Fingerprint Full-Length Proteoforms ?? Unlock Single-Cell Multi-Omics with Scbean ?? Integrate scDNA and scRNA with CCNMF ??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 24 | Date: 16 February 2024
?? Welcome to the Bioinformer Weekly Roundup!
In this newsletter, we curate and bring you the most captivating stories, developments, and breakthroughs from the world of bioinformatics. Whether you're a seasoned researcher, a student, or simply curious about the intersection of biology and data science, we've got you covered. Subscribe now to stay ahead in the exciting realm of bioinformatics!
?? Featured Research
The study introduces CCNMF, a computational framework for integrating scDNA and scRNA sequencing data. CCNMF links copy number and gene expression profiles to infer clonal structures, identifying coexisting clones with high correlations between genomic and transcriptomic data. Validation using simulated benchmarks and real-world datasets demonstrates CCNMF's accuracy and robustness, offering insights into cellular genomic differences and tumour evolution.
This article introduces RENIN, a computational tool designed to uncover gene regulatory networks involved in the transition of proximal tubule cells in chronic kidney disease (CKD). RENIN's approach allows researchers to prioritise and identify critical regulatory elements, including transcription factors like NFAT5, associated with CKD progression. The tool enhances understanding of CKD pathogenesis and identifies potential targets for therapeutic intervention, potentially leading to more effective treatments for this prevalent condition.
GCNFORMER is a novel algorithm that combines graph convolutional networks and transformers to predict lncRNA-disease associations accurately. It utilizes intraclass similarity and interclass connections to extract key features and understand global dependencies. The method has demonstrated effectiveness in case studies of breast, colon, and lung cancer. GCNFORMER has the potential to advance medical research by improving our understanding of disease mechanisms.
The study investigates tumour heterogeneity in ovarian cancer (OV) and proposes a prognostic signature, CCIS. By integrating single-cell RNA sequencing and bulk data, CCIS shows potential in prognosis assessment and patient stratification. Low-risk patients identified by CCIS display certain characteristics, including increased genomic variations and enhanced immune cell infiltration, which may offer insights for OV clinical management.
??? Latest Tools
The study introduces Control-FREEC Viewer, a user-friendly tool for visualising copy number data. It enables easy data loading, offers whole genome or single chromosome views, and facilitates the identification of gene-specific gains or losses. Users can store analysis parameters and export images in various formats. Compatible with Control-FREEC and similar tools, it provides an intuitive interface for data exploration.
The article introduces MRMPro, a new web application aimed at improving MRM data analysis for biomarker discovery. MRMPro addresses manual inspection challenges and enables collaborative review via cloud architecture, streamlining batch operations and peak selection. Its compatibility with multiple mass spectrometer vendors enhances efficiency and accuracy, representing a significant advancement in quantitative proteomics and metabolomics research.
This study introduces vissE, a tool designed to categorize data and provide visualization modules for analysis of complex biological systems. Its adaptability across various technologies allows for enhanced gene-set enrichment workflows and facilitates molecular discovery in biological research.
Introducing Scbean: A Python library developed for single-cell multi-omics analysis. It integrates various models to enable efficient exploration across omics modalities, offering features such as dimensionality reduction and batch effect elimination. By leveraging GPU acceleration via Tensorflow, Scbean handles large-scale datasets, potentially uncovering novel insights into cellular functionality.
The 123VCF filtering tool provides a method for variant filtration in research and clinical settings. It aims to assist the global scientific and clinical community in identifying disease-causing variants and advancing personalized medicine. Developed to tackle challenges in annotation-based variant filtering, the tool prioritizes accessibility, efficiency, and user-friendliness, potentially enhancing its usefulness in genomic analysis.
?? Community News
A new technique called FRET X utilizes fluorescence resonance energy transfer (FRET) to identify specific amino acids and post-translational modifications within single full-length protein molecules. This method enables precise localization of residues, facilitating discrimination among proteins with subtle differences. FRET X holds promise for advancing proteomics research and biomarker-based diagnostics.
领英推荐
A study of 1,500 blood proteins has discovered biomarkers predicting dementia risk up to 15 years before diagnosis, detailed in Nature Aging. By analyzing blood samples from 50,000 healthy adults, researchers identified four key proteins — GFAP, NEFL, GDF15, and LTBP2 — strongly associated with dementia.
Residents in the United States can now pre-order genetically engineered petunias from biotechnology firm Light Bio, based in Sun Valley, Idaho. Priced at $29.00, these plants glow faintly green in the dark while appearing white during the day. Partnering with Ginkgo Bioworks and approved by the USDA, Light Bio plans to ship a batch of 50,000 firefly petunias in April.
?? Upcoming Events
Discover essential bioinformatics resources tailored for NCI CCR researchers in this upcoming webinar. Explore programming classes (R, Unix, Python), next-gen sequencing tools (Partek, Qlucore, Qiagen), compute clusters (Biowulf/Helix), and cloud resources. Led by Amy Stonelake from BTEP, this session focuses on NCI-specific and NIH-wide offerings to enhance your research capabilities.
Join this webinar to explore enriching your drug discovery efforts by combining insights from the QIAGEN Biomedical Knowledge Base with meticulously curated disease datasets from QIAGEN OmicSoft Lands. This webinar welcomes participants of all levels, catering to both beginners and experts from industries and academic institutions alike.
Join Garry Nolan in a webinar to explore MaxFuse, a method for integrating cross-modal data in single-cell sequencing and spatial omics. MaxFuse consolidates proteomic, transcriptomic, and epigenomic data at single-cell resolution, enabling deeper insights into complex biological processes. A Q&A session with expert panellists will follow.
This forthcoming webinar on the QIIME platform in microbiome research, led by J. Gregory Caporaso, will cover its progression from marker gene analysis to multi-omics data science, including an introduction to new features such as the QIIME 2 Shotgun Metagenomics Distribution and Provenance Replay functionality. Additionally, attendees will have the opportunity to learn about methods for integrating QIIME 2 into various workflows through different interfaces.
?? Educational Corner
The blog introduces the importance of cytokines in immune-related diseases and presents Cui et al.'s immune dictionary. It proposes a local Python implementation for gene-cytokine inference using the paper's supplementary table. A mouse colon tissue dataset is used to demonstrate SCVI modelling for differential expression analysis and Pertpy's Enrichment.hypergeometric function for enrichment analysis.
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