St. Jude Children's Research Hospital的动态

Stanford University Scientists Discover New Lifeform Residing in Human Microbiome Though they are a mystery, once solved, Obelisks could lead to new biomarkers for clinical laboratory testing. Microbiologists and clinical laboratories know that human microbiota play many important roles in the body. Now, scientists from Stanford University have discovered an entirely new class of “viroid-like” lifeforms residing inside the human body. The researchers detected their presence in both the gut microbiome and saliva samples. Most interesting of all, the researchers are not sure what the lifeforms actually are. The Stanford researchers, led by PhD student Ivan Zheludev, called the new discovery “Obelisks” due to their RNA structures, which are short and can fold into structures that resemble rods. The scientists believe the Obelisks went undetected until now in the human microbiome due to their compact genetic elements, which are only around 1,000 characters or nucleotides in size. A typical human DNA structure consists of around three billion nucleotides. In an article they published on the biology preprint server bioRxiv titled, “Viroid-like Colonists of Human Microbiomes,” the Stanford researchers wrote, “Here, we describe the ‘Obelisks,’ a previously unrecognized class of viroid-like elements that we first identified in human gut metatranscriptomic data. … Obelisks comprise a class of diverse RNAs that have colonized and gone unnoticed in... Read the Dark Daily article at https://hubs.ly/Q02qqfJ10

While single-cell biology has witnessed remarkable advancements, transitioning from single-cell transcriptomics to spatial transcriptomics and even single-cell proteomics, the demand for single-cell RNA sequencing (scRNA-Seq) datasets remains substantial. Whether annotating spatial transcriptomics datasets, constructing single-cell atlases, or exploring other avenues, the analysis of scRNA-Seq datasets remains a pivotal challenge for researchers in the biological sciences. ? During my PhD journey, I contributed to addressing this challenge by developing a comprehensive pipeline for scRNA-Seq data analysis, published in "Dendritic Cell Protocols." It covers essential aspects, including normalization, clustering, cell type identification, trajectory inference, and gene set enrichment analysis. Notably, we introduced an innovative approach that moves beyond cluster-based methods for cell type identification, enabling the identification of cells at the single-cell level, harnessing the true power of scRNA-Seq data. For those interested, the GitHub link to the chapter is available at this link https://lnkd.in/eNitfMJb. ? ?? Are you grappling with unanalyzed bioinformatics data and unsure where to begin? Fear not! The Independent Data Lab is here to cater to all your bioinformatics data analysis needs. Our experts boast a diverse skill set, capable of tackling a spectrum of challenges within the bioinformatics domain. ?? Why Choose the Independent Data Lab? Holistic Solutions: From scRNA-Seq analysis to other bioinformatics complexities, we've got you covered. Expertise Across Domains: Our team's diverse skills ensure a comprehensive understanding of and solutions for various bioinformatics problems. Collaborative Support: Partner with us, and let's transform your raw data into meaningful insights. ?? Ready to Unlock the Potential of Your Data? Contact the Independent Data Lab! #SingleCellBiology #Bioinformatics #IndependentDataLab #scRNA #spatialbiology #computationalbiology #singlecellanalysis #cancerresearch #oncologyresearch #transcriptomics #ngs #datascience #machinelearning #deeplearning

Stanford University Scientists Discover New Lifeform Residing in Human Microbiome Though they are a mystery, once solved, Obelisks could lead to new biomarkers for clinical laboratory testing. Microbiologists and clinical laboratories know that human microbiota play many important roles in the body. Now, scientists from Stanford University have discovered an entirely new class of “viroid-like” lifeforms residing inside the human body. The researchers detected their presence in both the gut microbiome and saliva samples. Most interesting of all, the researchers are not sure what the lifeforms actually are. The Stanford researchers, led by PhD student Ivan Zheludev, called the new discovery “Obelisks” due to their RNA structures, which are short and can fold into structures that resemble rods. The scientists believe the Obelisks went undetected until now in the human microbiome due to their compact genetic elements, which are only around 1,000 characters or nucleotides in size. A typical human DNA structure consists of around three billion nucleotides. In an article they published on the biology preprint server bioRxiv titled, “Viroid-like Colonists of Human Microbiomes,” the Stanford researchers wrote, “Here, we describe the ‘Obelisks,’ a previously unrecognized class of viroid-like elements that we first identified in human gut metatranscriptomic data. … Obelisks comprise a class of diverse RNAs that have colonized and gone unnoticed in... Read the Dark Daily article at https://hubs.ly/Q02qq9F20

The success of precision medicine hinges on high-quality genetic and molecular data linked to detailed clinical insights. I highly recommend this review, which explores the increasing need for bioinformaticians with clinical skills to improve patient care and clinical trials. It highlights key global initiatives in precision medicine, introduces 'precision bioinformatics,' and discusses the integration of computational tools in health institutions. The review also covers the training needs for bioinformaticians, essential skills in the field, and future challenges. https://lnkd.in/dSkm3NE5 #PrecisionMedicine #Bioinformatics #ClinicalData #GenomicData #PatientCare #ClinicalTrials #HealthInnovation #DataIntegration #MedicalEducation #FutureHealthcare

