Oxford Science Enterprises’ Post

🔬 **Optical Genome Mapping (OGM) vs. Next-Generation Sequencing (NGS): Which is Better?** **What is Optical Genome Mapping (OGM)?** OGM is a cutting-edge technique that creates high-resolution, large-scale maps of the genome by physically stretching and labeling DNA molecules. This allows for the detection of structural variations and provides a visual representation of the genome's architecture. **Optical Genome Mapping (OGM):** ✅ Ideal for detecting large structural variations (insertions, deletions, duplications, inversions, translocations). ✅ Provides a high-resolution, visual representation of genome architecture. ✅ Effective in analyzing complex genomic regions. **Next-Generation Sequencing (NGS):** ✅ Excels at identifying small-scale variations (SNVs, indels). ✅ Essential for gene expression and transcriptome analysis. ✅ Comprehensive variant detection, cost-effective, and high throughput. 🔗 **Combined Use:** Leverage both technologies for a complete genomic view—OGM for structural insights and NGS for detailed sequence information. Choosing the right tool depends on your specific needs, whether it's large-scale structural insights or detailed genetic analysis. In many cases, integrating OGM and NGS offers the most comprehensive understanding of the genome. #Genomics #GenomeMapping #NextGenSequencing #OGM #NGS #Biotech #Research #HealthcareInnovation

CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments abs: https://lnkd.in/dtK6E9mM "Introduces CRISPR-GPT, a tailor-made LLM agent for automated designing of gene-editing experiments. Focuses on breaking experiment design down to a variety of substeps that the agents solve: selection of the CRISPR system, design of guide RNA, prediction of off-target effects, selection of delivery system, etc. The agent was validated with human evals and even wet-lab experiments where 4 gene knockout experiments were designed with CRISPR-GPT with successful results."

Genetically speaking, humans are 99.5-99.9% identical to one another. The remaining 0.1-0.5% of unique genetic material helps define our individuality. The landscape of human health is being transformed by Genome Sequencing. Large-scale genome sequencing projects, such as the UK Biobank's initiative to sequence half a million individuals, exemplify this shift. However, this also presents challenges, including the need to manage and interpret vast amounts of genomic data accurately to glean meaningful insights. Join us for our workshop on Clinical NGS Data Analysis, where we will delve into the analysis of large-scale NGS data to extract relevant information. This workshop is designed to provide comprehensive training on analyzing and interpreting genomic datasets. Participants will learn how to analyze NGS datasets from raw files, including variant calling, annotation, and clinical interpretation. Be part of this exciting workshop to prepare yourself for the future of healthcare. Register today: https://lnkd.in/dkVH735N 📅 Workshop Dates: March 27th to April 25th, 2024 🕒 Time: Every Wednesday and Thursday, 6:30 PM to 8:00 PM IST #precisionmedicine #bioinformatics #nextgenerationsequencing #precisionhealth

🧬 Spatial Transcriptomics Cell Type Annotation with Graph Contrastive Learning 🧬 The recent bioRxiv article by Qiaolin Lu and colleagues introduces "Focus," a new semi-supervised graph contrastive learning method that enhances cell type annotation in spatial transcriptomics by modeling the subcellular RNA distribution 🔍 Key Features of Focus: 🟣 Constructs gene neighborhood networks at the subcellular level to refine cell type identification. 🟢 Demonstrates superior accuracy over existing methods on platforms like CosMx SMI, MERFISH, and Xenium. 🟠 Assigns importance scores to genes, highlighting their roles in cell type-specific pathways and revealing potential regulatory mechanisms. 🔬 Impact on Research: Focus not only improves annotation accuracy but also provides deeper insights into molecular pathways and gene regulation at a subcellular level. This method has the potential to unlock new understanding in cellular function and disease progression. 📚 bioRxiv paper: https://buff.ly/3UbMcnh 👨💻 GitHub: https://buff.ly/3UrHhzQ 📢 Join the Conversation 📢 Share your ideas, methods, and tools in the comments! 👇 💬 #Bioinformatics #Transcriptomics #SpatialBiology #CellBiology #Genomics #Focus

Two decades after the unveiling of the human genome, our understanding of genomic complexity continues to evolve. The number of known protein-coding genes is stabilising below 19,500, but our understanding of noncoding RNA genes across the human genome remains in its early stages. While recent advancements pave the way towards understanding these genes and refining our gene catalogue, the challenge to identify and describe every gene for the benefit of biomedical research and genome interpretation remains. Find out more and what the future holds for the comprehensive annotation of human genes. https://lnkd.in/exmF5ikA #genomeresearch #emblebi #humangenome #genomics #bioinformatics #medicalgenetics #geneannotation EMBL National Center for Biotechnology Information (NCBI) Ensembl

