Tag: genome-wide

Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M. & Cunningham, P. Evidence for two independent domestications of cattle. Proc. Natl Acad. Sci. USA 91, 2757–2761 (1994). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Verdugo Marta, P. et al. Ancient cattle genomics, origins, and rapid turnover…

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Plants | Free Full-Text | The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms

The PacBio RS II sequencer has been effectively utilized to generate a 1.27 Gb genome assembly of Dendrobium officinale [70]. By utilizing advanced sequencing technologies such as Illumina HiSeq, Nanopore, PacBio, and Hi-C, the results have revealed remarkable N50 values of 44 Mb and 65.35 Mb for Gardenia jasminoides and…

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Genome haplarithmisis sheds light on complex genetic landscape of miscarriages

About 10-15% of pregnancies fail after conception has been recognized, amounting to 23 million losses a year. Chromosomal anomalies underlie many embryonic and fetal losses, but their exact frequency and localization to the embryo or placenta are still unclear. A new study published in Nature Medicine reports on a chromosomal…

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Capturing the ancient origins of humanity

DNA is the unseen constant in our world. Not only do its As, Ts, Cs, and Gs form the basis of all life on earth, but DNA that’s shed from living things will pervade the environment around us and, in some cases, will long outlive us. As a biomaterial, DNA is…

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What Is DNA Methylation? Definition & Overview

DNA methylation is a fundamental epigenetic modification mechanism that is crucial in regulating gene activity. It involves adding a methyl group to the DNA molecule, specifically to the cytosine base. This process is vital for various cellular functions, including regulating gene expression, where specific genes are activated or silenced based…

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Ancient diversity in host-parasite interaction genes in a model parasitic nematode

Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar  Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article  CAS  PubMed  Google…

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Head of the Medical Bioinformatics platform (m/f/d) – Kiel

Das Universitätsklinikum Schleswig-Holstein (UKSH) verbindet internationale Spitzenforschung mit interdisziplinärer Krankenversorgung. Wir sind einziger Maximalversorger und größter Arbeitgeber des Landes. Unsere mehr als 14.500 Mitarbeiter*innen stellen eine höchst individuelle Versorgung sicher – unverzichtbar für die Menschen in Schleswig-Holstein.The Institute of Clinical Molecular Biology (IKMB)The Medical Faculty together with the Institute of…

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Bioconductor Code: SNPRelate

SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data ==== ![GPLv3](http://www.gnu.org/graphics/gplv3-88×31.png) [GNU General Public License, GPLv3](http://www.gnu.org/copyleft/gpl.html) [![Availability](http://www.bioconductor.org/shields/availability/release/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![Years-in-BioC](http://www.bioconductor.org/shields/years-in-bioc/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![R](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml/badge.svg)](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml) ## Features Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R…

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Genome Sequencing in Field Crops: Unlocking Agricultural Potential

Genome Sequencing in Field Crops: Unlocking Agricultural Potential Rishabh Gupta Department of Genetics and Plant Breeding, Acharya Narendra Deva University of Agriculture and Technology, Kumarganj, Ayodhya, Uttar Pradesh (224229), India. Anuj Verma Department of Genetics and Plant Breeding, Acharya Narendra Deva University of Agriculture and Technology, Kumarganj, Ayodhya, Uttar Pradesh…

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The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids

Genome sequencing and assembly of R. tetraphylla After DNA extraction from young leaves and sequencing, the R. tetraphylla genome was first assembled into 1008 contigs with an N50 of 3.7 Mb. After haplotigs removal and a final pilon polishing, the 364,945,498 bp final assembly was distributed across 76 scaffolds with an N50…

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Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value

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…

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Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius

Khalifa, S. A. M. et al. Overview of bee pollination and Its economic value for crop production. Insects 12 (2021). Vanengelsdorp, D. et al. Colony collapse disorder: a descriptive study. PLoS ONE 4, e6481 (2009). Article  ADS  PubMed  PubMed Central  Google Scholar  Muli, E. et al. Evaluation of the distribution…

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Genome study unveils genetic ties between cannabis use disorder and lung cancer risk

In a recent study published in Nature Genetics, researchers conducted a genome-wide association study (GWAS) to gain novel insights into the pathophysiology of cannabis use disorder and public health concerns associated with the disorder. Study: Multi-ancestry genome-wide association study of cannabis use disorder yields insight into disease biology and public health…

