Alexis W
@alexiswe.bsky.social
Postdoc in the Hammarlund lab. C. elegans neurobiology, transcriptomics...
Reposted by Alexis W
They were circulated that way at the time, as a 3-paper bound reprint. They also have a collective title (frequently mistaken - including on the Nature website - as the title of the W&C paper): Molecular Structure of Nucleic Acids.
November 9, 2025 at 7:22 PM
They were circulated that way at the time, as a 3-paper bound reprint. They also have a collective title (frequently mistaken - including on the Nature website - as the title of the W&C paper): Molecular Structure of Nucleic Acids.
Reposted by Alexis W
I am seeing a lot of posts about Rosalind Franklin that themselves ignore her publication record on DNA!
In fact Franklin and Gosling's paper, including the famous Photograph #51, was published, along with Wilkins's paper, back-to-back with the Watson and Crick paper in Nature in 1953.
In fact Franklin and Gosling's paper, including the famous Photograph #51, was published, along with Wilkins's paper, back-to-back with the Watson and Crick paper in Nature in 1953.
November 9, 2025 at 6:43 PM
I am seeing a lot of posts about Rosalind Franklin that themselves ignore her publication record on DNA!
In fact Franklin and Gosling's paper, including the famous Photograph #51, was published, along with Wilkins's paper, back-to-back with the Watson and Crick paper in Nature in 1953.
In fact Franklin and Gosling's paper, including the famous Photograph #51, was published, along with Wilkins's paper, back-to-back with the Watson and Crick paper in Nature in 1953.
Reposted by Alexis W
“Overly honest methods”
November 10, 2025 at 7:33 PM
“Overly honest methods”
Reposted by Alexis W
🌍Open call: Junior Group Leader positions!
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
November 10, 2025 at 1:26 PM
🌍Open call: Junior Group Leader positions!
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Reposted by Alexis W
Check out our work on RNA structure in introns! Testing >100k base pairing patterns, we found that RNA structure can predictably tune gene expression. Just by changing intron sequence, we see a dynamic range of regulation comparable to messing e.g. with promoters. @karlaneugebauer.bsky.social
Control of gene output by intron RNA structure https://www.biorxiv.org/content/10.1101/2025.11.08.687378v1
November 10, 2025 at 5:32 PM
Check out our work on RNA structure in introns! Testing >100k base pairing patterns, we found that RNA structure can predictably tune gene expression. Just by changing intron sequence, we see a dynamic range of regulation comparable to messing e.g. with promoters. @karlaneugebauer.bsky.social
Reposted by Alexis W
If you believe either that Franklin discovered the double helix, and / or Watson and Crick stole her data, ask yourself how you know this. Then take a read of this article.
If I see one more stupid Rosalind Franklin take I'm going to lose my mind. Thank god for @matthewcobb.bsky.social and @nccomfort.bsky.social. www.nature.com/articles/d41...
What Rosalind Franklin truly contributed to the discovery of DNA’s structure
Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.
www.nature.com
November 8, 2025 at 7:32 AM
If you believe either that Franklin discovered the double helix, and / or Watson and Crick stole her data, ask yourself how you know this. Then take a read of this article.
Reposted by Alexis W
How many (active) C. elegans labs are there?
November 7, 2025 at 4:49 PM
How many (active) C. elegans labs are there?
Reposted by Alexis W
There still seems to be a lot of confusion about significance testing in psych. No, p-values *don’t* become useless at large N. This flawed point also used to be framed as "too much power". But power isn't the problem – it's 1) unbalanced error rates and 2) the (lack of a) SESOI. 1/ >
But here's, the thing, p values and significance become useless at such large sample sizes. When you're dividing the coefficient by the SE and the sample size is in the tens of thousands, EVERYTHING IS SIGNIFICANT. All you're testing is whether the coefficient is different than zero.
October 31, 2025 at 8:13 AM
There still seems to be a lot of confusion about significance testing in psych. No, p-values *don’t* become useless at large N. This flawed point also used to be framed as "too much power". But power isn't the problem – it's 1) unbalanced error rates and 2) the (lack of a) SESOI. 1/ >
Reposted by Alexis W
From the lab of Maxwell Heiman discussing the interesting topic of apical ECM and the function of sensing organs and how these ECM proteins can both mechanically and biochemically modulate the organ's functions.
doi.org/10.1016/j.cd...
doi.org/10.1016/j.cd...
