@bskytdp.bsky.social
Reposted
steven-senior.medium.com/it-wont-work...
It won’t work but at least it’ll be expensive: Why genomics could be an expensive distraction when it comes to preventing illness
@stevensenior.bsky.social
(At least I'm not the only cynic)
It won’t work but at least it’ll be expensive: Why genomics could be an expensive distraction when it comes to preventing illness
@stevensenior.bsky.social
(At least I'm not the only cynic)
It won’t work but at least it’ll be expensive: Why genomics could be an expensive distraction when…
The NHS 10 year plan puts a lot of stock in genomics for preventing people getting sick. For example, it envisages a“new genomics…
steven-senior.medium.com
July 10, 2025 at 12:36 PM
steven-senior.medium.com/it-wont-work...
It won’t work but at least it’ll be expensive: Why genomics could be an expensive distraction when it comes to preventing illness
@stevensenior.bsky.social
(At least I'm not the only cynic)
It won’t work but at least it’ll be expensive: Why genomics could be an expensive distraction when it comes to preventing illness
@stevensenior.bsky.social
(At least I'm not the only cynic)
Reposted
Another review/opinion piece about why studying proteoforms is important, this time when dealing with Anti-Microbial Resistance. Written by my super-talented PhD student @breyerwoodland.bsky.social with Piklu Roy Chowdhury and Matt O'Rourke.
doi.org/10.1016/j.ta...
doi.org/10.1016/j.ta...
Redirecting
doi.org
June 25, 2025 at 7:30 AM
Another review/opinion piece about why studying proteoforms is important, this time when dealing with Anti-Microbial Resistance. Written by my super-talented PhD student @breyerwoodland.bsky.social with Piklu Roy Chowdhury and Matt O'Rourke.
doi.org/10.1016/j.ta...
doi.org/10.1016/j.ta...
Reposted
The pulished version of the review is out: doi.org/10.1002/pmic.... Enjoy.
Sample Preparation for Multi‐Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow
Advances in methodologies and technologies over the past decade have led to an unprecedented depth of analysis of a cell's biomolecules, with entire genomes able to be sequenced in hours and up to 10...
doi.org
June 23, 2025 at 9:52 PM
The pulished version of the review is out: doi.org/10.1002/pmic.... Enjoy.
The morning started with assessing dogma, so let’s also look at the over-/mis-interpretation of Western blots. Considering proteoforms, ‘routine’ Westerns need to be better controlled & data more critically assessed before publishing any interpretations. DOI: 10.1016/j.talanta.2025.128266
June 22, 2025 at 2:33 PM
The morning started with assessing dogma, so let’s also look at the over-/mis-interpretation of Western blots. Considering proteoforms, ‘routine’ Westerns need to be better controlled & data more critically assessed before publishing any interpretations. DOI: 10.1016/j.talanta.2025.128266
Reposted
2024 Journal Impact Factors.
Molecular & Cellular Proteomics: 5.5
Proteomics: 3.9
Proteomes: 3.6
Journal of Proteome Research: 3.6
Journal of Proteomics: 2.8
Equal to JPR. I'll take that. 🎉
Molecular & Cellular Proteomics: 5.5
Proteomics: 3.9
Proteomes: 3.6
Journal of Proteome Research: 3.6
Journal of Proteomics: 2.8
Equal to JPR. I'll take that. 🎉
June 20, 2025 at 6:50 AM
2024 Journal Impact Factors.
Molecular & Cellular Proteomics: 5.5
Proteomics: 3.9
Proteomes: 3.6
Journal of Proteome Research: 3.6
Journal of Proteomics: 2.8
Equal to JPR. I'll take that. 🎉
Molecular & Cellular Proteomics: 5.5
Proteomics: 3.9
Proteomes: 3.6
Journal of Proteome Research: 3.6
Journal of Proteomics: 2.8
Equal to JPR. I'll take that. 🎉
Reposted
My talk at Aus-Omics was recorded and I have finally sync'd it with the slides and shoved it on YouTube.
youtu.be/mYjK5GCcqms
youtu.be/mYjK5GCcqms
Deep Visual Proteomics to Understand a Rare Cancer - AusOmics 2025
YouTube video by Matt Padula
youtu.be
June 14, 2025 at 10:32 AM
My talk at Aus-Omics was recorded and I have finally sync'd it with the slides and shoved it on YouTube.
youtu.be/mYjK5GCcqms
youtu.be/mYjK5GCcqms
Reposted
My paper on consultant-vampires Nous sucking the lifeblood of universities goes into more detail about how these guys operate (co-written with @bestqualitycrab.bsky.social) www.tandfonline.com/doi/full/10....
