david gfeller
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SwissTargetPrediction: a web server for target prediction of bioactive small molecules
D Gfeller, A Grosdidier, M Wirth, A Daina, O Michielin, V Zoete
Nucleic acids research 42 (W1), W32-W38, 2014
Intratumoral Tcf1+ PD-1+ CD8+ T cells with stem-like properties promote tumor control in response to vaccination and checkpoint blockade immunotherapy
I Siddiqui, K Schaeuble, V Chennupati, SAF Marraco, S Calderon-Copete, ...
Immunity 50 (1), 195-211. e10, 2019
Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data
J Racle, K de Jonge, P Baumgaertner, DE Speiser, D Gfeller
elife 6, e26476, 2017
Shaping the interaction landscape of bioactive molecules
D Gfeller, O Michielin, V Zoete
Bioinformatics 29 (23), 3073-3079, 2013
Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer
JL Tanyi, S Bobisse, E Ophir, S Tuyaerts, A Roberti, R Genolet, ...
Science translational medicine 10 (436), eaao5931, 2018
Key parameters of tumor epitope immunogenicity revealed through a consortium approach improve neoantigen prediction
DK Wells, MM van Buuren, KK Dang, VM Hubbard-Lucey, KCF Sheehan, ...
Cell 183 (3), 818-834. e13, 2020
EPIC: a tool to estimate the proportions of different cell types from bulk gene expression data
J Racle, D Gfeller
Bioinformatics for cancer immunotherapy: methods and protocols, 233-248, 2020
Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity
M Bassani-Sternberg, C Chong, P Guillaume, M Solleder, HS Pak, ...
PLoS computational biology 13 (8), e1005725, 2017
Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes
J Racle, J Michaux, GA Rockinger, M Arnaud, S Bobisse, C Chong, ...
Nature biotechnology 37 (11), 1283-1286, 2019
Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling
T Oka, E Remue, K Meerschaert, B Vanloo, C Boucherie, D Gfeller, ...
Biochemical Journal 432 (3), 461-478, 2010
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
R Tonikian, X Xin, CP Toret, D Gfeller, C Landgraf, S Panni, S Paoluzi, ...
PLoS biology 7 (10), e1000218, 2009
Complex network analysis of free-energy landscapes
D Gfeller, P De Los Rios, A Caflisch, F Rao
Proceedings of the National Academy of Sciences 104 (6), 1817-1822, 2007
Tumour-derived PGD2 and NKp30-B7H6 engagement drives an immunosuppressive ILC2-MDSC axis
S Trabanelli, MF Chevalier, A Martinez-Usatorre, A Gomez-Cadena, ...
Nature communications 8 (1), 593, 2017
Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer
A Cachot, M Bilous, YC Liu, X Li, M Saillard, M Cenerenti, GA Rockinger, ...
Science advances 7 (9), eabe3348, 2021
High-throughput and sensitive immunopeptidomics platform reveals profound interferonγ-mediated remodeling of the human leukocyte antigen (HLA) ligandome
C Chong, F Marino, HS Pak, J Racle, RT Daniel, M Müller, D Gfeller, ...
Molecular & Cellular Proteomics 17 (3), 533-548, 2018
ILC2-modulated T cell–to-MDSC balance is associated with bladder cancer recurrence
MF Chevalier, S Trabanelli, J Racle, B Salomé, V Cesson, D Gharbi, ...
The Journal of clinical investigation 127 (8), 2916-2929, 2017
Spectral coarse graining of complex networks
D Gfeller, P De Los Rios
Physical review letters 99 (3), 038701, 2007
Finding instabilities in the community structure of complex networks
D Gfeller, JC Chappelier, P De Los Rios
Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 72 (5 …, 2005
Predicting antigen presentation—what could we learn from a million peptides?
D Gfeller, M Bassani-Sternberg
Frontiers in immunology 9, 1716, 2018
Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing
A Ernst, D Gfeller, Z Kan, S Seshagiri, PM Kim, GD Bader, SS Sidhu
Molecular BioSystems 6 (10), 1782-1790, 2010
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