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Items: 40

1.

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

Tanyi JL, Bobisse S, Ophir E, Tuyaerts S, Roberti A, Genolet R, Baumgartner P, Stevenson BJ, Iseli C, Dangaj D, Czerniecki B, Semilietof A, Racle J, Michel A, Xenarios I, Chiang C, Monos DS, Torigian DA, Nisenbaum HL, Michielin O, June CH, Levine BL, Powell DJ Jr., Gfeller D, Mick R, Dafni U, Zoete V, Harari A, Coukos G, Kandalaft LE.

Sci Transl Med. 2018 Apr 11;10(436). pii: eaao5931. doi: 10.1126/scitranslmed.aao5931.

PMID:
29643231
2.

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 JL, Racle J, Stevenson BJ, Iseli C, Michel A, Le Bitoux MA, Guillaume P, Schmidt J, Bianchi V, Dangaj D, Fenwick C, Derré L, Xenarios I, Michielin O, Romero P, Monos DS, Zoete V, Gfeller D, Kandalaft LE, Coukos G, Harari A.

Nat Commun. 2018 Mar 15;9(1):1092. doi: 10.1038/s41467-018-03301-0.

3.

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 RT, Müller M, Gfeller D, Coukos G, Bassani-Sternberg M.

Mol Cell Proteomics. 2018 Mar;17(3):533-548. doi: 10.1074/mcp.TIR117.000383. Epub 2017 Dec 14.

4.

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

Racle J, de Jonge K, Baumgaertner P, Speiser DE, Gfeller D.

Elife. 2017 Nov 13;6. pii: e26476. doi: 10.7554/eLife.26476.

5.

'Hotspots' of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization.

Müller M, Gfeller D, Coukos G, Bassani-Sternberg M.

Front Immunol. 2017 Oct 20;8:1367. doi: 10.3389/fimmu.2017.01367. eCollection 2017.

6.

Tumour-derived PGD2 and NKp30-B7H6 engagement drives an immunosuppressive ILC2-MDSC axis.

Trabanelli S, Chevalier MF, Martinez-Usatorre A, Gomez-Cadena A, Salomé B, Lecciso M, Salvestrini V, Verdeil G, Racle J, Papayannidis C, Morita H, Pizzitola I, Grandclément C, Bohner P, Bruni E, Girotra M, Pallavi R, Falvo P, Leibundgut EO, Baerlocher GM, Carlo-Stella C, Taurino D, Santoro A, Spinelli O, Rambaldi A, Giarin E, Basso G, Tresoldi C, Ciceri F, Gfeller D, Akdis CA, Mazzarella L, Minucci S, Pelicci PG, Marcenaro E, McKenzie ANJ, Vanhecke D, Coukos G, Mavilio D, Curti A, Derré L, Jandus C.

Nat Commun. 2017 Sep 19;8(1):593. doi: 10.1038/s41467-017-00678-2.

7.

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 PO, Kandalaft LE, Coukos G, Gfeller D.

PLoS Comput Biol. 2017 Aug 23;13(8):e1005725. doi: 10.1371/journal.pcbi.1005725. eCollection 2017 Aug.

8.

ILC2-modulated T cell-to-MDSC balance is associated with bladder cancer recurrence.

Chevalier MF, Trabanelli S, Racle J, Salomé B, Cesson V, Gharbi D, Bohner P, Domingos-Pereira S, Dartiguenave F, Fritschi AS, Speiser DE, Rentsch CA, Gfeller D, Jichlinski P, Nardelli-Haefliger D, Jandus C, Derré L.

J Clin Invest. 2017 Aug 1;127(8):2916-2929. doi: 10.1172/JCI89717. Epub 2017 Jun 26.

9.

Identification of innate lymphoid cells in single-cell RNA-Seq data.

Suffiotti M, Carmona SJ, Jandus C, Gfeller D.

