Franca Fraternali

ImmunoMatch learns and predicts cognate pairing of heavy and light immunoglobulin chains

ImmunoMatch predicts cognate pairing of heavy and light immunoglobulin chains using a language model trained on paired sequences from human B cells.

Corylus avellana non-specific lipid-transfer protein Cor a 8 is a moonlighting enzyme with a new lipase activity

This study identifies Cor a 8, a non-specific lipid-transfer protein, as a novel lipase in hazelnuts that hydrolyzes triglycerides and contributes to lipid oxidation.

Assessing structure-function impacts on Vitellogenin by leveraging allelic variant occurring in honey bee subspecies Apis mellifera meliffera

The paper identifies a 9-nucleotide deletion in honey bee Vg alleles and shows it maintains protein structure and stability using structural bioinformatics and a transformer-based model.

Tuning antibody stability and function by rational designs of framework mutations

This study designs framework mutations in antibodies to improve stability and function using a computational-experimental approach, showing that FW modifications can affect immunological functions beyond binding affinity.

Tumor-infiltrating CD27-IgD- regulatory B cells suppress cytotoxic CD8+T cell responses in renal cell carcinoma

The paper identifies CD27-IgD- regulatory B cells in renal cell carcinoma that suppress CD8+T cell responses, linking them to poor prognosis.

Multi-step antibody class switching in a primary human response is restricted after IGHG2 and dependent on B cell maturation stage.

The paper investigates antibody class switching dynamics in a primary human immune response, revealing multistep progression and memory B cell subtype dependence beyond IGHG2.

Leveraging protein language models and scoring function for Indel characterisation and transfer learning

This paper introduces IndeLLM, a method for indel pathogenicity prediction using protein language models and transfer learning, achieving high performance across species.

TITINdb2 - Expanding Annotation and Structural Information for Protein Variants in the Giant Sarcomeric Protein Titin

TITINdb2 expands variant annotation and structural information for titin protein variants associated with myopathies.

Single Distal Mutation Enhances Activity of known PETases via Stabilisation of PET-binding

The paper reports an engineered PETase, Fast_2.9, with enhanced activity and stability for PET degradation, identified through high-throughput screening of PET nanoparticles.

VCAb: A web-tool for structure-guided antibody engineering

VCAb provides a web tool for antibody engineering by annotating antibody structures, isotypes, and mutation impacts across species.

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data

The "dark matter" of protein variants carries a distinct DNA signature and predicts damaging variant effects

The paper identifies a DNA mutational signature linked to damaging protein variants, showing it is under-sampled in tumor data and can predict variant impact using DMS data.

Missense variants in health and disease affect distinct functional pathways and proteomics features

This study identifies molecular differences between pathogenic and population missense variants by analyzing their effects on protein structure and function, revealing distinct patterns in protein domains and cellular processes.

SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals

The paper predicts SARS-CoV-2 spike protein interactions with ACE2 orthologues across 215 vertebrates, finds mutations in ACE2 are more detrimental, and shows human strains are present in animals.

Identifying extrinsic versus intrinsic drivers of variation in cell behaviour in human iPS cell lines from healthy donors

The paper integrates genetic and cell biological data from human iPSC lines to identify intrinsic and extrinsic factors driving inter-individual variability in cell behavior.

Short loop motif profiling of protein interaction networks in acute myeloid leukaemia

The paper develops an in-silico pipeline to analyze mutations and their effects on protein-protein interactions in acute myeloid leukaemia, identifying functional modules and potential drug targets.