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Middle Author Bioinformatics

@midauthorbio.bsky.social
63 followers 22 following 84 posts

Your friendly neighborhood bioinformaticians :) Learn more about the company here: midauthorbio.com Check out our free bioinformatics web app: omix.midauthorbio.com Follow bsky.app/profile/thedailypub.bsky.s…

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Reposted by Middle Author Bioinformatics
Arkadiy Garber @ironark.bsky.social · 07/08/2026
I am pleased to share the preprint of our MagicLamp paper, in collaboration with the Penn Geomicrobiology Lab headed by Dr. Pérez-Rodríguez: www.biorxiv.org/content/10.6...
biorxiv.org
MagicLamp: a web server and software toolkit for targeted gene annotation of microbial functions
Genome and metagenome annotation tools designed for large databases are ill-suited to the discovery of specialized, ecologically relevant microbial functions. MagicLamp (<https://github.com/Arkadiy-Ga...
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Middle Author Bioinformatics @midauthorbio.bsky.social · 12/05/2026
We're excited to launch the MAB Newsletter! Issue #1 is a step-by-step tutorial on FeGenie, a tool we use to identify iron-related genes in (meta)genomes. Written for wet-lab biologists and nascent bioinformaticians. Read and subscribe here → middleauthorbioinformatics.substack.com/p/using-fege...
middleauthorbioinformatics.substack.com
Using FeGenie to Identify Iron Genes in Microbial Genomes
A step-by-step tutorial for wet-lab biologists and early-career bioinformaticians. Estimated read time: 12 minutes
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Reposted by Middle Author Bioinformatics
Vaughn Cooper @vscooper.micropopbio.org · 28/04/2026
One more app: ✅ FeGenie, 🔎 iron-related genes and more "Genies" to come soon! If you could use bioinformatic support on a current or upcoming project, contact midauthorbio.com, and a friendly colleague with microbiology and genomics expertise will follow up with you! cc: @ironark.bsky.social
midauthorbio.com
Middle Author Bioinformatics
This website describes a start-up company that specializes in bioinformatics analysis, software development, and teaching/outreach.
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Reposted by Middle Author Bioinformatics
Vaughn Cooper @vscooper.micropopbio.org · 28/04/2026
🚨Microbial genomics researchers🚨 Terrific FREE web apps from @midauthorbio.bsky.social midauthorbio.com/#freetools No coding or command line required ✅ breseq, A+ microbial variant calling ✅ SprayNPray, taxonomic profiling of metagenomes ✅ Pseudofinder 🔎 pseudogenes ✅ GToTree, phylogenomic trees
midauthorbio.com
Middle Author Bioinformatics
This website describes a start-up company that specializes in bioinformatics analysis, software development, and teaching/outreach.
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Reposted by Middle Author Bioinformatics
BF Francis Ouellette @bffo.bsky.social · 27/04/2026
From #NCBI Insight | #GenBank Release 271.0 is out | 261,460,182 traditional records containing 7,289,942,983,522 base pairs of sequence data | #Bioinformatics #Proteomics #Genomics #OpenScience #OpenData | 🧬 🖥️ 🧪 🔓 ⬇️ ncbiinsights.ncbi.nlm.nih.gov/2026/04/27/g...
ncbiinsights.ncbi.nlm.nih.gov
GenBank Release 271.0 is Available! - NCBI Insights
GenBank release 271.0 (4/14/2026) is now available on the NCBI FTP site. This release has 53.90 trillion bases and 6.27 billion records.  The current release has:   261,460,182 traditional records con...
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Middle Author Bioinformatics @midauthorbio.bsky.social · 26/04/2026
(1/2) One of the easiest phylogenomics tools to use just got even easier. GToTree, by Mike Lee, is now available as a web application: midauthorbio.com/#gtotree #phylogenomics #genomics #gtotree #phylogenetics
midauthorbio.com
Middle Author Bioinformatics
This website describes a start-up company that specializes in bioinformatics analysis, software development, and teaching/outreach.
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Middle Author Bioinformatics @midauthorbio.bsky.social · 26/04/2026
(1/2) The goal of Middle Author Bioinformatics is to make bioinformatics more accessible to biologists. With that in mind, FeGenie is now available as a web app at midauthorbio.com/#fegenie, making it easier to use without the command line. #metagenomics #bioinformatics #genomics
midauthorbio.com
Middle Author Bioinformatics
This website describes a start-up company that specializes in bioinformatics analysis, software development, and teaching/outreach.