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High-throughput screening of genetic and cellular drivers of syncytium formation induced by the spike protein of SARS-CoV-2

Plasmid construction All the constructs used in this study were generated with standard cloning strategies, including PCR, overlapping PCR, oligo annealing, digestion and ligation. Primers were purchased from Genewiz. The plasmid sequence was verified by Sanger sequencing. The pCAG-spike(D614G)-GFP11-mCherry plasmid was modified from Addgene plasmid 158761. Briefly, GFP11 and mCherry…

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Gene expression profiles separate endometriosis lesion subtypes and indicate a sensitivity of endometrioma to estrogen suppressive treatments through elevated ESR2 expression | BMC Medicine

Cea Soriano L, López-Garcia E, Schulze-Rath R, Garcia Rodríguez LA. Incidence, treatment and recurrence of endometriosis in a UK-based population analysis using data from The Health Improvement Network and the Hospital Episode Statistics database. Eur J Contracept Reprod Health Care. 2017;22(5):334–43. Article  PubMed  Google Scholar  Guo SW. Recurrence of endometriosis…

Continue Reading Gene expression profiles separate endometriosis lesion subtypes and indicate a sensitivity of endometrioma to estrogen suppressive treatments through elevated ESR2 expression | BMC Medicine

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article  PubMed  Google Scholar  Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article  PubMed  Google Scholar  Amborella Genome Project et al. The Amborella…

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Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA

Summary Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY,…

Continue Reading Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA

Analyzing somatic mutations by single-cell whole-genome sequencing

Failla, G. The aging process and cancerogenesis. Ann. N. Y. Acad. Sci. 71, 1124–1140 (1958). Article  CAS  PubMed  Google Scholar  Szilard, L. On the nature of the aging process. Proc. Natl Acad. Sci. USA 45, 30–45 (1959). Article  CAS  PubMed  PubMed Central  Google Scholar  Vijg, J. & Dong, X. Pathogenic…

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Genome-Wide CRISPR Screens Identify Multiple Synthetic Lethal Targets That Enhance KRASG12C Inhibitor Efficacy | Cancer Research

Citation Suman Mukhopadhyay, Hsin-Yi Huang, Ziyan Lin, Michela Ranieri, Shuai Li, Soumyadip Sahu, Yingzhuo Liu, Yi Ban, Kayla Guidry, Hai Hu, Alfonso Lopez, Fiona Sherman, Yi Jer Tan, Yeuan Ting Lee, Amanda P. Armstrong, Igor Dolgalev, Priyanka Sahu, Tinghu Zhang, Wenchao Lu, Nathanael S. Gray, James G. Christensen, Tracy T….

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Sequencing 101: Tandem repeats – PacBio

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…

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Weaponized genomics: potential threats to international and human security

Lentzos, F. (ed.) Biological threats in the 21st century: The politics, people, science and historical roots (Imperial College Press, 2016). Kania, E. B. Minds at War: China’s pursuit of military dominance through the cognitive sciences and biotechnology. PRISM 8, 82–101 (2019). Google Scholar  Lentzos, F. Personalized war: How the genomics…

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What Is CRISPR Technology | CitizenSide

History of CRISPR Technology The history of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology traces back to the early 1990s when scientists first noticed repetitive DNA sequences in the genomes of certain bacteria. However, it wasn’t until 2005 that the true potential of CRISPR was realized. It was in…

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Unraveling the mitochondrial phylogenetic landscape of Thailand reveals complex admixture and demographic dynamics

Higham, C. Early Mainland Southeast Asia (Antiquity (River Books Press Dist A C, 2014). Google Scholar  O’Connell, J. F. et al. When did homo sapiens first reach Southeast Asia and Sahul?. Proc. Natl. Acad. Sci. U. S. A. 115, 8482–8490 (2018). Article  ADS  PubMed  PubMed Central  Google Scholar  Freidline, S….

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ARFID Genes and Environment (ARFID-GEN): study protocol | BMC Psychiatry

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…

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Multi-ancestry genome-wide association study of cannabis use disorder yields insight into disease biology and public health implications

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….

