Pablo Riesgo-Ferreiro
@priesgo.bsky.social
Bioinformatics Scientist @ BioNTech
#bioinformatics #AI #immunology #cancer #vaccines
Opinions my own
#bioinformatics #AI #immunology #cancer #vaccines
Opinions my own
Reposted by Pablo Riesgo-Ferreiro
Protein language models excel at generating functional yet remarkably diverse artificial sequences.
They however fail to naturally sample rare datapoints, like very high activities.
In our new preprint, we show that RL can solve this without the need for additional data:
arxiv.org/abs/2412.12979
They however fail to naturally sample rare datapoints, like very high activities.
In our new preprint, we show that RL can solve this without the need for additional data:
arxiv.org/abs/2412.12979
December 18, 2024 at 9:06 PM
Protein language models excel at generating functional yet remarkably diverse artificial sequences.
They however fail to naturally sample rare datapoints, like very high activities.
In our new preprint, we show that RL can solve this without the need for additional data:
arxiv.org/abs/2412.12979
They however fail to naturally sample rare datapoints, like very high activities.
In our new preprint, we show that RL can solve this without the need for additional data:
arxiv.org/abs/2412.12979
Reposted by Pablo Riesgo-Ferreiro
Thrilled to see this paper out!! 🧪
Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors!
Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social!
rdcu.be/d33uQ 🧵
Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors!
Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social!
rdcu.be/d33uQ 🧵
Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Nature - A spatially resolved single-cell transcriptomics map of the mouse brain at different ages reveals signatures of ageing, rejuvenation and disease, including ageing effects associated with T...
rdcu.be
December 18, 2024 at 10:40 PM
Thrilled to see this paper out!! 🧪
Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors!
Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social!
rdcu.be/d33uQ 🧵
Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors!
Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social!
rdcu.be/d33uQ 🧵
Reposted by Pablo Riesgo-Ferreiro
Cell is happy to connect (and re-connect) with scientists across all areas of biology on Bluesky! We aim to start posting in 2025. Until then, we'll be keeping an eye out for your exciting and interesting findings... 🔬👀
December 18, 2024 at 5:48 PM
Cell is happy to connect (and re-connect) with scientists across all areas of biology on Bluesky! We aim to start posting in 2025. Until then, we'll be keeping an eye out for your exciting and interesting findings... 🔬👀
Reposted by Pablo Riesgo-Ferreiro
One of the biggest questions we get is when will our journals be here. We thank you for your patience.
You can now follow our journals with this starter pack!
You can now follow our journals with this starter pack!
December 18, 2024 at 2:57 PM
One of the biggest questions we get is when will our journals be here. We thank you for your patience.
You can now follow our journals with this starter pack!
You can now follow our journals with this starter pack!
Reposted by Pablo Riesgo-Ferreiro
It took four days from submission to publication, and nearly five years from publication to retraction. After campaigning by many, many scientists, and an investigation by Elsevier, an infamous paper on hydroxychloroquine as a COVID-19 treatment has been retracted. 🧪
www.science.org/content/arti...
www.science.org/content/arti...
Infamous paper that popularized unproven COVID-19 treatment finally retracted
Study on hydroxychloroquine by Didier Raoult and colleagues gets pulled on ethical and scientific grounds
www.science.org
December 17, 2024 at 5:31 PM
It took four days from submission to publication, and nearly five years from publication to retraction. After campaigning by many, many scientists, and an investigation by Elsevier, an infamous paper on hydroxychloroquine as a COVID-19 treatment has been retracted. 🧪
www.science.org/content/arti...
www.science.org/content/arti...
Reposted by Pablo Riesgo-Ferreiro
Hi Bluesky community! 👋
Are you looking forward to 2025 as much as we are? 👀
We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look!
➡️ s.embl.org/poster-bl
#EMBLEvents #molecularbiology #lifesciencetraining
Are you looking forward to 2025 as much as we are? 👀
We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look!
➡️ s.embl.org/poster-bl
#EMBLEvents #molecularbiology #lifesciencetraining
December 13, 2024 at 9:06 AM
Hi Bluesky community! 👋
Are you looking forward to 2025 as much as we are? 👀
We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look!
➡️ s.embl.org/poster-bl
#EMBLEvents #molecularbiology #lifesciencetraining
Are you looking forward to 2025 as much as we are? 👀
We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look!
➡️ s.embl.org/poster-bl
#EMBLEvents #molecularbiology #lifesciencetraining
Reposted by Pablo Riesgo-Ferreiro
As I mentioned three weeks ago, Jevin West and I are developing a sort of followup course to Calling Bullshit.
We've got the basic scrollytelling tech worked out and now need to choose a design.
We're not designers and would like to simply buy an HTML5 template if only for the colors and fonts.
We've got the basic scrollytelling tech worked out and now need to choose a design.
We're not designers and would like to simply buy an HTML5 template if only for the colors and fonts.
Calling Bullshit: Data Reasoning in a Digital World
The world is awash in bullshit. Politicians are unconstrained by facts. Science is conducted by press release. Higher education rewards bullshit over analytic thought. Startup culture elevates bullshi...
callingbullshit.org
December 14, 2024 at 8:06 AM
As I mentioned three weeks ago, Jevin West and I are developing a sort of followup course to Calling Bullshit.
