Thomas Lemberger
@tlemberger.bsky.social
Life scientist. AI, q-bio, systems biology.
Head, Open Science, @embo.org
Project Lead, @reviewcommons.org
@embopress.org
Loves 🎶 and plays the 🎻
Views my own
Head, Open Science, @embo.org
Project Lead, @reviewcommons.org
@embopress.org
Loves 🎶 and plays the 🎻
Views my own
Reposted by Thomas Lemberger
Honored to be included in this reflection on 20 excellent years of MolSystBiol! From our first phosphotyrosine interactome in 2005 to proteome-wide networks - scale has grown exponentially. MS proteomics + AI is transforming systems-level understanding. Exciting times!
embopress.org/doi/pdf/10.1...
embopress.org/doi/pdf/10.1...
embopress.org
November 25, 2025 at 12:44 PM
Honored to be included in this reflection on 20 excellent years of MolSystBiol! From our first phosphotyrosine interactome in 2005 to proteome-wide networks - scale has grown exponentially. MS proteomics + AI is transforming systems-level understanding. Exciting times!
embopress.org/doi/pdf/10.1...
embopress.org/doi/pdf/10.1...
Reposted by Thomas Lemberger
IT'S HAPPENING! 💥 I'm psyched to launch the collaboration between @qedscience.bsky.social & @openrxiv.bsky.social @biorxivpreprint.bsky.social! Preprint + q.e.d = your science is out there, and anyone can appreciate it. Let's care about making discoveries, and not on “getting published” (1/3) 👇
November 6, 2025 at 2:49 PM
IT'S HAPPENING! 💥 I'm psyched to launch the collaboration between @qedscience.bsky.social & @openrxiv.bsky.social @biorxivpreprint.bsky.social! Preprint + q.e.d = your science is out there, and anyone can appreciate it. Let's care about making discoveries, and not on “getting published” (1/3) 👇
Very cool! I agree AI scientific review can be useful if it is transparent. It is all progressing very fast and will change everything. @qedScience @bioRxiv is a great first step. We are doing some human-based eval, so more soon from @EMBOPress @ReviewCommons with @qedScience. Watch this space ;-)
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Enabling options for review: from training and transparency to author-centered AI tools - openRxiv
Peer review is widely viewed as a critical aspect of biomedical communication. Ideally, it provides authors with feedback so they can improve manuscripts and gives readers, particularly nonspecialists...
openrxiv.org
November 6, 2025 at 3:21 PM
Very cool! I agree AI scientific review can be useful if it is transparent. It is all progressing very fast and will change everything. @qedScience @bioRxiv is a great first step. We are doing some human-based eval, so more soon from @EMBOPress @ReviewCommons with @qedScience. Watch this space ;-)
Reposted by Thomas Lemberger
Last week on 11–12 Sep, together with our publishing partner @springernature.com, EMBO hosted a workshop "AI to advance open science publishing” in Heidelberg, DE. 🧪 Participants engaged in demonstrations and experiments using tools developed by Springer Nature and EMBO for innovation in publishing.
September 15, 2025 at 4:53 PM
Last week on 11–12 Sep, together with our publishing partner @springernature.com, EMBO hosted a workshop "AI to advance open science publishing” in Heidelberg, DE. 🧪 Participants engaged in demonstrations and experiments using tools developed by Springer Nature and EMBO for innovation in publishing.
Reposted by Thomas Lemberger
Two metrics designed for measuring the impact of investments in the specific context of life sciences (in brief: the metrics assess the potential increase in life years attributable to the investment & the improvement in quality of life) ➡️ www.nature.com/articles/s41...
A new impact framework for investors in life sciences bridges financial returns and patient outcomes - Nature Biotechnology
A new model for quantifying the impact of capital investments in life science interventions could help investors, policymakers and healthcare stakeholders to assess, monitor and optimize the societal ...
www.nature.com
July 16, 2025 at 7:21 AM
Two metrics designed for measuring the impact of investments in the specific context of life sciences (in brief: the metrics assess the potential increase in life years attributable to the investment & the improvement in quality of life) ➡️ www.nature.com/articles/s41...
