Ralitsa Madsen
@ralitsamadsen.bsky.social
UKRI Future Leaders Fellow @MRC PPU, University of Dundee. Passionate about quantitative cell signalling, systems biology, human disease mechanisms, Open Science and research integrity. Incurably curious and obsessed with PI3K signalling, in particular!
Reposted by Ralitsa Madsen
Just out: new preprint (with @ralitsamadsen.bsky.social) is now #Reviewed at @eLife! "Non-equilibrium strategies for ligand specificity in signaling networks". We show how cells use non-equilibrium strategies to discriminate between ligands in surprising ways 🔗 elifesciences.org/reviewed-pre...
Non-equilibrium strategies for ligand specificity in signaling networks
elifesciences.org
July 30, 2025 at 10:13 AM
Just out: new preprint (with @ralitsamadsen.bsky.social) is now #Reviewed at @eLife! "Non-equilibrium strategies for ligand specificity in signaling networks". We show how cells use non-equilibrium strategies to discriminate between ligands in surprising ways 🔗 elifesciences.org/reviewed-pre...
Word of caution to fellow scientists:
If you're considering the RoboRocker platforms from NextAdvance: DON’T.
Despite claims on their website, these devices do not achieve in vivo-like shear stress in standard multiwell plates. That promise is why we bought them. It was misleading.
If you're considering the RoboRocker platforms from NextAdvance: DON’T.
Despite claims on their website, these devices do not achieve in vivo-like shear stress in standard multiwell plates. That promise is why we bought them. It was misleading.
April 9, 2025 at 7:44 PM
Word of caution to fellow scientists:
If you're considering the RoboRocker platforms from NextAdvance: DON’T.
Despite claims on their website, these devices do not achieve in vivo-like shear stress in standard multiwell plates. That promise is why we bought them. It was misleading.
If you're considering the RoboRocker platforms from NextAdvance: DON’T.
Despite claims on their website, these devices do not achieve in vivo-like shear stress in standard multiwell plates. That promise is why we bought them. It was misleading.
Reposted by Ralitsa Madsen
What's central to academic research & careers is not publishing papers.
What's central is exploring the unknown, making discoveries, communicating them rigorously & effectively, mentoring & teaching students, supporting colleagues, helping educate the public ...
Writing ...
🧵
What's central is exploring the unknown, making discoveries, communicating them rigorously & effectively, mentoring & teaching students, supporting colleagues, helping educate the public ...
Writing ...
🧵
April 7, 2025 at 12:06 PM
What's central to academic research & careers is not publishing papers.
What's central is exploring the unknown, making discoveries, communicating them rigorously & effectively, mentoring & teaching students, supporting colleagues, helping educate the public ...
Writing ...
🧵
What's central is exploring the unknown, making discoveries, communicating them rigorously & effectively, mentoring & teaching students, supporting colleagues, helping educate the public ...
Writing ...
🧵
Reposted by Ralitsa Madsen
This is fantastic! I missed Lauren has become an MP chairing science & technology. We were in the same PhD cohort in Dundee and I completely agree that Dundee life sciences is a jewel for UK science. It would be a pleasure to have you @laurensullivanmp.bsky.social visit @uniofeastanglia.bsky.social
Tropical disease researcher and parliamentarian Lauren Sullivan talks about difficulties of returning to the lab after a career break, juggling family, science and politics, and why Dundee’s life science sector must be supported. @jgro-the.bsky.social reports
#AcademicSky
#AcademicSky
Crick scientist-turned-Labour MP on supporting academic mothers
Tropical disease researcher and parliamentarian Lauren Sullivan talks about difficulties of returning to the lab after a career break, juggling family, science and politics, and why Dundee’s life scie...
www.timeshighereducation.com
March 19, 2025 at 12:27 PM
This is fantastic! I missed Lauren has become an MP chairing science & technology. We were in the same PhD cohort in Dundee and I completely agree that Dundee life sciences is a jewel for UK science. It would be a pleasure to have you @laurensullivanmp.bsky.social visit @uniofeastanglia.bsky.social
Reposted by Ralitsa Madsen
Provocative but important commentary from Sui Huang & co
Argues we need to change the paradigm of cancer origin from a somatic mutation theory to one grounded in gene regulatory networks & tissue organisation: a system level rather purely genetic mechanism
journals.plos.org/plosbiology/...