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Phenotype integration improves power and preserves specificity in biobank-based genetic studies of major depressive disorder

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…

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A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei,Nature Communications

Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification on rRNA in the two life stages of the parasite using four different genome-wide approaches. CRISPR-Cas9 knock-outs of all four snoRNAs guiding…

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Navigating the Road Ahead with Genomics and Polygenic Risk Scores, ET HealthWorld

by Dr Firoz Ahmad Cardiovascular diseases (CVD) as a result of coronary artery diseases (CAD) are a group of health issues that affect the heart and the blood vessels which are essential for optimal heart functioning. It is a leading cause of death worldwide, particularly in India, where it accounts…

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Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles

Introduction The CRISPR-Cas system is a widely used genome engineering technology because of its simple programmability, versatile scalability, and targeting efficiency (Wang & Doudna, 2023). Although researchers are rapidly developing CRISPR-Cas9 tools, the biggest challenge remains to overcome undesired on- and off-targeting outcomes. Previous studies have reported unintended genomic alterations,…

Continue Reading Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles

Novaseq read coverage needed for demultiplexing

Novaseq read coverage needed for demultiplexing 0 Hi, I am a new graduate student in biology and am relatively new to sequencing in general. I am planning on doing a genome-wide CRISPR screen over many days. I plan to extract genomic DNA from each condition and amplify the sg region…

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CRISPR-Cas13d screens identify KILR a breast cancer risk-associated lncRNA that regulates DNA replication and repair.

Abstract Long noncoding RNAs (lncRNAs) have surpassed the number of protein-coding genes, yet the majority have no known function. We previously discovered >800 lncRNAs at regions identified by breast cancer genome-wide association studies (GWAS). Here, we performed a pooled CRISPR-Cas13d RNA knockdown screen to identify which of these lncRNAs altered…

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MAJOR Computational Biology Research Lab

MAJOR Computational Biology Research Lab (MCBRL) uses computer science algorithms to solve biology related problems, bioinformatics software development and develop bioinformatics cloud computing platforms or services for handling and analyzing large-scale biological data.. The workflow of hdWGCNA analysis for Single-cell Spatial Transcriptomics data RNA-seq Schematicsc/nRNA-seq Schematic ” RNA-seq Schematic 空间转录共表达网络分析流程…

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Mutation of key signaling regulators of cerebrovascular development in vein of Galen malformations

Adams, R. H. & Eichmann, A. Axon guidance molecules in vascular patterning. Cold Spring Harb. Perspect. Biol. 2, a001875 (2010). Article  PubMed  PubMed Central  Google Scholar  Fish, J. E. & Wythe, J. D. The molecular regulation of arteriovenous specification and maintenance. Dev. Dyn. 244, 391–409 (2015). Article  CAS  PubMed  Google…

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Using Genomic Profiling to Provide Personalized Medicine in MDS

Myelodysplastic syndromes (MDS) is a group of clonal hematopoietic neoplasms characterized by the combination of persistent unexplained cytopenia (or cytopenias) and morphologic dysplasia and a propensity to progress to bone marrow failure or acute myeloid leukemia (AML).1 The treatment landscape for MDS is continually progressing and involves a multidisciplinary approach…

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Guidelines for performing ribosome profiling in plants including structural analysis of rRNA fragments

Abstract Ribosome profiling (or Ribo-seq) is a technique that provides genome-wide information on the translational landscape (translatome). Across different plant studies, variable methodological setups have been described which raises questions about the general comparability of data that were generated from diverging methodologies. Furthermore, a common problem when performing Ribo-seq are…

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Transgenerational epigenetic effects imposed by neonicotinoid thiacloprid exposure

This study is aimed at revealing the transgenerational effects of thia. We chose the developmental window from embryonic days 6.5 to E15.5 because of its importance in germ cell program establishment. The mice breeding was described in the Materials and Methods section “Mouse treatment and dissection.” The design of the…

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Postdoctoral fellow in Bioinformatics/Genomics

Postdoctoral Position – Institut Curie Paris The Genomics and Development of Childhood Cancers lab (institut-curie.org/team/saulnier), headed by Olivier Saulnier is looking for one postdoctoral position researcher in bioinformatics. The team focuses on using cutting-edge high-throughput genomic approaches and genome-wide data analyses to study the spatio-temporal origins of pediatric brain tumors….