Reposted by Thomas Lemberger
🤖✍️ How is #AI transforming scientific publishing? From trust to truth, @tlemberger.bsky.social @embopress.org explains what’s changing and why it matters for all of us.
youtu.be/k-_MuFEwFx0 @salmaamin.bsky.social @mkiwanski.bsky.social
youtu.be/k-_MuFEwFx0 @salmaamin.bsky.social @mkiwanski.bsky.social
Trust, Truth and AI in Scientific Publishing with Thomas Lemberger
YouTube video by Human Technopole
youtu.be
July 2, 2025 at 2:27 PM
🤖✍️ How is #AI transforming scientific publishing? From trust to truth, @tlemberger.bsky.social @embopress.org explains what’s changing and why it matters for all of us.
youtu.be/k-_MuFEwFx0 @salmaamin.bsky.social @mkiwanski.bsky.social
youtu.be/k-_MuFEwFx0 @salmaamin.bsky.social @mkiwanski.bsky.social
A message of hope and optimism in these crazy times: Gewandhaus Orchestra open air concert, in Leipzig, Germany, right now: 20,000 people peacefully listening to the music of Max Bruch. Beautiful event.
June 28, 2025 at 7:26 PM
A message of hope and optimism in these crazy times: Gewandhaus Orchestra open air concert, in Leipzig, Germany, right now: 20,000 people peacefully listening to the music of Max Bruch. Beautiful event.
An important, moving, and courageous piece from @juliosaezrod.bsky.social Respect!
"Becoming a patient has given me a new perspective on biomedical research. Despite my background in data analytics, I have found that I do not necessarily have access to the data or information I need..."
"Becoming a patient has given me a new perspective on biomedical research. Despite my background in data analytics, I have found that I do not necessarily have access to the data or information I need..."
I wrote a short piece on how becoming an IgA Nephropathy patient has changed my perspective on biomedical research, developing an appreciation for the challenges in data interpretability & availability and the importance of patient engagement www.nature.com/articles/s41...
Leveraging data as a patient–scientist: frustrations and opportunities - Nature Reviews Nephrology
The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability h...
www.nature.com
June 23, 2025 at 2:58 PM
An important, moving, and courageous piece from @juliosaezrod.bsky.social Respect!
"Becoming a patient has given me a new perspective on biomedical research. Despite my background in data analytics, I have found that I do not necessarily have access to the data or information I need..."
"Becoming a patient has given me a new perspective on biomedical research. Despite my background in data analytics, I have found that I do not necessarily have access to the data or information I need..."
Reposted by Thomas Lemberger
#TCTeAC - the Woodstock of Biology2 & #nightscience - was such an amazing event!! We met great scientists who creatively presented their high quality work. We dreamt and discussed in a very broad, open-minded setting. Talking science outside of our nutshell can be soo valuable - let's do this again!
June 14, 2025 at 7:44 AM
#TCTeAC - the Woodstock of Biology2 & #nightscience - was such an amazing event!! We met great scientists who creatively presented their high quality work. We dreamt and discussed in a very broad, open-minded setting. Talking science outside of our nutshell can be soo valuable - let's do this again!
Reposted by Thomas Lemberger
Let's not be #TCTeAC "The Conference To END All Conferences", but a new format of many more such events. Depating science outside of our typical nutshell (scientifically and mentally) has great potential - we could have come up with 50+ project proposals together. Let's bring fun back to science :)
June 14, 2025 at 7:48 AM
Let's not be #TCTeAC "The Conference To END All Conferences", but a new format of many more such events. Depating science outside of our typical nutshell (scientifically and mentally) has great potential - we could have come up with 50+ project proposals together. Let's bring fun back to science :)
Reposted by Thomas Lemberger
@paveltomancak.bsky.social and @itaiyanai.bsky.social fighting /debating about the hourglass idea
#theconferencetoendallconferences #TCTeAC
#theconferencetoendallconferences #TCTeAC
June 12, 2025 at 10:58 AM
@paveltomancak.bsky.social and @itaiyanai.bsky.social fighting /debating about the hourglass idea
#theconferencetoendallconferences #TCTeAC
#theconferencetoendallconferences #TCTeAC
Reposted by Thomas Lemberger
#fightforsciemce at #TCTeAC with #nightscience :) cell & gene people gather together.
(no scientist got hurt)
(no scientist got hurt)
June 12, 2025 at 11:00 AM
#fightforsciemce at #TCTeAC with #nightscience :) cell & gene people gather together.
(no scientist got hurt)
(no scientist got hurt)
Reposted by Thomas Lemberger
Our publishing process needs to be revolutionised @odedrechavi.bsky.social #TCTeAC high-quality AI generated peer review
June 11, 2025 at 1:40 PM
Our publishing process needs to be revolutionised @odedrechavi.bsky.social #TCTeAC high-quality AI generated peer review
Reposted by Thomas Lemberger
June 11, 2025 at 8:09 AM
Reposted by Thomas Lemberger
I'm late to review the "Illusion of Thinking" paper, so let me collect some of the best threads by and critical takes by @scaling01 in one place and sprinkle some of my own thoughts in as well.
