MetageNN - a memory efficient taxonomic classifier - is now out in BMC Bioinformatics #metagenomics #AI

MetageNN outperforms other machine learning-based metagenomic classifiers, and shows higher sensitivity than kmer-based tools Rafael Peres Chayaporn Nok Suphavilai

tinyurl.com/mvr5th8j

Let's implement & train this neural network step-by-step, from scratch using PyTorch!

1/n

Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes genomebiology.biomedcentral.com/articles/10.11…

The wound microbiota: microbial mechanisms of impaired wound healing and infection

rdcu.be/dDI0s

Grice & co explore the diversity of microbes present in wounds and examine the mechanisms through which they invade skin tissues, impair skin repair and cause infection.

Which one is better? AWS, Azure, or GCP?

The good news: This might not matter soon!

The guy who created the AWS CDK created Winglang, an open-source language designed from the ground up for the cloud.

Winglang abstracts the differences between cloud providers by defining a…

Excited to share the final version of our genomic language model (gLM) paper out in Nature Communications! gLM learns hidden evolutionary patterns from metagenomes to expand functional inference beyond sequence and structure to include genomic context. nature.com/articles/s4146…

Our recent work just published in Cell uncovering the connection between gut bacteria and the risk of cardiovascular diseases.

Excited to share our latest study uncovering gut microbes and microbial metabolites linked to cardiovascular health! We show that Oscillibacter is associated w/decreased cholesterol in human subjects & that these bacteria take up &metabolize cholesterol.

bit.ly/4cGpnjW

A new finding points towards possible treatments for high cholesterol levels go.nature.com/49gsj3S

Cholesterol-induced #SmoothMuscleCell phenotytic plasticity

Activation of KLF4 & Acquisition of atherogenic Macrophage-like or Fibroblast-like features are mediated by #IntegratedStressResponse #ERStress #UnfoldedProteinResponse (PERK arm)

Dianna Milewicz lab ATVB: An AHA Journal…

PROTGOAT : Improved automated protein function predictions using Protein Language Models biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Genes in Humans and Mice: Insights from Deep learning of 777K Bulk Transcriptomes biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

A new study finds that certain bacteria in the gut may help lower cholesterol levels and heart disease risk in people. broad.io/Oscillibacter-…

Discovery of gut microbiome constituents that lower cholesterol levels that may be used to reduce risk for heart disease
cell.com/cell/abstract/… Chenhao Li Xavier Lab Broad Institute Cell

🌟1/3: Introducing mm2-gb, GPU-accelerated Minimap2 for long-read DNA mapping!
🔥 mm2-gb accelerates Minimap2's bottleneck (chaining) on GPUs without compromising accuracy. 🚀 Kudos to Xueshen Liu Joy Dong, Satish Narayanasamy & Gina Sitaraman Computer Science and Engineering at Michigan AMD Michigan Engineering

We show the gut microbiota directly generates auto-antigens by modifying glycosylation of a human glycoprotein (IgA1) in an autoimmune disease called IgA nephropathy. Published Science Translational Medicine
bit.ly/4cw3gwD
Nicolas Benech Jonathan Chemouny Harry Sokol
Inserm APC Microbiome Ireland AP-HP

Single Cell Genomics Day starts tomorrow at 10AM ET!

Come for the awesome keynotes (Jason Buenrostro , Xiaowei Zhuang, IdoAmitLab) and to learn about our favorite new methods and trends for the field in the last year. All talks streamed on Youtube and satijalab.org/scgd

Microbes from the oral cavity sometimes find a new home in the inflamed gut.🔴🔵 Learn about their chemical repertoire in our recent work led by Schirmer Lab
and key players Daniel Rojas
Eric Brown Emily Temple Rachele Invernizzi Xavier Lab tinyurl.com/5c6r4r2z

You can use any free or paid version of ChatGPT or Claude for this. For the purposes of this post, I am using Claude 3 Opus.

Start by telling Claude/ChatGPT that you would like it act as your academic writing assistant.

Example prompt:

'I would like you to act as my academic…

BREAKING: CRISPR edited pig kidney transplanted into living patient. Scientists used CRISPR to make 69 changes to the pig kidney, removing harmful pig genes, adding human genes and making other edits to prevent the transmission of pig viruses. wbur.org/news/2024/03/2…