engl. J. Med. 383, 2557–2570. doi.org/10.1056/NEJMra1307118 (2020). Article  CAS  PubMed  Google Scholar  Jeselsohn, R. M. The evolving use of SERDs in estrogen receptor-positive, HER2-negative metastatic breast cancer. Clin. Adv. Hematol. Oncol. 19, 428–431 (2021). PubMed  Google Scholar  McAndrew,…

A recent research letter published in the journal Nature Cardiovascular Research describes two new genetic loci associated with coronary artery calcification (CAC). CAC is a measure of atherosclerosis and predicts coronary artery disease (CAD) events. Coronary calcification is a manifestation of atherosclerotic plaque. It is suggested to contribute to plaque…

The global Next Generation Sequencing market was valued at USD 8.26 Billion in 2022 and growing at a CAGR of 19.24% from 2023 to 2032. The market is expected to reach USD 48.01 Billion by 2032. The next-generation sequencing technologies (NGS) market has grown significantly since it was first commercialized….

Introduction Lung cancer remains the leading cause of cancer-related mortality worldwide, and the majority are non-small-cell lung cancer (NSCLC).1,2 Genetic variation is a typical feature of NSCLC that drives cancer initiation and progression.3 Understanding the role of mutated genes in NSCLC is the basis of the development of novel treatment…

Huang, X. et al. The landscape of mRNA nanomedicine. Nat. Med. 28, 2273–2287 (2022). Article  CAS  Google Scholar  Rohner, E., Yang, R., Foo, K. S., Goedel, A. & Chien, K. R. Unlocking the promise of mRNA therapeutics. Nat. Biotechnol. 40, 1586–1600 (2022). Article  CAS  Google Scholar  Brown, A., Shao, S.,…

B cells undergo a series of programmed genomic alterations that enable the immunoglobulin light and heavy chain loci to generate high-affinity antibodies against invading pathogens. First, B cells undergo variability, diversity and joining (VDJ) recombination in the bone marrow with subsequent somatic hypermutation (SHM) and class switch recombination (CSR) occurring…

Kornberg, R. D. & Lorch, Y. Primary role of the nucleosome. Mol. Cell 79, 371–375 (2020). Article  CAS  PubMed  Google Scholar  Zhu, F. et al. The interaction landscape between transcription factors and the nucleosome. Nature 562, 76–81 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Lee, C. K., Shibata, Y.,…

In a momentous landmark for medical research, UK Biobank has today [Thursday 30 November] unveiled incredible new data from whole genome sequencing of its half a million participants. This is set to drive the discovery of new diagnostics, treatments and cures and, uniquely, is available to approved researchers worldwide, via a protected…

A supply of nitrate triggers organ-specific changes of histone modifications at specific gene loci To investigate the organ specificity of dynamic histone modifications in response to N changes, we treated 3-week-old tomato seedlings (Solanum lycopersicum, cultivar M82) with four days of N starvation, followed by N-supply (2.8 mM NO3−; +N) or…

Tsui C, Kretschmer L, Rapelius S, Gabriel SS, Chisanga D, Knöpper K, et al. MYB orchestrates T cell exhaustion and response to checkpoint inhibition. Nature. 2022;609(7926):354–60. Article  CAS  PubMed  PubMed Central  Google Scholar  Zhu L, Zhou X, Gu M, Kim J, Li Y, Ko CJ, et al. Dapl1 controls NFATc2…

Background: Asthma is a chronic airway disease driven by complex genetic-environmental interactions. The role of epigenetic modifications in bronchial epithelial cells (BECs) in asthma is poorly understood. Methods: We piloted genome-wide profiling of the enhancer-associated histone modification H3K27ac in BECs from people with asthma (n=4) and healthy controls (n=3). Results:…

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…

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)….

