V. Celeste Lanclos, Ph.D.
@vclanclos.bsky.social
Bioinformatics Scientist @Biotech | Postdoc @ UC Berkeley Coates Lab | PhD @USC Thrash Lab. Gimme the 'omics and untamed environmental buggers. Bay Area, CA.
Reposted by V. Celeste Lanclos, Ph.D.
We now have a working proof-of-concept implementation of the mim-enabled fastq parser in Rust. It uses needletail for the actual parsing and is *already* ~30% faster than the C++ implementation! Very excited about where this will go! cc @curiouscoding.nl
December 3, 2025 at 2:32 PM
We now have a working proof-of-concept implementation of the mim-enabled fastq parser in Rust. It uses needletail for the actual parsing and is *already* ~30% faster than the C++ implementation! Very excited about where this will go! cc @curiouscoding.nl
Reposted by V. Celeste Lanclos, Ph.D.
Are you a postdoc or 4-5th year grad student working on any problem in environmental microbiology and are interested in giving a virtual seminar (via zoom) on your hard work to a crowd of interested researchers at Montana State's Thermal Biology Institute in spring? Email/DM me!
December 1, 2025 at 7:58 PM
Are you a postdoc or 4-5th year grad student working on any problem in environmental microbiology and are interested in giving a virtual seminar (via zoom) on your hard work to a crowd of interested researchers at Montana State's Thermal Biology Institute in spring? Email/DM me!
Reposted by V. Celeste Lanclos, Ph.D.
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
November 25, 2025 at 8:41 PM
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
Reposted by V. Celeste Lanclos, Ph.D.
Diving through the purple sulfur bacteria layer of Fayetteville Green Lake with our ROV last month. This is the most intense density of PSB that I've seen in many years!
November 8, 2025 at 6:30 PM
Diving through the purple sulfur bacteria layer of Fayetteville Green Lake with our ROV last month. This is the most intense density of PSB that I've seen in many years!
Reposted by V. Celeste Lanclos, Ph.D.
“There is a cult of ignorance in the US & there has always been. The strain of anti-intellectualism has been a constant thread winding its way through our political & cultural life, nurtured by the false notion that democracy means that 'my ignorance is just as good as your knowledge.” -Isaac Asimov
November 14, 2025 at 1:31 PM
“There is a cult of ignorance in the US & there has always been. The strain of anti-intellectualism has been a constant thread winding its way through our political & cultural life, nurtured by the false notion that democracy means that 'my ignorance is just as good as your knowledge.” -Isaac Asimov
Reposted by V. Celeste Lanclos, Ph.D.
Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
November 10, 2025 at 9:32 AM
Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Reposted by V. Celeste Lanclos, Ph.D.
OMG
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 7, 2025 at 12:03 AM
OMG
Reposted by V. Celeste Lanclos, Ph.D.
A very good read for machine learning if you using RUST 🦀 and Polars. so a very good book. ericfecteau.ca/data/rust-da.... You can use the Linfa or the smartcore for the implementation of the machine learning algorithm.
Data analysis in Rust - Data Analysis in Rust
ericfecteau.ca
November 6, 2025 at 4:28 PM
A very good read for machine learning if you using RUST 🦀 and Polars. so a very good book. ericfecteau.ca/data/rust-da.... You can use the Linfa or the smartcore for the implementation of the machine learning algorithm.
Reposted by V. Celeste Lanclos, Ph.D.
The government shutdown is especially tough on men, who are losing $1.00 for every 75¢ a woman loses.
October 22, 2025 at 9:46 AM
The government shutdown is especially tough on men, who are losing $1.00 for every 75¢ a woman loses.
Reposted by V. Celeste Lanclos, Ph.D.
No image has ever spoken so succinctly about the current situation in the US.
October 20, 2025 at 8:59 PM
No image has ever spoken so succinctly about the current situation in the US.
Reposted by V. Celeste Lanclos, Ph.D.