October 30, 2025 at 5:48 PM
From the lab of Maxwell Heiman discussing the interesting topic of apical ECM and the function of sensing organs and how these ECM proteins can both mechanically and biochemically modulate the organ's functions.
doi.org/10.1016/j.cd...
doi.org/10.1016/j.cd...
Reposted by Alexis W
The ECM is no longer in the back seat when it comes to development. Check out our special issue "Dynamics of the extracellular matrix in development, cell physiology and disease" with 8 selected articles to learn more: A 🧵 www.sciencedirect.com/special-issu...
Cells & Development | Dynamics of the extracellular matrix in development, cell physiology and disease. | ScienceDirect.com by Elsevier
Extracellular matrices (ECMs) are everywhere in our body– from the sheet-like basement membranes that line epithelia and other tissues - to the loose stromal arrays of mesenchyme - to the rigid struct...
www.sciencedirect.com
October 30, 2025 at 5:48 PM
The ECM is no longer in the back seat when it comes to development. Check out our special issue "Dynamics of the extracellular matrix in development, cell physiology and disease" with 8 selected articles to learn more: A 🧵 www.sciencedirect.com/special-issu...
Reposted by Alexis W
#TodayinHistory #dataviz #OTD 📊
🎂Oct 20, 1719 Gottfried Achenwall born in Elbing, Germany 🇩🇪
1749: First use of the term "statistik", meaning numbers of the state, and implying collection of data by government entities.
Sometimes called the Father of #Statistics.
🎂Oct 20, 1719 Gottfried Achenwall born in Elbing, Germany 🇩🇪
1749: First use of the term "statistik", meaning numbers of the state, and implying collection of data by government entities.
Sometimes called the Father of #Statistics.
October 21, 2025 at 12:55 AM
#TodayinHistory #dataviz #OTD 📊
🎂Oct 20, 1719 Gottfried Achenwall born in Elbing, Germany 🇩🇪
1749: First use of the term "statistik", meaning numbers of the state, and implying collection of data by government entities.
Sometimes called the Father of #Statistics.
🎂Oct 20, 1719 Gottfried Achenwall born in Elbing, Germany 🇩🇪
1749: First use of the term "statistik", meaning numbers of the state, and implying collection of data by government entities.
Sometimes called the Father of #Statistics.
Reposted by Alexis W
Registration is open for the next Genome Dynamics course at @institutcurie.bsky.social! This course will explore the full spectrum of genome biology bringing together international experts to share the latest experimental and computational advances ▶️ training.institut-curie.org/courses/Geno...
October 14, 2025 at 9:14 AM
Registration is open for the next Genome Dynamics course at @institutcurie.bsky.social! This course will explore the full spectrum of genome biology bringing together international experts to share the latest experimental and computational advances ▶️ training.institut-curie.org/courses/Geno...
Reposted by Alexis W
With @taleshape.bsky.social chart annotations are just another SQL query:
You can load calendar events or goal lines from any data source and display them in your charts.
And not only chart annotations - any text, label or dropdown in Shaper can be generated dynamically.
You can load calendar events or goal lines from any data source and display them in your charts.
And not only chart annotations - any text, label or dropdown in Shaper can be generated dynamically.
October 8, 2025 at 9:49 AM
With @taleshape.bsky.social chart annotations are just another SQL query:
You can load calendar events or goal lines from any data source and display them in your charts.
And not only chart annotations - any text, label or dropdown in Shaper can be generated dynamically.
You can load calendar events or goal lines from any data source and display them in your charts.
And not only chart annotations - any text, label or dropdown in Shaper can be generated dynamically.
Reposted by Alexis W
I did one of these over the weekend and it was really good fun and also did not take very long. One of the kids asked me if mummies can come back to life. 10/10 experience for any archaeologist I think.
Welp here we are again, fresh out of Archaeologists for Skype a Scientist matches.
This fall, we have matched 248 groups with Archaeologists for online Q&As. I have 38 more groups who need a match, but I'm out of Archaeologists!
Archaeologists! Please volunteer
www.skypeascientist.com/sign-up.html
This fall, we have matched 248 groups with Archaeologists for online Q&As. I have 38 more groups who need a match, but I'm out of Archaeologists!
Archaeologists! Please volunteer
www.skypeascientist.com/sign-up.html
a woman is smiling and holding a cup that says help me .