We've got the basic scrollytelling tech worked out and now need to choose a design.
We're not designers and would like to simply buy an HTML5 template if only for the colors and fonts.
We've got the basic scrollytelling tech worked out and now need to choose a design.
We're not designers and would like to simply buy an HTML5 template if only for the colors and fonts.
Reposted by Pablo Riesgo-Ferreiro
What if Eroom's law, the decreasing productivity of drug discovery, is a result of aggressive accounting whereby pharma companies consider as much stuff as possible as R&D to avoid taxes? I bet eroom's law holds in movies too - where losses are built to equal move revenue
December 9, 2024 at 11:34 PM
What if Eroom's law, the decreasing productivity of drug discovery, is a result of aggressive accounting whereby pharma companies consider as much stuff as possible as R&D to avoid taxes? I bet eroom's law holds in movies too - where losses are built to equal move revenue
Reposted by Pablo Riesgo-Ferreiro
In our work (EmbedGEM: doi.org/10.1093/bioa...) we developed the first formal evaluation framework for multivariate phenotypes that reports metrics for both heritability as well as disease relevance. The way we evaluate heritability is using several simple proxies: number of associations, (6/)
EmbedGEM: a framework to evaluate the utility of embeddings for genetic discovery
AbstractSummary. Machine learning-derived embeddings are a compressed representation of high content data modalities. Embeddings can capture detailed infor
academic.oup.com
December 5, 2024 at 6:27 AM
In our work (EmbedGEM: doi.org/10.1093/bioa...) we developed the first formal evaluation framework for multivariate phenotypes that reports metrics for both heritability as well as disease relevance. The way we evaluate heritability is using several simple proxies: number of associations, (6/)
This is possibly the last thing I was missing from R in python. Thanks for that!
Formulaic is the go-to way to specify design formulas in Python, e.g. ~treatment + timepoint.
To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline".
To make this easier, we developed "formulaic-contrasts":
formulaic-contrasts.readthedocs.io/en/latest/
To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline".
To make this easier, we developed "formulaic-contrasts":
formulaic-contrasts.readthedocs.io/en/latest/
December 8, 2024 at 4:49 AM
This is possibly the last thing I was missing from R in python. Thanks for that!
Reposted by Pablo Riesgo-Ferreiro
🎉Thrilled that #GenePT is published!
We show how to create #ChatGPT embeddings of genes and #singlecell --> improve gene function prediction + cell annotation/analyses🧬
📰 www.nature.com/articles/s41...
🌐 github.com/yiqunchen/Ge...
Great job Yiqun Chen! #LLM for bio.
We show how to create #ChatGPT embeddings of genes and #singlecell --> improve gene function prediction + cell annotation/analyses🧬
📰 www.nature.com/articles/s41...
🌐 github.com/yiqunchen/Ge...
Great job Yiqun Chen! #LLM for bio.
December 6, 2024 at 3:08 PM
🎉Thrilled that #GenePT is published!
We show how to create #ChatGPT embeddings of genes and #singlecell --> improve gene function prediction + cell annotation/analyses🧬
📰 www.nature.com/articles/s41...
🌐 github.com/yiqunchen/Ge...
Great job Yiqun Chen! #LLM for bio.
We show how to create #ChatGPT embeddings of genes and #singlecell --> improve gene function prediction + cell annotation/analyses🧬
📰 www.nature.com/articles/s41...
🌐 github.com/yiqunchen/Ge...
Great job Yiqun Chen! #LLM for bio.
Reposted by Pablo Riesgo-Ferreiro
Out in time for the #ASCB meeting an @science.org Review from Jody Rosenblatt and friends
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Imperfect wound healing sets the stage for chronic diseases
Although the age of the genome gave us much insight about how our organs fail with disease, it also suggested that diseases do not arise from mutations alone; rather, they develop as we age. In this R...
www.science.org
December 6, 2024 at 11:37 AM
Out in time for the #ASCB meeting an @science.org Review from Jody Rosenblatt and friends
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
www.frontiersin.org/journals/imm...
An approach to stratify AML patients in two immune groups based on expression profiles.
#paper #immunology
An approach to stratify AML patients in two immune groups based on expression profiles.
#paper #immunology
Frontiers | Immune-based subgroups uncover diverse tumor immunogenicity and implications for prognosis and precision therapy in acute myeloid leukemia
BackgroundAlthough a considerable proportion of acute myeloid leukemia (AML) patients achieve remission through chemotherapy, relapse remains a recurring and...
www.frontiersin.org
December 6, 2024 at 12:48 PM
www.frontiersin.org/journals/imm...
An approach to stratify AML patients in two immune groups based on expression profiles.
#paper #immunology
An approach to stratify AML patients in two immune groups based on expression profiles.
#paper #immunology
This is so arbitrary it's laughable in retrospective
CW: Scientific racism
You see, Haeckel has interpreted paleontology to be a constant road to higher development, a goal-driven “perfection” of the organisms over time. Lending itself to hierarchy, in which he had seen Mittellanderm (Germanics) as evolutionary superior to others.