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Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding

Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya…

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Seven Salk scientists named among best and most highly cited researchers in the world

November 15, 2023 Seven Salk scientists named among best and most highly cited researchers in the world November 15, 2023 LA JOLLA—Salk Professors Joseph Ecker, Ronald Evans, Satchidananda Panda, Rusty Gage, and Kay Tye, as well as Assistant Professor Jesse Dixon, have been named to the Highly Cited Researchers list…

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MD Anderson Research Highlights for November 15, 2023

Newswise — 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…

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Inhibition of providencia vermicola FabD

Introduction Microbial resistance has become a problem in the contemporary medical environment due to the inadequate development of new antibiotics and the asinine prescription of antibiotics in both developed and developing nations. Antimicrobial resistance (AMR), which affects wealthy and developing nations, is a global concern.1 AMR is a problem for…

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Cis- and trans-eQTL TWAS of breast and ovarian cancer identify more than 100 risk associated genes in the BCAC and OCAC consortia

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…

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IJMS | Free Full-Text | CRISPR/Cas9-Mediated Genome Editing in Cancer Therapy

1. Introduction Recently, the morbidity and mortality rates of cancer have been increasing rapidly, posing a significant threat to human health. Cancer, a refractory and multifaceted disease, fundamentally originates from a cumulative series of mutations in the cellular genome and epigenome. These mutations activate oncogenes and deactivate tumor suppressors, leading…

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Personalized medicine: “Tyranny of the gene”

Dr Priya Hays, Ph.D., CEO/Science Writer at Hays Documentation Specialists, LLC, responds to “Tyranny of the Gene.” Is personalized medicine a threat to public health? Not really, but yes, it’s an argument for price controls and perhaps more regulations; we hear Tyranny of the Gene: Personalized Medicine’s Threat to Public…

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The effects of methylphenidate and atomoxetine on Drosophila brain at single-cell resolution and potential drug repurposing for ADHD treatment

Both MPH and ATX increase the locomotor activity of wild-type Drosophila To investigate the cell type-specific molecular mechanisms of ADHD drugs in the brain at single-cell resolution, we conducted behavioral experiments and scRNASEQ in wild-type (WT) adult male Drosophila melanogaster following exposure to MPH, ATX, and control treatment. Here, we…

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ABCB1 and immune genes in breast cancer

Introduction Chemoresistance is a major challenge for breast cancer treatment.1 The mechanisms of chemoresistance are complex because of crosstalk between receptor tyrosine kinases and downstream pathways, deregulation of cell-cycle and apoptosis regulators, and modulation of tumor-infiltrating immune cells.2 The ATP-binding cassette (ABC) superfamily is one of the largest families of…

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Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…

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Whole genome sequencing in high-grade cervical intraepitheli… : Medicine

1. Introduction Cervical cancer (CC) is the third most common cancer in women worldwide and has a high mortality rate among women. In 2008, CC was responsible for 275,000 deaths, thereby being the fourth leading cause of cancer death in females worldwide.[1,2] In China, CC is the second most…

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DNA microarray technique for infectious disease diagnostics.

Introduction Infectious diseases are illnesses caused by pathogenic microbes such as bacteria, viruses, parasites, or fungus, which can be transmitted directly or indirectly from one person to another.1 Throughout human history, infectious illnesses have been a major cause of morbidity and mortality. One-third of all death worldwide is caused by…

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Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders

Kessler, R. C. et al. Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Arch. Gen. Psychiatry 62, 593–602 (2005). Article  PubMed  Google Scholar  Kessler, R. C. et al. Prevalence, persistence, and sociodemographic correlates of DSM-IV disorders in the National Comorbidity Survey Replication Adolescent Supplement….

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Most large structural variants in cancer genomes can be detected without long reads

JaBbA v1 outperforms previous CN algorithms We enhanced our previous JaBbA (v0.1; ref. 4) model with several methodological innovations to increase robustness to read depth waviness, improve algorithm convergence and enforce junction balance for allele-specific as well as total CN (Extended Data Fig. 1a–d and Methods). We also rigorously defined…

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Genome interpretation in a federated learning context allows the multi-center exome-based risk prediction of Crohn’s disease patients

Goodwin, S., McPherson, J. D. & Richard McCombie, W. Coming of age: Ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17(6), 333–351 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Van Dijk, E. L., Auger, H., Jaszczyszyn, Y. & Thermes, C. Ten years of next-generation sequencing technology. Trends Genet….