Sequencing technologies are evolving rapidly, continuously delivering improved accuracy and lower costs that are driving genomics forwards. From long-read technology that allows detection of modifications to single-cell sequencing platforms that offer incredible resolution, sequencing is the backbone of genomics research.? ? At The Festival of Genomics & Biodata in London, we’re delighted to host talks on sequencing including: ? Fireside Chat: The Past, Present and Future of Genomics? - J.Craig Venter, Founder, Chairman and CEO, J. Craig Venter Institute Capturing Targeted Single-Cell Long-Read Transcripts to Dissect Tumour Heterogeneity? - Rachel Thijssen, Assistant Professor, Amsterdam University Medical Center Long-Read Whole Genome Sequencing of Human Individuals, Populations and Single Cells?? - Adam Ameur, Associate Professor & Senior Bioinformatician, SciLife Lab, Uppsala University Identifying m6A RNA Modifications in Neuroblastoma Cell Lines Using Nanopore Sequencing?? - Jade Forster, Postdoctoral Fellow, University of Southampton ? Updates on Nanopore-Based High Quality Assembly, Applications of Nanopore Methylation to Primary Cells, and Direct RNA (+cDNA) Nanopore Analysis of Transcripts in Human Cells and Tissue?? - Miten Jain, Assistant Professor, Northeastern University Genome-wide Single-Molecule Analysis of Long-Read DNA Methylation Reveals Heterogeneous Methylation Patterns at Heterochromatin?? - Lyndsay Kerr, Chancellor’s Fellow, Department of Mathematics and Statistics, University of Strathclyde All in a Day's Work – From Raw Data to Manuscript Figures in Under a Day? - John Cole, Research Scientist, University of Glasgow Comparative Analysis of Longread Approaches for Isoform Resolved Single-Cell Transcriptomics? - Anita Scoones, Postdoctoral Researcher, Macaulay, Earlham Institute Mining the CNS Transcriptome for Novel Therapeutic Targets: The Cerevance NETSseq Platform? - Steve Sheardown, Head of Molecular Biology and Cell Engineering, Cerevance All in a Day's Work – From Raw Data to Manuscript Figures in Under a Day? - John Cole, Research Scientist, University of Glasgow Whole Exome Sequencing at Scale for Drug Discovery and Development? - Mary Haas, Senior Manager, Cardiovascular, Metabolic and Skeletal Disease Genetics, Regeneron Genetics Center Deep Learning Improves Pancreatic Cancer Diagnosis Using RNA-Based Variants? - Michael Schroeder, Professor in Bioinformatics, TU Dresden?? ? Don’t wait – get your ticket today: https://hubs.la/Q025rLKP0??? #FOG2024 #NGS #sequencing #genomics

Professor Juan Alfonzo, executive director of the new RNA Center at Brown University, shares insights on the groundbreaking research happening at the center. From advancing our understanding of RNA to its potential applications in medicine and beyond, the center is at the forefront of a scientific revolution. As #RNA study becomes a central focus at Brown’s Warren Alpert Medical School, this Q&A highlights why this research is crucial for the future of healthcare. ?? Dive into the full conversation with Alfonzo and discover what the future holds for RNA research. #RNAResearch #MolecularBiology

In this year's NCI Spring School of Algorithmic Cancer Biology (SSACB), I and Vishaka Gopalan modulated a panel discussion on a special topic: the mutual impact of research reproducibility and scientific publication on each other. As expected, this topic aroused fervent discussion, or even debates, from the attendees. Here are some interesting opinions/comments: - Education on how to handle complexity in study design and result evaluation is mostly lacking among performers of experiments (like me), as well as reviewers for such experimental studies (like me again). - To make a "complete" story (from initial finding to hypothesis, and then to validation on literally every aspect), the content of a paper in a high-profile journal become increasingly heavy. Such requirement for publication make a study too complicated and fragmented to be handled appropriately. - However, the reviewers do not have sufficient support and/or tools to evaluate such heavy and increasingly complicated results. The overloading in task seriously impairs the capability of review outcomes, reducing the quality/reproducibility while promoting fraud of research. - Introducing resource/technologies such as benchmark database or AI (e.g. ChatGPT) may help to relieve the overloading of review task. However, there's concern that these tools will become target of system gaming, turning the measurement to goal (again). - Can preprints in bioRxiv with invited review comments replace publication in scientific journals, reducing the stress of "Publish or Perish", so the researchers can focus on one important question each time, thus promoting the quality of study? - Can we innovate in scientific publication to address these issues? For example, can the study be published in a series of papers, like a TV drama series? This mode will give credit to more authors, and each "episode" can focus on one specific question while bringing up the next one? OK, I stop here, and I will appreciate very, very much if you can give any comment. I want more discussion because I do think the current research/publication model is not sustainable. I really worry that if we don't change, the new generation will lose interest in academic research.

