Mice in space, cancer microbiome, AI in science, and ATAC-seq benchmarking

??? Hello LinkedIn Network!

Welcome to Week 31 of the Bioinformer Newsletter! In this weekly digest, we'll keep you informed about the most exciting developments, tools, and research in the world of bioinformatics, all in a concise and easy-to-read format. Let's get started with this week's highlights:

?? Research Briefs

• In a critical analysis of a recent extensive cancer-microbiome study, Salzberg et al identify significant flaws in both data and methodologies. Notably, errors in the genome database and computational methods resulted in millions of incorrect positive bacterial read identifications, primarily due to misclassified human sequences as bacteria.

• This article discusses how artificial intelligence (AI) is being used to enhance scientific discovery by aiding hypothesis generation, experiment design, data interpretation, and insight generation. It highlights recent breakthroughs in self-supervised learning, geometric deep learning, and generative AI methods.

• This study evaluates eight scATAC-seq methods on PBMCs, highlighting biases in library complexity and tagmentation that affect annotation, peak calling, and motif enrichment. They introduce the PUMATAC preprocessing pipeline and offer insights into sample extraction, method choice, and data processing for improved research. The study provides a large dataset and analysis code for future benchmarking.

• This perspective outlines how rising interest in human microbiome research has led to misinformation. The authors highlight baseless myths and stress the need for accurate, nuanced understanding to avoid undermining progress and trust in the field.

• Did you know NASA recently flew twenty mice to the ISS for over a month? Eli Lilly and Co. and the Center for the Advancement of Science in Space sponsored the Rodent Research-3 (RR-3) mission to test a countermeasure against muscle and bone loss in space.

??? Tool Spotlight

• The Matthias Mann lab have released AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics.

• The nf-core community have released the first version of a best-practice analysis pipeline for pangenome graph construction.

• The Manu Setty lab have released Mellon: a novel computational algorithm for high-resolution estimation of cell-state densities from single-cell data.

?? Tutorials & Seminars

• Learn about how non-coding variants in GWAS studies can be explored using CRISPR inhibition to identify target genes and pathways.

?? Ming "Tommy" Tang has posted a video on common problems and best practices for using spreadsheets to organise data for easier processing.

?? Upcoming Events

• The training and development team at EMBL have revealed their courses and conferences programme for 2024.

• The 3rd Annual Single Cell Symposium at Johns Hopkins Bloomberg School of Public Health will take place on November 9 & 10, 2023 in Baltimore, MD.?Registration for the event is required.

• The deadline to submit an abstract for the Nextflow summit taking place hosted by Seqera has been extended until August 11

• Experience the unveiling of Xenium, an innovative spatial in situ profiling product by 10x Genomics , during a global tour led by experts and senior leaders. Select an event near you and register below.

?? Job Postings

LatchBio are hiring for a full-time bioinformatics data engineer in San Francisco

Seqera are hiring for full-time bioinformatics engineers in both North America and Europe

Wrapping Up

That's it for this week's newsletter! ???? We hope this succinct roundup of bioinformatics updates has been informative and engaging. If you want more in-depth insights or have specific questions, don't hesitate to reach out.

Follow us for regular updates on all things bioinformatics, and let's continue our journey into the fascinating world of data-driven life sciences!