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brophage.bsky.social
ⵃⴰⵎⵣⴰ - Hamza
@brophage.bsky.social
330 followers 400 following 7 posts
Sciencer, phage phanatic, mutants maker, viral dark matter explorer, polyglot, happy goat.
Posts Replies Media Videos
Reposted by ⵃⴰⵎⵣⴰ - Hamza
baym.lol
The only thing more scientifically dispiriting than reading a potentially exciting paper that turns out to be a ton of hype and little else is seeing your colleagues uncritically holding it up as a breakthrough
October 28, 2025 at 1:04 AM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
joshuasweitz.bsky.social
Pres. Garimella for U of Arizona:

"As a result, the university has not agreed to the terms outlined in the draft proposal, but instead submitted a Statement of Principles to the Department of Education that I am sharing with you."

president.arizona.edu/news/update-...
October 20, 2025 at 9:47 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
danudwary.secondarymetabolism.com
It integrates with Benchling. I can't possibly see how letting an LLM document your research could possibly go wrong... 🙄
October 20, 2025 at 9:53 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
jenshoer.bsky.social
Are you interested in studying RNA phages? We are looking for a PhD student and a postdoc to join the lab!

For more information and how to apply, see below 👇

Please RT!
October 17, 2025 at 12:52 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
stcmicrobeblog.bsky.social
#PhageSky ! (because j ≠ h)
October 16, 2025 at 7:58 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
mbeisen.bsky.social
Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com
October 15, 2025 at 6:33 AM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
odedrechavi.bsky.social
I’m dying for you to TRY IT, and it’s very simple - just drop a paper (the link to the website is in the replies👇) - it’s completely secure, private, and free, and you get results fast. Please show your support, SHARE, tell your friends, and let’s be the revolution 🫵!
October 15, 2025 at 12:22 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
avantikalal.bsky.social
I'm happy to share that our gReLU package is now published in Nature Methods!

www.nature.com/articles/s41...
gReLU: a comprehensive framework for DNA sequence modeling and design - Nature Methods
gReLU advances deep-learning-based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications.
www.nature.com
October 15, 2025 at 9:21 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
binomicalabs.org
Retrying GNU #Guix, test driving it for some bioinformatics workflows, learning scheme scripting and etc. I wrote up a quick walkthrough on how to install it as a package manager on non-selinux systems, if anyone's interested.

naturepoker.wordpress.com/2025/10/15/s...
Setting up GNU Guix package manager
It’s been a hot minute since last update on this lab note page. Things since last write up had been quite hectic, both in good and bad sense. I hopped on a train across continental US to atte…
naturepoker.wordpress.com
October 15, 2025 at 10:30 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
vscooper.micropopbio.org
Terrific writeup of our new paper led by @nanamikubota.bsky.social, thanks Pitt media!

www.medschool.pitt.edu/news/bacteri...
Bacteria Can Use Viruses to Kill Other Bacteria, Pitt Researchers Find | School of Medicine | University of Pittsburgh
Many bacteria, including the opportunistic pathogen Pseudomonas aeruginosa, are chronically infected by viruses that can reproduce without killing the cell. These viruses, called filamentous phages, t...
www.medschool.pitt.edu
October 15, 2025 at 8:31 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
elliejameson.bsky.social
Day 13, Loss 3/4. One of the phages finds a host, while the other losses out and perishes... #Drawtober #PhageSky #SciArt
Black and white ink cartoon of a smiling firey sun shining down on the sea. some of the sun's rays go into the sea hitting a phage that is limp with crosses for eyes, the cyanobacteria looks shocked as a second phage lands on its underside. The phage that survived looks shocked as its friend is no more Black and white ink cartoon with four panels, three contain drawings and the fourth is empty. Three of them show the sea with the sun first asleep and just visible over the waves in the top right, then with eyes open and fire haloing it, but still the lower portion behind the waves, in the thrid it is in the centre above the waves no longer hidden. under the waves are 2 phages, firstly alone, then there is a cyanobacteria in the second panel smiling at the sun whilst one phage looks panicked, in the third panel some of the sun's rays go into the sea hitting a phage that is limp with crosses for eyes, the cyanobacteria looks shocked as a second phage lands on its underside. The phage that survived looks shocked as its friend is no more.
October 13, 2025 at 3:23 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
cpavloud.bsky.social
If you feel like contributing your microbial growth data, take a look at μGrowthDB

mgrowthdb.gbiomed.kuleuven.be

You can also read the preprint: www.biorxiv.org/content/10.1...