Alt: a woman is smiling and holding a cup that says help me .
media.tenor.com
October 6, 2025 at 8:05 PM
I did one of these over the weekend and it was really good fun and also did not take very long. One of the kids asked me if mummies can come back to life. 10/10 experience for any archaeologist I think.
Reposted by Alexis W
Some day, I am going to win the Ig Nobel just to see what they come up with (apparently this is a thing they do, and it slaps)
Video: a Japanese scientist was attacked by flies while giving the acceptance speech for his Ig Nobel Prize-winning research paper that proved painting Zebra-like stripes on cows led to a decrease in biting fly attacks.
October 4, 2025 at 7:37 PM
Some day, I am going to win the Ig Nobel just to see what they come up with (apparently this is a thing they do, and it slaps)
Reposted by Alexis W
2. Map of <some far away country/city> generated with the same prompt.
Try and discuss how accurate it is - this is hard because we're unfamiliar with the (literal) territory. 😶🌫️
3. "When you hand in work done with an LLM, imagine when *I* (expert) are that *you* (novice) don't." 🤨
Try and discuss how accurate it is - this is hard because we're unfamiliar with the (literal) territory. 😶🌫️
3. "When you hand in work done with an LLM, imagine when *I* (expert) are that *you* (novice) don't." 🤨
October 2, 2025 at 6:41 AM
2. Map of <some far away country/city> generated with the same prompt.
Try and discuss how accurate it is - this is hard because we're unfamiliar with the (literal) territory. 😶🌫️
3. "When you hand in work done with an LLM, imagine when *I* (expert) are that *you* (novice) don't." 🤨
Try and discuss how accurate it is - this is hard because we're unfamiliar with the (literal) territory. 😶🌫️
3. "When you hand in work done with an LLM, imagine when *I* (expert) are that *you* (novice) don't." 🤨
Reposted by Alexis W
Added 3 slides to my "dear students, don't use LLMs" slidedeck. Here's how it works:
1. Generated map of <our country/city> from prompt "Generate an image: a schematic map of the <X> with major roads, cities, and landmarks."
Discuss how obviously wrong it is. Very fun, many lolz, silly LLM. 🤣
1. Generated map of <our country/city> from prompt "Generate an image: a schematic map of the <X> with major roads, cities, and landmarks."
Discuss how obviously wrong it is. Very fun, many lolz, silly LLM. 🤣
October 2, 2025 at 6:41 AM
Added 3 slides to my "dear students, don't use LLMs" slidedeck. Here's how it works:
1. Generated map of <our country/city> from prompt "Generate an image: a schematic map of the <X> with major roads, cities, and landmarks."
Discuss how obviously wrong it is. Very fun, many lolz, silly LLM. 🤣
1. Generated map of <our country/city> from prompt "Generate an image: a schematic map of the <X> with major roads, cities, and landmarks."
Discuss how obviously wrong it is. Very fun, many lolz, silly LLM. 🤣
Reposted by Alexis W
What are people using for calling m6A from pacbio revio data? This is for analysis of fiberseq library. Any suggestions appreciated, we are newbies with m6A analysis!
September 29, 2025 at 2:31 AM
What are people using for calling m6A from pacbio revio data? This is for analysis of fiberseq library. Any suggestions appreciated, we are newbies with m6A analysis!
Reposted by Alexis W
If you're wondering why we're hosting the pre-print via dropbox, its because arXiv (and bioRxiv) did not accept it (because it is a review). Its a bit disconcerting, because a review is precisely the type of paper that would benefit a lot from pre-publication dissemination and feedback.
Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.
September 25, 2025 at 1:25 PM
If you're wondering why we're hosting the pre-print via dropbox, its because arXiv (and bioRxiv) did not accept it (because it is a review). Its a bit disconcerting, because a review is precisely the type of paper that would benefit a lot from pre-publication dissemination and feedback.
Reposted by Alexis W
:)
I think it’s people like us that prompted @milesmcbain.bsky.social to write github.com/MilesMcBain/...
I think it’s people like us that prompted @milesmcbain.bsky.social to write github.com/MilesMcBain/...
GitHub - MilesMcBain/gistfo: Turn your RStudio untitled tabs into gists. You monsters.
Turn your RStudio untitled tabs into gists. You monsters. - MilesMcBain/gistfo
github.com
September 24, 2025 at 9:59 PM
:)
I think it’s people like us that prompted @milesmcbain.bsky.social to write github.com/MilesMcBain/...
