osn-scott.bsky.social
@osn-scott.bsky.social
Synthetic biologist, passionate about levelling the playing field in bioinnovation - open source biostack.
Open Science Network Society, Creator of the Open Yeast Collection and Yeast Protein Expression Toolkit, Reclone.org, iGEM Eng. Team, FreeGenes
Open Science Network Society, Creator of the Open Yeast Collection and Yeast Protein Expression Toolkit, Reclone.org, iGEM Eng. Team, FreeGenes
Reposted by osn-scott.bsky.social
First time on Bsky and first big announcement!
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
Estimation and mapping of the missing heritability of human phenotypes - Nature
WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...
www.nature.com
November 12, 2025 at 5:57 PM
First time on Bsky and first big announcement!
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
Reposted by osn-scott.bsky.social
Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on.
(Please repost to reach a broad audience.)
(Please repost to reach a broad audience.)
November 12, 2025 at 4:49 AM
Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on.
(Please repost to reach a broad audience.)
(Please repost to reach a broad audience.)
Reposted by osn-scott.bsky.social
Better than making Marmite. 😝
Beer yeast leftovers spun into a promising sustainable yarn 50% stronger than wool
www.chemistryworld.com/news/beer-ye...
www.chemistryworld.com/news/beer-ye...
Beer yeast leftovers spun into a promising sustainable yarn 50% stronger than wool
Brewery waste can be turned into a cheap, environmentally-friendly textile
www.chemistryworld.com
November 9, 2025 at 8:11 PM
Better than making Marmite. 😝
Reposted by osn-scott.bsky.social
'When Mendel began his investigation, his first inclination was to try breeding mice of different colors. However, before his mice experiment really got going, Mendel was forced to switch the subject of his experiments to peas by a prudish bishop uncomfortable with animals having sex in the abbey.'
Origins of the Lab Mouse
How the mouse found its way from Victorian novelty to a biomedical mainstay.
www.asimov.press
November 3, 2025 at 6:25 PM
'When Mendel began his investigation, his first inclination was to try breeding mice of different colors. However, before his mice experiment really got going, Mendel was forced to switch the subject of his experiments to peas by a prudish bishop uncomfortable with animals having sex in the abbey.'
Reposted by osn-scott.bsky.social
My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...
Remembering Hamilton O. Smith
Hamilton O. Smith
August 31, 1931 – October 25, 2025
It is with profound sorrow that we announce the loss of Hamilton O. Smith, M.D., a...
www.jcvi.org
October 29, 2025 at 11:26 PM
My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...
Reposted by osn-scott.bsky.social
R.I.P Hamilton Smith, 1978 Nobel Laureate for the discovery of type II restriction-modification systems (HindII).
October 26, 2025 at 6:54 PM
R.I.P Hamilton Smith, 1978 Nobel Laureate for the discovery of type II restriction-modification systems (HindII).
Reposted by osn-scott.bsky.social
13 years ago, the revolutionary genetic tool #CRISPR/Cas9 was published in Science, work that Emmanuelle Charpentier and Jennifer Doudna won a #NobelPrize for in 2020.
On #WorldCRISPRDay, read the landmark paper that describes the discovery: https://scim.ag/42JHuSN
On #WorldCRISPRDay, read the landmark paper that describes the discovery: https://scim.ag/42JHuSN
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
A prokaryotic RNA–directed targeting system can be designed to cleave any DNA sequence.
scim.ag
October 20, 2025 at 7:33 PM
13 years ago, the revolutionary genetic tool #CRISPR/Cas9 was published in Science, work that Emmanuelle Charpentier and Jennifer Doudna won a #NobelPrize for in 2020.
On #WorldCRISPRDay, read the landmark paper that describes the discovery: https://scim.ag/42JHuSN
On #WorldCRISPRDay, read the landmark paper that describes the discovery: https://scim.ag/42JHuSN
Reposted by osn-scott.bsky.social
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Reposted by osn-scott.bsky.social
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 osn-scott.bsky.social
Related but cool combo of cytogenetics and phenotype. Know when the first QTL was mapped?