- DrSeq Clinical NGS Services: Harness the power of Next-Generation Sequencing (NGS) using the Illumina NovaSeq 6000 technology. This advanced platform enables us to precisely identify Single Nucleotide Variants (SNVs) and Copy Number Variations (CNVs) within your genome, providing in-depth genetic insights. - Custom Panels and Structural Variation Analysis: Tailor your genetic analysis with our custom panel design. We focus on specific genes and regions of interest, allowing us to unravel structural variations that may hold significant relevance to your health and genetic profile. - Targeted Resequencing Services: Dive deeper into your genetic makeup with our targeted resequencing services. We customize the analysis to match your unique genetic interests, ensuring a comprehensive examination of the genes and regions that matter most to you. Your genetic story, uncovered with precision. - HiFI Sequencing on Pacbio Sequel II: Experience the extraordinary with our HiFI sequencing technology on the Pacbio Sequel II. This cutting-edge platform allows us to unveil macro structural variants within your genome, providing a level of genetic detail that was once hidden in the shadows. Your genetic research is waiting to be discovered. Contact DrSeq Lab by Nucleome today to embark on your journey of self-discovery, and let our expert team reveal the mysteries hidden within your DNA. Contact us today and take the first step towards understanding your genetic destiny. Your story begins here. 🧬🌟 #Genomics #DNA #DiscoverYourGenes More information: www.DrSeq.com

🔬 New Tools for Niche Analysis in Spatial Transcriptomics 🔬 A recent study in Genome Biology (https://buff.ly/3UhE3PM) introduces two innovative tools, Niche-DE and Niche-LR, set to transform our approach to spatial transcriptomics. 🌐 Key Highlights: 🔵 Niche-DE Analysis: This new statistical procedure identifies cell-type-specific niche-associated genes, revealing how they are differentially expressed in specific spatial niches. 🔵 Niche-LR Method: Developed alongside Niche-DE, Niche-LR uncovers ligand-receptor signaling mechanisms that drive niche-differential gene expression patterns. 🔵 Versatility: Both tools are applicable to a range of spatial transcriptomics data, from low-resolution spot-based to single-cell or subcellular resolution. 🔵 Focus on Cell-Cell Interactions: Niche-DE delves into local gene expression changes driven by cell-cell interactions, offering a deeper understanding of cellular communication. 🔵 Niche-DE uses a kernel-smoothed density of cell-type compositions, characterizing the spatial niche of a cell as a vector measuring the concentration of different cell types in its neighborhood. 🔵 Integration Across Studies: These tools can integrate data from multiple tissue slides and patients, adjusting for tissue- and slide-batch effects. 🔵 Intercellular Communication: Niche-LR integrates niche-DE statistics with ligand-target matrices, identifying cell-cell signaling channels between cell types. 👩💻 Github page: https://buff.ly/3Ug1edm 📢 Join the Conversation 📢 How can Niche-DE and Niche-LR enhance your research? Share your thoughts, methods, and tools in the comments 👇 💬  #SpatialTranscriptomics #Genomics #Bioinformatics #CellBiology #NicheDE #NicheLR #InnovationInScience

CHESS 3 is an enhanced human gene catalog derived from almost 10,000 RNA-seq experiments across 54 body sites, incorporating advanced algorithms, machine learning, and new protein structure prediction methods. It lists 41,356 genes with distinctive features, including 14,863 protein-coding transcripts not found in other databases and an additional 129 protein-coding genes on the CHM13 human genome. https://lnkd.in/gzhdWUWi

❗️Save the date! Join us on December 7th for our upcoming #free Webinar on Transcriptome sequencing analysis. 👩 Xuan Yang, Junior Bioinformatics Analysis Engineer at BMKGENE, will be sharing valuable insights on Transcriptome sequencing analysis. 🤔 Transcriptome sequencing analysis is important because it can provide insights into gene expression, regulation, and function. By analyzing the transcriptome, researchers can identify which genes are turned on or off under different conditions, and how they are regulated. This information can be used to understand how genes contribute to the development of biological processes and diseases. 🔗 Register today: https://lnkd.in/gVefjz7k ⏰ Date and Time: Thursday, 7th December | 2:00 pm-3:00 pm CEST #Webinar #TranscriptomeSequencing #RNASeq #Genomics #BMKCloud #Sequencing #Bioinformtics

https://lnkd.in/ecnKsFiC We at CHCF believe that if we are to better understand the root causes of diseases including abnormal neurodevelopment we need to generate a large database of robust genetic and epigenetic information that can be linked to behavioral symptoms in a manner that is unbiased, powered statistically and standardized across many observational and longtitudinal studies nationally and internationally. Genetic information is only the groundwork but clearly it is not sufficient. Let’s hope stakeholders and policymakers recognize the importance of correlating our individual genetic structure and blueprint to what has to be ultimately addressed therapeutically which is the “phenotype” of many life threatening conditions and diseases. #nci #nih #ninds #nimh #niehs #neuroscience #biomarkers #genetics #epigenetics #translationalresearch #braindevelopment #neurodevelopment #chcf