USC is also rejecting Trump's compact
Update from Interim President Kim
October 16, 2025 Dear Trojan Family, Earlier today, I sent this letter to the U.S. Department of Education regarding the Compact for Academic Excellence in Higher Education. I appreciate the various p...
www.president.usc.edu
October 16, 2025 at 9:12 PM
USC is also rejecting Trump's compact
This was a fun one- images remind me of the planet in Scavenger's Reign
What if a time traveler accidentally killed Asgard archaea, and eukaryotes never emerged? Giant sulfur bacteria might still develop complex life. Using neural networks, I try to show this alternative living world 🧪🦠
#BiologyWeek
communities.springernature.com/posts/altern...
#BiologyWeek
communities.springernature.com/posts/altern...
Alternative history of life on Earth: complex life evolving from giant sulfur bacteria
What if a time traveler accidentally killed Asgard archaea, and eukaryotes never emerged? Giant sulfur bacteria might still develop complex life. Using neural networks, I try to show this alternative ...
communities.springernature.com
October 17, 2025 at 2:05 PM
This was a fun one- images remind me of the planet in Scavenger's Reign
Reposted by V. Celeste Lanclos, Ph.D.
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
blog.genesmindsmachines.com/p/we-still-c...
We still can’t predict much of anything in biology
Biology is hard. Yes, even for AI.
blog.genesmindsmachines.com
October 7, 2025 at 4:11 PM
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
blog.genesmindsmachines.com/p/we-still-c...
Reposted by V. Celeste Lanclos, Ph.D.
Please circulate among your bioinformatics students! 🧬🖥️❄️🦠
📢 PLEASE RT!
❄️ M2 Masters Internship: Metagenomic analysis of microbial cold adaptation in the cryosphere
🧬 Compile & curate ice nucleation & cold-adaptation protein database
🖥️ Build HMM profiles
🦠 Analyze existing metagenomic data using HMMs
☀️ Marseille, France
Apply by 15 Oct
❄️ M2 Masters Internship: Metagenomic analysis of microbial cold adaptation in the cryosphere
🧬 Compile & curate ice nucleation & cold-adaptation protein database
🖥️ Build HMM profiles
🦠 Analyze existing metagenomic data using HMMs
☀️ Marseille, France
Apply by 15 Oct
September 22, 2025 at 11:09 AM
Please circulate among your bioinformatics students! 🧬🖥️❄️🦠
Reposted by V. Celeste Lanclos, Ph.D.
Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
AllTheBacteria - all bacterial genomes assembled, available and searchable
The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...
www.biorxiv.org
August 28, 2025 at 12:16 PM
Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by V. Celeste Lanclos, Ph.D.
It's like you can see the interaction between ecology and evolution happening right in front of you. 💚🦠🧬
#mevosky #bluesci
www.science.org/doi/10.1126/...
#mevosky #bluesci
www.science.org/doi/10.1126/...
Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution
An integrated analysis framework shows a strong association between within-population genetic variation and protein structure.
www.science.org
August 26, 2025 at 4:09 PM
It's like you can see the interaction between ecology and evolution happening right in front of you. 💚🦠🧬
#mevosky #bluesci
www.science.org/doi/10.1126/...
#mevosky #bluesci
www.science.org/doi/10.1126/...
Reposted by V. Celeste Lanclos, Ph.D.
Cell Geometry Limits Bacterial Metabolic Efficiency www.biorxiv.org/content/10.1... #jcampubs
August 15, 2025 at 4:06 PM
Cell Geometry Limits Bacterial Metabolic Efficiency www.biorxiv.org/content/10.1... #jcampubs
Reposted by V. Celeste Lanclos, Ph.D.
GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction. #Genomics #Rust #GenomeAnnotation #GFF #GenomicFeatures @biorxiv-bioinfo.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
August 16, 2025 at 5:07 PM
GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction. #Genomics #Rust #GenomeAnnotation #GFF #GenomicFeatures @biorxiv-bioinfo.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by V. Celeste Lanclos, Ph.D.
SingleRust: A High-Performance Toolkit for Single-Cell Data Analysis at Scale. #SingleCell #scRNAseq #Rust #Bioinformatics @biorxiv-bioinfo.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
August 17, 2025 at 9:15 AM
SingleRust: A High-Performance Toolkit for Single-Cell Data Analysis at Scale. #SingleCell #scRNAseq #Rust #Bioinformatics @biorxiv-bioinfo.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by V. Celeste Lanclos, Ph.D.
