Martina Milighetti
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View article: Data-Driven Discovery of Biophysical T Cell Receptor Cospecificity Rules
Data-Driven Discovery of Biophysical T Cell Receptor Cospecificity Rules Open
The biophysical interactions between the T cell receptor (TCR) and its ligands determine the specificity of the cellular immune response. However, the immense diversity of receptors and ligands has made it challenging to discover generaliz…
View article: Data-Driven Discovery of Biophysical T Cell Receptor Cospecificity Rules
Data-Driven Discovery of Biophysical T Cell Receptor Cospecificity Rules Open
The biophysical interactions between the T cell receptor (TCR) and its ligands determine the specificity of the cellular immune response. However, the immense diversity of receptors and ligands has made it challenging to discover generaliz…
View article: RNA neoantigen vaccines prime long-lived CD8+ T cells in pancreatic cancer
RNA neoantigen vaccines prime long-lived CD8+ T cells in pancreatic cancer Open
View article: Treg fitness signatures as a biomarker for disease activity in Juvenile Idiopathic Arthritis
Treg fitness signatures as a biomarker for disease activity in Juvenile Idiopathic Arthritis Open
Juvenile Idiopathic Arthritis (JIA) is an autoimmune condition characterised by flares of joint inflammation. However, no reliable biomarker exists to predict the erratic disease course. Normally, regulatory T cells (Tregs) maintain tolera…
View article: IL-33-activated ILC2s induce tertiary lymphoid structures in pancreatic cancer
IL-33-activated ILC2s induce tertiary lymphoid structures in pancreatic cancer Open
View article: Contrastive learning of T cell receptor representations
Contrastive learning of T cell receptor representations Open
Computational prediction of the interaction of T cell receptors (TCRs) and their ligands is a grand challenge in immunology. Despite advances in high-throughput assays, specificity-labeled TCR data remain sparse. In other domains, the pre-…
View article: DiffPaSS—high-performance differentiable pairing of protein sequences using soft scores
DiffPaSS—high-performance differentiable pairing of protein sequences using soft scores Open
Motivation Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and featur…
View article: Limits on inferring T cell specificity from partial information
Limits on inferring T cell specificity from partial information Open
A key challenge in molecular biology is to decipher the mapping of protein sequence to function. To perform this mapping requires the identification of sequence features most informative about function. Here, we quantify the amount of info…
View article: DiffPaSS -- High-performance differentiable pairing of protein sequences using soft scores
DiffPaSS -- High-performance differentiable pairing of protein sequences using soft scores Open
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature correlati…
View article: Contrastive learning of T cell receptor representations
Contrastive learning of T cell receptor representations Open
Computational prediction of the interaction of T cell receptors (TCRs) and their ligands is a grand challenge in immunology. Despite advances in high-throughput assays, specificity-labelled TCR data remains sparse. In other domains, the pr…
View article: Systematic analysis of CDR contacts and sequence constraints between T cell receptor <i>αβ</i> chains
Systematic analysis of CDR contacts and sequence constraints between T cell receptor <i>αβ</i> chains Open
The six complementarity determining regions (CDRs) of the T cell receptor (TCR) form multiple contacts with cognate peptide and major histocompatibility complex, thus determining antigen specificity. However, the contacts between the CDRs …
View article: Single-cell analysis of bronchoalveolar cells in inflammatory and fibrotic post-COVID lung disease
Single-cell analysis of bronchoalveolar cells in inflammatory and fibrotic post-COVID lung disease Open
Background Persistent radiological lung abnormalities are evident in many survivors of acute coronavirus disease 2019 (COVID-19). Consolidation and ground glass opacities are interpreted to indicate subacute inflammation whereas reticulati…
View article: Treg fitness as a biomarker for disease activity in Juvenile Idiopathic Arthritis
Treg fitness as a biomarker for disease activity in Juvenile Idiopathic Arthritis Open
Juvenile Idiopathic Arthritis (JIA) is an autoimmune condition characterised by persistent flares of joint inflammation. However, no reliable biomarker exists to predict the erratic disease course. Normally, regulatory T cells (Tregs) main…
View article: Limits on Inferring T-cell Specificity from Partial Information
Limits on Inferring T-cell Specificity from Partial Information Open
A key challenge in molecular biology is to decipher the mapping of protein sequence to function. To perform this mapping requires the identification of sequence features most informative about function. Here, we quantify the amount of info…
View article: S84 Single-cell landscape of bronchoalveolar cells in inflammatory and fibrotic post-COVID residual lung abnormalities
S84 Single-cell landscape of bronchoalveolar cells in inflammatory and fibrotic post-COVID residual lung abnormalities Open
Background Approximately 10% of patients hospitalised with COVID-19 have residual lung abnormalities (RLAs) at 12 months. In clinical practice, CT scan appearances are often used to guide management. Whether such radiological changes relia…
View article: The proteomic landscape of soft tissue sarcomas
The proteomic landscape of soft tissue sarcomas Open
View article: Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection
Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection Open
View article: Single-cell analysis of bronchoalveolar cells in inflammatory and fibrotic post-COVID lung disease
Single-cell analysis of bronchoalveolar cells in inflammatory and fibrotic post-COVID lung disease Open
A bstract Background Persistent radiological lung abnormalities are evident in many survivors of acute coronavirus disease 2019 (COVID-19). Consolidation and ground glass opacities are interpreted to indicate subacute inflammation whereas …
View article: Large Clones of Pre-Existing T Cells Drive Early Immunity Against SARS-COV-2 and LCMV Infection
Large Clones of Pre-Existing T Cells Drive Early Immunity Against SARS-COV-2 and LCMV Infection Open
View article: Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection
Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection Open
We analyzed the dynamics of the earliest T cell response to SARS-COV-2. A wave of TCRs strongly but transiently expand during infection, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enrich…
View article: Corrigendum: Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes
Corrigendum: Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes Open
[This corrects the article DOI: 10.3389/fphys.2021.730908.].
View article: Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes
Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes Open
The physical interaction between the T cell receptor (TCR) and its cognate antigen causes T cells to activate and participate in the immune response. Understanding this physical interaction is important in predicting TCR binding to a targe…
View article: Predicting T cell receptor antigen specificity from structural features derived from homology models of receptor-peptide-major histocompatibility complexes
Predicting T cell receptor antigen specificity from structural features derived from homology models of receptor-peptide-major histocompatibility complexes Open
1 Abstract The physical interaction between the T cell receptor (TCR) and its cognate antigen causes T cells to activate and participate in the immune response. Understanding this physical interaction is important in predicting TCR binding…
View article: Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry
Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry Open
Soft tissue sarcomas (STS) are a group of rare and heterogeneous cancers. While large-scale genomic and epigenomic profiling of STS have been undertaken, proteomic analysis has thus far been limited. Here we utilise sequential window acqui…
View article: Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry
Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry Open
Soft tissue sarcomas (STS) are a group of rare and heterogeneous cancers. While large-scale genomic and epigenomic profiling of STS have been undertaken, proteomic analysis has thus far been limited. Here we utilise sequential window acqui…