Genentech-NVIDIA Partnership ??, DecontPro: Single-Cell Noise Cleanup??, RNA-Seq Pseudotime Framework ??, Containers for Reproducibility ??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 14 | Date: 24 November 2023
?? 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 highlights that in large-scale multi-subject single-cell data, the use of pseudobulk can lead to significant errors in differential gene expression analysis, and offers practical solutions depending on the study design.
?? The first author, Hanbin Lee, has posted a Twitter thread describing the motivation and results of the research.
This study introduces Lamian, a novel computational framework for differential multi-sample pseudotime analysis in scRNA-seq data, enhancing the accuracy of studying cellular gene expression programs by accounting for cross-sample variability and adjusting for batch effects.
This study introduces SPACEL, a deep learning-based method for spatial transcriptomics data analysis, effectively addressing challenges in 3D reconstruction and analysis of tissue slices, and outperforming existing methods in cell type deconvolution and spatial domain identification.
??? Latest Tools
This study presents RoseTTAFoldNA, an extension of the RoseTTAFold approach, which successfully predicts structures of protein–nucleic acid complexes with higher accuracy than current methods, aiding in understanding and designing these crucial biological complexes.
This study introduces DecontPro, a Bayesian hierarchical model for decontaminating antibody derived tag data in CITE-seq by identifying and removing noise sources, significantly enhancing downstream analysis accuracy by better distinguishing true cell signals from artifacts.
This study presents EUGENe, a FAIR deep learning toolkit for genomic analysis, offering an adaptable and comprehensive approach for data processing, model training, and interpretation in regulatory genomics.
?? Community News
Genentech and NVIDIA have announced a strategic collaboration to enhance AI-driven drug discovery and development. This partnership combines Genentech's AI capabilities, biological data, and research expertise with NVIDIA's advanced computing and AI, aiming to expedite the creation and delivery of new medicines.
?? Genentech and NVIDIA have released a video along with their announcement to help explain what the partnership means for drug discovery.
领英推荐
Bioconductor has decided to discontinue its presence on Twitter/X, citing a misalignment with the platform’s current direction and Bioconductor's commitment to a harassment-free community.
In this edition of the Channels Podcast, Geraldine Van der Auwera interviews Raquel Manzano, Edmund Miller, Rieke Hanssen, and Francesco Lescai, members of the Nextflow community, during the 2023 nf-core hackathon at the Nextflow Summit in Barcelona.
?? Upcoming Events
This workshop, co-organized by the National Microbiome Data Collaborative (NMDC), NASA GeneLab, and NMDC Ambassadors, focuses on hands-on training for standardized bioinformatics workflows and multi-omic data processing for microbial samples.
?? Educational Corner
Spacedeconv is a comprehensive interface that integrates 31 different deconvolution tools, specifically tailored for spatial transcriptomics datasets. It can directly estimate the proportions of immune cells and is capable of deconvoluting various cell types given an annotated single-cell reference dataset.
This primer outlines the growing use of containers in scientific research to address software complexity and compatibility issues, highlighting their role in ensuring reproducibility and efficient collaboration in computational science, and offering guidance on their implementation across various platforms, including high-performance computing clusters.
The blog post emphasizes the critical role of data dictionaries in project documentation, highlighting their dual function in data cleaning processes: as a reference guide for necessary data transformations and as an integral part of the cleaning script, where they can be directly utilized within functions.
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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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