Immunogenetics. 2017 Jul;69(7):439-450. doi: 10.1007/s00251-017-1002-x. Epub 2017 May 22.

PMID:
28534222
10.

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 OA, Schneiter R.

J Biol Chem. 2017 May 19;292(20):8304-8314. doi: 10.1074/jbc.M117.781880. Epub 2017 Apr 1.

PMID:
28365570
11.

Broad and Conserved Immune Regulation by Genetically Heterogeneous Melanoma Cells.

Neubert NJ, Tillé L, Barras D, Soneson C, Baumgaertner P, Rimoldi D, Gfeller D, Delorenzi M, Fuertes Marraco SA, Speiser DE.

Cancer Res. 2017 Apr 1;77(7):1623-1636. doi: 10.1158/0008-5472.CAN-16-2680. Epub 2017 Jan 19.

12.

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

Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ, Cvejic A, Gfeller D.

Genome Res. 2017 Mar;27(3):451-461. doi: 10.1101/gr.207704.116. Epub 2017 Jan 13.

13.

Current tools for predicting cancer-specific T cell immunity.

Gfeller D, Bassani-Sternberg M, Schmidt J, Luescher IF.

Oncoimmunology. 2016 Apr 25;5(7):e1177691. doi: 10.1080/2162402X.2016.1177691. eCollection 2016 Jul. Review.

14.

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

Bassani-Sternberg M, Gfeller D.

J Immunol. 2016 Sep 15;197(6):2492-9. doi: 10.4049/jimmunol.1600808. Epub 2016 Aug 10.

15.

Protein homology reveals new targets for bioactive small molecules.

Gfeller D, Zoete V.

Bioinformatics. 2015 Aug 15;31(16):2721-7. doi: 10.1093/bioinformatics/btv214. Epub 2015 Apr 21.

PMID:
25900917
16.

Assessment of the nonoperated root after apical surgery of the other root in mandibular molars: a 5-year follow-up study.

Kraus RD, von Arx T, Gfeller D, Ducommun J, Jensen SS.

J Endod. 2015 Apr;41(4):442-6. doi: 10.1016/j.joen.2014.11.024. Epub 2015 Feb 12.

PMID:
25684434
17.

A structural portrait of the PDZ domain family.

Ernst A, Appleton BA, Ivarsson Y, Zhang Y, Gfeller D, Wiesmann C, Sidhu SS.

J Mol Biol. 2014 Oct 23;426(21):3509-19. doi: 10.1016/j.jmb.2014.08.012. Epub 2014 Aug 23.

PMID:
25158098
18.

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

Gfeller D, Grosdidier A, Wirth M, Daina A, Michielin O, Zoete V.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W32-8. doi: 10.1093/nar/gku293. Epub 2014 May 3.

19.

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

Gfeller D, Ernst A, Jarvik N, Sidhu SS, Bader GD.

PLoS One. 2014 Apr 10;9(4):e94507. doi: 10.1371/journal.pone.0094507. eCollection 2014.

20.

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.

J Lipid Res. 2014 May;55(5):883-94. doi: 10.1194/jlr.M047126. Epub 2014 Mar 5.

21.

Shaping the interaction landscape of bioactive molecules.

Gfeller D, Michielin O, Zoete V.

Bioinformatics. 2013 Dec 1;29(23):3073-9. doi: 10.1093/bioinformatics/btt540. Epub 2013 Sep 17.

PMID:
24048355
22.

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

Chen S, Gfeller D, Buth SA, Michielin O, Leiman PG, Heinis C.

Chembiochem. 2013 Jul 22;14(11):1316-22. doi: 10.1002/cbic.201300228. Epub 2013 Jul 4.

PMID:
23828687
23.

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

Rahm N, Gfeller D, Snoeck J, Martinez R, McLaren PJ, Ortiz M, Ciuffi A, Telenti A.

Virology. 2013 Jul 5;441(2):162-70. doi: 10.1016/j.virol.2013.03.021. Epub 2013 Apr 17.

