raw9371

crates.iocrates.io: Rust Package Registrycrates.io serves as a central registry for sharing crates, which are packages or libraries written in Rust that you can use to enhance your projects

💥 You asked. RAW Lab delivered. DYNAMITE-ORFs v1.1.0 🧬 ✅ Prodigal gap controls ✅ Gene-calling fixes ⚡ E. coli auto mode: 20.6 → 9.2s in our benchmark Messy genomes. Meet DYNAMITE. crates.io/crates/dynam... #Bioinformatics #Rust

🚨 5 BIOINFORMATICS TOOLS. 3 NEW QC ENGINES. 1 RUST BINARY. 🦀🔥 Introducing 🛡️ SENTINEL-X! 🧬 CheckV + CheckM2 + BUSCO + EukCC + viralVerify ⚡ No Python runtime! 🔬 Viral, bacterial & eukaryotic QC ONE TOOL. EVERY DOMAIN OF LIFE. 🚀 crates.io/crates/senti... #RustLang

microbialite.orgmicrobialite.org: 3.5 billion years of microbialites, stromatolites and microbial matsHow microbes learned to build rock, and kept building it for three and a half billion years: the story of microbialites, stromatolites and microbial mats.

🚨 What if the future of carbon capture is 3.5 BILLION YEARS OLD? 🦠 Microbialites turn carbon into STONE. 🪨 Nature's engineers could inspire NET-ZERO building materials. 🌍 We're searching for life on Mars while overlooking Earth's oldest ecosystems. 🔬 Check out microbialite.org We need your help!!

crates.iocrates.io: Rust Package Registrycrates.io serves as a central registry for sharing crates, which are packages or libraries written in Rust that you can use to enhance your projects

🦀 Rust is coming for bioinformatics. Meet Cleaver-X — one binary for: ✂️ Trimming + QC 🧬 FASTA/FASTQ/SAM/BAM 📊 Counting + demux ⚡ Constant-memory streaming 180 MB in 0.17 sec. ~7 MB RAM. No Python. No C/C++. Just Rust. 🦀 #Rust #rustsky Crates crates.io/crates/Cleav...

crates.iocrates.io: Rust Package Registrycrates.io serves as a central registry for sharing crates, which are packages or libraries written in Rust that you can use to enhance your projects

27 Aug

🧙‍♂️ I built Merlin. A pure-Rust RNA gene finder that detects tRNA, tmRNA & rRNAs. 🦀 No C ⚡ Parallel 🔮 Real HMMER Plan7 📦 No external tools or databases Fast. Parallel. Honest. Modern RNA gene finding. Crates crates.io/crates/merli... GitHub github.com/raw-lab/merl...

crates.iocrates.io: Rust Package Registrycrates.io serves as a central registry for sharing crates, which are packages or libraries written in Rust that you can use to enhance your projects

13 Aug

💥 I built DYNAMITE. 7 gene-calling engines. Phages, viruses, bacteria, archaea, eukaryotes. One command. Pure Rust. No Python. No dependencies circus. Crates crates.io/crates/dynam... GitHub github.com/raw-lab/dynamite 🧬 Genome in. Genes out. #Bioinformatics #Rust #Genomics

journals.asm.orgHigh-throughput viral enumeration of aquatic ecosystems via flow cytometry | Applied and Environmental MicrobiologyViruses represent the most numerically abundant biological entity on planet Earth. Enumeration of viruses within aquatic ecosystems (e.g., lakes and oceans) is essential to viral ecology and our under...

7 July

🌊🦠 Viruses are everywhere. Counting them shouldn’t be the bottleneck. Our new 96-well, hands-free flow cytometry workflow counts 60 aquatic samples in 2.25 hours—faster, cleaner, and more reproducible. In AEM Today journals.asm.org/doi/10.1128/... #phagesky #microbesky #phage #flow

lnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn

24 June

Python got bioinformatics started. Rust will scale it. 🦀 Today we released rustyomestats, our first Rust crate for genome assembly statistics. Fast. Memory safe. Built for massive genomic datasets. Crates: lnkd.in/dP88c83F GitHub: lnkd.in/dDw2KNuX Rust is the way. #RustLang #Bioinformatics

lnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn

24 June

Most high-performance bioinformatics software written 10 years from now will be in Rust. 🦀 Today we released rustyomestats — our first Rust crate ⚡ Genome size 🧬 GC content 📊 N50/L50/U50 🔬 Codon density 🚀 FASTA parsing GitHub: lnkd.in/dDw2KNuX Rust is the way. #RustLang #Bioinformatics

lnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn

19 June

github.com/raw-lab/rustyomestats crates.io/crates/rusty...

