Santiago Carmona 🧬 🖥️ 🧑🏾🔬
@carmonation.bsky.social
Computational biologist, associate professor at University of Geneva, Department of Pathology and Immunology. Single-cell omics, bio data science, immunology & cancer research
Pinned
📢 We have an open position at University of Geneva for a PhD student with CS/Math/Physics background to study adaptive immune responses using deep learning. If interested please contact me directly!
Cool paper on scRNA T cell annotation. However, a note for ProjecTILs users: I wouldn’t rely on the ProjecTILs benchmark in this work, as it was run using a mouse reference map to classify human T cells (even though human CD4/CD8 T cell maps are available github.com/carmonalab/P...)
October 31, 2025 at 1:01 PM
Cool paper on scRNA T cell annotation. However, a note for ProjecTILs users: I wouldn’t rely on the ProjecTILs benchmark in this work, as it was run using a mouse reference map to classify human T cells (even though human CD4/CD8 T cell maps are available github.com/carmonalab/P...)
Your favourite single-cell gene signature scoring method now in Python #scverse and much faster!
pypi.org/project/pyuc...
pypi.org/project/pyuc...
Client Challenge
pypi.org
October 27, 2025 at 1:56 PM
Your favourite single-cell gene signature scoring method now in Python #scverse and much faster!
pypi.org/project/pyuc...
pypi.org/project/pyuc...
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
Introducing ParTIpy, a python package for Pareto Task Inference that scales to large-scale datasets, including single-cell and spatial transcriptomics.
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
September 15, 2025 at 8:40 AM
Introducing ParTIpy, a python package for Pareto Task Inference that scales to large-scale datasets, including single-cell and spatial transcriptomics.
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
Evaluating the practical aspects and performance of
commercial single-cell RNA sequencing technologies
www.biorxiv.org/content/10.1...
commercial single-cell RNA sequencing technologies
www.biorxiv.org/content/10.1...
Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies
The rapid development of updated and new commercially available single-cell transcriptomics platforms provides users with a range of experimental options. Cost, sensitivity, throughput, flexibility, a...
www.biorxiv.org
October 1, 2025 at 7:58 AM
Evaluating the practical aspects and performance of
commercial single-cell RNA sequencing technologies
www.biorxiv.org/content/10.1...
commercial single-cell RNA sequencing technologies
www.biorxiv.org/content/10.1...
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
A new review on the challenges of identifying cancer cells in single-cell data, summarizing current computational solutions as well as underexplored features of malignancy. From scientists @sib.swiss
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Identification of malignant cells in single-cell transcriptomics data - Communications Biology
This review article discusses the challenges of identifying cancer cells in single-cell data, summarizing current computational solutions as well as underexplored features of malignancy.
www.nature.com
August 25, 2025 at 7:47 PM
A new review on the challenges of identifying cancer cells in single-cell data, summarizing current computational solutions as well as underexplored features of malignancy. From scientists @sib.swiss
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Identifying malignant cells in single-cell transcriptomics data – from first principles to computational solutions, framed around the hallmarks of cancer
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Identification of malignant cells in single-cell transcriptomics data - Communications Biology
This review article discusses the challenges of identifying cancer cells in single-cell data, summarizing current computational solutions as well as underexplored features of malignancy.
www.nature.com
August 22, 2025 at 4:05 PM
Identifying malignant cells in single-cell transcriptomics data – from first principles to computational solutions, framed around the hallmarks of cancer
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
Interested in T cell immunity in TB? Check out our new pre-print on antigen-agnostic identification of generalisable human in vivo Mtb-reactive T cell responses: www.biorxiv.org/content/10.1...
with @qimmuno.bsky.social & @innate2adaptive.bsky.social
with @qimmuno.bsky.social & @innate2adaptive.bsky.social
Evolution of T cell responses in the tuberculin skin test reveals generalisable Mtb-reactive T cell metaclones.
T cells contribute to immune protection and pathogenesis in tuberculosis, but measurements of polyclonal responses have failed to resolve correlates of outcome. We report the first temporal…
www.biorxiv.org
April 21, 2025 at 5:28 PM
Interested in T cell immunity in TB? Check out our new pre-print on antigen-agnostic identification of generalisable human in vivo Mtb-reactive T cell responses: www.biorxiv.org/content/10.1...
with @qimmuno.bsky.social & @innate2adaptive.bsky.social
with @qimmuno.bsky.social & @innate2adaptive.bsky.social
Foundation Model Attributions Reveal Shared Inflammatory Program Across Diseases www.biorxiv.org/content/10.1...