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Bioconductor – FitHiC

DOI: 10.18129/B9.bioc.FitHiC     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see FitHiC. Confidence estimation for intra-chromosomal contact maps Bioconductor version: 3.11 Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as…

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Study unveils complex admixture in European ancestry populations

A recent study published in the journal Nature Communications provides evidence of subcontinental admixture in people with European ancestry, in contrast to previous genetic association studies that recognize European ancestry populations as stratified and not as admixed.   Study: Unappreciated subcontinental admixture in Europeans and European Americans and implications for genetic epidemiology…

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Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges

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…

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Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network | Genome Medicine

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  Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E,…

Continue Reading Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network | Genome Medicine

TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons

Padeken, J., Methot, S. P. & Gasser, S. M. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat. Rev. Mol. Cell Biol. 23, 623–640 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Tchasovnikarova, I. A. et al. Epigenetic silencing by the HUSH complex mediates position-effect variegation…

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Mapping Mammalian 3D Genome Interactions with Micro-C-XL

A protocol for mapping the three-dimensional genome organization with nucleosome resolution using the genome-wide chromosome conformation capture method Micro-C-XL is presented here. This protocol is significant as it shows high resolution chromosome loops and other short-range interaction features. The main advantage of this technique is the mapping of the 3D…

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Pharmacogenomics holds promise for personalized dementia therapies

In a recent article published in the Genes Journal, researchers discussed the significance of pharmacogenomics-based studies in the research for personalized therapeutics for dementia, including drugs targeting both cognitive and non-cognitive symptoms. They discussed pharmacotherapy approaches for Alzheimer’s disease (AD), vascular dementia (VaD), frontotemporal disease (FTD), and Lewy body disease (LBD). In…

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Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls

World Health Organization. Facts sheet: suicide. www.who.int/news-room/fact-sheets/detail/suicide. National Institute of Mental Health. Suicide. www.nimh.nih.gov/health/statistics/suicide. Nock MK, Hwang I, Sampson N, Kessler RC, Angermeyer M, Beautrais A, et al. Cross-national analysis of the associations among mental disorders and suicidal behavior: findings from the WHO world mental health surveys. PLoS Med. 2009;6:e1000123….

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IJMS | Free Full-Text | CRISPR/Cas9 Landscape: Current State and Future Perspectives

1. Introduction Genome editing has taken a leading position among genome modification technologies in a short time and is now widely used in gene therapy. To date, there are three main systems for genome editing: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas nucleases. Genome editing has…

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Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer | Military Medical Research

Zhu J, Ke Y, Liu Q, Yang J, Liu F, Xu R, et al. Engineered Lactococcus lactis secreting Flt3L and OX40 ligand for in situ vaccination-based cancer immunotherapy. Nat Commun. 2022;13(1):7466. Article  CAS  PubMed  PubMed Central  Google Scholar  Evans ER, Bugga P, Asthana V, Drezek R. Metallic nanoparticles for cancer…

Continue Reading Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer | Military Medical Research

Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau

Abebe TD, Naz AA, Léon J (2015) Landscape genomics reveal signatures of local adaptation in barley (Hordeum vulgare L.). Front Plant Sci 6:813 Article  PubMed  PubMed Central  Google Scholar  Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 Article  CAS  PubMed …

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Genes that shape facial features

After turning up hundreds of genes with hard-to-predict effects, some scientists are now probing the grander developmental processes that shape face geometry When Eric Mueller, who was adopted, first saw a photograph of his birth mother, he was overcome by how alike their faces were. It was, he wrote, “the…

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Characterization of the genomic alterations in poorly differentiated thyroid cancer

Cancer Genome Atlas Research, N. Integrated genomic characterization of papillary thyroid carcinoma. Cell 159, 676–690. doi.org/10.1016/j.cell.2014.09.050 (2014). Sherman, S. I. Thyroid carcinoma. Lancet 361, 501–511. doi.org/10.1016/s0140-6736(03)12488-9 (2003). Article  PubMed  Google Scholar  Tong, J. et al. Poorly differentiated thyroid carcinoma: a clinician’s perspective. Eur. Thyroid J. 11, doi.org/10.1530/ETJ-22-0021 (2022). Asioli, S….

