List of works - David Gfeller

A structural portrait of the PDZ domain family

scientific article

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins

scientific article

Beyond the binding site: the role of the β₂-β₃ loop and extra-domain structures in PDZ domains

scientific article published on 8 March 2012

Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing

article published in 2010

Complex network analysis of free-energy landscapes

scholarly article

Current tools for predicting cancer-specific T cell immunity

scientific article published on 25 April 2016

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity.

scientific article

Expanding molecular modeling and design tools to non-natural sidechains

scientific article published on 14 April 2012

Finding instabilities in the community structure of complex networks

scientific article published on 29 November 2005

Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling

scientific article published on December 2010

How to visually interpret biological data using networks

scientific article

Improving binding affinity and stability of peptide ligands by substituting glycines with D-amino acids

scientific article

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets

scientific article

Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer.

scientific article published in April 2018

Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins.

scientific article published on 21 May 2018

Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs

scientific article

Protein homology reveals new targets for bioactive small molecules

scientific article published on 21 April 2015

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

scientific article published on 14 October 2019

SH3 interactome conserves general function over specific form.

scientific article published in January 2013

Sensitive identification of neoantigens and cognate TCRs in human solid tumors

scientific article published on 15 November 2021

Sequence determinants of a microtubule tip localization signal (MtLS).

scientific article

Shaping the interaction landscape of bioactive molecules.

scientific article

Simultaneous Enumeration Of Cancer And Immune Cell Types From Bulk Tumor Gene Expression Data

article

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

scientific article published on 13 November 2017

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

scientific article published on 13 January 2017

Single-cell transcriptomics identifies multiple pathways underlying antitumor function of TCR- and CD8αβ-engineered human CD4+ T cells

scientific article published on 03 July 2020

Spectral Coarse Graining and Synchronization in Oscillator Networks

scientific article published in Physical Review Letters

Spectral Coarse Graining of Complex Networks

scientific article published in Physical Review Letters

Susceptibility and adaptation to human TRIM5α alleles at positive selected sites in HIV-1 capsid

scientific article published on 17 April 2013

SwissSidechain: a molecular and structural database of non-natural sidechains

scientific article published on 26 October 2012

SwissTargetPrediction: a web server for target prediction of bioactive small molecules

scientific article published on 3 May 2014

The C-terminal extension landscape of naturally presented HLA-I ligands

article published in the Proceedings of the National Academy of Sciences of the United States of America

The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands

scientific article published on 14 November 2018

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

scientific article (publication date: 4 January 2016)

The caveolin-binding motif of the pathogen-related yeast protein Pry1, a member of the CAP protein superfamily, is required for in vivo export of cholesteryl acetate.

scientific article published on 05 March 2014

The length distribution and multiple specificity of naturally presented HLA-I ligands

The multiple-specificity landscape of modular peptide recognition domains ⬇️

scientific journal article

Uncovering new aspects of protein interactions through analysis of specificity landscapes in peptide recognition domains ⬇️

scientific article published on 03 April 2012

Uncovering the topology of configuration space networks

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide-HLA Interactions

scientific article

List of works by David Gfeller

A structural portrait of the PDZ domain family

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins

Beyond the binding site: the role of the β₂-β₃ loop and extra-domain structures in PDZ domains

Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing

Complex network analysis of free-energy landscapes

Current tools for predicting cancer-specific T cell immunity

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity.

Expanding molecular modeling and design tools to non-natural sidechains

Finding instabilities in the community structure of complex networks

Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling

How to visually interpret biological data using networks

Improving binding affinity and stability of peptide ligands by substituting glycines with D-amino acids

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets

Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer.

Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins.

Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs

Protein homology reveals new targets for bioactive small molecules

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

SH3 interactome conserves general function over specific form.

Sensitive identification of neoantigens and cognate TCRs in human solid tumors

Sequence determinants of a microtubule tip localization signal (MtLS).

Shaping the interaction landscape of bioactive molecules.

Simultaneous Enumeration Of Cancer And Immune Cell Types From Bulk Tumor Gene Expression Data

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

Single-cell transcriptomics identifies multiple pathways underlying antitumor function of TCR- and CD8αβ-engineered human CD4+ T cells

Spectral Coarse Graining and Synchronization in Oscillator Networks

Spectral Coarse Graining of Complex Networks

Susceptibility and adaptation to human TRIM5α alleles at positive selected sites in HIV-1 capsid

SwissSidechain: a molecular and structural database of non-natural sidechains

SwissTargetPrediction: a web server for target prediction of bioactive small molecules

The C-terminal extension landscape of naturally presented HLA-I ligands

The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The caveolin-binding motif of the pathogen-related yeast protein Pry1, a member of the CAP protein superfamily, is required for in vivo export of cholesteryl acetate.

The length distribution and multiple specificity of naturally presented HLA-I ligands

The multiple-specificity landscape of modular peptide recognition domains ⬇️

Uncovering new aspects of protein interactions through analysis of specificity landscapes in peptide recognition domains ⬇️

Uncovering the topology of configuration space networks

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide-HLA Interactions