🧬🖥️🧪🦠🧫
October 14, 2025 at 3:07 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
vivekmutalik.bsky.social
😳

#phage #phagesky #microsky
antimicrobial.bsky.social Antimicrobial resistance #AMR @antimicrobial.bsky.social · Oct 13
WHO reports 1 in 6 bacterial infections worldwide are antibiotic-resistant, with resistance rising sharply since 2018. Gram-negative bacteria like E. coli and K. pneumoniae pose the biggest threat. Action on #AMR surveillance and responsible antibiotic use is needed.

www.who.int/news/item/13...
WHO warns of widespread resistance to common antibiotics worldwide
One in six laboratory-confirmed bacterial infections causing common infections in people worldwide in 2023 were resistant to antibiotic treatments, according to a new World Health Organization (WHO) r...
www.who.int
October 13, 2025 at 11:17 AM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
viromegirl.bsky.social
We're hiring for several positions (a post-bac researcher in #transcriptomics, a #phage #postdoc, a senior researcher (broad topics) and a graduate student to work on #ciliates) - find info here: www.marine.usf.edu/genomics/app...
Apply - Genomics
www.marine.usf.edu
October 2, 2025 at 5:29 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
beatrizbeamud.bsky.social
Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky

www.nature.com/articles/s41...
Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases - Nature Communications
Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.
www.nature.com
October 8, 2025 at 8:59 AM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
evelienadri.bsky.social
For those of you working on tailed #phages, this is the virus realm for you!
#Duplodnaviria #virus #taxonomy

The Profile in #JGenVirol provides the citable reference. More details in the chapter on the ICTV website: ictv.global/report/chapt...
October 10, 2025 at 8:07 AM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
elliejameson.bsky.social
Day 11, Drink, 1/4. Drink might be a bit of a stretch, just floating in the sea! This is the first of four panels and the story of these oceanic cyanophage. They were released into the world at dusk and now dawn approaches... #Drawtober #SciArt #PhageSky
Black and white comic panel of the sea with a cartoon sun peeping over the surface with both eyes still shut wearing a sleep cap. In the sea are two phages floating on their sides next to each other
October 11, 2025 at 8:38 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
vscooper.micropopbio.org
🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
Faculty Professor Associate - Full-Time | Vaughn Cooper
We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...
www.linkedin.com
September 23, 2025 at 10:31 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
gtrubl.bsky.social
New paper alert with @alexjprobst.bsky.social.

enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication
The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, inc...
enviromicro-journals.onlinelibrary.wiley.com
September 19, 2025 at 7:43 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
uncultured.carinilab.com
New post up about Generative AI in academic research settings.

tl;dr : I'm mostly in favor of it, but with increased transparency.
open.substack.com/pub/carinila...
AI Is Already in Your Lab
The Honor System Won't Save You
open.substack.com
September 20, 2025 at 12:01 AM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
annizlab.bsky.social
Our new tool "X-Mapper: fast and accurate sequence alignment via gapped x-mers" now published on Genome Biology! Please try it if you work on DNA sequences :) github.com/mathjeff/Map...
genomebiology.biomedcentral.com/articles/10....
X-Mapper: fast and accurate sequence alignment via gapped x-mers - Genome Biology
Sequence alignment is foundational to many bioinformatic analyses. Many aligners start by splitting sequences into contiguous, fixed-length seeds, called k-mers. Alignment is faster with longer, uniqu...
genomebiology.biomedcentral.com
August 30, 2025 at 1:45 AM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
thejoesorg.bsky.social
We're hiring! 5 tenure track assistant professors. 2 #microbiology, 2 #Evolution, 1 #biologicalclocks

jobs.sciencecareers.org/job/675062/f...
Five Tenure-Track Assistant Professor Positions in Microbiology, Evolution, and Biological Clocks - College Station, Texas job with Department of Biology - TAMU | 675062
Texas A&M University (TAMU) invites applications for five full-time, tenure-track Assistant Professor positions
jobs.sciencecareers.org
September 12, 2025 at 6:11 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
joachimbaumann.bsky.social
🚨 New paper alert 🚨 Using LLMs as data annotators, you can produce any scientific result you want. We call this **LLM Hacking**.

Paper: arxiv.org/pdf/2509.08825
We present our new preprint titled "Large Language Model Hacking: Quantifying the Hidden Risks of Using LLMs for Text Annotation". We quantify LLM hacking risk through systematic replication of 37 diverse computational social science annotation tasks. For these tasks, we use a combined set of 2,361 realistic hypotheses that researchers might test using these annotations. Then, we collect 13 million LLM annotations across plausible LLM configurations. These annotations feed into 1.4 million regressions testing the hypotheses. For a hypothesis with no true effect (ground truth $p > 0.05$), different LLM configurations yield conflicting conclusions. Checkmarks indicate correct statistical conclusions matching ground truth; crosses indicate LLM hacking -- incorrect conclusions due to annotation errors. Across all experiments, LLM hacking occurs in 31-50\% of cases even with highly capable models. Since minor configuration changes can flip scientific conclusions, from correct to incorrect, LLM hacking can be exploited to present anything as statistically significant.
September 12, 2025 at 10:33 AM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
alicemaestri.bsky.social
We're looking for a technician at Institut Pasteur for experimental work on satellite-phage-bacteria interactions, working directly with @jmouradesousa.bsky.social and myself in the lab of @epcrocha.bsky.social ! ANR funded.

Link to the job emploi.pasteur.fr/offre-de-emp...
Thx for sharing!
INSTITUT PASTEUR - Technicien de recherche Microbiologie H/F
emploi.pasteur.fr
September 12, 2025 at 2:42 PM
Reposted by ⵃⴰⵎⵣⴰ - Hamza
zaminiqbal.bsky.social
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM