Single Molecule Delivery into Cells ?? Spatial Transcriptomics at Micron Scale ?? Raman2RNA: Predicting RNA Profiles ??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 19 | Date: 12 January 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
This study introduces a nanoinjection platform utilising nanopipettes for the precise delivery of macromolecules like DNA and proteins into cells, achieving single molecule resolution and inducing observable phenotypic changes.
This research introduces TIME-seq, an efficient and cost-effective method for applying epigenetic 'clocks' based on DNA methylation, demonstrating its accuracy and robustness in various tissues and cells.
This study presents a novel high-resolution DNA chip for spatial transcriptomics, offering enhanced mapping of cell types and gene expression patterns in a mouse model.
This paper presents CytoCommunity, an algorithm that identifies tissue cellular neighbourhoods (TCNs) using a graph neural network model, demonstrating its superior ability to discern condition-specific TCNs in spatial omics data.
??? Latest Tools
This research introduces SPLASH, a novel genomic analysis method that bypasses reference sequence alignment, enabling the discovery of various types of sequence variations including complex mutation patterns and regulated RNA isoforms.
?? Paper author, Tavor Baharav, has posted a Twitter thread describing the analysis method and implications.
This study introduces scGOclust, a computational tool leveraging the Gene Ontology knowledge-base to compare cell type expression profiles across species, demonstrating its ability to identify functional similarities and divergences in cell types.
?? Paper author, Yuyao Song, has posted a Twitter thread describing the tool and highlighting its application.
This study introduces Raman2RNA (R2R), a novel method combining hyperspectral Raman microscopy with domain translation to infer single-cell RNA sequencing profiles nondestructively, demonstrating its superiority over brightfield image inferences.
This paper presents Sopa, a technology-agnostic and memory-efficient pipeline for analyzing various spatial-omics data, including spatial-transcriptomics and multiplex imaging. Sopa offers a unified platform for tasks like segmentation and spatial analysis, and produces accessible web reports and visualizer files.
This study introduces scDirect, a computational framework designed to identify key transcription factors (TFs) from single-cell multi-omics data, overcoming limitations of traditional methods that rely on cell population data.
?? Community News
Landmark national study demonstrates how the integration of health data with whole genome sequence (WGS) data in cancer patients enables doctors to deliver more personalised and effective care.
This reports highlights the impact of the UK Biobank's pioneering study design and data access policies on its ability to greatly enhance the capacity for formulating and validating hypotheses concerning the underlying causes of human diseases.
Visium HD Spatial Gene Expression is now available for pre-order, offering whole transcriptome spatial gene expression with single-cell scale resolution.
领英推荐
This video from CZI showcases how emerging technologies and bioengineering cells are revolutionising our approach to solving complex problems and expanding our knowledge of human biology.
NVIDIA's Parabricks GPU-accelerated genomics tools have been integrated into Nextflow modules, offering researchers the ability to speed up genomics workloads by up to 100 times.
The potential of therapeutic genome editing to cure rare diseases is immense, yet germline editing currently faces a ban. However, with extensive societal discourse and the backing of national and transnational legislation, there could be a path forward for permitting germline editing under specific circumstances.
In today's biotechnology landscape, startups face a challenging funding paradox: they need preliminary data to secure funding, but require funding to generate this data. To move forward, these startups must find creative solutions to overcome the early-stage funding hurdle.
?? Upcoming Events
ISB's free virtual workshop on Spatial Multi-Omics for Cancer Systems Biology includes sessions on experimental and computational methods, practical tutorials, and targets a diverse scientific audience.
The ISCO conference focuses on single-cell and spatial technologies, computational methods, and medical applications, offering networking opportunities for PhD students and postdocs.
?? Educational Corner
HRT Atlas v1.0 is a web-based database that provides accurate lists of housekeeping genes and transcripts in humans and mice, utilizing extensive RNA-seq data and offering resources for qPCR experiments and regulatory elements.
This free course covers advanced statistical computing programming paradigms and workflows required for the research and application of statistical methods. The course is developed and maintained by Stephanie Hicks .
This free course will provide a comprehensive introduction to fundamental concepts and experimental approaches in the analysis and interpretation of experimental genomics data. The course is developed and maintained by Aaron Quinlan .
This essay advocates for a shift away from the dominant focus on statistical power in experiment sample size determination, suggesting a new approach that emphasizes better study designs, (pre)registration, obligatory reporting of all results, team science, multi-institutional collaboration, and prospective and living meta-analyses to enhance the effectiveness and equity of scientific research.
In this interview, Rob and Kelsey discuss how genomic surveillance has changed since the COVID pandemic, and how Seqera Platform and Nextflow pipelines have substantially lowered the barrier to entry for bioinformaticians running workflows in public health labs and in the field.
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Disclaimer: The information provided in this newsletter is for educational and informational purposes only and does not constitute professional advice.
Editor: James Ashmore | Contact: [email protected]
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