Foundation Model Attributions Reveal Shared Inflammatory Program Across Diseases
Determining a gene’s functional significance within a specific cellular context has long been a challenge. We introduce a framework for quantifying gene importance by leveraging attributions learned b...
www.biorxiv.org
August 13, 2025 at 7:46 AM
Foundation Model Attributions Reveal Shared Inflammatory Program Across Diseases www.biorxiv.org/content/10.1...
📢 We have an open position at University of Geneva for a PhD student with CS/Math/Physics background to study adaptive immune responses using deep learning. If interested please contact me directly!
August 5, 2025 at 10:06 AM
📢 We have an open position at University of Geneva for a PhD student with CS/Math/Physics background to study adaptive immune responses using deep learning. If interested please contact me directly!
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
Check out how we tackled one of the fundamental challenges in immunology, out today @cp-cellsystems.bsky.social: www.cell.com/cell-systems.... Our major innovations are BATCAVE and BATMAN, two new players to get us closer to solving TCR-pMHC predictions!
T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database
Banerjee et al. present a comprehensive T cell receptor cross-reactivity database
and a hierarchical Bayesian framework to predict T cell receptor targets. Together,
they reveal structural and biochem...
www.cell.com
July 25, 2025 at 3:00 PM
Check out how we tackled one of the fundamental challenges in immunology, out today @cp-cellsystems.bsky.social: www.cell.com/cell-systems.... Our major innovations are BATCAVE and BATMAN, two new players to get us closer to solving TCR-pMHC predictions!
AI-driven predictive biomarker discovery with contrastive learning to improve clinical trial outcomes: Cancer Cell www.cell.com/cancer-cell/...
AI-driven predictive biomarker discovery with contrastive learning to improve clinical trial outcomes
Arango-Argoty et al. introduce the Predictive Biomarker Modeling Framework (PBMF),
an AI-driven contrastive learning framework to identify putative predictive, rather
than prognostic, biomarkers for c...
www.cell.com
April 22, 2025 at 5:55 AM
AI-driven predictive biomarker discovery with contrastive learning to improve clinical trial outcomes: Cancer Cell www.cell.com/cancer-cell/...
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
Excited to share our new study revealing the intricate dynamics of pregnancy & postpartum physiology! We analyzed 40M lab tests from 300K pregnancies and 160K women (cross-sectional) and mapped week-by-week changes starting from preconception to months-long postpartum recovery.
March 27, 2025 at 12:44 PM
Excited to share our new study revealing the intricate dynamics of pregnancy & postpartum physiology! We analyzed 40M lab tests from 300K pregnancies and 160K women (cross-sectional) and mapped week-by-week changes starting from preconception to months-long postpartum recovery.
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
Exited to share our recent work on TF isoforms! Amazing work by @kaiamattioli.bsky.social Luke Lambourne and Clarissa Santoso and many other collaborators.
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
March 26, 2025 at 5:37 PM
Exited to share our recent work on TF isoforms! Amazing work by @kaiamattioli.bsky.social Luke Lambourne and Clarissa Santoso and many other collaborators.
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 31, 2024 at 8:11 PM
scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
The recent "Mal-ID" paper in Science diagnoses diseases from immune repertoires. But a powerful model like Mal-ID can learn differences between groups of immune repertoires that are unrelated to the diseases of interest. We explore these pitfalls in our eLetter response.
Disease diagnostics using machine learning of B cell and T cell receptor sequences
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...
www.science.org
March 19, 2025 at 10:35 PM
The recent "Mal-ID" paper in Science diagnoses diseases from immune repertoires. But a powerful model like Mal-ID can learn differences between groups of immune repertoires that are unrelated to the diseases of interest. We explore these pitfalls in our eLetter response.
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
🔥 Unveiling the Future of Genomics with Genome Language Models (gLMs)! 🔥
Our comprehensive review, "Transformers and genome language models," is finally published in Nature Machine Intelligence!
Link: nature.com/articles/s42...
Our comprehensive review, "Transformers and genome language models," is finally published in Nature Machine Intelligence!
Link: nature.com/articles/s42...
