Publications by authors named "David Gfeller"

58Publications

Structural dissimilarity from self drives neoepitope escape from immune tolerance.

Nat Chem Biol 2020 Nov 17;16(11):1269-1276. Epub 2020 Aug 17.

Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.

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http://dx.doi.org/10.1038/s41589-020-0610-1DOI Listing
November 2020

Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma.

Cancer Cell 2020 05 23;37(5):674-689.e12. Epub 2020 Apr 23.

Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2020.03.016DOI Listing
May 2020

Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq.

Oncoimmunology 2020 12;9(1):1737369. Epub 2020 Mar 12.

Department of Oncology UNIL CHUV, University of Lausanne, Epalinges, Switzerland.

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http://dx.doi.org/10.1080/2162402X.2020.1737369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153840PMC
March 2020

EPIC: A Tool to Estimate the Proportions of Different Cell Types from Bulk Gene Expression Data.

Methods Mol Biol 2020 ;2120:233-248

Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1007/978-1-0716-0327-7_17DOI Listing
January 2020

Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands.

Mol Cell Proteomics 2020 02 17;19(2):390-404. Epub 2019 Dec 17.

Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland

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http://dx.doi.org/10.1074/mcp.TIR119.001641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000122PMC
February 2020

Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands.

Front Immunol 2019 22;10:2731. Epub 2019 Nov 22.

Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.3389/fimmu.2019.02731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883762PMC
November 2019

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

Nat Biotechnol 2019 11 14;37(11):1283-1286. Epub 2019 Oct 14.

Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1038/s41587-019-0289-6DOI Listing
November 2019

Computational KIR copy number discovery reveals interaction between inhibitory receptor burden and survival.

Pac Symp Biocomput 2019 ;24:148-159

School of Medicine, University of California, San Diego, 9500 Gilman Dr., San Diego, CA 92093, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417817PMC
August 2019

Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores.

J Mol Biol 2019 01 22;431(2):336-350. Epub 2018 Nov 22.

The Donnelly Centre for Cellular and Biomolecular Research. University of Toronto, Toronto, ON M5S 3E1, Canada; Banting and Best Department of Medical Research. University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics. University of Toronto, Toronto, ON M5S 3E1, Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00222836183111
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http://dx.doi.org/10.1016/j.jmb.2018.11.018DOI Listing
January 2019

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

J Immunol 2018 12 14;201(12):3705-3716. Epub 2018 Nov 14.

Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland.

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http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1800914
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http://dx.doi.org/10.4049/jimmunol.1800914DOI Listing
December 2018

Predicting Antigen Presentation-What Could We Learn From a Million Peptides?

Front Immunol 2018 25;9:1716. Epub 2018 Jul 25.

Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.3389/fimmu.2018.01716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6068240PMC
July 2018

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

PLoS Comput Biol 2018 05 21;14(5):e1006188. Epub 2018 May 21.

Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Switzerland.

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http://dx.doi.org/10.1371/journal.pcbi.1006188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5983860PMC
May 2018

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

Proc Natl Acad Sci U S A 2018 05 30;115(20):5083-5088. Epub 2018 Apr 30.

Ludwig Institute for Cancer Research, Department of Fundamental Oncology, University of Lausanne, 1066 Epalinges, Switzerland;

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http://dx.doi.org/10.1073/pnas.1717277115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5960288PMC
May 2018

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

Elife 2017 11 13;6. Epub 2017 Nov 13.

Ludwig Centre for Cancer Research, Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland.

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http://dx.doi.org/10.7554/eLife.26476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718706PMC
November 2017

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

Front Immunol 2017 20;8:1367. Epub 2017 Oct 20.

Ludwig Cancer Research Center, University of Lausanne, Epalinges, Switzerland.

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http://dx.doi.org/10.3389/fimmu.2017.01367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654951PMC
October 2017

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

Immunogenetics 2017 07 22;69(7):439-450. Epub 2017 May 22.

Ludwig Centre for Cancer Research, University of Lausanne, 1066, Epalinges, Switzerland.

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http://dx.doi.org/10.1007/s00251-017-1002-xDOI Listing
July 2017

The pathogen-related yeast protein Pry1, a member of the CAP protein superfamily, is a fatty acid-binding protein.

J Biol Chem 2017 05 1;292(20):8304-8314. Epub 2017 Apr 1.

From the Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland,

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http://dx.doi.org/10.1074/jbc.M117.781880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437237PMC
May 2017

Broad and Conserved Immune Regulation by Genetically Heterogeneous Melanoma Cells.

Cancer Res 2017 04 19;77(7):1623-1636. Epub 2017 Jan 19.

Ludwig Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1158/0008-5472.CAN-16-2680DOI Listing
April 2017

Current tools for predicting cancer-specific T cell immunity.

Oncoimmunology 2016 Jul 25;5(7):e1177691. Epub 2016 Apr 25.

