David Gfeller

Publications | Phd and Masters theses

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60 publications

In press | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2005 |
 
Structural dissimilarity from self drives neoepitope escape from immune tolerance.
Devlin J.R., Alonso J.A., Ayres C.M., Keller GLJ, Bobisse S., Vander Kooi C.W., Coukos G., Gfeller D., Harari A., Baker B.M. Nature chemical biology. Peer-reviewed.
 
Single-cell transcriptomics identifies multiple pathways underlying antitumor function of TCR- and CD8αβ-engineered human CD4<sup>+</sup> T cells.
Rath J.A., Bajwa G., Carreres B., Hoyer E., Gruber I., Martínez-Paniagua M.A., Yu Y.R., Nouraee N., Sadeghi F., Wu M. et al., 2020/07. Science advances, 6 (27) pp. eaaz7809. Peer-reviewed.
 
Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma.
Dheilly E., Battistello E., Katanayeva N., Sungalee S., Michaux J., Duns G., Wehrle S., Sordet-Dessimoz J., Mina M., Racle J. et al., 2020/05/11. Cancer cell, 37 (5) pp. 674-689.e12. Peer-reviewed.
 
Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands.
Solleder M., Guillaume P., Racle J., Michaux J., Pak H.S., Müller M., Coukos G., Bassani-Sternberg M., Gfeller D., 2020/02. Molecular & cellular proteomics, 19 (2) pp. 390-404. Peer-reviewed.
Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq
Carmona Santiago J., Siddiqui Imran, Bilous Mariia, Held Werner, Gfeller David, 2020/01/01. OncoImmunology, 9 (1) p. 1737369. Peer-reviewed.
 
EPIC: A Tool to Estimate the Proportions of Different Cell Types from Bulk Gene Expression Data.
Racle J., Gfeller D., 2020. Methods in molecular biology, 2120 pp. 233-248. Peer-reviewed.
CD56 as a marker of an ILC1-like population with NK cell properties that is functionally impaired in AML.
Salomé B., Gomez-Cadena A., Loyon R., Suffiotti M., Salvestrini V., Wyss T., Vanoni G., Ruan D.F., Rossi M., Tozzo A. et al., 2019/11/26. Blood advances, 3 (22) pp. 3674-3687. Peer-reviewed.
 
Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment.
Newey A., Griffiths B., Michaux J., Pak H.S., Stevenson B.J., Woolston A., Semiannikova M., Spain G., Barber L.J., Matthews N. et al., 2019/11/18. Journal for immunotherapy of cancer, 7 (1) p. 309. Peer-reviewed.
 
Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes.
Racle J., Michaux J., Rockinger G.A., Arnaud M., Bobisse S., Chong C., Guillaume P., Coukos G., Harari A., Jandus C. et al., 2019/11. Nature biotechnology, 37 (11) pp. 1283-1286. Peer-reviewed.
A Phase Ib Study of the Combination of Personalized Autologous Dendritic Cell Vaccine, Aspirin, and Standard of Care Adjuvant Chemotherapy Followed by Nivolumab for Resected Pancreatic Adenocarcinoma—A Proof of Antigen Discovery Feasibility in Three Patients
Bassani-Sternberg Michal, Digklia Antonia, Huber Florian, Wagner Dorothea, Sempoux Christine, Stevenson Brian J., Thierry Anne-Christine, Michaux Justine, Pak HuiSong, Racle Julien et al., 2019/08/08. Frontiers in Immunology, 10. Peer-reviewed.
 
Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores.
Ben-David M., Huang H., Sun MGF, Corbi-Verge C., Petsalaki E., Liu K., Gfeller D., Garg P., Tempel W., Sochirca I. et al., 2019/01/18. Journal of molecular biology, 431 (2) pp. 336-350. Peer-reviewed.
Intratumoral Tcf1<sup>+</sup>PD-1<sup>+</sup>CD8<sup>+</sup> T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy.
Siddiqui I., Schaeuble K., Chennupati V., Fuertes Marraco S.A., Calderon-Copete S., Pais Ferreira D., Carmona S.J., Scarpellino L., Gfeller D., Pradervand S. et al., 2019/01/15. Immunity, 50 (1) pp. 195-211.e10. Peer-reviewed.
 
Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands.
Perez MAS, Bassani-Sternberg M., Coukos G., Gfeller D., Zoete V., 2019. Frontiers in immunology, 10 p. 2731. Peer-reviewed.
 
Computational KIR copy number discovery reveals interaction between inhibitory receptor burden and survival.
Pyke R.M., Genolet R., Harari A., Coukos G., Gfeller D., Carter H., 2019. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 24 pp. 148-159. Peer-reviewed.
 
The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands.
Gfeller D., Guillaume P., Michaux J., Pak H.S., Daniel R.T., Racle J., Coukos G., Bassani-Sternberg M., 2018/12/15. Journal of immunology, 201 (12) pp. 3705-3716. Peer-reviewed.
 
Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome.
Mylonas R., Beer I., Iseli C., Chong C., Pak H.S., Gfeller D., Coukos G., Xenarios I., Müller M., Bassani-Sternberg M., 2018/12. Molecular & cellular proteomics, 17 (12) pp. 2347-2357. Peer-reviewed.
The C-terminal extension landscape of naturally presented HLA-I ligands.
Guillaume P., Picaud S., Baumgaertner P., Montandon N., Schmidt J., Speiser D.E., Coukos G., Bassani-Sternberg M., Filippakopoulos P., Gfeller D., 2018/05/15. Proceedings of the National Academy of Sciences of the United States of America, 115 (20) pp. 5083-5088. Peer-reviewed.
Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins.
Dib L., Salamin N., Gfeller D., 2018/05. PLoS computational biology, 14 (5) pp. e1006188. Peer-reviewed.
 
Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer
Tanyi Janos L., Bobisse Sara, Ophir Eran, Tuyaerts Sandra, Roberti Annalisa, Genolet Raphael, Baumgartner Petra, Stevenson Brian J., Iseli Christian, Dangaj Denarda et al., 2018/04/11. Science Translational Medicine, 10 (436) pp. eaao5931.
 
Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer.
Tanyi J.L., Bobisse S., Ophir E., Tuyaerts S., Roberti A., Genolet R., Baumgartner P., Stevenson B.J., Iseli C., Dangaj D. et al., 2018/04/11. Science translational medicine, 10 (436) pp. NA. Peer-reviewed.
Sensitive and frequent identification of high avidity neo-epitope specific CD8 + T cells in immunotherapy-naive ovarian cancer.
Bobisse S., Genolet R., Roberti A., Tanyi J.L., Racle J., Stevenson B.J., Iseli C., Michel A., Le Bitoux M.A., Guillaume P. et al., 2018/03/15. Nature communications, 9 (1) p. 1092. Peer-reviewed.
 
High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome.
Chong C., Marino F., Pak H., Racle J., Daniel R.T., Müller M., Gfeller D., Coukos G., Bassani-Sternberg M., 2018/03. Molecular & cellular proteomics, 17 (3) pp. 533-548. Peer-reviewed.
 
Predicting Antigen Presentation-What Could We Learn From a Million Peptides?
Gfeller D., Bassani-Sternberg M., 2018. Frontiers in immunology, 9 p. 1716. Peer-reviewed.
Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data.
Racle J., de Jonge K., Baumgaertner P., Speiser D.E., Gfeller D., 2017/11/13. eLife, 6 pp. 1-25. Peer-reviewed.
Tumour-derived PGD2 and NKp30-B7H6 engagement drives an immunosuppressive ILC2-MDSC axis.
Trabanelli S., Chevalier M.F., Martinez-Usatorre A., Gomez-Cadena A., Salomé B., Lecciso M., Salvestrini V., Verdeil G., Racle J., Papayannidis C. et al., 2017/09/19. Nature communications, 8 (1) p. 593. Peer-reviewed.
 
Identification of innate lymphoid cells in single-cell RNA-Seq data.
Suffiotti M., Carmona S.J., Jandus C., Gfeller D., 2017/07. Immunogenetics, 69 (7) pp. 439-450. Peer-reviewed.
 
The pathogen-related yeast protein Pry1, a member of the CAP protein superfamily, is a fatty acid-binding protein.
Darwiche R., Mène-Saffrané L., Gfeller D., Asojo O.A., Schneiter R., 2017/05/19. The Journal of biological chemistry, 292 (20) pp. 8304-8314. Peer-reviewed.
 