You see, Haeckel has interpreted paleontology to be a constant road to higher development, a goal-driven “perfection” of the organisms over time. Lending itself to hierarchy, in which he had seen Mittellanderm (Germanics) as evolutionary superior to others.
December 4, 2024 at 10:07 PM
This is so arbitrary it's laughable in retrospective
Reposted by Pablo Riesgo-Ferreiro
Imagine your notebook surviving for centuries to be studied by historians. This happened to transcriptions by Nicholai Miklouho-Maclay, Russian of Ukrainian Cossack descent, of a palaeontology class delivered by Ernst Haeckel (1866) This unlikely record, captures the rise of race science in Germany🧵
December 4, 2024 at 7:46 PM
Imagine your notebook surviving for centuries to be studied by historians. This happened to transcriptions by Nicholai Miklouho-Maclay, Russian of Ukrainian Cossack descent, of a palaeontology class delivered by Ernst Haeckel (1866) This unlikely record, captures the rise of race science in Germany🧵
Reposted by Pablo Riesgo-Ferreiro
What are shapley interactions and why should you care about them?
This is a guest post by Julia, Max, Fabian and Hubert on my newsletter Mindful Modeler.
I also learned a lot from this post and definitely recommend checking out the shapiq package.
mindfulmodeler.substack.com/p/what-are-s...
This is a guest post by Julia, Max, Fabian and Hubert on my newsletter Mindful Modeler.
I also learned a lot from this post and definitely recommend checking out the shapiq package.
mindfulmodeler.substack.com/p/what-are-s...
What Are Shapley Interactions, and Why Should You Care?
A guest post by Julia, Max, Fabian and Hubert.
mindfulmodeler.substack.com
December 3, 2024 at 3:45 PM
What are shapley interactions and why should you care about them?
This is a guest post by Julia, Max, Fabian and Hubert on my newsletter Mindful Modeler.
I also learned a lot from this post and definitely recommend checking out the shapiq package.
mindfulmodeler.substack.com/p/what-are-s...
This is a guest post by Julia, Max, Fabian and Hubert on my newsletter Mindful Modeler.
I also learned a lot from this post and definitely recommend checking out the shapiq package.
mindfulmodeler.substack.com/p/what-are-s...
Reposted by Pablo Riesgo-Ferreiro
December 3, 2024 at 6:36 PM
Reposted by Pablo Riesgo-Ferreiro
A nice analysis of different tokenization strategies (BPE, wordpiece, sentencepiece) on protein sequences.
arxiv.org/abs/2411.17669
arxiv.org/abs/2411.17669
December 2, 2024 at 9:34 PM
A nice analysis of different tokenization strategies (BPE, wordpiece, sentencepiece) on protein sequences.
arxiv.org/abs/2411.17669
arxiv.org/abs/2411.17669
Reposted by Pablo Riesgo-Ferreiro
Design of high specificity binders for peptide-MHC-I complexes https://www.biorxiv.org/content/10.1101/2024.11.28.625793v1
Design of high specificity binders for peptide-MHC-I complexes https://www.biorxiv.org/content/10.1101/2024.11.28.625793v1
Class I MHC molecules present peptides derived from intracellular antigens on the cell surface for i
www.biorxiv.org
November 29, 2024 at 5:15 AM
Design of high specificity binders for peptide-MHC-I complexes https://www.biorxiv.org/content/10.1101/2024.11.28.625793v1
Reposted by Pablo Riesgo-Ferreiro
Our Herpesfolds paper is out in Nature Communications! rdcu.be/d1uM7 Congrats to Timothy Soh,
@sofiaaognibene
, Saskia Sanders, Robin Schaeper and Benedikt Kaufer!
Have a look at our database at herpesfolds.org by Malte Kansy
@sofiaaognibene
, Saskia Sanders, Robin Schaeper and Benedikt Kaufer!
Have a look at our database at herpesfolds.org by Malte Kansy
November 26, 2024 at 9:28 AM
Our Herpesfolds paper is out in Nature Communications! rdcu.be/d1uM7 Congrats to Timothy Soh,
@sofiaaognibene
, Saskia Sanders, Robin Schaeper and Benedikt Kaufer!
Have a look at our database at herpesfolds.org by Malte Kansy
@sofiaaognibene
, Saskia Sanders, Robin Schaeper and Benedikt Kaufer!
Have a look at our database at herpesfolds.org by Malte Kansy
Reposted by Pablo Riesgo-Ferreiro
Immune cells change in proportions with age - naive go down, effector go up. www.science.org/doi/10.1126/...
A panoramic view of cell population dynamics in mammalian aging
To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, se...
www.science.org
November 29, 2024 at 8:37 AM
Immune cells change in proportions with age - naive go down, effector go up. www.science.org/doi/10.1126/...
Reposted by Pablo Riesgo-Ferreiro
The danger theory of immunity strikes back... rdcu.be/d1uQN
November 26, 2024 at 6:13 PM
The danger theory of immunity strikes back... rdcu.be/d1uQN