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University of Oklahoma hiring Postdoctoral Researcher in Bioinformatics & Computational Biology in Norman, OK

Description Description The candidate is responsible for analyzing and mining multi-omics data using computational techniques, such as deep learning, generalized linear mixed models, and biological network analysis. This may require development of new computer algorithms and/or construction of computational workflows on computer clusters. The types of multi-omics data will include…

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Correction of a homoplasmic mitochondrial tRNA mutation in patient-derived iPSCs via a mitochondrial base editor

Human induced pluripotent stem cells (iPSCs) Reprogramming and Culture This study was ethically approved by the Medical Ethics Committee of Nanjing Maternal and Child Health Care Hospital (2021KY-131), and informed consents were obtained from the patient’s legal guardian as well as the healthy donors, in accordance with the Declaration of…

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Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms

Bond, R. & Loeffler, A. What’s happened to Staphylococcus intermedius? Taxonomic revision and emergence of multi-drug resistance. J. Small Anim. Pr. 53, 147–154 (2012). Article  CAS  Google Scholar  Carroll, K. C., Burnham, C. D. & Westblade, L. F. From canines to humans: clinical importance of Staphylococcus pseudintermedius. PLoS Pathog. 17,…

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Generating, modeling, and evaluating a large-scale set of CRISPR/Cas9 off-target sites with bulges

CRISPR/Cas9 system is widely used in a broad range of gene-editing applications. While the CRISPR editing technique is quite accurate in the target region, there may be many unplanned off-target sites (OTS). Consequently, a plethora of high-throughput experimental assays have been developed to measure OTS in a genome-wide manner. Based…

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The Hidden Mechanisms Behind Rapid Tumor Evolution: AR Amplification on Extrachromosomal DNA I Prostate Cancer

Read the Full Video Transcript Andrea Miyahira: Hi everyone, I’m Andrea Miyahira at the Prostate Cancer Foundation. Presenting today is Dr. Scott Dehm, a professor at the University of Minnesota on his recent paper, “Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer,” published…

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HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases

HLA allele calling from WES HLA-HD was used to call HLA alleles for 454,824 participants at 3-field resolution (representing the allele’s serological specificity, HLA protein, and synonymous variants). We used the UKB whole-genome genotyping (unavailable in 1283 participants) projected on the 1000 Genome reference to estimate genetic ancestry. We found…

Continue Reading HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases

Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo

Introduction The non-random packaging of chromatin within the nucleus is a universal feature of eukaryotic genomes. The three-dimensional (3D) spatial organization of chromatin could be partitioned at different levels based on the interaction frequency between two given loci in the genome. Advances in sequencing technologies have led to the identification…

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Structural Variants in gnomAD v4

Today, we are thrilled to announce the release of genome-wide structural variants (SVs) for 63,046 unrelated samples with genome sequencing (GS) data. All site-level information for 1,199,117 high-quality SVs discovered in these samples is browsable in the gnomAD browser (gnomAD SV v4) and downloadable from the gnomAD downloads page. For…

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Functional Genomics Scientific Capabilities | National Center for Advancing Translational Sciences

Historically, a lack of methods to properly interpret the results of genome-wide screens, a lack of collaborative expertise to perform RNAi experiments, and the absence of comprehensive RNAi data in public databases for researchers to reference all have limited RNAi’s usefulness. To address these problems, NCATS operates a state-of-the-art RNAi…

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Bacterial SNPs in the human gut microbiome associate with host BMI

Lynch, S. V. & Pedersen, O. The human intestinal microbiome in health and disease. N. Engl. J. Med. 375, 2369–2379 (2016). Article  CAS  PubMed  Google Scholar  Manichanh, C. et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55, 205–211 (2006). Article  CAS  PubMed …

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Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus

Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been the molecular markers of choice to identify admixed individuals. However, with the advent of high-throughput sequencing easing the generation of genome-wide datasets, incorrect reports of hybridization resulting…

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Diet-induced rewiring of the Wnt gene regulatory network connects aberrant splicing to fatty liver and liver cancer in DIAMOND mice

DIAMOND mice develop HCC in the context of obesity and insulin resistance To investigate in depth the genome-wide transcriptional and epigenetic changes that occur during development of MAFLD and obesity-related hepatocellular carcinoma (HCC), we performed RNA-sequencing (RNA-seq) and Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) of liver tumours (HCC) and liver control tissue (FL)…