Broad and Conserved Immune Regulation by Genetically Heterogeneous Melanoma Cells.
Neubert N.J., Tillé L., Barras D., Soneson C., Baumgaertner P., Rimoldi D., Gfeller D., Delorenzi M., Fuertes Marraco S.A., Speiser D.E., 2017/04/01. Cancer research, 77 (7) pp. 1623-1636. Peer-reviewed.
Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.
Carmona S.J., Teichmann S.A., Ferreira L., Macaulay I.C., Stubbington M.J., Cvejic A., Gfeller D., 2017/03. Genome research, 27 (3) pp. 451-461. Peer-reviewed.
'Hotspots' of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization.
Müller M., Gfeller D., Coukos G., Bassani-Sternberg M., 2017. Frontiers in Immunology, 8 p. 1367. Peer-reviewed.
Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity.
Bassani-Sternberg M., Chong C., Guillaume P., Solleder M., Pak H., Gannon P.O., Kandalaft L.E., Coukos G., Gfeller D., 2017. PLoS Computational Biology, 13 (8) pp. e1005725. Peer-reviewed.
ILC2-modulated T cell-to-MDSC balance is associated with bladder cancer recurrence.
Chevalier M.F., Trabanelli S., Racle J., Salomé B., Cesson V., Gharbi D., Bohner P., Domingos-Pereira S., Dartiguenave F., Fritschi A.S. et al., 2017. The Journal of Clinical Investigation, 127 (8) pp. 2916-2929. Peer-reviewed.
 
Current tools for predicting cancer-specific T cell immunity.
Gfeller D., Bassani-Sternberg M., Schmidt J., Luescher I.F., 2016. Oncoimmunology, 5 (7) pp. e1177691. Peer-reviewed.
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.
SIB Swiss Institute of Bioinformatics Members, 2016. Nucleic Acids Research, 44 (D1) pp. D27-D37.
 
Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide-HLA Interactions.
Bassani-Sternberg M., Gfeller D., 2016. Journal of Immunology (baltimore, Md. : 1950), 197 (6) pp. 2492-2499. Peer-reviewed.
Protein homology reveals new targets for bioactive small molecules.
Gfeller D., Zoete V., 2015. Bioinformatics, 31 (16) pp. 2721-2727. Peer-reviewed.
 
A structural portrait of the PDZ domain family.
Ernst A., Appleton B.A., Ivarsson Y., Zhang Y., Gfeller D., Wiesmann C., Sidhu S.S., 2014. Journal of Molecular Biology, 426 (21) pp. 3509-3519. Peer-reviewed.
Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs.
Gfeller D., Ernst A., Jarvik N., Sidhu S.S., Bader G.D., 2014. PloS One, 9 (4) pp. e94507. Peer-reviewed.
SwissTargetPrediction: a web server for target prediction of bioactive small molecules.
Gfeller D., Grosdidier A., Wirth M., Daina A., Michielin O., Zoete V., 2014. Nucleic Acids Research, 42 (W1) pp. W32-W38.
 
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.
Choudhary V., Darwiche R., Gfeller D., Zoete V., Michielin O., Schneiter R., 2014. Journal of Lipid Research, 55 (5) pp. 883-894. Peer-reviewed.
 
Improving binding affinity and stability of peptide ligands by substituting glycines with D-amino acids.
Chen S., Gfeller D., Buth S.A., Michielin O., Leiman P.G., Heinis C., 2013. Chembiochem, 14 (11) pp. 1316-1322. Peer-reviewed.
SH3 interactome conserves general function over specific form.
Xin X., Gfeller D., Cheng J., Tonikian R., Sun L., Guo A., Lopez L., Pavlenco A., Akintobi A., Zhang Y. et al., 2013. Molecular Systems Biology, 9 p. 652. Peer-reviewed.
Shaping the interaction landscape of bioactive molecules.
Gfeller D., Michielin O., Zoete V., 2013. Bioinformatics, 29 (23) pp. 3073-3079.
Susceptibility and adaptation to human TRIM5α alleles at positive selected sites in HIV-1 capsid.
Rahm N., Gfeller D., Snoeck J., Martinez R., McLaren P.J., Ortiz M., Ciuffi A., Telenti A., 2013. Virology, 441 (2) pp. 162-170.
SwissSidechain: a molecular and structural database of non-natural sidechains.
Gfeller D., Michielin O., Zoete V., 2013. Nucleic Acids Research, 41 (D1) pp. D327-D332. Peer-reviewed.
Beyond the binding site: the role of the β₂-β₃ loop and extra-domain structures in PDZ domains.
Mostarda S., Gfeller D., Rao F., 2012. PLoS Computational Biology, 8 (3) pp. e1002429. Peer-reviewed.
 