19 June

github.comGitHub - raw-lab/RustyOmeStatsContribute to raw-lab/RustyOmeStats development by creating an account on GitHub.

lnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn

19 June

1 May

Its official as of today - I am now an Associate Professor with Tenure at the University of North Carolina at Charlotte Dept of Bioinformatics & Genomics. A promise to my father - 20 years ago this Jan is finally complete. Never give up on your dreams - believe. #tenure

20 Apr

Bat Immunological Training Education (BITE) outreach at Discovery Place yesterday. We had 171 visitors at our booths today. We will continue to educate the public about diseases and immune responses. At Discovery Place every 3rd Saturday of the month. #microsky #bats #Stem Great job team!

Most RNA-seq pipelines are doing this wrong. They run differential expression… and stop there. You’re leaving biological signal on the table. I built pygage to fix that 👇 pip install pygage #Bioinformatics #rnaseq #computation #computationalbiology

Where this shines: • small RNA-seq studies (n < 5/group) • fast exploratory analysis • pipeline integration (pandas/NumPy workflows) Basically: real-world data!!

If you’re already doing differential expression in Python: This drops in directly. No exporting. No context switching. That alone saves time!! ALSO outputs feed pathview-plus our pathway tool! pip install pygage pip install pathview-plus #Bioinformatics #rnaseq #computationalbiology

Hot take: Most people don’t need more advanced enrichment methods! They need ones they’ll actually run. #rnaseq #bioinformatics #computational

Limitations (important): • ignores gene–gene correlation • pathway size affects variance Not perfect. But the tradeoff → speed + stability is often worth it. But that is corrected in our pathway level tool -> pathview-plus when you feed pyGAGE outputs to it!!

Under the hood: For a gene set S: → compute mean(d_g) → build null by sampling random gene sets of same size → compute Z-score vs that null No permutations. No heavy compute. This is why it’s fast! Its not analysis that takes long - its testing 50 tools that don't run to get some data back!!

7/ Output: • Z-scores • up/down pathway direction • FDR-corrected significance Fast, interpretable, reproducible! Now and today!!

8/ It’s not the fanciest method. But it actually works in real pipelines. And now it works natively in Python. #bioinformatics #rnaseq #genomics

5/ That last part matters. Most methods rely on sample permutation. That breaks when n is small (which is most datasets).

6/ pyGAGE avoids that. Gene randomization → stable inference even at low sample size

3/ So I built pygage — a Python implementation of GAGE. No bridges. No friction. Just runs.

4/ The method is simple and solid: → compute gene-level differential signal → aggregate into pathways → compare to a null via gene randomization

2/ Gene-level stats ≠ biological interpretation. You need pathway-level signals. That’s where gene set enrichment comes in. But most tools are: • slow • fragile with small n • stuck in R

link.springer.comResolving and quantifying viral-like particles via blind deconvolution - BMC MethodsBMC Methods - Viruses represent the most numerous’biological entities’on Earth; but the direct quantification of viruses within ecosystems is a significant challenge. The classical...

18 Apr

#Bioinformatics #computationalbiology #datascience

raw9371@raw937.bsky.social

🔬 Pathview-plus = powerful pathway visualization for bioinformatics 🚀 Thousands of pathway maps (KEGG + SBGNview) and super easy to use. Install in seconds: pip install pathview-plus GitHub: github.com/raw-lab/path... PyPI: pypi.org/project/path... #Bioinformatics #DataScience #Omics

The first automated computer vision–based software enabling the detection, enumeration, and sizing of virus-like particles from epifluorescence microscopy (EFM) images of environmental samples. Published online in BMC methods today. #giantvirus #phagesky Paper link.springer.com/article/10.1...

Genome Biology and Evolution

9 Feb

Send us a mail. We are always developing it.

Works well for bacteria as well in mixtures with viruses.

raw9371 reposted

@genomebiolevol.bsky.social

12 Dec 2025

@bhuwanabbot.bsky.social @morgancarterphd.bsky.social @raw937.bsky.social @andrabuchan.bsky.social et al. present a pangenome analysis of the endofungal genus Mycetohabitans, showing bacteria-fungus coevolution. 🔗 doi.org/10.1093/gbe/evaf231 #genome #evolution #pangenome #MicrobeSky

doi.orgComparative Genomics Reveals Multipartite Genomes Undergoing Loss in the Fungal Endosymbiotic Genus MycetohabitansAbstract. Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they b

7 Dec 2025

Bat Immunological Training Education (BITE) outreach at Discovery Place yesterday. We had 324 visitors at our booths today. We will continue to educate the public about diseases and immune responses. At Discovery Place every 3rd Saturday of the month. #microsky #bats Great job team!

academic.oup.comComparative genomics reveals multipartite genomes undergoing loss in the fungal endosymbiotic genus MycetohabitansAbstract. Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they b