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Reposted by Middle Author Bioinformatics
Vaughn Cooper @vscooper.micropopbio.org · 17/02/2026
Dear friends and fans of evolutionary biology & medicine (#EvMed), deadlines for the 2026 meeting in Kiel Germany are coming up. Looks to be excellent! March 1, 2026: Abstract submission deadline and travel award decisions April 1, 2026: Abstract decisions open.substack.com/pub/evmedrev...
open.substack.com
Abstracts due for the July Evolution and Medicine Conference in Kiel, Germany!
Early discounted registration is also open
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 07/12/2025
The hologenome in brain health and disease.
doi.org
The hologenome in brain health and disease.
Published in Neuron
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 04/12/2025
Performance of cabin air filters used in waste collection trucks.
doi.org
Performance of cabin air filters used in waste collection trucks.
Published in Journal of the Air & Waste Management Association (1995)
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Middle Author Bioinformatics @midauthorbio.bsky.social · 26/10/2025
Did you know that some bacteria can break down plastics? One such microbe is Ideonella sakaiensis. Using our web platform MagicLamp, and its built-in module PlasticGenie, you can now identify plastic-degradation–related genes in any Ideonella genome that's on RefSeq. www.magiclamp.midauthorbio.com
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Middle Author Bioinformatics @midauthorbio.bsky.social · 04/10/2025
Did you know that FeGenie has a simple-to-use GUI that requires no command-line experience? omix.midauthorbio.com Simply drop your (meta)genomes in and get results in minutes! We dropped in several hundred Prochlorococcus genomes to investigate their potential for iron acquisition and storage.
Dot plot showing number if genes classified as belonging to one of four iron-gene categories shown (there are more categories not shown)
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 01/10/2025
Wastewater can tell a lot about antibiotic resistance trends. A study of sewage from a university and nearby town found that resistance genes were higher in the town's wastewater, but levels evened out when antibiotics usage spiked at the university. Reducing antibiotic use doesn't quickly lower...
doi.org
Relating antimicrobial use to wastewater resistance gene patterns via metagenomic analysis of two neighboring treatment plants circa the COVID-19 pandemic.
Published in npj antimicrobials and resistance
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Reposted by Middle Author Bioinformatics
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 21/09/2025
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com
nature.com
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 12/09/2025
Bifidobacteria, the good microbes linked to health, have evolved alongside their animal hosts. Kujawska and the team found that these bacteria adapt based on the host's species, diet, and family line over generations. Their research gives insight into how these friendly microbes became such impor...
doi.org
Microbial matchmakers: Bifidobacterium evolution across animal hosts.
Published in Cell host & microbe
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Middle Author Bioinformatics @midauthorbio.bsky.social · 12/09/2025
Plasmodium falciparum is the protozoan parasite behind the most severe form of malaria, transmitted by Anopheles mosquitoes. If you want to see where P. falciparum sits in the tree of life, you can now do so easily with our microbial omics web app: omix.midauthorbio.com in less than 1 min!
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 08/09/2025
Turns out hosts and their microbes have a complicated relationship. A cool model shows microbes can help hosts handle environmental changes smoothly. When parents pass their microbes to offspring, high transfer boosts microbe fitness, but low transfer helps the host. Balancing this can keep the m...
doi.org
Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change.
Published in FEMS microbiology ecology
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 08/09/2025
Fighting the tough Mycobacterium abscessus is getting a bit easier! A new study suggests checking drug resistance in just a week could be as good as traditional tests. They found that a specific pattern in the bacteria's reaction to treatment predicted drug resistance pretty well. This method cou...
doi.org
Optimizing macrolide resistance detection for Mycobacterium abscessus: a potential low-cost, time-saving alternative.
Published in Microbiology spectrum
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Reposted by Middle Author Bioinformatics
Arkadiy Garber @ironark.bsky.social · 01/09/2025
Cool system. I was surprised to learn about circadian rhythms in bacteria. To aid in the identification of this system in genomes and metagenomes, @zombiephylotype.bsky.social and I included this pathway as part of our MagicLamp functional annotation suite: www.magiclamp.midauthorbio.com
magiclamp.midauthorbio.com
BinfoTools
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Vaughn Cooper @vscooper.micropopbio.org · 31/08/2025
Our efforts to govern research on mirror life covered by USA Today, featuring quotes by ⭐ @kateadamala.bsky.social and me. Good article, alarmist headline notwithstanding www.usatoday.com/story/news/n...
usatoday.com
Scientists fear microscopic 'mirror life' could wipe out humanity
Can a research ban save us?