Argues we need to change the paradigm of cancer origin from a somatic mutation theory to one grounded in gene regulatory networks & tissue organisation: a system level rather purely genetic mechanism
journals.plos.org/plosbiology/...
The end of the genetic paradigm of cancer
Genome sequencing results and single-cell transcriptomics continue to produce findings that challenge the idea that cancer is purely a ‘genetic disease’. This Essay delves into cancer omics data that ...
journals.plos.org
March 19, 2025 at 8:52 AM
Provocative but important commentary from Sui Huang & co
Argues we need to change the paradigm of cancer origin from a somatic mutation theory to one grounded in gene regulatory networks & tissue organisation: a system level rather purely genetic mechanism
journals.plos.org/plosbiology/...
Argues we need to change the paradigm of cancer origin from a somatic mutation theory to one grounded in gene regulatory networks & tissue organisation: a system level rather purely genetic mechanism
journals.plos.org/plosbiology/...
Reposted by Ralitsa Madsen
It’s incredibly hard to see a national treasure like the NIH descend into the atrocious servitude of stripping out an image of one of their most successful Institute Directors in an effort to please the thinnest skinned President of all time.
March 15, 2025 at 9:12 PM
It’s incredibly hard to see a national treasure like the NIH descend into the atrocious servitude of stripping out an image of one of their most successful Institute Directors in an effort to please the thinnest skinned President of all time.
Reposted by Ralitsa Madsen
Together with fellow @biologists.bsky.social EiCs we've written about the unprecedented cuts & policy changes to research in the US
We stand with our US colleagues during this challenging time
Science transcends borders—setbacks in one nation affect us all
journals.biologists.com/dev/article/...
We stand with our US colleagues during this challenging time
Science transcends borders—setbacks in one nation affect us all
journals.biologists.com/dev/article/...
Science under siege: protecting scientific progress in turbulent times
As Editors-in-Chief of The Company of Biologists' journals, we have been watching with growing concern the policy changes in the United States of America (USA) and the challenges that these are creati...
journals.biologists.com
March 13, 2025 at 9:13 PM
Together with fellow @biologists.bsky.social EiCs we've written about the unprecedented cuts & policy changes to research in the US
We stand with our US colleagues during this challenging time
Science transcends borders—setbacks in one nation affect us all
journals.biologists.com/dev/article/...
We stand with our US colleagues during this challenging time
Science transcends borders—setbacks in one nation affect us all
journals.biologists.com/dev/article/...
Please read the human story behind this. Horrific and so sad. I hope there will be a solution that is better than what has been put forward.
The lengthy letter I sent that this was responding to:
March 14, 2025 at 12:08 AM
Please read the human story behind this. Horrific and so sad. I hope there will be a solution that is better than what has been put forward.
Reposted by Ralitsa Madsen
I think scientists should prioritize direct measurements, reliable conclusions, and rigor over throughput & convenience.
Throughput and convenience are important and highly desirable but after we have secured direct measurements & rigor.
Otherwise, noise rules.
Throughput and convenience are important and highly desirable but after we have secured direct measurements & rigor.
Otherwise, noise rules.
As nosy data & predictions are scaled up, we get more noisy results.
Designing good experiments, measuring directly what matters, and improving quality may be harder, but it's also more productive & rewarding.
Designing good experiments, measuring directly what matters, and improving quality may be harder, but it's also more productive & rewarding.
A common problem is that high-throughput data (and models) often focus on what can be easily measured at high-throughput rather that what should be measured (and modeled) to answer scientific questions.
Just scaling up is not enough.
nikolai.slavovlab.net/high-through...
Just scaling up is not enough.
nikolai.slavovlab.net/high-through...
March 9, 2025 at 4:55 PM
I think scientists should prioritize direct measurements, reliable conclusions, and rigor over throughput & convenience.
Throughput and convenience are important and highly desirable but after we have secured direct measurements & rigor.