“Nousferatu”: Are corporate consultants extracting the lifeblood from universities?
Universities and management consultants are locked in a danse macabre. We turn to the vampire genre to elaborate on the relationship of consulting companies to the university sector, focusing on th...
www.tandfonline.com
June 14, 2025 at 12:16 AM
My paper on consultant-vampires Nous sucking the lifeblood of universities goes into more detail about how these guys operate (co-written with @bestqualitycrab.bsky.social) www.tandfonline.com/doi/full/10....
Reposted
4/
In fact,
Over 32,755 published articles were based on misidentified cell lines.
These were cited by an estimated half a million other papers.
Source: journals.plos.org/plosone/art...
In fact,
Over 32,755 published articles were based on misidentified cell lines.
These were cited by an estimated half a million other papers.
Source: journals.plos.org/plosone/art...
The ghosts of HeLa: How cell line misidentification contaminates the scientific literature
While problems with cell line misidentification have been known for decades, an unknown number of published papers remains in circulation reporting on the wrong cells without warning or correction. Here we attempt to make a conservative estimate of this ‘contaminated’ literature. We found 32,755 articles reporting on research with misidentified cells, in turn cited by an estimated half a million other papers. The contamination of the literature is not decreasing over time and is anything but restricted to countries in the periphery of global science. The decades-old and often contentious attempts to stop misidentification of cell lines have proven to be insufficient. The contamination of the literature calls for a fair and reasonable notification system, warning users and readers to interpret these papers with appropriate care.
journals.plos.org
May 31, 2025 at 1:15 PM
4/
In fact,
Over 32,755 published articles were based on misidentified cell lines.
These were cited by an estimated half a million other papers.
Source: journals.plos.org/plosone/art...
In fact,
Over 32,755 published articles were based on misidentified cell lines.
These were cited by an estimated half a million other papers.
Source: journals.plos.org/plosone/art...
Reposted
We’re pleased to have the opportunity to support our Editor-in-Chief, @mattpadula.bsky.social, and Editorial Board Member, Dr. Matthew O'Rourke, with travel grants to attend #AUSoMicS 2025 conference. Congratulations to both on their successful presentations! 🎉
#proteomics #proteomes #proteoforms
#proteomics #proteomes #proteoforms
May 26, 2025 at 7:59 AM
We’re pleased to have the opportunity to support our Editor-in-Chief, @mattpadula.bsky.social, and Editorial Board Member, Dr. Matthew O'Rourke, with travel grants to attend #AUSoMicS 2025 conference. Congratulations to both on their successful presentations! 🎉
#proteomics #proteomes #proteoforms
#proteomics #proteomes #proteoforms
Reposted
#proteomics tip: if you want to find high occupancy S/T+phosphoryl acceptors, you can't go wrong looking for S/T residues wedged between short low complexity regions with different side chain charges. If there are a few prolines scattered around, it's a party!
PRPLKKRSSITEPEGPG
PRPLKKRSSITEPEGPG
May 19, 2025 at 3:31 PM
#proteomics tip: if you want to find high occupancy S/T+phosphoryl acceptors, you can't go wrong looking for S/T residues wedged between short low complexity regions with different side chain charges. If there are a few prolines scattered around, it's a party!
PRPLKKRSSITEPEGPG
PRPLKKRSSITEPEGPG
Reposted
New to proteomics?? We have like one rule! Make your data available!! proteomicsnews.blogspot.com/2025/04/subm...
Submitting your first proteomics paper? Do this or don't bother submitting it!
We are SO SO SO very excited that you are moving past the GENotype and are intertested in actually measuring PHENOtypic data (or close to it...
proteomicsnews.blogspot.com
April 30, 2025 at 1:21 PM
New to proteomics?? We have like one rule! Make your data available!! proteomicsnews.blogspot.com/2025/04/subm...
