ImmunoNodes – graphical development of complex immunoinformatics workflows

por Schubert, Benjamin, de la Garza, Luis, Mohr, Christopher, Walzer, Mathias, Kohlbacher, Oliver
Publicado 2017

FRED 2: an immunoinformatics framework for Python

por Schubert, Benjamin, Walzer, Mathias, Brachvogel, Hans-Philipp, Szolek, András, Mohr, Christopher, Kohlbacher, Oliver
Publicado 2016

Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry

por Aiche, Stephan, Sachsenberg, Timo, Kenar, Erhan, Walzer, Mathias, Wiswedel, Bernd, Kristl, Theresa, Boyles, Matthew, Duschl, Albert, Huber, Christian G, Berthold, Michael R, Reinert, Knut, Kohlbacher, Oliver
Publicado 2015

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

por Walzer, Mathias, García-Seisdedos, David, Prakash, Ananth, Brack, Paul, Crowther, Peter, Graham, Robert L., George, Nancy, Mohammed, Suhaib, Moreno, Pablo, Papatheodorou, Irene, Hubbard, Simon J., Vizcaíno, Juan Antonio
Publicado 2022

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

por Griss, Johannes, Perez-Riverol, Yasset, Lewis, Steve, Tabb, David L., Dianes, José A., del-Toro, Noemi, Rurik, Marc, Walzer, Mathias W., Kohlbacher, Oliver, Hermjakob, Henning, Wang, Rui, Vizcaíno, Juan Antonio
Publicado 2016

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

por Perez-Riverol, Yasset, Bai, Jingwen, Bandla, Chakradhar, García-Seisdedos, David, Hewapathirana, Suresh, Kamatchinathan, Selvakumar, Kundu, Deepti J, Prakash, Ananth, Frericks-Zipper, Anika, Eisenacher, Martin, Walzer, Mathias, Wang, Shengbo, Brazma, Alvis, Vizcaíno, Juan Antonio
Publicado 2021

The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics([Image: see text])

por Walzer, Mathias, Qi, Da, Mayer, Gerhard, Uszkoreit, Julian, Eisenacher, Martin, Sachsenberg, Timo, Gonzalez-Galarza, Faviel F., Fan, Jun, Bessant, Conrad, Deutsch, Eric W., Reisinger, Florian, Vizcaíno, Juan Antonio, Medina-Aunon, J. Alberto, Albar, Juan Pablo, Kohlbacher, Oliver, Jones, Andrew R.
Publicado 2013

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

por Deutsch, Eric W., Orchard, Sandra, Binz, Pierre-Alain, Bittremieux, Wout, Eisenacher, Martin, Hermjakob, Henning, Kawano, Shin, Lam, Henry, Mayer, Gerhard, Menschaert, Gerben, Perez-Riverol, Yasset, Salek, Reza M., Tabb, David L., Tenzer, Stefan, Vizcaíno, Juan Antonio, Walzer, Mathias, Jones, Andrew R.
Publicado 2017

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics

por Vizcaíno, Juan Antonio, Mayer, Gerhard, Perkins, Simon, Barsnes, Harald, Vaudel, Marc, Perez-Riverol, Yasset, Ternent, Tobias, Uszkoreit, Julian, Eisenacher, Martin, Fischer, Lutz, Rappsilber, Juri, Netz, Eugen, Walzer, Mathias, Kohlbacher, Oliver, Leitner, Alexander, Chalkley, Robert J., Ghali, Fawaz, Martínez-Bartolomé, Salvador, Deutsch, Eric W., Jones, Andrew R.
Publicado 2017

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

por Perez-Riverol, Yasset, Csordas, Attila, Bai, Jingwen, Bernal-Llinares, Manuel, Hewapathirana, Suresh, Kundu, Deepti J, Inuganti, Avinash, Griss, Johannes, Mayer, Gerhard, Eisenacher, Martin, Pérez, Enrique, Uszkoreit, Julian, Pfeuffer, Julianus, Sachsenberg, Timo, Yılmaz, Şule, Tiwary, Shivani, Cox, Jürgen, Audain, Enrique, Walzer, Mathias, Jarnuczak, Andrew F, Ternent, Tobias, Brazma, Alvis, Vizcaíno, Juan Antonio
Publicado 2019

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience

por Griss, Johannes, Jones, Andrew R., Sachsenberg, Timo, Walzer, Mathias, Gatto, Laurent, Hartler, Jürgen, Thallinger, Gerhard G., Salek, Reza M., Steinbeck, Christoph, Neuhauser, Nadin, Cox, Jürgen, Neumann, Steffen, Fan, Jun, Reisinger, Florian, Xu, Qing-Wei, del Toro, Noemi, Pérez-Riverol, Yasset, Ghali, Fawaz, Bandeira, Nuno, Xenarios, Ioannis, Kohlbacher, Oliver, Vizcaíno, Juan Antonio, Hermjakob, Henning
Publicado 2014