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Novel Rett syndrome variant shines light on n

Rett syndrome is a rare devastating neurological disorder that primarily affects young girls and manifests as an impaired ability to walk and talk, along with characteristic ‘hand-wringing’ movements, seizures, and cognitive disability. This incurable condition results from mutations in the methyl-CpG binding protein 2 (MECP2) gene that impairs the role…

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epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data | GigaScience

Abstract Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5–8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new…

Continue Reading epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data | GigaScience

Bioinformatics Staff Scientist at the Center for Functional Genomics

Job Description We are seeking a highly motivated and skilled computational staff scientist to join our team in Center for Functional Genomics and Tissue Plasticity (ATLAS) for a four-year position, focusing on supporting and coordinating computational analyses on NGS data. The position is available from January 1, 2024 or as…

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Help with genome comparison between two strains.

Help with genome comparison between two strains. 1 Hi, I’m new to bioinformatics and I need to compare two bacterial genomes. These genomes come from different strains of the same species. and both genomes are available in NCBI What I need to do is a genome wide comparison to find…

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MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing | Genome Biology

Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang C-Z, Wala J, Mermel CH. Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013;45:1134–40. Article  CAS  PubMed  PubMed Central  Google Scholar  Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı…

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Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing

Study population We included 67,390 participants from 19 TOPMed studies: Genetics of Cardiometabolic Health in the Amish (n = 1,109) (ref. 32), Atherosclerosis Risk in Communities Study (n = 3,780) (ref. 33), Barbados Genetics Asthma Study (n = 980), Mount Sinai BioMe Biobank (n = 9,392) (ref. 34), Coronary Artery Risk Development in Young Adults (n = 3,293) (ref. 35),…

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Decoding Life’s Secrets: Researchers Solve Protein Mystery

Proteins in human cells commonly undergo N-terminal acetylation, a modification by the enzyme group N-terminal acetyltransferases (NATs), the function of which has been largely mysterious. Recent research using CRISPR-Cas9 technology and collaborative studies in fruit flies reveal that this modification protects proteins from degradation, playing a crucial role in longevity…

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Sequencing and Genotyping / Technological Facilities / Facilities / CRI – Fondazione E. Mach

Instruments MISEQ ILLUMINA NGS sequencing platform that allows to generate up to 25 million reads from 25 to 300 nucleotides in paired end mode (PE 2X300)  MinION ONT Portable real time device for DNA and RNA sequencing by nanopore technology 3730xl GENETIC ANALYZER Capillary electrophoresis platform for high throughput genetic…

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Microorganisms | Free Full-Text | Identification, Genome Sequencing, and Characterizations of Helicobacter pylori Sourced from Pakistan

1. Introduction The incidence of H. pylori infection differs across different regions and populations, but according to an estimate, more than 50% of the global population may be infected with this bacterium. It is particularly prevalent in underdeveloped nations such as Pakistan, where over 80% of the population carries H….

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Unlocking the genetic potential of poplars: A

The Populus genus, commonly known as poplars, cottonwoods, and aspens, consists of approximately 30 tree species native to the northern hemisphere. Because of their diverse usages in landscape, agriculture, bioenergy, and industry, Populus species have been the focus of many tree breeding and genetic improvement programs. Modern biotechnologies, including both genomics and genetic…

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Increased binding of anti-dsDNA antibodies to short oligonucleotides modified with topoisomerase I reveals a potential new enzyme function independent from DNA relaxation | BMC Research Notes

Lee MP, Brown SD, Chen A, Hsieh TS. DNA topoisomerase I is essential in Drosophila melanogaster. Proc Natl Acad Sci U S A. 1993;90(14):6656–60. doi.org/10.1073/pnas.90.14.6656. [published Online First: Epub Date]|. Article  CAS  PubMed  PubMed Central  Google Scholar  Morham SG, Kluckman KD, Voulomanos N, Smithies O. Targeted disruption of the mouse…

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Study identifies new mutations with potential link to EDS

Through a genetic analysis of more than 170 patients, researchers have identified new genetic mutations that may cause Ehlers-Danlos syndrome (EDS). “Our results are consistent with the complex genetic architecture of EDS and suggest a number of novel … candidate genes and pathways,” the researchers wrote in the study, “Genetic…