Reposted
Thanks @benneely.com for your words. Another nice coincidence this week, the Proteomics FAIR and OS was published pubs.acs.org/doi/10.1021/... 🔥
Open-Source and FAIR Research Software for Proteomics
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and in...
pubs.acs.org
April 25, 2025 at 3:42 PM
Thanks @benneely.com for your words. Another nice coincidence this week, the Proteomics FAIR and OS was published pubs.acs.org/doi/10.1021/... 🔥
Reposted
Since we seem to be living in "The Age of Atlases" (there were 3 new ones in my feed this morning), what is it that differentiates a data "atlas" from an "archive"? The way the data is collected, the way it is displayed, the mechanism for looking up features or something else entirely? #proteomics
April 11, 2025 at 2:17 PM
Since we seem to be living in "The Age of Atlases" (there were 3 new ones in my feed this morning), what is it that differentiates a data "atlas" from an "archive"? The way the data is collected, the way it is displayed, the mechanism for looking up features or something else entirely? #proteomics
Reposted
I bet you guys have already discussed this one but it was new to me this morning and very very strange. proteomicsnews.blogspot.com/2025/04/prep...
Preprint compares 7 plasma proteomics methods - and doesn't get a single good correlation!
Title is overstated, I guess, there are some "strong correlations" but not the ones I really care about. SomaScan 11k vs 7k get a strong. Sa...
proteomicsnews.blogspot.com
April 10, 2025 at 12:34 PM
I bet you guys have already discussed this one but it was new to me this morning and very very strange. proteomicsnews.blogspot.com/2025/04/prep...
Reposted
RNA binding domains seem to come in 2 flavours: those smeared with conditionally occupied acetyl/ubiquityl acceptors & those that are not. Has there been any work done on the functional significance of this duality? #proteomics
April 9, 2025 at 2:53 PM
RNA binding domains seem to come in 2 flavours: those smeared with conditionally occupied acetyl/ubiquityl acceptors & those that are not. Has there been any work done on the functional significance of this duality? #proteomics
Reposted
'Omics has suffered from the imbalance between the great amount of effort that has been put into generating more data and the lack of any significant effort into the more difficult problem of how to use the resulting information effectively.
April 7, 2025 at 4:15 PM
'Omics has suffered from the imbalance between the great amount of effort that has been put into generating more data and the lack of any significant effort into the more difficult problem of how to use the resulting information effectively.
Reposted
After a VERY long time, it got published: rdcu.be/d8KyK.
My deep thanks to Sonja, Matthias and the other authors for analysing my own cancer. Now to convince my clinicians to use it for treating me. The battle is far from over.
My deep thanks to Sonja, Matthias and the other authors for analysing my own cancer. Now to convince my clinicians to use it for treating me. The battle is far from over.
Deep visual proteomics reveals DNA replication stress as a hallmark of signet ring cell carcinoma
npj Precision Oncology - Deep visual proteomics reveals DNA replication stress as a hallmark of signet ring cell carcinoma
rdcu.be
February 5, 2025 at 8:25 PM
After a VERY long time, it got published: rdcu.be/d8KyK.
My deep thanks to Sonja, Matthias and the other authors for analysing my own cancer. Now to convince my clinicians to use it for treating me. The battle is far from over.
My deep thanks to Sonja, Matthias and the other authors for analysing my own cancer. Now to convince my clinicians to use it for treating me. The battle is far from over.
Reposted
Are you an ECR and want to make a positive contribution to the field? Then apply to join Proteomes ECR Editorial Board! You will get to work with me and Jens to ensure our published articles are rigorously and properly reviewed. Details at the link (ignore deadline).
www.mdpi.com/about/announ...
www.mdpi.com/about/announ...
Recruiting Early Career Editorial Board Members for Proteomes
In order to further enhance the international outreach and influence of our journal Proteomes (ISSN: 2227-7382), promote a global academic...
www.mdpi.com
January 16, 2025 at 7:09 AM
Are you an ECR and want to make a positive contribution to the field? Then apply to join Proteomes ECR Editorial Board! You will get to work with me and Jens to ensure our published articles are rigorously and properly reviewed. Details at the link (ignore deadline).
www.mdpi.com/about/announ...
www.mdpi.com/about/announ...
Reposted
I find it both disturbing and annoying that the word "proteoform" does not appear in this article.
DOI: 10.1021/acs.jproteome.4c00776
DOI: 10.1021/acs.jproteome.4c00776
December 15, 2024 at 10:30 PM
I find it both disturbing and annoying that the word "proteoform" does not appear in this article.
DOI: 10.1021/acs.jproteome.4c00776
DOI: 10.1021/acs.jproteome.4c00776