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1

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

Astrid Slany, Verena J. Haudek, Nina C. Gundacker, Johannes Griss, Thomas Mohr, Helge Wimmer, Maria Eisenbauer, Leonilla Elbling, Christopher Gerner

Journal:

ELECTROPHORESIS

Year:

2009

Language:

english

File:

PDF, 286 KB

english, 2009

2

Introducing the CPL/MUW proteome database: Interpretation of human liver and liver cancer proteome profiles by referring to isolated primary cells

Helge Wimmer, Nina C. Gundacker, Johannes Griss, Verena J. Haudek, Stefan Stättner, Thomas Mohr, Hannes Zwickl, Verena Paulitschke, David M. Baron, Wolfgang Trittner, Markus Kubicek, Editha Bayer, Ast

Journal:

ELECTROPHORESIS

Year:

2009

Language:

english

File:

PDF, 752 KB

english, 2009

3

GPDE: A biological proteomic database for biomarker discovery and evaluation

Johannes Griss, Verena Haudek-Prinz, Christopher Gerner

Journal:

Year:

2011

Language:

english

File:

PDF, 318 KB

english, 2011

4

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

Joseph M. Foster, Sven Degroeve, Laurent Gatto, Matthieu Visser, Rui Wang, Johannes Griss, Rolf Apweiler, Lennart Martens

Journal:

Year:

2011

Language:

english

File:

PDF, 468 KB

english, 2011

5

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets

Johannes Griss, María Martín, Claire O'Donovan, Rolf Apweiler, Henning Hermjakob, Juan Antonio Vizcaíno

Journal:

Year:

2011

Language:

english

File:

PDF, 183 KB

english, 2011

6

GPDE: A biological proteomic database for biomarker discovery and evaluation

Johannes Griss, Verena Haudek-Prinz, Christopher Gerner

Journal:

PROTEOMICS - Clinical Applications

Year:

2011

Language:

english

File:

PDF, 92 KB

english, 2011

7

PRIDE Inspector: a tool to visualize and validate MS proteomics data

Wang, Rui, Fabregat, Antonio, Ríos, Daniel, Ovelleiro, David, Foster, Joseph M, Côté, Richard G, Griss, Johannes, Csordas, Attila, Perez-Riverol, Yasset, Reisinger, Florian

Journal:

Nature Biotechnology

Year:

2012

Language:

english

File:

PDF, 372 KB

english, 2012

8

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

Johannes Griss, Florian Reisinger, Henning Hermjakob, Juan Antonio Vizcaíno

Journal:

Year:

2012

Language:

english

File:

PDF, 1.27 MB

english, 2012

9

Proteome signatures of inflammatory activated primary human peripheral blood mononuclear cells

Haudek-Prinz, Verena J., Klepeisz, Philip, Slany, Astrid, Griss, Johannes, Meshcheryakova, Anastasia, Paulitschke, Verena, Mitulovic, Goran, Stöckl, Johannes, Gerner, Christopher

Journal:

Journal of Proteomics

Year:

2012

Language:

english

File:

PDF, 1.51 MB

english, 2012

10

PRIDE Cluster: building a consensus of proteomics data

Griss, Johannes, Foster, Joseph M, Hermjakob, Henning, Vizcaíno, Juan Antonio

Journal:

Year:

2013

Language:

english

File:

PDF, 2.46 MB

english, 2013

11

Functional Classification of Cellular Proteome Profiles Support the Identification of Drug Resistance Signatures in Melanoma Cells

Paulitschke, Verena, Haudek-Prinz, Verena, Griss, Johannes, Berger, Walter, Mohr, Thomas, Pehamberger, Hubert, Kunstfeld, Rainer, Gerner, Christopher

Journal:

Journal of Proteome Research

Year:

2013

Language:

english

File:

PDF, 3.03 MB

english, 2013

12

Cytoplasmic Proteome and Secretome Profiles of Differently Stimulated Human Dendritic Cells

Gundacker, Nina C., Haudek, Verena J., Wimmer, Helge, Slany, Astrid, Griss, Johannes, Bochkov, Valery, Zielinski, Christoph, Wagner, Oswald, Stöckl, Johannes, Gerner, Christopher

Journal:

Journal of Proteome Research

Year:

2009

Language:

english

File:

