ML for Microbiologists ?? JASPAR @ 20 Years ?? Single-Cell Tech Tradeoffs ?? Gene Regulatory Encyclopaedia ??
Bioinformer Weekly Roundup
Stay Updated with the Latest in Bioinformatics!
Issue: 13 | Date: 17 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 review discusses the impact of Large Language Models in genomics, analyzing their strengths and limitations, and speculates on future genomic modeling techniques, aiming to guide computational biologists and educate traditional biologists on upcoming shifts in genomic data analysis.
?? The last author, Bo Wang, has posted a Twitter thread summarising the contents of the review. Additionally, Anshul Kundaje has also provided insights on the paper through his own Twitter thread.
This review discusses the progress in single-cell and spatial proteomics technologies, emphasizing the need for robust computational tools to manage and interpret the resulting high-dimensional datasets, and highlights benchmarking studies that evaluate the strengths and weaknesses of existing computational methods, underscoring the importance of developing advanced analysis tools alongside these evolving technologies.
This article provides a detailed overview of the latest developments in single-cell transcriptomic analysis, focusing on the trade-off between profiling a high number of cells and achieving full-length transcript coverage. It discusses emerging solutions that enhance cellular throughput, gene detection sensitivity, and full-length transcript capture, including advancements in long-read sequencing techniques for single-cell transcripts, and highlights the pros and cons of various approaches in this rapidly evolving field.
??? Latest Tools
This article introduces Decipher, a tool that leverages variational auto-encoders to harmonise and visualize single-cell RNA-seq data from both normal and disease states, effectively mapping out the disrupted cell-state transitions in diseases.
?? The first author, Achille Nazaret, has posted a Twitter thread describing the motivation and details of the method.
This article introduces ENCODE-rE2G, a new predictive model developed by integrating CRISPR experiments, eQTLs, GWAS variants, and other data, to create a comprehensive map of over 13 million enhancer-gene interactions across various cell types and tissues, offering valuable insights into gene regulation and the genetic basis of diseases.
This article introduces ZEBRA, a comprehensive single-cell and single-nucleus RNA-seq database that integrates and normalizes gene expression data from over 4.2 million human and mouse brain cells across 39 regions. It includes samples from neurodegenerative diseases like Alzheimer's, Parkinson's, and Multiple Sclerosis and employs scVI for data integration. The database provides tools for exploring cell-type and disease-specific markers, thus enhancing the understanding of brain function during aging and disease.
?? Community News
The article highlights the 10th edition and 20th-anniversary update of JASPAR, a transcription factor DNA-binding profile database. This latest release introduces 329 new profiles, updates to existing profiles, refined prediction algorithms, and enriched metadata.
?? The last author, Anthony Mathelier, has posted a Twitter thread announcing all of the updates to the 10th edition.
领英推荐
This review explores key machine learning concepts and applications in microbiology, providing a fundamental toolkit for microbiologists to understand and apply machine learning techniques in experimental and clinical research, including tasks like antibiotic resistance prediction
?? Upcoming Events
The 9th annual Festival of Genomics & Biodata, offering inspirational talks, the latest in research and technology, and excellent networking opportunities, will be held in London on January 24-25, 2024.
?? Educational Corner
This talk by Ricard Argelaguet addresses the challenges in integrating single-cell multimodal data, first discussing key principles and issues in data integration, followed by a case study on combining gene expression and chromatin accessibility to predict transcription factor binding sites, infer gene regulatory networks, and simulate transcription factor perturbations.
This video by Melissa Van Bussel provides a concise, 5-minute guide on setting up GitHub Copilot and ChatGPT within RStudio, covering the necessary steps for integrating the RStudio Copilot and using the 'chattr' package to interact with Large Language Models like OpenAI's ChatGPT and LLaMA models.
This article from 10x Genomics describes which files you need to send to public databases such as NCBI GEO/SRA depending on the workflow or chemistry version used to create the data. It has a table showing which files are best to submit for different 10x Genomics chemistries.
This blog post by Yoseph Barash and Benjamin Wales-McGrath discusses the impact of different STAR aligner settings on RNA splicing analysis, focusing on the choice between 1-pass and 2-pass alignment and its implications for RNA splicing quantification.
?? Connect with Us
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Editor: James Ashmore | Contact: [email protected]
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