🧬 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
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One of the most fundamental sequencing methods is bulk, short read RNA-sequencing. Touch up your knowledge about it with our most recent blog article!
🧬 Thursday's Technique: Bulk RNA-seq 🧬 Welcome to the third part of our "Thursday's Technique" series! This week, we're diving deep into bulk RNA Sequencing (RNA-seq) - a cornerstone technique in #lifescience that has revolutionised our understanding of gene expression and cellular functions. Whether you're a seasoned researcher or new to the field, our latest blog post offers a comprehensive look at bulk #RNAseq, from its basic principles to its vast applications in #diseasestudies, #developmentalbiology, and beyond. Discover the power of bulk RNA-seq in providing a holistic view of the #transcriptome and how it can elevate your research to new heights. Read the blogpost here: https://lnkd.in/dxGYXasc #BulkRNASeq #Bioinformatics #NextGenSequencing #LifeSciences #OmiqaBioinformatics
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We created another blogpost! This one is about bulk short-read RNA sequencing. Check it out!
🧬 Thursday's Technique: Bulk RNA-seq 🧬 Welcome to the third part of our "Thursday's Technique" series! This week, we're diving deep into bulk RNA Sequencing (RNA-seq) - a cornerstone technique in #lifescience that has revolutionised our understanding of gene expression and cellular functions. Whether you're a seasoned researcher or new to the field, our latest blog post offers a comprehensive look at bulk #RNAseq, from its basic principles to its vast applications in #diseasestudies, #developmentalbiology, and beyond. Discover the power of bulk RNA-seq in providing a holistic view of the #transcriptome and how it can elevate your research to new heights. Read the blogpost here: https://lnkd.in/dxGYXasc #BulkRNASeq #Bioinformatics #NextGenSequencing #LifeSciences #OmiqaBioinformatics
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🧬 Thursday's Technique: Bulk RNA-seq 🧬 Welcome to the third part of our "Thursday's Technique" series! This week, we're diving deep into bulk RNA Sequencing (RNA-seq) - a cornerstone technique in #lifescience that has revolutionised our understanding of gene expression and cellular functions. Whether you're a seasoned researcher or new to the field, our latest blog post offers a comprehensive look at bulk #RNAseq, from its basic principles to its vast applications in #diseasestudies, #developmentalbiology, and beyond. Discover the power of bulk RNA-seq in providing a holistic view of the #transcriptome and how it can elevate your research to new heights. Read the blogpost here: https://lnkd.in/dxGYXasc #BulkRNASeq #Bioinformatics #NextGenSequencing #LifeSciences #OmiqaBioinformatics
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Happy RNA Day! Today, we join the global scientific community to celebrate the essential role of ribonucleic acid (RNA) in biology and research. Established in 2018, RNA Day is observed on August 1st to honor the "AUG" start codon - the universal signal for the beginning of protein synthesis in cells. AmpSeq is proud to be a leader in the field of RNA sequencing. This powerful technique enables us to explore the transcriptome and gain deep insights into gene expression, regulation, and cellular responses. On this special day, we recognize the remarkable achievements in RNA research and the transformative impact of RNA-Seq. Follow us to find out more about RNA and its critical role in advancing our understanding of life at the molecular level! #RNAday #AmpSeq #NGSSolutionsForAll #NGS #NextGenerationSequencing #sequencing #science #biotech #DNA #RNA #genomics #genetics
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Ready to explore the next frontier in transcriptomics? Discover the power of the Zymo-Seq RiboFree® Total RNA Library Kit. The innovative probe-free rRNA depletion method of the Zymo-Seq RiboFree® Total RNA Library Kit enables coding and non-coding gene expression studies across all species in total RNA sequencing. This groundbreaking technology has been featured in diverse peer-reviewed publications, exploring topics such as resilient coral species and bacterial responses in wine production. Shop now with us: https://lnkd.in/e3CzrEFa #GeneExpression #RNASeq #Biotech #Innovation #Transcriptomics #MolecularBiology #Genomics #RNASequencing #NGS #NextGenerationSequencing
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📍 Revealing gene function with statistical inference at single-cell resolution Trapnell highlights statistical concepts, models, tools and algorithms that can be repurposed to solve problems now arising or becoming increasingly urgent in genetic and molecular biology studies of development and disease. Key points ☑ The workflow for phenotyping with single-cell molecular profiling, including differential cell composition and gene expression analysis ☑ Strategies for quantitatively modelling a gene’s regulation, for understanding lineage relationships and cell-cell signalling interactions, and for inferring gene regulatory networks ☑ The problem of forecasting cell fate, briefly touching on the promise of advanced artificial intelligence systems. ➡ More details: https://lnkd.in/e_HFKNxa #UniversityofWashington #spatialomics #spatialbiology #singlecellanalysis #singlecell
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🔍 Explore the fascinating world of mRNA abundance analysis, where you uncover the secrets of gene expression! 🧬 Dive into understanding how genes behave across different conditions and samples. Excited to learn more about these interesting concepts? 🚀 Enroll in OmicsLogic Transcriptomics for Biomedical Research Program for a deep dive into transcriptomics. 📚 Don't miss out on this chance to enhance your skills! 🔗Register Here: https://lnkd.in/gXza_9Rt #Transcriptomics #Bioinformatics #OmicsLogic #SummerTraining #GeneExpression #mRNA #Genomics #DataScience #BigData #BioinformaticsTraining #GeneAnalysis #ComputationalBiology #LifeSciences #ScientificResearch #Research #BioinformaticsCommunity #Biology #LearnBioinformatics
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🔬 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
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Working with single-cell RNA-Seq data?🔍 scRNA-Seq data provides high-resolution information on complex tissues that can be used to understand the relative contributions of cell populations to bulk RNA-Seq data. Moreover, it also captures heterogeneity present in populations of cells and empowers the discovery of gene expression programs that vary over time, developmental trajectories, mutational burden, and disease conditions. Existing databases have been adapted to accept single-cell data and new databases have been created specifically for its curation and exploration. Here are the top 7: ➡️ GEO/SRA hosted by the National Center for Biotechnology Information (NCBI) ➡️ Single Cell Expression Atlas by EMBL ➡️ Single Cell Portal by Broad Institute of MIT and Harvard ➡️ CZ Cell x Gene Discover in partnership with Chan Zuckerberg Initiative ➡️ scRNAseq package on Bioconductor ➡️ PanglaoDB by the Karolinska Institutet ➡️ The Allen Brain Cell Atlas by Allen Institute for Brain Science Learn more about public databases and how to access them at https://lnkd.in/ewsR2Kgy --- Analyze and visualize your RNA-Seq data interactively with Omics Playground! Try it now 👉 https://lnkd.in/eUnFPwEt #scRNAseq #rnaseq #omicsdata #omicsdataanalysis #computationalbiology #bioinformatics
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🔍 Explore the fascinating world of mRNA abundance analysis, where you uncover the secrets of gene expression! 🧬 Dive into understanding how genes behave across different conditions and samples. Excited to learn more about these interesting concepts? 🚀 Enroll in OmicsLogic Transcriptomics for Biomedical Research Program for a deep dive into transcriptomics. 📚 Don't miss out on this chance to enhance your skills! 🔗Register Here: https://lnkd.in/gXza_9Rt #Transcriptomics #Bioinformatics #OmicsLogic #SummerTraining #GeneExpression #mRNA #Genomics #DataScience #BigData #BioinformaticsTraining #GeneAnalysis #ComputationalBiology #LifeSciences #ScientificResearch #Research #BioinformaticsCommunity #Biology #LearnBioinformatics
