Middle Author Bioinformatics

Excited to announce a web GUI for FeGenie!

Are you interested in iron-related genes in your (meta)genomic datasets, but no experience with the command-line? You can now drag-and-drop and, with the click of a button, find all the iron genes: omix.midauthorbio.com

www.frontiersin.org/journals/mic...

Lactic acid bacteria have been a staple in fermentation, but now they're stepping up in new roles like probiotics and as natural factories for chemicals. Navigating their full potential is tricky with old tech, but CRISPR technology is changing the game, revolutionizing how these bacteria are eng...

Dimetrodon skeleton

Edaphosaurus skeleton

Dazzled by Dimetrodon? Enchanted by Edaphosaurus?
If you’ve ever wanted to write for Eons and the Permian is your jam, please DM me!

#FossilFriday #scicomm 🧪

A new tool called BGC-Prophet is shaking up the search for hidden microbial compounds by analyzing genes in a groundbreaking way. After examining over 94,000 genomes and metagenomes, it revealed a treasure trove of gene clusters involved in producing important chemicals, suggesting they evolved w...

PlantPan is shaking up plant research! With data from 195 genomes in 11 plant species, it offers a treasure trove of information for studying species evolution and crop breeding. It features millions of genes and variations, making it a powerful tool for researchers to explore gene functions, res...

check out the 🧵 below for info about the apps👇🏻. feedback welcome! cc: @ironark.bsky.social

Bioinformatics without the command line? Yes please.
We just launched a free app where non-comp bio folks can run bioinformatics software like SprayNPray, Megahit, Bakta, and more, via simple GUIs.

Get your FASTAs ready!

omix.midauthorbio.com

Tiny bacteria, part of the Candidate Phyla Radiation, thrive in extreme serpentinite environments, making up a significant chunk of the microbial population. They might lack full pathways for some nutrients but are gene-rich for essential folate vitamins, hinting at a metabolic tag team with thei...

Antimicrobial resistance is rising partly due to biofilms, which shield bacteria and foster resistance spread. In places like refugee camps, where healthcare is scarce, these biofilms in wastewater become breeding grounds for tougher germs. Watching these biofilms could be crucial in tackling hid...

Scientists have found a new way to detect DNA swaps in microbes without messy phylogenetic trees. Their method uses an advanced information technique to spot unique DNA patterns, making it much faster and easier to identify these genetic exchanges. This could transform our understanding of microb...

Studying how communities bounce back from disruptions is vital. Turns out, exposure to the same disturbance before and some "mix and mingle" from undisturbed areas can boost resilience. Antibiotic tests showed that prior exposure helps species evolve resistance and stay stable, even if their neig...

New breakthroughs in making efficient and cheap oxygen-evolving catalysts! Innovative use of bacteria helps form awesome nanosheets on nickel foam. These nanosheets boost performance, needing only 220 mV for a solid reaction rate. The secret? Bacteria aid in creating a catalyst packed with active...

Antimicrobial-resistant bacteria are becoming a big health issue. The gut microbiome plays a key role in this problem, as it can harbor bacteria resistant to antibiotics. These resistant bacteria can flourish due to antibiotics and potentially lead to infections. To tackle this, strategies like p...

Embracing the systems complexity of microbial ecology and evolution: call for papers.
https://doi.org/10.1128/msystems.00091-25

Ancient reef-building corals had a little help from microbial friends.
https://doi.org/10.1038/d41586-025-00650-x

Delighted that Pitt libraries renewed “all-inclusive” @asm.org journal subscriptions for 2025 including the 6 S2O "legacy" journals.

➡️Pitt authors can publish open access in any of the 6 S2O journals this year without paying OA publishing fees/APCs. ➡️More info: journals.asm.org/s2o-author-faq

Messy gene alignment rendered in terminal

A question while writing up a study proposal:

What are characters of a good prokaryotic gene alignment?

The way I learned it from no-one is a good alignment gives well-scoring inferred tree later, but that feels a bit iffy and takes too long to confirm. Any great articles/insights on this? 🦠🧫🧬💻

Preeclampsia, a serious pregnancy complication, is tough to predict. New machine learning models show promise in forecasting this condition without racial bias. Key predictors include BMI, blood pressure, and certain placental measures. Fixing bias improved accuracy for all moms-to-be.

Detecting genetic changes linked to hereditary diseases is tough, but there's new insight. After testing 12 different tools, ClinCNV and GATK-gCNV emerged as top performers, with GATK-gCNV especially sensitive. A new guide, CNVbenchmarker2, can now help others optimize these tools effectively.

Evolve and resequence FTW, congrats Elizabeth and the lab!

Digitalization has revolutionized health care, but not everyone benefits equally. A study in Sweden found that older age and less internet use are linked to lower eHealth literacy. To close this digital gap, eHealth must be tailored to individual needs, boosting motivation and access for all.

Researchers developed a deep learning model using 3D CNNs on fMRI scans for early Alzheimer's detection, achieving 92.8% accuracy, without added genetic data benefits. This study highlights the potential of AI in healthcare but also its challenges with small, imbalanced datasets.

Researchers engineered Yarrowia lipolytica yeast to boost taxifolin production, a flavonoid with health benefits, by modifying genes and optimizing methods. Innovations increased yields substantially, paving the way for more sustainable, large-scale production of this valuable compound.

Researchers explored a smart, eco-friendly wastewater treatment system using constructed wetlands and microbial fuel cells. The study found that certain plants and materials boost both cleaning efficiency and energy generation, offering sustainable solutions for tropical areas.

Scientists discovered how the immune and blood clotting systems talk to each other. They found that the immune system can help control blood clots and that clots can affect immunity. These insights could lead to new ways to treat clots and bleeding by targeting the immune system.

Researchers found that the traditional Chinese herb Ampelopsis japonica can boost the effectiveness of radiotherapy for lung cancer. It slows tumor growth more effectively by interfering with certain cell pathways.

Scientists studied rare ovarian cancer, finding it might come from germ cells in teratomas. Key genetic changes, like TP53 mutations, were common, helping distinguish primary from metastatic cases. This research could guide better diagnosis and treatment options.

Scientists discovered that a gene called CCT6A is involved in the spread of liver cancer by helping cancer cells move and invade. This is linked to how cancer cells use energy. Targeting CCT6A might be a new way to slow down or stop liver cancer from spreading.

Scientists engineered a yeast to efficiently produce taxifolin, a powerful antioxidant with health benefits. By tweaking the yeast’s genes and using a cost-effective method, they doubled taxifolin production, offering a more sustainable way to make this valuable compound.

Platinum chemo drugs help fight cancer but can harm kidneys, making treatment tricky. Doctors tweak treatments and use kidney-safe meds to help. Early detection tools are improving. Teamwork between specialists is key, but more research is needed to find better ways to prevent kidney damage.