Do you like coastal/estuarine microbiology, time-series data, and/or metagenomics? Have we got a dataset for you #NSFfunded
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series - Scientific Data
Scientific Data - Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series
www.nature.com
August 11, 2025 at 4:37 PM
Do you like coastal/estuarine microbiology, time-series data, and/or metagenomics? Have we got a dataset for you #NSFfunded
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs
Reposted by V. Celeste Lanclos, Ph.D.
InterProScan 6 (beta) is here 🎉
A Nextflow-powered, containerised overhaul for scalable, reproducible protein annotation—decoupled software/data, automated data handling, and smoother runs across HPC and cloud.
Feedback welcome!
github.com/ebi-pf-team/...
💻🧪🧬
A Nextflow-powered, containerised overhaul for scalable, reproducible protein annotation—decoupled software/data, automated data handling, and smoother runs across HPC and cloud.
Feedback welcome!
github.com/ebi-pf-team/...
💻🧪🧬
August 8, 2025 at 9:32 AM
InterProScan 6 (beta) is here 🎉
A Nextflow-powered, containerised overhaul for scalable, reproducible protein annotation—decoupled software/data, automated data handling, and smoother runs across HPC and cloud.
Feedback welcome!
github.com/ebi-pf-team/...
💻🧪🧬
A Nextflow-powered, containerised overhaul for scalable, reproducible protein annotation—decoupled software/data, automated data handling, and smoother runs across HPC and cloud.
Feedback welcome!
github.com/ebi-pf-team/...
💻🧪🧬
Reposted by V. Celeste Lanclos, Ph.D.
Sassy is out now!
Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!
Available now wherever you get your code
With @rickbitloo.bsky.social
curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!
Available now wherever you get your code
With @rickbitloo.bsky.social
curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
July 18, 2025 at 8:20 PM
Sassy is out now!
Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!
Available now wherever you get your code
With @rickbitloo.bsky.social
curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!
Available now wherever you get your code
With @rickbitloo.bsky.social
curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
Reposted by V. Celeste Lanclos, Ph.D.
Are you a top US-based scientist wanting to relocate to Australia? We are now calling for formal applications from both Australian and non-Australian citizens based in the US whose work is internationally recognised as exceptional.
📅 Applications close: Aug 29, 2025
🔗 science.org.au/gtap/?utm_so...
📅 Applications close: Aug 29, 2025
🔗 science.org.au/gtap/?utm_so...
July 11, 2025 at 12:21 AM
Are you a top US-based scientist wanting to relocate to Australia? We are now calling for formal applications from both Australian and non-Australian citizens based in the US whose work is internationally recognised as exceptional.
📅 Applications close: Aug 29, 2025
🔗 science.org.au/gtap/?utm_so...
📅 Applications close: Aug 29, 2025
🔗 science.org.au/gtap/?utm_so...
Reposted by V. Celeste Lanclos, Ph.D.
We're looking for someone with expertise in bacterial TEM that could help us interpret some images.
Bonus points for familiarity with images of endospores, BMCs, or cellulosomes. Please DM/email me if it's you, or have any leads. Thank you!
Bonus points for familiarity with images of endospores, BMCs, or cellulosomes. Please DM/email me if it's you, or have any leads. Thank you!
July 1, 2025 at 12:18 PM
We're looking for someone with expertise in bacterial TEM that could help us interpret some images.
Bonus points for familiarity with images of endospores, BMCs, or cellulosomes. Please DM/email me if it's you, or have any leads. Thank you!
Bonus points for familiarity with images of endospores, BMCs, or cellulosomes. Please DM/email me if it's you, or have any leads. Thank you!
Reposted by V. Celeste Lanclos, Ph.D.
Hi folks, we had a last minute cancellation at MBL STAMPS, the microbiome data analysis course in Woods Hole that runs from July 14th to July 24th. We can provide housing space for a woman. If you or anyone you know is interested, pls drop me an e-mail at ctbrown@ucdavis.edu. Thx!
June 27, 2025 at 6:48 PM
Hi folks, we had a last minute cancellation at MBL STAMPS, the microbiome data analysis course in Woods Hole that runs from July 14th to July 24th. We can provide housing space for a woman. If you or anyone you know is interested, pls drop me an e-mail at ctbrown@ucdavis.edu. Thx!