PDF, 2.21 MB

english, 2009

13

jmzTab: A Java interface to the mzTab data standard

Xu, Qing-Wei, Griss, Johannes, Wang, Rui, Jones, Andrew R., Hermjakob, Henning, Vizcaíno, Juan Antonio

Journal:

Year:

2014

Language:

english

File:

PDF, 346 KB

english, 2014

14

Comprehensive Comparative and Semiquantitative Proteome of a Very Low Number of Native and Matched Epstein–Barr-Virus-Transformed B Lymphocytes Infiltrating Human Melanoma

Maurer, Margarita, Müller, André C., Parapatics, Katja, Pickl, Winfried F., Wagner, Christine, Rudashevskaya, Elena L., Breitwieser, Florian P., Colinge, Jacques, Garg, Kanika, Griss, Johannes, Bennet

Journal:

Journal of Proteome Research

Year:

2014

Language:

english

File:

PDF, 4.54 MB

english, 2014

15

Identifying novel biomarkers through data mining-A realistic scenario?

Griss, Johannes, Perez-Riverol, Yasset, Hermjakob, Henning, Vizcaíno, Juan Antonio

Journal:

PROTEOMICS - Clinical Applications

Year:

2015

Language:

english

File:

PDF, 788 KB

english, 2015

16

Analysis of the tryptic search space in UniProt databases

Alpi, Emanuele, Griss, Johannes, da Silva, Alan Wilter Sousa, Bely, Benoit, Antunes, Ricardo, Zellner, Hermann, Ríos, Daniel, O'Donovan, Claire, Vizcaíno, Juan Antonio, Martin, Maria J.

Journal:

Year:

2015

Language:

english

File:

PDF, 452 KB

english, 2015

17

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets

Perez-Riverol, Yasset, Xu, Qing-Wei, Wang, Rui, Uszkoreit, Julian, Griss, Johannes, Sanchez, Aniel, Reisinger, Florian, Csordas, Attila, Ternent, Tobias, del-Toro, Noemi, Dianes, Jose A., Eisenacher,

Journal:

Molecular & Cellular Proteomics

Year:

2016

Language:

english

File:

PDF, 1.12 MB

english, 2016

18

Orally Administered Rapamycin, Dacarbazine or Both for Treatment of Human Melanoma Evaluated in Severe Combined Immunodeficiency Mice

Thallinger, Christiane, Skorjanec, Sophie, Soleiman, Afschin, Tzaneva, Stanislava, Griss, Johannes, Rous, Wolfgang, Poeppl, Wolfgang, Weinlich, Georg, Karimian-Teherani, Daniela, Joukhadar, Christian

Journal:

Year:

2008

Language:

english

File:

PDF, 304 KB

english, 2008

19

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

Schittmayer, Matthias, Fritz, Katarina, Liesinger, Laura, Griss, Johannes, Birner-Gruenberger, Ruth

Journal:

Journal of Proteome Research

Year:

2016

Language:

english

File:

PDF, 1.28 MB

english, 2016

20

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

Garg, Kanika, Maurer, Margarita, Griss, Johannes, Brüggen, Marie-Charlotte, Wolf, Ingrid H., Wagner, Christine, Willi, Niels, Mertz, Kirsten D., Wagner, Stephan N.

Journal:

Human Pathology

Year:

2016

Language:

english

File:

PDF, 505 KB

english, 2016

21

2016 update of the PRIDE database and its related tools

Vizcaíno, Juan Antonio, Csordas, Attila, del-Toro, Noemi, Dianes, José A., Griss, Johannes, Lavidas, Ilias, Mayer, Gerhard, Perez-Riverol, Yasset, Reisinger, Florian, Ternent, Tobias, Xu, Qing-Wei, Wa

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 2.59 MB

english, 2016

22

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

Griss, Johannes, Perez-Riverol, Yasset, Lewis, Steve, Tabb, David L, Dianes, José A, del-Toro, Noemi, Rurik, Marc, Walzer, Mathias, Kohlbacher, Oliver, Hermjakob, Henning, Wang, Rui, Vizcaíno, Juan An

Journal:

Year:

2016

Language:

english

File:

PDF, 1.24 MB

english, 2016

23

Spectral library searching in proteomics

Griss, Johannes

Journal:

Year:

2016

Language:

english

File:

PDF, 261 KB

english, 2016

24

2016 update of the PRIDE database and its related tools

Vizcaíno, Juan Antonio, Csordas, Attila, del-Toro, Noemi, Dianes, José A., Griss, Johannes, Lavidas, Ilias, Mayer, Gerhard, Perez-Riverol, Yasset, Reisinger, Florian, Ternent, Tobias, Xu, Qing-Wei, Wa

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 35 KB

english, 2016

25

Digital image analysis improves precision of programmed death ligand 1 (PD-L1) scoring in cutaneous melanoma

Koelzer, Viktor H., Gisler, Aline, Hanhart, Jonathan C., Griss, Johannes, Wagner, Stephan N., Willi, Niels, Cathomas, Gieri, Sachs, Melanie, Kempf, Werner, Thommen, Daniela S., Mertz, Kirsten D.

Journal:

Year:

2018

Language:

english

File:

PDF, 629 KB

english, 2018

26

Response to: “Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra”

Griss, Johannes, Perez-Riverol, Yasset, The, Matthew, Käll, Lukas, Vizcaíno, Juan A.

Journal:

Journal of Proteome Research

Year:

2018

Language:

english

File:

PDF, 405 KB

english, 2018

27

Future prospects of spectral clustering approaches in proteomics

Perez-Riverol, Yasset, Vizcaíno, Juan Antonio, Griss, Johannes

Journal:

Year:

2018

Language:

english

File:

PDF, 1.19 MB

english, 2018

28

The PRIDE database and related tools and resources in 2019: improving support for quantification data

Perez-Riverol, Yasset, Csordas, Attila, Bai, Jingwen, Bernal-Llinares, Manuel, Hewapathirana, Suresh, Kundu, Deepti J, Inuganti, Avinash, Griss, Johannes, Mayer, Gerhard, Eisenacher, Martin, Pérez, En

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 2.09 MB

english, 2018

29

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

Griss, Johannes, Stanek, Florian, Hudecz, Otto, Dürnberger, Gerhard, Perez-Riverol, Yasset, Vizcaíno, Juan Antonio, Mechtler, Karl

Journal:

Journal of Proteome Research

Year:

2019

Language:

english

File:

PDF, 740 KB

english, 2019

30

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

Griss, Johannes, Vinterhalter, Goran, Schwämmle, Veit

Journal:

Journal of Proteome Research

Year:

2019

Language:

english

File:

PDF, 1.09 MB

english, 2019

31

Separating Golgi proteins from cis to trans reveals underlying properties of cisternal localization

Parsons, Harriet T, Stevens, Tim J, McFarlane, Heather E., Vidal-Melgosa, Silvia, Griss, Johannes, Lawrence, Nicola, Butler, Richard, Sousa, Mirta M.L., Salemi, Michelle, Willats, William George Tycho

Journal:

Year:

2019

Language:

english

File:

PDF, 9.77 MB

english, 2019

32

B cells sustain inflammation and predict response to immune checkpoint blockade in human melanoma

Griss, Johannes, Bauer, Wolfgang, Wagner, Christine, Simon, Martin, Chen, Minyi, Grabmeier-Pfistershammer, Katharina, Maurer-Granofszky, Margarita, Roka, Florian, Penz, Thomas, Bock, Christoph, Zhang,

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 4.77 MB

english, 2019

33

B cells sustain inflammation and predict response to immune checkpoint blockade in human melanoma

Griss, Johannes, Bauer, Wolfgang, Wagner, Christine, Simon, Martin, Chen, Minyi, Grabmeier-Pfistershammer, Katharina, Maurer-Granofszky, Margarita, Roka, Florian, Penz, Thomas, Bock, Christoph, Zhang,

Journal:

Nature Communications

Year:

2019

File:

PDF, 4.77 MB

2019

34

ÃGDV PreistrÃ¤ger stellen sich vor: Der Wissenschaftspreis der ÃGDV 2019 ging an Dr.Â Johannes Griss und Dr.Â Philipp Tschandl

Griss, Johannes, Tschandl, Philipp

Journal:

JDDG: Journal der Deutschen Dermatologischen Gesellschaft

Year:

2020

File:

PDF, 409 KB

2020

35

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis

Griss, Johannes, Viteri, Guilherme, Sidiropoulos, Konstantinos, Nguyen, Vy, Fabregat, Antonio, Hermjakob, Henning

Journal:

Molecular & Cellular Proteomics

Year:

2020

File:

PDF, 598 KB

2020

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