Transformers and genome language models - Nature Machine Intelligence
Micaela Consens et al. discuss and review the recent rise of transformer-based and large language models in genomics. They also highlight promising directions for genome language models beyond the tra...
nature.com
March 17, 2025 at 2:58 PM
🔥 Unveiling the Future of Genomics with Genome Language Models (gLMs)! 🔥
Our comprehensive review, "Transformers and genome language models," is finally published in Nature Machine Intelligence!
Link: nature.com/articles/s42...
Our comprehensive review, "Transformers and genome language models," is finally published in Nature Machine Intelligence!
Link: nature.com/articles/s42...
Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data | bioRxiv
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data
Cells regulate their functions through gene expression, driven by a complex interplay of transcription factors and other regulatory mechanisms that together can be modeled as gene regulatory networks ...
www.biorxiv.org
March 18, 2025 at 8:51 AM
Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data | bioRxiv
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
1) I am delighted to share a manuscript long in the making (7 years), elucidating the forces that shape metastatic adaptation PDAC using scRNA-seq across multiple organs from a rapid autopsy combined with a powerful new clonal phylogeny inference algorithm www.biorxiv.org/content/10.1...
Transcriptomic plasticity is a hallmark of metastatic pancreatic cancer
Metastasis is the leading cause of cancer deaths; nonetheless, how tumor cells adapt to vastly different organ contexts is largely unknown. To investigate this question, we generated a transcriptomic ...
www.biorxiv.org
March 7, 2025 at 11:26 AM
1) I am delighted to share a manuscript long in the making (7 years), elucidating the forces that shape metastatic adaptation PDAC using scRNA-seq across multiple organs from a rapid autopsy combined with a powerful new clonal phylogeny inference algorithm www.biorxiv.org/content/10.1...
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
Thrilled to share new work led by @jieyang437.bsky.social in the lab published today in @Nature. We find that Aspirin prevents metastasis by releasing T cells from immune suppression by platelet TXA2. @Cambridge_Uni @CRUKCamCentre rdcu.be/eci1U
March 5, 2025 at 6:56 PM
Thrilled to share new work led by @jieyang437.bsky.social in the lab published today in @Nature. We find that Aspirin prevents metastasis by releasing T cells from immune suppression by platelet TXA2. @Cambridge_Uni @CRUKCamCentre rdcu.be/eci1U
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
The Biozentrum in Basel, Switzerland @biozentrum.unibas.ch welcomes students from all over the world. You can apply directly to individual labs or through our fellowship program. It is very similar to US programs. Rotations followed by choice of lab. www.biozentrum.unibas.ch/phd/internat...
PhD Program - Biozentrum
PhD students can expect an extraordinary wealth of research expertise, a wide range of courses, intensive individual mentoring, an international community of researchers from over 40 countries and a l...
www.biozentrum.unibas.ch
March 1, 2025 at 12:46 PM
The Biozentrum in Basel, Switzerland @biozentrum.unibas.ch welcomes students from all over the world. You can apply directly to individual labs or through our fellowship program. It is very similar to US programs. Rotations followed by choice of lab. www.biozentrum.unibas.ch/phd/internat...
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
I'm really excited to join the University of Geneva as associate professor. I look forward to expanding our research program in systems immunology within the Department of Pathology and Immunology and contributing to advance the Faculty's data science capabilities!
JOB OPPORTUNITY👇
JOB OPPORTUNITY👇
February 28, 2025 at 3:40 PM
I'm really excited to join the University of Geneva as associate professor. I look forward to expanding our research program in systems immunology within the Department of Pathology and Immunology and contributing to advance the Faculty's data science capabilities!
JOB OPPORTUNITY👇
JOB OPPORTUNITY👇
Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾🔬
In a new Science study, researchers present ESM3, a protein language model that enables the programmed generation of protein structure and sequence in response to user prompts.
Learn more: scim.ag/40l2z3J
Learn more: scim.ag/40l2z3J
Simulating 500 million years of evolution with a language model
More than 3 billion years of evolution have produced an image of biology encoded into the space of natural proteins. Here, we show that language models trained at scale on evolutionary data can genera...
scim.ag
February 26, 2025 at 8:08 PM
In a new Science study, researchers present ESM3, a protein language model that enables the programmed generation of protein structure and sequence in response to user prompts.
Learn more: scim.ag/40l2z3J
Learn more: scim.ag/40l2z3J