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Genetic diversity and phylogenetic analyses of Asian lineage Zika virus whole genome sequences derived from Culex quinquefasciatus mosquitoes and urine of patients during the 2020 epidemic in Thailand

Hayes, E. B. Zika virus outside Africa. Emerg. Infect. Dis. 15(9), 1347–1350. doi.org/10.3201/eid1509.090442 (2009). Article  PubMed  PubMed Central  Google Scholar  Faye, O. et al. Molecular evolution of Zika virus during its emergence in the 20th century. PLoS Negl. Trop. Dis. 8(1), e2636. doi.org/10.1371/journal.pntd.0002636 (2014). Article  CAS  PubMed  PubMed Central  Google…

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T cell receptor therapeutics: immunological targeting of the intracellular cancer proteome

Hedrick, S. M., Cohen, D. I., Nielsen, E. A. & Davis, M. M. Isolation of cDNA clones encoding T cell-specific membrane-associated proteins. Nature 308, 149–153 (1984). Article  CAS  PubMed  Google Scholar  Yanagi, Y. et al. A human T cell-specific cDNA clone encodes a protein having extensive homology to immunoglobulin chains….

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Researchers Uncover the Answer to Protein Mystery

Register for free to listen to this article Thank you. Listen to this article using the player above. ✖ Want to listen to this article for FREE? Complete the form below to unlock access to ALL audio articles. Proteins are key to all processes in our cells…

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Comparative Analysis of Structural Variant Callers on Short-Read Whole-Genome Sequencing Data

Pang, A.W., MacDonald, J.R., Pinto, D., et al., Towards a comprehensive structural variation map of an individual human genome, Genome Biol., 2010, vol. 11, no. 5, p. R52. doi.org/10.1186/gb-2010-11-5-r52 Article  CAS  PubMed  PubMed Central  Google Scholar  The International HapMap Consortium, The international HapMap project, Nature, 2003, pp. 789—796. doi.org/10.1038/nature02168 Sudmant,…

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TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells

Animal models Animal studies were approved by the Institutional Animal Care Use Committee of the Institute of Biosciences and Technology, Texas A&M University (AUP 2020-0195). Most mouse strains bear a C57BL/6 genetic background unless otherwise noted. All the animals were housed in a certified animal facility with a standard dark/light…

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NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology

Patient characteristics and tissue context The clinical interpretation of molecular alterations starts with evaluating relevant patient characteristics and the tissue context in which a genetic profile occurs. The former relates, in particular, to previous therapies, in addition to disease stage and clinical performance status. For example, prior targeted therapies warrant…

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Single Nucleotide Polymorphism (SNP) Genotyping Market Report

Single Nucleotide Polymorphism (SNP) Genotyping Market The Business Research Company’s global market reports are now updated with the latest market sizing information for the year 2023 and forecasted to 2032 The Business Research Company’s Single Nucleotide Polymorphism (SNP) Genotyping Global Market Report 2023 identifies ncreasing burden of chronic conditions as…

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MICA: a multi-omics method to predict gene regulatory networks in early human embryos

Introduction After the fusion of the oocyte and sperm, the zygote undergoes a series of cell divisions until it forms a blastocyst before implantation into the uterus. A human blastocyst is formed of a fluid-filled cavity and ∼200 cells that comprise three distinct cell types: the trophectoderm (TE), which gives…

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Leishmania genetic exchange is mediated by IgM natural antibodies

Rapaka, R. R. et al. Conserved natural IgM antibodies mediate innate and adaptive immunity against the opportunistic fungus Pneumocystis murina. J. Exp. Med. 207, 2907–2919 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  Boehm, T., Iwanami, N. & Hess, I. Evolution of the immune system in the lower vertebrates. Annu….

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Why is COVID-19 more severe in some people? Researchers use genetics, data science to find out

Why do some people have a more severe course of COVID-19 disease than others? A genome sequence database created by an international collaboration of researchers, including many from the University of Toronto and partner hospitals, may hold the answers to this question – and many more. The origins of the Canadian…

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Identification of asthma-related genes using asthmatic blood eQTLs of Korean patients

Background: More than 200 asthma-associated genetic variants have been identified in genome-wide association studies (GWASs). Expression quantitative trait loci (eQTL) data resources can help identify causal genes of the GWAS signals, but it can be difficult to find an eQTL that reflects the disease state because most eQTL data are…

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