A novel collection of genomes from Cabinda, Angola and Maputo, Mozambique Genomic DNA was extracted using saliva samples collected with informed consent and sequenced using the Illumina HiSeq X™ platform to an average autosomal read depth of ~12X from 300 individuals sampled in Cabinda and 50 individuals sampled in Maputo…

DOI: 10.18129/B9.bioc.semisup   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see semisup. Semi-Supervised Mixture Model Bioconductor version: 3.16 Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis…

After five years, more than 350,000 hours of genome sequencing, and over £200 million of investment, UK Biobank is releasing the world’s largest-by-far single set of human sequencing data—completing the most ambitious project of its kind ever undertaken. The new data, whole genome sequences of its half a million participants,…

UK Biobank has shared new data from its world’s largest whole genome sequencing project with researchers worldwide for the discovery of new diagnostics, treatments and cures. The set of sequencing data is the biggest ever seen globally and was curated across five years, with more than 350,000 hours of genome…

FBXW7 is a commonly mutated tumor suppressor gene that functions to regulate numerous oncogenes involved in cell cycle regulation. Genome-wide CRISPR fitness screens identified a signature of DNA repair and DNA damage response genes as required for the growth of FBXW7-knockout cells. Guided by these findings, we show that FBXW7…

Abstract A major unmet need in the cystic fibrosis (CF) therapeutic landscape is the lack of effective treatments for nonsense CFTR mutations, which affect approximately 10% of CF patients. Correction of nonsense CFTR mutations via genomic editing represents a promising therapeutic approach. In this study, we tested whether prime editing,…

Individuals with higher quantities of cancer signal from cell-free DNA (cfDNA) prior to treatment had a significantly increased likelihood of recurrence post-treatment Adela’s tissue-agnostic platform shows potential to inform treatment decisions by predicting prognosis FOSTER CITY, Calif., Nov. 30, 2023 /PRNewswire/ — Adela, Inc., an innovator in blood testing for minimal…

Abstract The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals…

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,…

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…

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…

Introduction Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) are characterized by chronic pain, fatigue, and weakness. Patients with these symptoms also suffer from sleep abnormalities and report affected cognitive processes such as memory. The diagnosis of these two syndromes is challenging and is based on questionnaires that make the diagnosis…

SAN DIEGO, Nov. 29, 2023 (GLOBE NEWSWIRE) — Bionano Genomics, Inc. (Nasdaq: BNGO) today announced a publication demonstrating the use of optical genome mapping (OGM) to identify structural variations (SVs) introduced by CRISPR-Cas9 gene editing of CD4+ T-cells that could potentially limit the therapeutic use of such edited cells. The research…

Introduction Thiopurine S-methyltransferase (TPMT) is a cytoplasmic enzyme that catalyzes the S-methylation of purine analogs, including azathioprine, 6-mercaptopurine (6-MP), and thioguanine.1 The metabolism of these drugs results in two types of metabolites: S-methylmercaptopurine and S-methylthioguanine, which are generally described as inactive metabolites, and S-methyl-thioinosine monophosphate, an inhibitor of de novo…

CMI Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when annotating genomes and interpreting biological meaning. It is used for biological experiments and computations to determine relationships among biological systems. Burlingame, Nov. 28, 2023 (GLOBE NEWSWIRE) — According to Coherent Market Insights,…

In recent decades, the development of computational and bioinformatics tools and websites for life sciences has increased exponentially. This great development has gone hand in hand with the availability of genome, proteome and macromolecule structure databases, and also of functional experiments, including microarray and RNAseq expression data, RNA-protein interactions, ChIP-seq,…

Dimitrov, D. S. Virus entry: molecular mechanisms and biomedical applications. Nat. Rev. Microbiol. 2004 22 2, 109–122 (2004). Google Scholar  Chen, W., Zarnitsyna, V. I., Sarangapani, K. K., Huang, J. & Zhu, C. Measuring Receptor-Ligand Binding Kinetics on Cell Surfaces: From Adhesion Frequency to Thermal Fluctuation Methods. Cell. Mol. Bioeng….

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…

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