Are you a medical laboratory technologist? Have you ever wondered how we can detect a single mutation in a vast sea of DNA? ?? As medical laboratory technologists, it's vital for us to stay updated with the latest developments in molecular biology. Let's break down some key concepts of molecular biology. ??Understanding Molecular Biology ?? Molecular biology is the study of molecular mechanisms behind the structure, function, and regulation of proteins and nucleic acids (DNA and RNA). ?? Key Techniques and Their Uses 1?? Polymerase Chain Reaction (PCR): This technique amplifies DNA, enabling precise detection and identification of pathogens. It's crucial in infectious disease testing, genetic mutation analysis, and forensic science. ???? 2?? Next-Generation Sequencing (NGS): NGS offers comprehensive genomic analysis, helping us identify genetic mutations linked to various diseases. It’s transformative in personalized medicine, oncology, and rare genetic disorder research. ???? 3?? CRISPR-Cas9: This genome-editing tool allows precise DNA modifications, paving the way for potential cures for genetic disorders. It’s also used in developing disease-resistant crops and new cancer therapies. ????? ?? Recent Breakthroughs 1?? Liquid Biopsies: These non-invasive tests detect cancer-related genetic mutations from a blood sample, offering a less intrusive alternative to traditional biopsies. ???? 2?? Epigenetics: This research field is revealing how gene expression is regulated by chemical modifications to DNA and histones, providing information about developmental processes and disease mechanisms. ???? ?? Why It Matters for Us Our role is crucial in implementing and interpreting these advanced techniques. By mastering molecular biology, we can: 1?? Improve diagnostic accuracy ?? 2?? Drive innovations in patient care ?? 3?? Contribute to the personalized treatment plans ?? What molecular biology techniques do you find most exciting or useful in your work? Share your thoughts in the comments! ???? Regards, Abdullah Bin Arshad #MolecularBiology #MedicalLaboratoryTechnology

[#Webinar] D-8 until our next QuanTIM Webinar! ? ? The webinar will start at 05.30 pm (Paris time) ? ?? Learning from Data in Single-Cell Transcriptomics ???Sandrine Dudoit?(Associate Dean for Faculty and Research, College of Computing, Data Science, and Society Professor, Department of Statistics and Division of Biostatistics/School of Public Health University of California, Berkeley) ???https://lnkd.in/dM-CB8Eg ?? Abstract ?? The ability to measure gene expression levels for individual cells (vs. pools of cells) is crucial to address many important biological questions, such as the study of stem cell differentiation, the detection of rare mutations in cancer, or the discovery of cellular subtypes in the brain. Single-cell transcriptome sequencing (RNA-Seq) allows the high-throughput measurement of gene expression levels for entire genomes at the resolution of single cells. RNA-Seq studies provide a great example of the range of questions one encounters in a Data Science workflow, where the data are complex in a variety of ways, there are multiple analysis steps, and drawing on rigorous statistical principles and methods is essential to derive reliable and interpretable biological results. In this talk, I will provide a survey of statistical questions related to the analysis of single-cell RNA-Seq data to investigate the differentiation of stem cells in the brain, including, exploratory data analysis, dimensionality reduction, normalization, expression quantitation, cluster analysis, and the inference of cellular lineages. About the speaker:?https://lnkd.in/dFY_qnZx #Transcriptomics #SingleCell #LineageInference #DifferentialExpression #StemCell #PublicHealth Cc.?Aix-Marseille Université,?IRD,?Santé publique France,?ISSPAM,?Société Fran?aise de Santé Publique (SFSP),?Collège de Liaison des Internes de Santé Publique (CLISP),?EUPHA - European Public Health Association,?EuroHealthNet,?European Public Health Alliance (EPHA),?Young WFPHA

?? Swipe to read D2R’s 6 Foundational Axes ?? ?? D2R is structured around six Foundational Axes that drive cutting-edge research in genomics and RNA therapeutics. These axes foster interdisciplinary collaborations and aim to advance genomic medicine for the benefit of all. 1?? Population Studies and Genomic Medicine: Innovating genomic methods to identify biomarkers and guide health determinants in prioritized areas. Promoting genomic medicine for improved health care and equitable research. 2?? RNA Therapeutics: Studying RNA biology to enhance therapeutic profiles for novel RNA-based drugs. Creating platforms for pre-clinical and clinical RNA research. 3?? Bioprocessing, Biomanufacturing, and Nanotechnology: Developing and testing nanotechnology for targeted RNA delivery. Providing platforms for designing and testing novel RNA delivery systems. 4?? Clinical Research, Acceleration, and Implementation: Expanding genomic and personalized medicine approaches for diagnostics and patient care. Conducting clinical investigations on disease markers, environmental modulators, and drug repurposing. 5?? Data Science, Bioinformatics, and Computing in Personalized Medicine: Developing integrative omics analysis methods and computational tools for biomarker discovery. Ensuring inclusive genomic studies and robust data governance. 6?? Ethical, Socioeconomic, and Cultural Dimensions in Genomic Research: Promoting responsible research and effective data governance. Engaging with Indigenous communities and patient organizations to ensure equity in research. Find out more: https://buff.ly/3YpjHX4 #D2R #RNA #GenomicResearch