I think it’s people like us that prompted @milesmcbain.bsky.social to write github.com/MilesMcBain/...
Reposted by Alexis W
Excited to share Modanovo, our transformer-based method for de novo peptide sequencing, which supports a broad range of post-translational modifications (PTMs)!
www.biorxiv.org/content/10.1...
#proteomics #massspectrometry #PTM
www.biorxiv.org/content/10.1...
#proteomics #massspectrometry #PTM
Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides
Post-translational modifications (PTMs) play a central role in cellular regulation and are implicated in numerous diseases. Database searching remains the standard for identifying modified peptides fr...
www.biorxiv.org
September 18, 2025 at 7:59 AM
Excited to share Modanovo, our transformer-based method for de novo peptide sequencing, which supports a broad range of post-translational modifications (PTMs)!
www.biorxiv.org/content/10.1...
#proteomics #massspectrometry #PTM
www.biorxiv.org/content/10.1...
#proteomics #massspectrometry #PTM
Reposted by Alexis W
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Reposted by Alexis W
📢 Lancement de la campagne ATIP-Avenir 2026
@cnrsbiologie.bsky.social et @inserm.fr ouvre la campagne ATIP-Avenir 2026, destinée à soutenir des projets de recherche innovants portés par de jeunes chercheuses et chercheurs.
📅 Toutes les informations : buff.ly/5DH6mpd
@cnrsbiologie.bsky.social et @inserm.fr ouvre la campagne ATIP-Avenir 2026, destinée à soutenir des projets de recherche innovants portés par de jeunes chercheuses et chercheurs.
📅 Toutes les informations : buff.ly/5DH6mpd
September 15, 2025 at 8:45 AM
📢 Lancement de la campagne ATIP-Avenir 2026
@cnrsbiologie.bsky.social et @inserm.fr ouvre la campagne ATIP-Avenir 2026, destinée à soutenir des projets de recherche innovants portés par de jeunes chercheuses et chercheurs.
📅 Toutes les informations : buff.ly/5DH6mpd
@cnrsbiologie.bsky.social et @inserm.fr ouvre la campagne ATIP-Avenir 2026, destinée à soutenir des projets de recherche innovants portés par de jeunes chercheuses et chercheurs.
📅 Toutes les informations : buff.ly/5DH6mpd
Reposted by Alexis W
Based on feedback from applicants, reviewers and broader research community, the ERC Scientific Council decided to make changes in the 2026–27 calls for proposal for research funding.
More details from the ERC President 👉 europa.eu/!hP3WWF
What’s your take on this? Tell us! 👇
More details from the ERC President 👉 europa.eu/!hP3WWF
What’s your take on this? Tell us! 👇
September 15, 2025 at 9:48 AM
Based on feedback from applicants, reviewers and broader research community, the ERC Scientific Council decided to make changes in the 2026–27 calls for proposal for research funding.
More details from the ERC President 👉 europa.eu/!hP3WWF
What’s your take on this? Tell us! 👇
More details from the ERC President 👉 europa.eu/!hP3WWF
What’s your take on this? Tell us! 👇
Changes in ERC eligibilty windows:
"researchers will be eligible to apply for a Starting Grant immediately after defending their PhD, and at any time within the following ten-year period. Consolidator Grant applicants will be eligible to apply between five and fifteen years after defending"
"researchers will be eligible to apply for a Starting Grant immediately after defending their PhD, and at any time within the following ten-year period. Consolidator Grant applicants will be eligible to apply between five and fifteen years after defending"
Based on feedback from applicants, reviewers and broader research community, the ERC Scientific Council decided to make changes in the 2026–27 calls for proposal for research funding.
More details from the ERC President 👉 europa.eu/!hP3WWF
What’s your take on this? Tell us! 👇
More details from the ERC President 👉 europa.eu/!hP3WWF
What’s your take on this? Tell us! 👇
September 15, 2025 at 10:38 AM
Changes in ERC eligibilty windows:
"researchers will be eligible to apply for a Starting Grant immediately after defending their PhD, and at any time within the following ten-year period. Consolidator Grant applicants will be eligible to apply between five and fifteen years after defending"
"researchers will be eligible to apply for a Starting Grant immediately after defending their PhD, and at any time within the following ten-year period. Consolidator Grant applicants will be eligible to apply between five and fifteen years after defending"