Otherwise, noise rules.
Throughput and convenience are important and highly desirable but after we have secured direct measurements & rigor.
Otherwise, noise rules.
Today, we were all 🦓 in support of #RareDiseaseDay #ShowYourStripes
Mysel and @olimruk.bsky.social were raising awareness about PIK3CA-related overgrowth spectrum (PROS) disorders including CLOVES 🍀☘️ clovessyndrome.org
Mysel and @olimruk.bsky.social were raising awareness about PIK3CA-related overgrowth spectrum (PROS) disorders including CLOVES 🍀☘️ clovessyndrome.org
February 28, 2025 at 5:26 PM
Today, we were all 🦓 in support of #RareDiseaseDay #ShowYourStripes
Mysel and @olimruk.bsky.social were raising awareness about PIK3CA-related overgrowth spectrum (PROS) disorders including CLOVES 🍀☘️ clovessyndrome.org
Mysel and @olimruk.bsky.social were raising awareness about PIK3CA-related overgrowth spectrum (PROS) disorders including CLOVES 🍀☘️ clovessyndrome.org
Reposted by Ralitsa Madsen
A whole generation of early career scientists and physician-scientists, including colleagues and myself, are particularly vulnerable to these funding freezes and cuts, with jobs and careers depending on federal grants.
#IDsky
#Medsky
#Episky
www.science.org/content/arti...
#IDsky
#Medsky
#Episky
www.science.org/content/arti...
U.S. early-career researchers struggling amid chaos
Uncertain funding, government firings, and distressed universities hit vulnerable groups especially hard
www.science.org
February 22, 2025 at 12:08 PM
A whole generation of early career scientists and physician-scientists, including colleagues and myself, are particularly vulnerable to these funding freezes and cuts, with jobs and careers depending on federal grants.
#IDsky
#Medsky
#Episky
www.science.org/content/arti...
#IDsky
#Medsky
#Episky
www.science.org/content/arti...
Reposted by Ralitsa Madsen
"Genes are... the easy part" @philipcball.bsky.social argues biologists need to embrace complexity from the start, rather than beginning with oversimplified "one gene, one trait" models
+1
www.cell.com/cell-systems...
+1
www.cell.com/cell-systems...
Should biology put complexity first?
The dictum “Everything should be made as simple as possible, but no simpler” poses
a problem for biology. How simply can it be told without doing damage to its complex
nature? The answer might be foun...
www.cell.com
February 21, 2025 at 7:44 AM
"Genes are... the easy part" @philipcball.bsky.social argues biologists need to embrace complexity from the start, rather than beginning with oversimplified "one gene, one trait" models
+1
www.cell.com/cell-systems...
+1
www.cell.com/cell-systems...
Reposted by Ralitsa Madsen
New study in @cellpress.bsky.social by Allen Distinguished Investigator @elowitzlab.bsky.social and collaborators explores the versatility of protein dimers. #FrontierScience
🔗 www.cell.com/cell/fulltex...
🔗 www.cell.com/cell/fulltex...
February 19, 2025 at 6:42 PM
New study in @cellpress.bsky.social by Allen Distinguished Investigator @elowitzlab.bsky.social and collaborators explores the versatility of protein dimers. #FrontierScience
🔗 www.cell.com/cell/fulltex...
🔗 www.cell.com/cell/fulltex...
Reposted by Ralitsa Madsen
Autophagy UK & Proteostasis UK joint meeting -June 3-5. Exploring the lifecycle of cellular components from synthesis to degradation. Going to be a great meeting and we look forward to welcoming you to Dundee! Exciting lineup of speakers and opportunities for ECRs
Register here: tinyurl.com/mr3p49f9
Register here: tinyurl.com/mr3p49f9
Joint 2025 Autophagy UK and Proteostasis UK conference | University of Dundee, UK
Welcome to the 2025 joint “Autophagy UK and Proteostasis UK” conference!
tinyurl.com
February 16, 2025 at 6:56 AM
Autophagy UK & Proteostasis UK joint meeting -June 3-5. Exploring the lifecycle of cellular components from synthesis to degradation. Going to be a great meeting and we look forward to welcoming you to Dundee! Exciting lineup of speakers and opportunities for ECRs
Register here: tinyurl.com/mr3p49f9
Register here: tinyurl.com/mr3p49f9
Reposted by Ralitsa Madsen
What is a Differentially Expressed Gene? www.biorxiv.org/content/10....
