André Soares

@geomicrosoares.bsky.social

🇵🇹 Staff Scientist @probstlab.bsky.social (@unidue.bsky.social - 🇩🇪). Microbial genomics in the One Health context, biogeochemistry of cave microbiomes, alga-microbe symbioses.

Come work with us, we're really cool people to hang out with 😁 You'll get to do interdisciplinary research exploring microbial metabolisms during the Archean Eon by investigating the deep biosphere in high-CO₂ ecosystems hundreds of meters below ground. Please retweet and spread the word! 🧬 💻

The Probst Lab@probstlab.bsky.social · 2mo ago

We're looking for a Postdoctoral Researcher (f/m/d) for the ERC Synergy project “Archean Park”! 📍 Location: Essen, Germany ⏱ Duration: 36 months (Full-time | EG 13 TV-L) 📅 Start Date: As soon as possible ⏰ Application Deadline: September 2, 2026 www.uni-due.de/karriere/ste...

🤯 Manual MAG refinement? Still doing it by hand?? We’ve been there... You could just leave those messy, ill-assigned contigs/scaffolds in your data for NCBI to pick up during your submission… …OR you could add itBins, our new automated MAG refiner by @jmk-ude.bsky.social, to your pipeline!! 🔥

Figure 1 shows the conceptual workflow of the algorithm. It first loads the configuration file and the input data of one or multiple binned metagenomes, yet evaluates each bin individually. It then iteratively processes each candidate bin in the input, going through the refinement tasks, potentially multiple times. The refinement either stops when the last step or a preset stop task have been reached or an unrecoverable error has been encountered. The algorithm tasks can be configured individually.

"Working in academia can be stressful. Laurel Raffington suggests treating it as ‘just a job’ to reduce performance pressure and advocate for structural improvements." "Academia is just a job" by @laraffington.bsky.social (2025, Nature Human Behavior) www.nature.com/articles/s41...

Academia is just a job - Nature Human Behaviour

Working in academia can be stressful. Laurel Raffington suggests treating it as ‘just a job’ to reduce performance pressure and advocate for structural improvements.

nature.com

Hi #bioinformatics folk, I want to quickly extract metagenome reads that map to medium-sized piles of reference genomes (100s-1000s, but not 10_000s). I don't _necessarily_ care about the exact position. I'm using minimap2 right now but it's kinda choking on 1000 microbial genomes at once. Thoughts?

Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2

GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing

A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim

github.com

Evidence from 14 research funding programmes confirms that early winners tend to keep winning (Matthew effect). But the idea that an early setback makes you stronger later doesn’t replicate widely. buff.ly/UEtcRd4

eLife Assessment

This important study reports the results of efforts to replicate two phenomena of significant interest to early-career scientists and scientific policymakers: the Matthew effect and the early-career setback effect. Several previous studies of these effects have focused on early-career researchers with grant proposals that fell just below or just above a funding threshold. Those just above the threshold were more likely to be successful when they applied for funding later in the career (an example of the well-known Matthew effect), while those just below were more likely to go on to have stronger publication records (the early-career setback effect). In this study the Matthew effect was found to be robust across funders, and to generalize from those close to the funding threshold to the whole population. The early-career setback effect was not robust across funders and did not generalize to the whole population. The evidence reported is convincing.

Are you, or someone you know, looking for a PhD, starting in Oct 2026? Do you like bacteria, genomics & puzzles?🦠🧬🧩 Do you wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social? Please apply or share by 2 Dec 🗓️ #PhDposition #academicsky Find out more ⬇️

PhD Out of order: investigating genetic and environmental drivers of genome rearrangement (LANGRIDGE_Q26DTP) 2026/27 | UEA

PhD Out of order: investigating genetic and environmental drivers of genome rearrangement (LANGRIDGE_Q26DTP) 2026/27 | UEA

uea.ac.uk

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Rob Patro@robp.bsky.social · 12mo ago

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j.... If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!