2 Dec 2025

Awesome work. With some phageyness at the end. #phage #phagesky #microsky #evolution

Morgan Carter@morgancarterphd.bsky.social

We are excited to present the accepted paper on the Mycetohabitans pangenome now in @genomebiolevol.bsky.social! 🧬🦠 Thanks to @bhuwanabbot.bsky.social for leading and collaborators: @raw937.bsky.social @andrabuchan.bsky.social academic.oup.com/gbe/advance-...

raw9371 reposted

Rita Ramalhete

@ritaramalhete.bsky.social

25 Nov 2025

Latest in our #Phage collection Through #experimentalevolution, researchers at @ucsandiego.bsky.social trained #phages to increase their ability to inhibit multidrug-resistant and extensively drug-resistant Klebsiella pneumoniae 🧫 @natcomms.nature.com www.nature.com/articles/s41...

nature.comExperimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates - Nature CommunicationsGhatbale et al. adapted a co-evolutionary technique to develop Klebsiella pneumoniae phages to be highly active longitudinally against K. pneumoniae clinical isolates, including drug resistant isolate...

raw9371 reposted

Emmanuele Severi

@emmseveri.bsky.social

20 Nov 2025

#microsky #phagesky #phage

Ákos T Kovács@evolvedbiofilm.bsky.social

Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates -in @natcomms.nature.com www.nature.com/articles/s41...

20 Nov 2025

Thanks for the repost

Ákos T Kovács@evolvedbiofilm.bsky.social

Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates -in @natcomms.nature.com www.nature.com/articles/s41...

19 Nov 2025

Congratulations to my student Josh Hensley and our amazing collaborators at UCSD David Pride lab! In press today, we developed a technique to evolve phages to broaden bacterial host range to tackle bacteria that evade antibiotics. #phagesky #phage #microsky #virussky www.nature.com/articles/s41...

17 Nov 2025

Bat Immunological Training Education (BITE) outreach at Discovery Place today. We had 193 visitors at our booths today. We will continue to educate the public about bats, rodents, infectious diseases, and immune responses. At Discovery Place every 3rd Saturday of the month. #BITE #teamraw #rawlab

biorxiv.orgPhylogeny-agnostic strain-level prediction of phage-host interactions from genomesBacteriophages offer promising alternatives to antibiotics for treating drug-resistant infections and engineering microbiomes, but applications are limited by inability to select phages infecting spec...

17 Nov 2025

Cool 😎 paper @vivekmutalik.bsky.social www.biorxiv.org/content/10.1...

3 Nov 2025

In a world where an ancient evil has been awaken. Tom Cruise in "Phage." Coming Summer 2026 Needed a laugh/joke today. #phage #microsky #giantvirus #phagesky

phys.orgPhage G genome: AI analysis maps out world's largest cultivated bacteria-killing virusThrough cutting-edge methods and advanced artificial intelligence analysis, UNC Charlotte researchers leading a multidisciplinary team across four universities have successfully resolved the entire ge...

2 Nov 2025

#phage #phagesky

raw9371@raw937.bsky.social

Take a look y'all phys.org/news/2025-10... #phage #phagesky #bacteriophage

2 Nov 2025

Take a look y'all phys.org/news/2025-10... #phage #phagesky #bacteriophage

23 Oct 2025

Happy World Phage Day! May the phage be with you always! #bacteriophage #phage

bioengineer.orgDecoding the Genome of a Cultivated MegaphageIn an era where the microscopic realm constantly challenges our understanding of life’s boundaries, a groundbreaking study has thrust megaphages into the scientific spotlight. These colossal v

11 Oct 2025

Are these articles AI generated about our paper on phage G? Not even a phage shape. It looks like a CoV or InfA. #phage #phagesky Here is the real article about it cci.charlotte.edu/2025/10/10/c... Bioengineer - AI? bioengineer.org/decoding-the... Scienmag - AI? scienmag.com/decoding-the...

cci.charlotte.eduUNC Charlotte researchers use AI to map out world’s largest cultivated bacteria-killing virus - College of Computing and InformaticsThrough cutting-edge methods and advanced artificial intelligence analysis, UNC Charlotte researchers leading a multidisciplinary team across four universities have successfully resolved the entire ge...

10 Oct 2025

Andra Buchan and Stephanie Wiedman completing the multiome of the only cultivated megaphage on Earth. #phage #phagesky cci.charlotte.edu/2025/10/10/c...

share.googleUnlocking the genomic repertoire of a cultivated megaphage - npj Virusesnpj Viruses - Unlocking the genomic repertoire of a cultivated megaphage

30 Sept 2025

Multiomic analysis of the only megaphage in culture. In press today. Unlocking the genomic repertoire of a cultivated megaphage | npj Viruses share.google/HgU1cjRnaHWv... #phage #bacteriophage