What is a Differentially Expressed Gene?
The concept of ‘Differentially Expressed Genes’ (DEGs) is central to RNA-Seq studies, yet their identification suffers from reproducibility issues. This is largely a consequence of the inherent biological and technical variation that cannot be captured with small numbers of replicates. When thresholds for p-values and log2 fold changes are introduced, this variability can propagate an incomplete description of the data, leading to differing interpretations. Here, we compare traditional binary DEG classification with a rank-based method, grounded in Bayesian statistics, using a published yeast dataset comprising over 40 replicates. This analysis reveals how the choice of thresholds and number of replicates results in discrepancies between studies and potentially interesting genes being overlooked. Furthermore, by comparing wild-type with wild-type samples, we show how variability in gene expression can be mistaken for differential expression. Evaluating current practices for navigating
www.biorxiv.org
February 15, 2025 at 2:45 PM
What is a Differentially Expressed Gene? www.biorxiv.org/content/10....
elifesciences.org/articles/94420 - important study for the PI3K/insulin signallers out there!
Paradoxical dominant negative activity of an immunodeficiency-associated activating PIK3R1 variant
PIK3R1 mutations that cause immunodeficiency through PI3-kinase hyperactivation also cause SHORT syndrome, due to PI3-kinase hypofunction, attributable to PI3-kinase destabilisation and outcompetition...
elifesciences.org
February 15, 2025 at 4:41 PM
elifesciences.org/articles/94420 - important study for the PI3K/insulin signallers out there!
Reposted by Ralitsa Madsen
An intuitive explanation:
At fast growth, protein clearance rates are very similar across the proteome (green distribution below).
At slow growth, protein clearance rates vary widely across the proteome (purple distribution below).
bsky.app/profile/andr...
At fast growth, protein clearance rates are very similar across the proteome (green distribution below).
At slow growth, protein clearance rates vary widely across the proteome (purple distribution below).
bsky.app/profile/andr...
When comparing growing and non-growing cells, the difference in clearance rates is more substantial for long lived proteins, and thus their abundance is reduced in the growing state unless synthesis rates compensate. We find this compensation is insufficient to explain these changes.
February 13, 2025 at 1:20 PM
An intuitive explanation:
At fast growth, protein clearance rates are very similar across the proteome (green distribution below).
At slow growth, protein clearance rates vary widely across the proteome (purple distribution below).
bsky.app/profile/andr...
At fast growth, protein clearance rates are very similar across the proteome (green distribution below).
At slow growth, protein clearance rates vary widely across the proteome (purple distribution below).
bsky.app/profile/andr...
Reposted by Ralitsa Madsen
What explains the divergence between RNA and protein levels ?
Protein degradation is a HUGE factor.
It accounts for up to 50 % of protein variation across proteins & tissue types.
www.biorxiv.org/content/10.1...
🧵
Protein degradation is a HUGE factor.
It accounts for up to 50 % of protein variation across proteins & tissue types.
www.biorxiv.org/content/10.1...
🧵
February 13, 2025 at 1:03 PM
What explains the divergence between RNA and protein levels ?
Protein degradation is a HUGE factor.
It accounts for up to 50 % of protein variation across proteins & tissue types.
www.biorxiv.org/content/10.1...
🧵
Protein degradation is a HUGE factor.
It accounts for up to 50 % of protein variation across proteins & tissue types.
www.biorxiv.org/content/10.1...
🧵
Reposted by Ralitsa Madsen
I'm looking forward to this Signalling Symposium which celebrates the achievements of Len Stephens and Phill Hawkins during their 30-yr tenure at the Babraham Institute @babrahaminst.bsky.social
Registration details below
Registration details below
📢 Calling all Signallers! Join us for this celebratory smorgasbord of signalling research on 1-2 May with sessions on #proteostasis, #PI3K, #autophagy, #redox biology and #nuclear signalling. 🧪
Latest Institute research with special guests ⤵️
www.eventbrite.co.uk/e/cellular-s...