Sax, K. 1923. The association of size differences with seed coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552-560.
Sax, K. 1923. The association of size differences with seed coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552-560.
August 27, 2025 at 3:12 AM
Related but cool combo of cytogenetics and phenotype. Know when the first QTL was mapped?
Sax, K. 1923. The association of size differences with seed coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552-560.
Sax, K. 1923. The association of size differences with seed coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552-560.
Reposted by osn-scott.bsky.social
A reminder you/your lab can support FlyBase at Cambridge through the following link. Every bit helps. Please share if you yourself can't donate.
www.philanthropy.cam.ac.uk/give-to-camb...
www.philanthropy.cam.ac.uk/give-to-camb...
August 14, 2025 at 5:25 AM
A reminder you/your lab can support FlyBase at Cambridge through the following link. Every bit helps. Please share if you yourself can't donate.
www.philanthropy.cam.ac.uk/give-to-camb...
www.philanthropy.cam.ac.uk/give-to-camb...
Reposted by osn-scott.bsky.social
May 27, 2025 at 5:54 AM
Reposted by osn-scott.bsky.social
We’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social!
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM
May 26, 2025 at 4:56 PM
We’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social!
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM
Reposted by osn-scott.bsky.social
🚨 Teaching bioinformatics? Or learning it solo?
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩💻
📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!
#bioinformatics #opensource #STEMeducation
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩💻
📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!
#bioinformatics #opensource #STEMeducation
GitHub - lskatz/fundamentals-of-bioinformatics
Contribute to lskatz/fundamentals-of-bioinformatics development by creating an account on GitHub.
github.com
May 12, 2025 at 6:00 PM
🚨 Teaching bioinformatics? Or learning it solo?
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩💻
📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!
#bioinformatics #opensource #STEMeducation
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩💻
📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!
#bioinformatics #opensource #STEMeducation
Reposted by osn-scott.bsky.social
"As with software, open DNA & strains promotes innovation around the world. I wish to extend Open Yeast & Yeast Protein Expression Toolkits, now in 50 countries, to permit engineering of Yarrowia lipolytica & creating truly open chassis to support boots on the ground innovators."
May 12, 2025 at 2:38 PM
"As with software, open DNA & strains promotes innovation around the world. I wish to extend Open Yeast & Yeast Protein Expression Toolkits, now in 50 countries, to permit engineering of Yarrowia lipolytica & creating truly open chassis to support boots on the ground innovators."
Reposted by osn-scott.bsky.social
Here's another #MegabaseSpark submission, from
@osn-scott.bsky.social: "The Open Yarrowia Collection" (detail in reply) Like and repost if you like this idea! #SynBio #RootPath
@osn-scott.bsky.social: "The Open Yarrowia Collection" (detail in reply) Like and repost if you like this idea! #SynBio #RootPath
May 12, 2025 at 2:37 PM
Here's another #MegabaseSpark submission, from
@osn-scott.bsky.social: "The Open Yarrowia Collection" (detail in reply) Like and repost if you like this idea! #SynBio #RootPath
@osn-scott.bsky.social: "The Open Yarrowia Collection" (detail in reply) Like and repost if you like this idea! #SynBio #RootPath
Reposted by osn-scott.bsky.social
AlphaFold is amazing but gives you static structures 🧊
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
April 17, 2025 at 7:11 PM
AlphaFold is amazing but gives you static structures 🧊
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
Reposted by osn-scott.bsky.social
chinnadevarapu.bsky.social has updated his tiny, low cost Pocket Spectrometer design that uses an M5StickC microcontroller and AS7341 spectral sensor - simplified hardware connections and software improvements. Nice job! Details at: github.com/scientistnob...