24.

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, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD.

Mol Syst Biol. 2013;9:652. doi: 10.1038/msb.2013.9.

25.

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

Gfeller D, Michielin O, Zoete V.

Nucleic Acids Res. 2013 Jan;41(Database issue):D327-32. doi: 10.1093/nar/gks991. Epub 2012 Oct 26.

26.

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

Gfeller D.

FEBS Lett. 2012 Aug 14;586(17):2764-72. doi: 10.1016/j.febslet.2012.03.054. Epub 2012 Apr 3. Review.

27.

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

Buey RM, Sen I, Kortt O, Mohan R, Gfeller D, Veprintsev D, Kretzschmar I, Scheuermann J, Neri D, Zoete V, Michielin O, de Pereda JM, Akhmanova A, Volkmer R, Steinmetz MO.

J Biol Chem. 2012 Aug 17;287(34):28227-42. doi: 10.1074/jbc.M112.373928. Epub 2012 Jun 13.

28.

Expanding molecular modeling and design tools to non-natural sidechains.

Gfeller D, Michielin O, Zoete V.

J Comput Chem. 2012 Jul 5;33(18):1525-35. doi: 10.1002/jcc.22982. Epub 2012 Apr 14.

PMID:
22505320
29.

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

Mostarda S, Gfeller D, Rao F.

PLoS Comput Biol. 2012;8(3):e1002429. doi: 10.1371/journal.pcbi.1002429. Epub 2012 Mar 8.

30.

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

Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM.

Nucleic Acids Res. 2012 Mar;40(6):e47. doi: 10.1093/nar/gkr1294. Epub 2011 Dec 30.

31.

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, Sidhu SS, Bader GD, Kim PM.

Mol Syst Biol. 2011 Apr 26;7:484. doi: 10.1038/msb.2011.18.

32.

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 GD, Sidhu SS, Vandekerckhove J, Gettemans J, Sudol M.

Biochem J. 2010 Dec 15;432(3):461-72. doi: 10.1042/BJ20100870.

PMID:
20868367
33.

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

Ernst A, Gfeller D, Kan Z, Seshagiri S, Kim PM, Bader GD, Sidhu SS.

Mol Biosyst. 2010 Oct;6(10):1782-90. doi: 10.1039/c0mb00061b. Epub 2010 Aug 11.

PMID:
20714644
34.

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

Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Currell B, Seshagiri S, Yu H, Winsor B, Vidal M, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C.

PLoS Biol. 2009 Oct;7(10):e1000218. doi: 10.1371/journal.pbio.1000218. Epub 2009 Oct 20.

35.

How to visually interpret biological data using networks.

Merico D, Gfeller D, Bader GD.

Nat Biotechnol. 2009 Oct;27(10):921-4. doi: 10.1038/nbt.1567.

36.

Spectral coarse graining and synchronization in oscillator networks.

Gfeller D, De Los Rios P.

Phys Rev Lett. 2008 May 2;100(17):174104. Epub 2008 May 2.

PMID:
18518293
37.

Uncovering the topology of configuration space networks.

Gfeller D, de Lachapelle DM, De Los Rios P, Caldarelli G, Rao F.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Aug;76(2 Pt 2):026113. Epub 2007 Aug 27.

PMID:
17930110
38.

Spectral coarse graining of complex networks.

Gfeller D, De Los Rios P.

Phys Rev Lett. 2007 Jul 20;99(3):038701. Epub 2007 Jul 19.

PMID:
17678338
39.

Complex network analysis of free-energy landscapes.

Gfeller D, De Los Rios P, Caflisch A, Rao F.

Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1817-22. Epub 2007 Jan 31.

40.

Finding instabilities in the community structure of complex networks.

Gfeller D, Chappelier JC, De Los Rios P.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Nov;72(5 Pt 2):056135. Epub 2005 Nov 29.

PMID:
16383716

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