David Gfeller
@dgfeller.bsky.social
📤 313
đź“Ą 16
đź“ť 44
Fascinated by computational biology applied to cancer immune cell recognition
Happy the share our latest perspective on T-cell epitope recognition predictions for cancer immunotherapy:
rdcu.be/fdKu6
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Advances in predicting T cell epitope recognition for cancer immunotherapy
Nature Cancer - Gfeller et al. discuss the recent technological and computational advances in prediction of TCR–epitope recognition and the therapeutic applications in cancer immunotherapy.
https://rdcu.be/fdKu6
about 1 month ago
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Happy to share the work of Aisha Shah about training predictors of TCR-epitope recognition with unpaired TCRa + TCRb sequences:
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.03.16.711991v1
2 months ago
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Interested in understanding how epitope recognition specificity is encoded in your TCR sequences? Try our new interactive page for building TCR specificity profiles on the TCR Motif Atlas:
tcrmotifatlas.unil.ch/Building_mot...
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Building Motifs
https://tcrmotifatlas.unil.ch/Building_motifs
3 months ago
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Happy to share the beautiful manuscript of Leonard Herault:
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.02.19.706848v1
3 months ago
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Very proud of the work of Dana Moreno about statistical modelling of CDR3 sequences in TCR repertoires:
www.biorxiv.org/content/10.6...
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Statistical modelling of CDR3 sequences provides robust quality control for TCR repertoire datasets
T-Cell Receptors (TCRs) show extensive sequence diversity across T cells. This diversity arises from different choices of V and J genes and from insertions and deletions at the V(D)J junction within t...
https://www.biorxiv.org/content/10.64898/2025.12.11.693618v1
6 months ago
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Nice results:
rdcu.be/eTNVr
. Looks like the decision to develop specific ML models of TCR-epitope interactions for each epitope was a reasonable choice.
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Assessing data size requirements for training generalizable sequence-based TCR specificity models via pan-allelic MHC-I point-mutation ligandome evaluation
Scientific Reports - Assessing data size requirements for training generalizable sequence-based TCR specificity models via pan-allelic MHC-I point-mutation ligandome evaluation
https://rdcu.be/eTNVr
6 months ago
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For those who followed the IMMREP25 competition and are interested in understanding how specificity was encoded for each epitope, check our TCR Motif Atlas IMMREP25 page:
tcrmotifatlas.unil.ch/Browse_epito...
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Model Motif Atlas
https://tcrmotifatlas.unil.ch/Browse_epitopes_IMMREP25
6 months ago
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Very happy to share our latest manuscript about TCR-epitope recognition specificity:
www.biorxiv.org/content/10.1...
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https://www.biorxiv.org/content/10.1101/2025.11.17.688817v1
6 months ago
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reposted by
David Gfeller
Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬
7 months ago
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...
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add a skeleton here at some point
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Interested in unraveling specificity in epitope recognition by TCRs and KIRs in the context of graft-versus-host diseases. We have an open post-doc position in the group. Do not hesitate to share the word.
11 months ago
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Happy to share the great work of Giancarlo Croce: Phage display enables machine learning discovery of cancer antigen–specific TCRs | Science Advances
www.science.org/doi/10.1126/...
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Phage display enables machine learning discovery of cancer antigen–specific TCRs
Phage display and machine learning join forces to identify cancer-specific TCRs.
https://www.science.org/doi/10.1126/sciadv.ads5589
12 months ago
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Call for abstract open at BC2 2025:
bc2.ch/talks-poster...
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Call for talks and posters
The [BC]2 Basel Computational Biology Conference is Switzerland's main event in the domain of Computational Biology and one of the major events of its kind in Europe. The conference unites scientists ...
https://bc2.ch/talks-posters-call
over 1 year ago
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Matei Teleman's SuperSpot paper out in Bioinformatics:
academic.oup.com/bioinformati...
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SuperSpot: Coarse Graining Spatial Transcriptomics Data into Metaspots
AbstractSummary. Spatial Transcriptomics is revolutionizing our ability to phenotypically characterize complex biological tissues and decipher cellular nic
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae734/7919601?login=true
over 1 year ago
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