March 9, 2025 at 6:47 PM
chinnadevarapu.bsky.social has updated his tiny, low cost Pocket Spectrometer design that uses an M5StickC microcontroller and AS7341 spectral sensor - simplified hardware connections and software improvements. Nice job! Details at: github.com/scientistnob...
Reposted by osn-scott.bsky.social
🚀 First Bluesky Post! 🎉 VMD 2.0 Alpha is here! Released today at BPS 2025, this is the biggest update in 30 years—new UI, real-time ray tracing, fast surfaces, UHD & touchscreen support. Monthly updates coming in 2025! Try it now! #VMD #BPS2025 #MolecularVisualization
www.ks.uiuc.edu/Research/vmd...
www.ks.uiuc.edu/Research/vmd...
February 17, 2025 at 6:56 AM
🚀 First Bluesky Post! 🎉 VMD 2.0 Alpha is here! Released today at BPS 2025, this is the biggest update in 30 years—new UI, real-time ray tracing, fast surfaces, UHD & touchscreen support. Monthly updates coming in 2025! Try it now! #VMD #BPS2025 #MolecularVisualization
www.ks.uiuc.edu/Research/vmd...
www.ks.uiuc.edu/Research/vmd...
Reposted by osn-scott.bsky.social
Re DNA sequence DBs: While sequence is shared across #INSDC databases #ENA #Genbank #DDBJ, the presentation and granularity of annotations/metadata can differ notably, with diff. benefits, impacting searches and downstream analyses. All INSDC databases must be maintained - annotations are important
February 22, 2025 at 9:00 PM
Reposted by osn-scott.bsky.social
Delighted to share our latest paper describing a method to read the levels of hundreds of metabolites or drugs in parallel using DNA sequencing. This method, which we call ‘smol-seq’ (Small MOLecule sequencing), harnesses the power of DNA sequencing for metabolite detection:
rdcu.be/d8xLv (1/6)
rdcu.be/d8xLv (1/6)
Quantifying metabolites using structure-switching aptamers coupled to DNA sequencing
Nature Biotechnology - Metabolites can be quantified using a combination of aptamers and DNA barcodes.
rdcu.be
February 4, 2025 at 1:54 PM
Delighted to share our latest paper describing a method to read the levels of hundreds of metabolites or drugs in parallel using DNA sequencing. This method, which we call ‘smol-seq’ (Small MOLecule sequencing), harnesses the power of DNA sequencing for metabolite detection:
rdcu.be/d8xLv (1/6)
rdcu.be/d8xLv (1/6)
Reposted by osn-scott.bsky.social
What limits rubisco function? Is it the chemical mechanism? Evolution? In this paper, @prywes.bsky.social et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7) doi.org/10.1038/s415...
January 24, 2025 at 8:27 PM
What limits rubisco function? Is it the chemical mechanism? Evolution? In this paper, @prywes.bsky.social et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7) doi.org/10.1038/s415...
Reposted by osn-scott.bsky.social
New Journal Article: “Trust in #Scientists and Their Role in Society Across 68 Countries” www.infodocket.com/2025/01/20/j... #science #trustinscience
January 20, 2025 at 6:33 PM
New Journal Article: “Trust in #Scientists and Their Role in Society Across 68 Countries” www.infodocket.com/2025/01/20/j... #science #trustinscience
Reposted by osn-scott.bsky.social
Two new studies provide some insights on red meat intake, with respect to both potential risks and how they can be mitigated.
erictopol.substack.com/p/the-update...
erictopol.substack.com/p/the-update...
January 19, 2025 at 5:16 PM
Two new studies provide some insights on red meat intake, with respect to both potential risks and how they can be mitigated.
erictopol.substack.com/p/the-update...
erictopol.substack.com/p/the-update...
Reposted by osn-scott.bsky.social
This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics https://www.biorxiv.org/content/10.1101/2025.01.16.633422v1
January 17, 2025 at 8:53 PM
This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after