Ludwig Center for Cancer Research, University of Lausanne , Epalinges, Switzerland.

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http://dx.doi.org/10.1080/2162402X.2016.1177691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006903PMC
July 2016

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

J Immunol 2016 09 10;197(6):2492-9. Epub 2016 Aug 10.

Ludwig Center for Cancer Research of the University of Lausanne, 1066 Epalinges, Switzerland; and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland

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http://dx.doi.org/10.4049/jimmunol.1600808DOI Listing
September 2016

Protein homology reveals new targets for bioactive small molecules.

Bioinformatics 2015 Aug 21;31(16):2721-7. Epub 2015 Apr 21.

Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btv214DOI Listing
August 2015

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

J Endod 2015 Apr 12;41(4):442-6. Epub 2015 Feb 12.

Department of Oral and Maxillofacial Surgery, Copenhagen University Hospital, Copenhagen, Denmark.

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http://dx.doi.org/10.1016/j.joen.2014.11.024DOI Listing
April 2015

A structural portrait of the PDZ domain family.

J Mol Biol 2014 Oct 23;426(21):3509-19. Epub 2014 Aug 23.

Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, The Donnelly Centre, 160 College Street, Toronto, ON M5S 3E1, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2014.08.012DOI Listing
October 2014

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

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

Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland

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http://nar.oxfordjournals.org/content/early/2014/05/03/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gku293
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http://dx.doi.org/10.1093/nar/gku293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086140PMC
July 2014

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

PLoS One 2014 10;9(4):e94507. Epub 2014 Apr 10.

The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094507PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983204PMC
December 2014

Shaping the interaction landscape of bioactive molecules.

Bioinformatics 2013 Dec 17;29(23):3073-9. Epub 2013 Sep 17.

Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland, Ludwig Institute for Cancer Research and Pluridisciplinary Center for Clinical Oncology, Centre Hospitalier Universitaire Vaudois, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btt540DOI Listing
December 2013

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

Chembiochem 2013 Jul 4;14(11):1316-22. Epub 2013 Jul 4.

Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, BCH 5305 (Batochime), Avenue Forel 2, 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1002/cbic.201300228DOI Listing
July 2013

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

Virology 2013 Jul 17;441(2):162-70. Epub 2013 Apr 17.

Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1016/j.virol.2013.03.021DOI Listing
July 2013

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

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

Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/nar/gks991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531096PMC
January 2013

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

Authors:
David Gfeller

FEBS Lett 2012 Aug 3;586(17):2764-72. Epub 2012 Apr 3.

Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.

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http://doi.wiley.com/10.1016/j.febslet.2012.03.054
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http://dx.doi.org/10.1016/j.febslet.2012.03.054DOI Listing
August 2012

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

J Comput Chem 2012 Jul 14;33(18):1525-35. Epub 2012 Apr 14.

Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland.

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http://doi.wiley.com/10.1002/jcc.22982
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http://dx.doi.org/10.1002/jcc.22982DOI Listing
July 2012

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

PLoS Comput Biol 2012 8;8(3):e1002429. Epub 2012 Mar 8.

Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1002429DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297566PMC
June 2012

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

Nucleic Acids Res 2012 Mar 30;40(6):e47. Epub 2011 Dec 30.

The Donnelly Centre, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5S 3E1.

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http://dx.doi.org/10.1093/nar/gkr1294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315295PMC
March 2012

The multiple-specificity landscape of modular peptide recognition domains.

Mol Syst Biol 2011 Apr;7:484

Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/msb.2011.18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097085PMC
April 2011

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

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

Banting and Best Department of Medical Research, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada.

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http://xlink.rsc.org/?DOI=c0mb00061b
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http://dx.doi.org/10.1039/c0mb00061bDOI Listing
October 2010

How to visually interpret biological data using networks.

Nat Biotechnol 2009 Oct;27(10):921-4

Terrence Donnelly Centre for Cellular and Biomolecular Research and Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.

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http://www.nature.com/articles/nbt.1567
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http://dx.doi.org/10.1038/nbt.1567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154490PMC
October 2009

Spectral coarse graining and synchronization in oscillator networks.

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

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1.

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http://dx.doi.org/10.1103/PhysRevLett.100.174104DOI Listing
May 2008

Uncovering the topology of configuration space networks.

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

Laboratoire de Biophysique Statistique, SB/ITP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.

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http://dx.doi.org/10.1103/PhysRevE.76.026113DOI Listing
August 2007

Spectral coarse graining of complex networks.

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

Laboratoire de Biophysique Statistique, SB/ITP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.

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http://dx.doi.org/10.1103/PhysRevLett.99.038701DOI Listing
July 2007

Finding instabilities in the community structure of complex networks.

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

Laboratoire de Biophysique Statistique, SB/ITP, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1103/PhysRevE.72.056135DOI Listing
November 2005