A community proposal to integrate proteomics activities in ELIXIR

por Vizcaíno, Juan Antonio, Walzer, Mathias, Jiménez, Rafael C., Bittremieux, Wout, Bouyssié, David, Carapito, Christine, Corrales, Fernando, Ferro, Myriam, Heck, Albert J.R., Horvatovich, Peter, Hubalek, Martin, Lane, Lydie, Laukens, Kris, Levander, Fredrik, Lisacek, Frederique, Novak, Petr, Palmblad, Magnus, Piovesan, Damiano, Pühler, Alfred, Schwämmle, Veit, Valkenborg, Dirk, van Rijswijk, Merlijn, Vondrasek, Jiri, Eisenacher, Martin, Martens, Lennart, Kohlbacher, Oliver
Publicado 2017

qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments

por Walzer, Mathias, Pernas, Lucia Espona, Nasso, Sara, Bittremieux, Wout, Nahnsen, Sven, Kelchtermans, Pieter, Pichler, Peter, van den Toorn, Henk W. P., Staes, An, Vandenbussche, Jonathan, Mazanek, Michael, Taus, Thomas, Scheltema, Richard A., Kelstrup, Christian D., Gatto, Laurent, van Breukelen, Bas, Aiche, Stephan, Valkenborg, Dirk, Laukens, Kris, Lilley, Kathryn S., Olsen, Jesper V., Heck, Albert J. R., Mechtler, Karl, Aebersold, Ruedi, Gevaert, Kris, Vizcaíno, Juan Antonio, Hermjakob, Henning, Kohlbacher, Oliver, Martens, Lennart
Publicado 2014

Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient

por Löffler, Markus W., Chandran, P. Anoop, Laske, Karoline, Schroeder, Christopher, Bonzheim, Irina, Walzer, Mathias, Hilke, Franz J., Trautwein, Nico, Kowalewski, Daniel J., Schuster, Heiko, Günder, Marc, Carcamo Yañez, Viviana A., Mohr, Christopher, Sturm, Marc, Nguyen, Huu-Phuc, Riess, Olaf, Bauer, Peter, Nahnsen, Sven, Nadalin, Silvio, Zieker, Derek, Glatzle, Jörg, Thiel, Karolin, Schneiderhan-Marra, Nicole, Clasen, Stephan, Bösmüller, Hans, Fend, Falko, Kohlbacher, Oliver, Gouttefangeas, Cécile, Stevanović, Stefan, Königsrainer, Alfred, Rammensee, Hans-Georg
Publicado 2016

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

por Löffler, Markus W., Mohr, Christopher, Bichmann, Leon, Freudenmann, Lena Katharina, Walzer, Mathias, Schroeder, Christopher M., Trautwein, Nico, Hilke, Franz J., Zinser, Raphael S., Mühlenbruch, Lena, Kowalewski, Daniel J., Schuster, Heiko, Sturm, Marc, Matthes, Jakob, Riess, Olaf, Czemmel, Stefan, Nahnsen, Sven, Königsrainer, Ingmar, Thiel, Karolin, Nadalin, Silvio, Beckert, Stefan, Bösmüller, Hans, Fend, Falko, Velic, Ana, Maček, Boris, Haen, Sebastian P., Buonaguro, Luigi, Kohlbacher, Oliver, Stevanović, Stefan, Königsrainer, Alfred, Rammensee, Hans-Georg
Publicado 2019

Erratum to “Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient”

por Löffler, Markus W., Chandran, P. Anoop, Laske, Karoline, Schroeder, Christopher, Bonzheim, Irina, Walzer, Mathias, Hilke, Franz J., Trautwein, Nico, Kowalewski, Daniel J., Schuster, Heiko, Günder, Marc, Carcamo Yañez, Viviana A., Mohr, Christopher, Sturm, Marc, Nguyen, Huu-Phuc, Riess, Olaf, Bauer, Peter, Nahnsen, Sven, Nadalin, Silvio, Zieker, Derek, Glatzle, Jörg, Thiel, Karolin, Schneiderhan-Marra, Nicole, Clasen, Stephan, Bösmüller, Hans, Fend, Falko, Kohlbacher, Oliver, Gouttefangeas, Cécile, Stevanović, Stefan, Königsrainer, Alfred, Rammensee, Hans-Georg
Publicado 2017

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

por Deutsch, Eric W., Vizcaíno, Juan Antonio, Jones, Andrew R., Binz, Pierre-Alain, Lam, Henry, Klein, Joshua, Bittremieux, Wout, Perez-Riverol, Yasset, Tabb, David L., Walzer, Mathias, Ricard-Blum, Sylvie, Hermjakob, Henning, Neumann, Steffen, Mak, Tytus D., Kawano, Shin, Mendoza, Luis, Van Den Bossche, Tim, Gabriels, Ralf, Bandeira, Nuno, Carver, Jeremy, Pullman, Benjamin, Sun, Zhi, Hoffmann, Nils, Shofstahl, Jim, Zhu, Yunping, Licata, Luana, Quaglia, Federica, Tosatto, Silvio C. E., Orchard, Sandra E.
Publicado 2023

Expression Atlas update: gene and protein expression in multiple species

por Moreno, Pablo, Fexova, Silvie, George, Nancy, Manning, Jonathan R, Miao, Zhichiao, Mohammed, Suhaib, Muñoz-Pomer, Alfonso, Fullgrabe, Anja, Bi, Yalan, Bush, Natassja, Iqbal, Haider, Kumbham, Upendra, Solovyev, Andrey, Zhao, Lingyun, Prakash, Ananth, García-Seisdedos, David, Kundu, Deepti J, Wang, Shengbo, Walzer, Mathias, Clarke, Laura, Osumi-Sutherland, David, Tello-Ruiz, Marcela Karey, Kumari, Sunita, Ware, Doreen, Eliasova, Jana, Arends, Mark J, Nawijn, Martijn C, Meyer, Kerstin, Burdett, Tony, Marioni, John, Teichmann, Sarah, Vizcaíno, Juan Antonio, Brazma, Alvis, Papatheodorou, Irene
Publicado 2021