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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Saez-Rodriguez Group @saezlab.bsky.social · 23d

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

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · 7d

Evaluating the practical aspects and performance of
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

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · Aug 29

www.nature.com/articles/s41...

Mechanical confinement governs phenotypic plasticity in melanoma - Nature

Mechanical confinement of cancer cells at the tumour–microenvironment interface induces phenotype switching through chromatin remodelling by HMGB2, leading to a more invasive and drug-resistant state ...

www.nature.com

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Communications Biology @commsbio.nature.com · Aug 25

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...

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

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · Aug 22

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...

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

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Mahdad Noursadeghi @mnoursad.bsky.social · Apr 21

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

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

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · Aug 13

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

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · Aug 5

📢 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!

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Hannah Meyer @hannahvmeyer.bsky.social · Jul 25

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

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · Jul 17

Thank you for supporting our project!

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · May 7

Exciting, congrats!

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · Apr 22

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

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Uri Alon @urialonlab.bsky.social · Mar 27

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.

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Juan Fuxman Bass @fuxmanlab.bsky.social · Mar 26

Exited to share our recent work on TF isoforms! Amazing work by @kaiamattioli.bsky.social Luke Lambourne and Clarissa Santoso and many other collaborators.

Kaia Mattioli @kaiamattioli.bsky.social · Mar 26

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...

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Nick Borcherding @thehumanborch.bsky.social · Dec 31

scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling
www.biorxiv.org/content/10.1...

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Damon May @the-dee-em.bsky.social · Mar 19

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

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Bo Wang @bowang87.bsky.social · Mar 17

🔥 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...

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

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · Mar 18

Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data | bioRxiv
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

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · Mar 11

Great news, Congratulations!

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

danapeer.bsky.social @danapeer.bsky.social · Mar 7

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

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Jeff Mold @jeffmold.bsky.social · Mar 5

Cool www.nature.com/articles/s41...

Clonal dynamics and somatic evolution of haematopoiesis in mouse - Nature

Isolating and studying haematopoietic stem cells in young and aged mice demonstrates evolutionary processes related to blood production and provides a framework for interpreting future work using labo...

www.nature.com

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Roychoudhuri Lab @roychoudhurilab.bsky.social · Mar 5

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

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Alex Schier @schierlab.bsky.social · Mar 1

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

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Reposted by Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬

Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · Mar 1

Here is our centralized Calls for PhD students at University of Geneva.

lifesciencesphd.unige.ch

University of Geneva - PhD School of Life Sciences | Welcome to the PhD School in Life Sciences at the Faculties of Medicine and Science

The University of Geneva Faculties of Medicine and Science join their forces to offer an outstanding study and research environment in Life Sciences. Highly motivated students with a Master’s degree o...

lifesciencesphd.unige.ch

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Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · Mar 1

Gracias, Fer! Te esperamos