Expanding molecular modeling and design tools to non-natural sidechains.
Gfeller D., Michielin O., Zoete V., 2012. Journal of Computational Chemistry, 33 (18) pp. 1525-1535.
MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets.
Kim T., Tyndel M.S., Huang H., Sidhu S.S., Bader G.D., Gfeller D., Kim P.M., 2012. Nucleic Acids Research, 40 (6) pp. e47. Peer-reviewed.
 
Sequence determinants of a microtubule tip localization signal (MtLS).
Buey R.M., Sen I., Kortt O., Mohan R., Gfeller D., Veprintsev D., Kretzschmar I., Scheuermann J., Neri D., Zoete V. et al., 2012. Journal of Biological Chemistry, 287 (34) pp. 28227-28242. Peer-reviewed.
 
Uncovering new aspects of protein interactions through analysis of specificity landscapes in peptide recognition domains.
Gfeller D., 2012. FEBS Letters, 586 (17) pp. 2764-2772. Peer-reviewed.
The multiple-specificity landscape of modular peptide recognition domains.
Gfeller D., Butty F., Wierzbicka M., Verschueren E., Vanhee P., Huang H., Ernst A., Dar N., Stagljar I., Serrano L. et al., 2011. Molecular Systems Biology, 7 p. 484. Peer-reviewed.
 
Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing.
Ernst A., Gfeller D., Kan Z., Seshagiri S., Kim P.M., Bader G.D., Sidhu S.S., 2010. Molecular BioSystems, 6 (10) pp. 1782-1790. Peer-reviewed.
 
Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling.
Oka T., Remue E., Meerschaert K., Vanloo B., Boucherie C., Gfeller D., Bader G.D., Sidhu S.S., Vandekerckhove J., Gettemans J. et al., 2010. Biochemical Journal, 432 (3) pp. 461-472. Peer-reviewed.
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.
Tonikian R., Xin X., Toret C.P., Gfeller D., Landgraf C., Panni S., Paoluzi S., Castagnoli L., Currell B., Seshagiri S. et al., 2009. PLoS Biology, 7 (10) pp. e1000218. Peer-reviewed.
 
How to visually interpret biological data using networks.
Merico D., Gfeller D., Bader G.D., 2009. Nature Biotechnology, 27 (10) pp. 921-924. Peer-reviewed.
 
Spectral coarse graining and synchronization in oscillator networks.
Gfeller D., De Los Rios P., 2008. Physical Review Letters, 100 (17) p. 174104. Peer-reviewed.
 
Complex network analysis of free-energy landscapes.
Gfeller D., De Los Rios P., Caflisch A., Rao F., 2007. Proceedings of the National Academy of Sciences of the United States of America, 104 (6) pp. 1817-1822. Peer-reviewed.
 
Spectral coarse graining of complex networks.
Gfeller D., De Los Rios P., 2007. Physical Review Letters, 99 (3) p. 038701. Peer-reviewed.
 
Uncovering the topology of configuration space networks.
Gfeller D., de Lachapelle D.M., De Los Rios P., Caldarelli G., Rao F., 2007. Physical review. E, Statistical, nonlinear, and soft matter physics, 76 (2 Pt 2) p. 026113. Peer-reviewed.
 
Finding instabilities in the community structure of complex networks.
Gfeller D., Chappelier J.C., De Los Rios P., 2005. Physical review. E, Statistical, nonlinear, and soft matter physics, 72 (5 Pt 2) p. 056135. Peer-reviewed.
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