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The Daily Pub @thedailypub.bsky.social · 27/08/2025
A groundbreaking study has successfully cultivated 627 unique microbial strains from Central European lakes. These strains represent a significant portion of the world's most common freshwater bacteria, many of which were previously uncultured. This new collection not only expands the knowledge o...
doi.org
Bringing the uncultivated microbial majority of freshwater ecosystems into culture.
Published in Nature communications
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 27/08/2025
Using advanced long-read metagenomics, scientists uncovered crucial genetic variations, known as structural variants (SVs), in marine microbes and viruses. These SVs help microbes adapt to their environments by affecting nutrient uptake and metabolism. In nutrient-poor seas like the Mediterranean...
doi.org
The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity.
Published in Environmental microbiome
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Reposted by Middle Author Bioinformatics
Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 25/08/2025
Adaptive radiation during long-term experimental evolution of the multicellular bacterium #Streptomyces www.biorxiv.org/content/10.1...
biorxiv.org
Adaptive radiation during long-term experimental evolution of the multicellular bacterium, Streptomyces
The rapid diversification of a single lineage into novel ecological niches underpins evolution of biodiversity, with adaptive radiations being important drivers of ecological diversity across the tree...
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Reposted by Middle Author Bioinformatics
Microbiome Virtual International Forum @microbiomevif.bsky.social · 22/08/2025
Program for #GloMiNe2025 "Preservation of microbial diversity” by @microbiotavault.bsky.social ‬and #MVIF is OUT: cassyni.com/s/mvif-glomi... 1/3
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 18/08/2025
Lung cancer microbiomes might hold the secret to better treatments. A study analyzing lung tissue microbiome from tumors found remarkable consistency in microbial diversity across different tissues and patients, suggesting these microbes are resilient even in cancer. Although the diversity seems...
doi.org
Assessing Diversity Scaling in Lung Cancer Microbiome Across Individuals and Tissue Types.
Published in MicrobiologyOpen
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Reposted by Middle Author Bioinformatics
ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · 18/08/2025
We're having a significant leptospirosis outbreak among sea lions along the California coast with significant mortality from kidney failure in the mammals Make sure your pet dogs who love the beach are vaccinated and don't get too close Remember: leptospirosis is the most common zoonosis of humans
newsweek.com
Disease outbreak among sea lions could spread to pets
As dozens of sea lions in California contract a bacterial infection, experts warn it could spread to humans and pets.
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Middle Author Bioinformatics @midauthorbio.bsky.social · 17/08/2025
Ever wondered how many genomes of your favorite bug have been sequenced and from where? We built a simple web app (GenBanker) that takes genus/species as name input and provides metadata sheet, including all relevant information from NCBI's GenBank database. main.d2btq5ga9882fz.amplifyapp.com
Results from a sample run.

Genus: Shewanella
Species: oneidensis
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Reposted by Middle Author Bioinformatics
Emma R. Hasson @dodecalemma.bsky.social · 14/08/2025
Writing stories like this for @sciam.bsky.social, and getting to speak to all the people involved who are brilliant and so committed to making other people's lives better always gives me hope. I hope you all enjoy! 🧪🧠
scientificamerican.com
This Brain Implant Can Read Out Your Inner Monologue
A new brain prosthesis can read out inner thoughts in real time, helping people with ALS and brain stem stroke communicate fast and comfortably
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Reposted by Middle Author Bioinformatics
Lilian Caesar @liliancaesar.bsky.social · 14/08/2025
Hey #microbiome folks :) What’s the current best approach to quantify absolute abundance of fungi in a sample? qPCR of a certain gene (not ITS due to variable/high copy number)? Spike-in before extraction with a known alien-fungus cell count? Thank you!