Latest Institute research with special guests ⤵️
www.eventbrite.co.uk/e/cellular-s...
Cellular signals for health & disease
A symposium marking the contributions of Len Stephens and Phillip Hawkins
www.eventbrite.co.uk
February 12, 2025 at 2:54 PM
I'm looking forward to this Signalling Symposium which celebrates the achievements of Len Stephens and Phill Hawkins during their 30-yr tenure at the Babraham Institute @babrahaminst.bsky.social
Registration details below
Registration details below
Reposted by Ralitsa Madsen
Members of the U.K. and international scientific community are invited to sign to show their support: docs.google.com/forms/d/e/1F...
Open letter to the President of the Royal Society – time to stand up for your values
If you wish to show your support for the letter below regarding apparent inaction by the Royal Society in the face of breaches of its code of conduct by Elon Musk FRS, please sign below. I invite anyo...
docs.google.com
February 11, 2025 at 5:17 PM
Members of the U.K. and international scientific community are invited to sign to show their support: docs.google.com/forms/d/e/1F...
Reposted by Ralitsa Madsen
Bluetorial-A dream and a bit of a nightmare
Serving as Editor-in-Chief at Science was fascinating. I greatly enjoyed working with talented and committed editorial, news, graphics, and production staff. But the inside look into scientific publishing and AAAS was also deeply disillusioning.
Serving as Editor-in-Chief at Science was fascinating. I greatly enjoyed working with talented and committed editorial, news, graphics, and production staff. But the inside look into scientific publishing and AAAS was also deeply disillusioning.
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
January 21, 2025 at 5:56 PM
Bluetorial-A dream and a bit of a nightmare
Serving as Editor-in-Chief at Science was fascinating. I greatly enjoyed working with talented and committed editorial, news, graphics, and production staff. But the inside look into scientific publishing and AAAS was also deeply disillusioning.
Serving as Editor-in-Chief at Science was fascinating. I greatly enjoyed working with talented and committed editorial, news, graphics, and production staff. But the inside look into scientific publishing and AAAS was also deeply disillusioning.
Reposted by Ralitsa Madsen
Taking the "on" out of the PIK3CA oncogene: a paradigm shift in PI3K signaling just out from @ralitsamadsen.bsky.social
Ralista will be talking about this in the New frontiers in inositol lipid signaling at the #ASBMB annual meeting this April - don’t miss it!
www.asbmb.org/annual-meeti...
Ralista will be talking about this in the New frontiers in inositol lipid signaling at the #ASBMB annual meeting this April - don’t miss it!
www.asbmb.org/annual-meeti...
January 7, 2025 at 3:57 PM
Taking the "on" out of the PIK3CA oncogene: a paradigm shift in PI3K signaling just out from @ralitsamadsen.bsky.social
Ralista will be talking about this in the New frontiers in inositol lipid signaling at the #ASBMB annual meeting this April - don’t miss it!
www.asbmb.org/annual-meeti...
Ralista will be talking about this in the New frontiers in inositol lipid signaling at the #ASBMB annual meeting this April - don’t miss it!
www.asbmb.org/annual-meeti...
Thanks for the fantastic publishing experience @molsystbiol.bsky.social - enjoyed the professionalism and the passion for Open Science!
Work by @ralitsamadsen.bsky.social showing oncogenic PIK3CAH1047R reduces biochemical information transfer, corrupts growth factor signaling specificity and increases single-cell heterogeneity ➡️ www.embopress.org/doi/full/10....
January 7, 2025 at 11:04 PM
Thanks for the fantastic publishing experience @molsystbiol.bsky.social - enjoyed the professionalism and the passion for Open Science!
Spotted today in of the local Tesco stores in Dundee.. EASTER??? It’s not even 2025 yet!
December 30, 2024 at 9:37 PM
Spotted today in of the local Tesco stores in Dundee.. EASTER??? It’s not even 2025 yet!