Publications by authors named "Johannes Griss"

44Publications

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis.

Mol Cell Proteomics 2020 Sep 9. Epub 2020 Sep 9.

European Bioinformatics Institute, Wellcome Trust Genome Campus, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/mcp.TIR120.002155DOI Listing
September 2020

Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins.

J Proteome Res 2019 04 22;18(4):1477-1485. Epub 2019 Mar 22.

Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00377
Publisher Site
http://dx.doi.org/10.1021/acs.jproteome.8b00377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456873PMC
April 2019

IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments.

J Proteome Res 2019 04 20;18(4):1751-1759. Epub 2019 Mar 20.

Department for Biochemistry and Molecular Biology , University of Southern Denmark , Campusvej 55 , 5230 Odense , Denmark.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00968
Publisher Site
http://dx.doi.org/10.1021/acs.jproteome.8b00968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456869PMC
April 2019

Future Prospects of Spectral Clustering Approaches in Proteomics.

Proteomics 2018 07;18(14):e1700454

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/pmic.201700454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6099476PMC
July 2018

Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra".

J Proteome Res 2018 05 25;17(5):1993-1996. Epub 2018 Apr 25.

European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD , United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.7b00824DOI Listing
May 2018

Digital image analysis improves precision of PD-L1 scoring in cutaneous melanoma.

Histopathology 2018 Sep 5;73(3):397-406. Epub 2018 Jun 5.

Cantonal Hospital Baselland, Institute of Pathology, Liestal, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/his.13528DOI Listing
September 2018

2016 update of the PRIDE database and its related tools.

Nucleic Acids Res 2016 12 28;44(22):11033. Epub 2016 Sep 28.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkw880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159556PMC
December 2016

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

Nat Methods 2016 Aug 27;13(8):651-656. Epub 2016 Jun 27.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.3902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968634PMC
August 2016

Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification.

Anal Chem 2016 06 24;88(11):5733-41. Epub 2016 May 24.

Department of Biomedical Informatics, Vanderbilt University , Nashville, Tennessee 37203, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.analchem.6b00021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996967PMC
June 2016

Tumor-associated B cells in cutaneous primary melanoma and improved clinical outcome.

Hum Pathol 2016 08 21;54:157-64. Epub 2016 Apr 21.

Division of Immunology Allergy and Infectious Diseases (DIAID), Department of Dermatology, Medical University of Vienna, Vienna, Austria, A-1090. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.humpath.2016.03.022DOI Listing
August 2016

Cleaning out the Litterbox of Proteomic Scientists' Favorite Pet: Optimized Data Analysis Avoiding Trypsin Artifacts.

J Proteome Res 2016 Apr 22;15(4):1222-9. Epub 2016 Mar 22.

Research Unit Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz , 8010 Graz, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.5b01105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820788PMC
April 2016

Spectral library searching in proteomics.

Authors:
Johannes Griss

Proteomics 2016 Mar 9;16(5):729-40. Epub 2016 Feb 9.

Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1002/pmic.201500296
Publisher Site
http://dx.doi.org/10.1002/pmic.201500296DOI Listing
March 2016

2016 update of the PRIDE database and its related tools.

Nucleic Acids Res 2016 Jan 2;44(D1):D447-56. Epub 2015 Nov 2.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK National Center for Protein Sciences, Beijing, China.

View Article

Download full-text PDF

Source
http://nar.oxfordjournals.org/content/44/D1/D447.full.pdf
Web Search
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gkv1145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702828PMC
January 2016

Autoantibody Levels and Clinical Disease Severity in Patients with Pemphigus: Comparison of Aggregated Anti-desmoglein ELISA Values and Indirect Immunofluorescence Titres.

Acta Derm Venereol 2015 May;95(5):559-64

Department of Dermatology, Division of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria.

View Article

Download full-text PDF

Source
http://www.medicaljournals.se/acta/content/?doi=10.2340/0001
Publisher Site
http://dx.doi.org/10.2340/00015555-2023DOI Listing
May 2015

Identifying novel biomarkers through data mining-a realistic scenario?

Proteomics Clin Appl 2015 Apr 12;9(3-4):437-43. Epub 2015 Jan 12.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1002/prca.201400107
Publisher Site
http://dx.doi.org/10.1002/prca.201400107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833187PMC
April 2015

Analysis of the tryptic search space in UniProt databases.

Proteomics 2015 Jan 3;15(1):48-57. Epub 2014 Dec 3.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/pmic.201400227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298651PMC
January 2015

Comprehensive comparative and semiquantitative proteome of a very low number of native and matched epstein-barr-virus-transformed B lymphocytes infiltrating human melanoma.

J Proteome Res 2014 Jun 6;13(6):2830-45. Epub 2014 May 6.

Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna , Waehringer Guertel 18-20, A-1090 Vienna, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr401270yDOI Listing
June 2014

jmzTab: a java interface to the mzTab data standard.

Proteomics 2014 Jun 29;14(11):1328-32. Epub 2014 Apr 29.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Computer Science and Technology, Hubei University of Education, Wuhan, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/pmic.201300560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230411PMC
June 2014

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

Proteomics 2012 Mar;12(6):795-8

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/pmic.201100578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472022PMC
March 2012

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.

Mol Cell Proteomics 2011 Sep 23;10(9):M111.008490. Epub 2011 Jun 23.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://www.mcponline.org/lookup/doi/10.1074/mcp.M111.008490
Publisher Site
http://dx.doi.org/10.1074/mcp.M111.008490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3186200PMC
September 2011

A posteriori quality control for the curation and reuse of public proteomics data.

Proteomics 2011 Jun 2;11(11):2182-94. Epub 2011 May 2.

EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/pmic.201000602DOI Listing
June 2011

GPDE: A biological proteomic database for biomarker discovery and evaluation.

Proteomics 2011 Mar 27;11(5):1000-4. Epub 2011 Jan 27.

Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/pmic.201000507DOI Listing
March 2011

Introducing a new parameter for quality control of proteome profiles: consideration of commonly expressed proteins.

Electrophoresis 2009 Apr;30(8):1306-28

Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/elps.200800440DOI Listing
April 2009

Cytoplasmic proteome and secretome profiles of differently stimulated human dendritic cells.

J Proteome Res 2009 Jun;8(6):2799-811

Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr8011039DOI Listing
June 2009