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 12/08/2025
Iron-oxidizing microbes aren’t ancient relics. Their iron metabolism evolved relatively recently due to shifting iron availability. This study suggests traits that aren't always useful might vanish and reappear throughout history, showing evolution isn't just about survival of the oldest but adap...
doi.org
Recent origin of iron oxidation in extant microbial groups and low clade fidelity of iron metabolisms.
Published in Applied and environmental microbiology
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 11/08/2025
Goodbye, harmful petrochemical plastics! This review dives into the world of PHAs—the eco-friendly, biodegradable plastics that mimic traditional materials. Exciting advances in production and application mean PHAs could revolutionize everything from packaging to medicine. There's still work to d...
doi.org
PHA, the Greenest Plastic So Far: Advancing Microbial Synthesis, Recovery, and Sustainable Applications for Circularity.
Published in ACS omega
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Reposted by Middle Author Bioinformatics
Arkadiy Garber @ironark.bsky.social · 18/05/2025
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...
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 01/05/2025
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...
doi.org
Current application and future prospects of CRISPR-Cas in lactic acid Bacteria: A review.
Published in Food research international (Ottawa, Ont.)
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Reposted by Middle Author Bioinformatics
Darcy Shapiro @darcyshapiro.bsky.social · 25/04/2025
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 🧪
Dimetrodon skeleton Edaphosaurus skeleton
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 14/04/2025
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...
doi.org
Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model.
Published in Nucleic acids research
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 13/04/2025
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...
doi.org
PlantPan: A comprehensive multi-species plant pan-genome database.
Published in The Plant journal : for cell and molecular biology
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Reposted by Middle Author Bioinformatics
Vaughn Cooper @vscooper.micropopbio.org · 08/04/2025
check out the 🧵 below for info about the apps👇🏻. feedback welcome! cc: @ironark.bsky.social
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Middle Author Bioinformatics @midauthorbio.bsky.social · 07/04/2025
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
omix.midauthorbio.com
Microbial Omics
A suite of bioinformatics tools for microbial genome and metagenome analysis.
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 07/04/2025
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...
doi.org
Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications.
Published in Microbiome
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 07/04/2025
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...
doi.org
Biofilms as potential reservoirs of antimicrobial resistance in vulnerable settings.
Published in Frontiers in public health
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 24/03/2025
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...
doi.org
What Do We Gain When Tolerating Loss? The Information Bottleneck Wrings Out Recombination.
Published in Molecular biology and evolution
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 24/03/2025
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...
doi.org
Pre-exposure of abundant species to disturbance improves resilience in microbial metacommunities.
Published in Nature ecology & evolution
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 24/03/2025
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...
doi.org
Microbial-induced Synthesis of nano NiFe LDH for High-efficiency Oxygen Evolution.
Published in Chemistry (Weinheim an der Bergstrasse, Germany)
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The Daily Pub @thedailypub.bsky.social · 23/03/2025
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...
doi.org
Exploring the role of gut microbiota in antibiotic resistance and prevention.
Published in Annals of medicine
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 22/03/2025
Embracing the systems complexity of microbial ecology and evolution: call for papers. doi.org/10.1128/msystems.00091-25
doi.org
Embracing the systems complexity of microbial ecology and evolution: call for papers.
Published in mSystems
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Reposted by Middle Author Bioinformatics
The Daily Pub @thedailypub.bsky.social · 22/03/2025
Ancient reef-building corals had a little help from microbial friends. doi.org/10.1038/d41586-025-00650-x
doi.org
Ancient reef-building corals had a little help from microbial friends.
Published in Nature
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Reposted by Middle Author Bioinformatics
Vaughn Cooper @vscooper.micropopbio.org · 18/03/2025
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
journals.asm.org
S2O Author FAQ
Discover how ASM's Subscribe to Open model benefits authors. Learn about ASM Journals author discounts, open access publishing, and funder compliance for 2025.
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naturepoker @binomicalabs.org · 17/03/2025
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? 🦠🧫🧬💻
Messy gene alignment rendered in terminal
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The Daily Pub @thedailypub.bsky.social · 24/12/2024
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.
doi.org
A comprehensive and bias-free machine learning approach for risk prediction of preeclampsia with severe features in a nulliparous study cohort.
Published in BMC pregnancy and childbirth
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The Daily Pub @thedailypub.bsky.social · 13/12/2024
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.
doi.org
Detection of germline CNVs from gene panel data: benchmarking the state of the art.
Published in Briefings in bioinformatics
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