Middle Author Bioinformatics
@midauthorbio.bsky.social
Your friendly neighborhood bioinformaticians :)
Learn more about the company here: midauthorbio.com
Check out our free bioinformatics web app: omix.midauthorbio.com
Follow https://bsky.app/profile/thedailypub.bsky.social
Learn more about the company here: midauthorbio.com
Check out our free bioinformatics web app: omix.midauthorbio.com
Follow https://bsky.app/profile/thedailypub.bsky.social
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
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
October 26, 2025 at 1:28 AM
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
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
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.
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.
October 4, 2025 at 3:40 PM
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.
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.
Reposted by Middle Author Bioinformatics
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...
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
doi.org
October 1, 2025 at 1:00 PM
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...
Reposted by Middle Author Bioinformatics
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
📄 www.nature.com/articles/s41...
💿 mmseqs.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...
www.nature.com
September 21, 2025 at 8:06 AM
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
📄 www.nature.com/articles/s41...
💿 mmseqs.com
Reposted by Middle Author Bioinformatics
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...
Microbial matchmakers: Bifidobacterium evolution across animal hosts.
Published in Cell host & microbe
doi.org
September 12, 2025 at 7:00 AM
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...
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!
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!
September 12, 2025 at 3:23 PM
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!
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!
Reposted by Middle Author Bioinformatics
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...
Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change.
Published in FEMS microbiology ecology
doi.org
September 8, 2025 at 7:00 PM
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...
Reposted by Middle Author Bioinformatics
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...
Optimizing macrolide resistance detection for Mycobacterium abscessus: a potential low-cost, time-saving alternative.
Published in Microbiology spectrum
doi.org
September 8, 2025 at 7:00 PM
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...
Reposted by Middle Author Bioinformatics
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
September 1, 2025 at 9:31 PM
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
Reposted by Middle Author Bioinformatics
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...
www.usatoday.com/story/news/n...
Scientists fear microscopic 'mirror life' could wipe out humanity
Can a research ban save us?
www.usatoday.com
August 31, 2025 at 5:20 PM
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...
www.usatoday.com/story/news/n...
Reposted by Middle Author Bioinformatics
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...
Bringing the uncultivated microbial majority of freshwater ecosystems into culture.
Published in Nature communications
doi.org
August 27, 2025 at 7:00 AM
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...
Reposted by Middle Author Bioinformatics
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...
The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity.
Published in Environmental microbiome
doi.org
August 27, 2025 at 1:00 PM
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...
Reposted by Middle Author Bioinformatics
Adaptive radiation during long-term experimental evolution of the multicellular bacterium #Streptomyces www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
August 25, 2025 at 8:27 PM
Adaptive radiation during long-term experimental evolution of the multicellular bacterium #Streptomyces www.biorxiv.org/content/10.1...
Reposted by Middle Author Bioinformatics
Program for #GloMiNe2025 "Preservation of microbial diversity” by @microbiotavault.bsky.social and #MVIF is OUT:
cassyni.com/s/mvif-glomi...
1/3
cassyni.com/s/mvif-glomi...
1/3
August 22, 2025 at 11:42 AM
Program for #GloMiNe2025 "Preservation of microbial diversity” by @microbiotavault.bsky.social and #MVIF is OUT:
cassyni.com/s/mvif-glomi...
1/3
cassyni.com/s/mvif-glomi...
1/3
Reposted by Middle Author Bioinformatics
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...
Assessing Diversity Scaling in Lung Cancer Microbiome Across Individuals and Tissue Types.
Published in MicrobiologyOpen
doi.org
August 18, 2025 at 1:00 PM
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...
Reposted by Middle Author Bioinformatics
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
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
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.
www.newsweek.com
August 18, 2025 at 12:36 AM
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
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
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
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
August 17, 2025 at 5:10 PM
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
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
Reposted by Middle Author Bioinformatics
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! 🧪🧠
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
www.scientificamerican.com
August 14, 2025 at 3:07 PM
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! 🧪🧠
Reposted by Middle Author Bioinformatics
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!
August 14, 2025 at 4:23 PM
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!
Reposted by Middle Author Bioinformatics
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...
Recent origin of iron oxidation in extant microbial groups and low clade fidelity of iron metabolisms.
Published in Applied and environmental microbiology
doi.org
August 12, 2025 at 7:00 PM
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...
Reposted by Middle Author Bioinformatics
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...
PHA, the Greenest Plastic So Far: Advancing Microbial Synthesis, Recovery, and Sustainable Applications for Circularity.
Published in ACS omega
doi.org
August 11, 2025 at 7:00 PM
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...
Reposted by 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...
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...
May 18, 2025 at 7:05 PM
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...
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...
Reposted by Middle Author Bioinformatics
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...
Current application and future prospects of CRISPR-Cas in lactic acid Bacteria: A review.
Published in Food research international (Ottawa, Ont.)
doi.org
May 1, 2025 at 7:00 AM
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...
Reposted by Middle Author Bioinformatics
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 🧪
If you’ve ever wanted to write for Eons and the Permian is your jam, please DM me!
#FossilFriday #scicomm 🧪
April 25, 2025 at 4:57 PM
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 🧪
If you’ve ever wanted to write for Eons and the Permian is your jam, please DM me!
#FossilFriday #scicomm 🧪
Reposted by Middle Author Bioinformatics
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...
Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model.
Published in Nucleic acids research
doi.org
April 14, 2025 at 7:00 PM
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...