The paper is rather critical of reasoning LLMs (LRMs):
x.com/MFarajtabar...
The paper is rather critical of reasoning LLMs (LRMs):
x.com/MFarajtabar...
June 9, 2025 at 9:49 PM
I'm late to review the "Illusion of Thinking" paper, so let me collect some of the best threads by and critical takes by @scaling01 in one place and sprinkle some of my own thoughts in as well.
The paper is rather critical of reasoning LLMs (LRMs):
x.com/MFarajtabar...
The paper is rather critical of reasoning LLMs (LRMs):
x.com/MFarajtabar...
Reposted by Thomas Lemberger
We quantify the aggregation of >100,000 random protein sequences to train CANYA, a convolution-attention hybrid neural network to predict aggregation from sequence. With @bennibolo.bsky.social www.science.org/doi/10.1126/...
Massive experimental quantification allows interpretable deep learning of protein aggregation
xAI trained on >100,000 random peptides predicts and elucidates primary sequence determinants of aggregation.
www.science.org
May 4, 2025 at 10:40 AM
We quantify the aggregation of >100,000 random protein sequences to train CANYA, a convolution-attention hybrid neural network to predict aggregation from sequence. With @bennibolo.bsky.social www.science.org/doi/10.1126/...
Reposted by Thomas Lemberger
A kind of cat https://www.wikiart.org/en/paul-klee/a-kind-of-cat-1937
May 5, 2025 at 8:02 AM
A kind of cat https://www.wikiart.org/en/paul-klee/a-kind-of-cat-1937
Reposted by Thomas Lemberger
Many of the moons orbiting Jupiter and Saturn appear to host subsurface oceans. Mysteries abound as to what fills these deep sea worlds. But the hints that we’ve already gathered make them tantalizing targets in the search for life beyond Earth.
🧵
🧵
April 16, 2025 at 3:54 PM
Many of the moons orbiting Jupiter and Saturn appear to host subsurface oceans. Mysteries abound as to what fills these deep sea worlds. But the hints that we’ve already gathered make them tantalizing targets in the search for life beyond Earth.
🧵
🧵
Very sad news!
Sad news. Benny Shilo, a pioneer in dev bio & Drosophila genetics, has died.
I'll remember the infectious enthusiasm and burning curiosity he brought to every conversation I had with him.
I'll remember the infectious enthusiasm and burning curiosity he brought to every conversation I had with him.
Our field has lost an amazing scientist, mentor, and old friend. Benny, along with Mike Hoffman, had a brilliant idea in the early 1980s. The first oncogenes were being cloned and they realized if we wanted to understand their roles in cancer, we needed to understand their normal function 1/n 🧪
April 17, 2025 at 12:49 PM
Very sad news!
Reposted by Thomas Lemberger
On the anniversary of the sinking of the Titanic, we thought we'd answer a question that's often asked,
"If they raised the Mary Rose, why not raise the Titanic?"
Allow our scaled diagram to explain...
"If they raised the Mary Rose, why not raise the Titanic?"
Allow our scaled diagram to explain...
April 15, 2025 at 8:21 AM
On the anniversary of the sinking of the Titanic, we thought we'd answer a question that's often asked,
"If they raised the Mary Rose, why not raise the Titanic?"
Allow our scaled diagram to explain...
"If they raised the Mary Rose, why not raise the Titanic?"
Allow our scaled diagram to explain...
Reposted by Thomas Lemberger
Woohoo it’s arrived!!! If it’s even 25% as good as Civilizations it’ll be amazing…
April 13, 2025 at 1:00 AM
Woohoo it’s arrived!!! If it’s even 25% as good as Civilizations it’ll be amazing…
Reposted by Thomas Lemberger
We then used a physics-based model to predict DNA linkers between the nucleosomes obtained by cryo-ET. This allowed us to visualize kbp-long chromatin fragments from inside human cells.
April 11, 2025 at 9:04 AM
We then used a physics-based model to predict DNA linkers between the nucleosomes obtained by cryo-ET. This allowed us to visualize kbp-long chromatin fragments from inside human cells.
Reposted by Thomas Lemberger
New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇
April 11, 2025 at 9:04 AM
New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇
Reposted by Thomas Lemberger
The Courtyard of the Hospital in Arles, 1889 #artbots #vangogh
https://botfrens.com/collections/46/contents/14663
https://botfrens.com/collections/46/contents/14663
March 28, 2025 at 3:00 PM
The Courtyard of the Hospital in Arles, 1889 #artbots #vangogh
https://botfrens.com/collections/46/contents/14663
https://botfrens.com/collections/46/contents/14663