The bacterial proteogenomic pipeline

por Uszkoreit, Julian, Plohnke, Nicole, Rexroth, Sascha, Marcus, Katrin, Eisenacher, Martin
Publicado 2014

Let me infuse this for you – A way to solve the first YPIC challenge

por Eggers, Britta, Pacharra, Sandra, Eisenacher, Martin, Marcus, Katrin, Uszkoreit, Julian
Publicado 2019

Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs

por Schork, Karin, Turewicz, Michael, Uszkoreit, Julian, Rahnenführer, Jörg, Eisenacher, Martin
Publicado 2022

Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition

por Barkovits, Katalin, Pacharra, Sandra, Pfeiffer, Kathy, Steinbach, Simone, Eisenacher, Martin, Marcus, Katrin, Uszkoreit, Julian
Publicado 2020

Dataset containing physiological amounts of spike-in proteins into murine C2C12 background as a ground truth quantitative LC-MS/MS reference

por Uszkoreit, Julian, Barkovits, Katalin, Pacharra, Sandra, Pfeiffer, Kathy, Steinbach, Simone, Marcus, Katrin, Eisenacher, Martin
Publicado 2022

Quality Control—A Stepchild in Quantitative Proteomics: A Case Study for the Human CSF Proteome

por Rozanova, Svitlana, Uszkoreit, Julian, Schork, Karin, Serschnitzki, Bettina, Eisenacher, Martin, Tönges, Lars, Barkovits-Boeddinghaus, Katalin, Marcus, Katrin
Publicado 2023

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics

por Perez-Riverol, Yasset, Uszkoreit, Julian, Sanchez, Aniel, Ternent, Tobias, del Toro, Noemi, Hermjakob, Henning, Vizcaíno, Juan Antonio, Wang, Rui
Publicado 2015

Proceedings of the EuBIC Winter School 2019

por Kopczynski, Dominik, Bittremieux, Wout, Bouyssié, David, Dorfer, Viktoria, Locard-Paulet, Marie, Van Puyvelde, Bart, Schwämmle, Veit, Soggiu, Alessio, Willems, Sander, Uszkoreit, Julian
Publicado 2019

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

por 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, Martin, Hermjakob, Henning, Vizcaíno, Juan Antonio
Publicado 2016

Homozygous expression of the myofibrillar myopathy-associated p.W2710X filamin C variant reveals major pathomechanisms of sarcomeric lesion formation

por Schuld, Julia, Orfanos, Zacharias, Chevessier, Frédéric, Eggers, Britta, Heil, Lorena, Uszkoreit, Julian, Unger, Andreas, Kirfel, Gregor, van der Ven, Peter F. M., Marcus, Katrin, Linke, Wolfgang A., Clemen, Christoph S., Schröder, Rolf, Fürst, Dieter O.
Publicado 2020

Ten Simple Rules for Taking Advantage of Git and GitHub

por Perez-Riverol, Yasset, Gatto, Laurent, Wang, Rui, Sachsenberg, Timo, Uszkoreit, Julian, Leprevost, Felipe da Veiga, Fufezan, Christian, Ternent, Tobias, Eglen, Stephen J., Katz, Daniel S., Pollard, Tom J., Konovalov, Alexander, Flight, Robert M., Blin, Kai, Vizcaíno, Juan Antonio
Publicado 2016

Spatial proteomics revealed a CX(3)CL1-dependent crosstalk between the urothelium and relocated macrophages through IL-6 during an acute bacterial infection in the urinary bladder

por Bottek, Jenny, Soun, Camille, Lill, Julia K., Dixit, Akanksha, Thiebes, Stephanie, Beerlage, Anna-Lena, Horstmann, Marius, Urbanek, Annett, Heuer, Heike, Uszkoreit, Julian, Eisenacher, Martin, Bracht, Thilo, Sitek, Barbara, Hoffmann, Franziska, Vijitha, Nirojah, von Eggeling, Ferdinand, Engel, Daniel R.
Publicado 2020

Plasma Proteomics Enable Differentiation of Lung Adenocarcinoma from Chronic Obstructive Pulmonary Disease (COPD)

por Bracht, Thilo, Kleefisch, Daniel, Schork, Karin, Witzke, Kathrin E., Chen, Weiqiang, Bayer, Malte, Hovanec, Jan, Johnen, Georg, Meier, Swetlana, Ko, Yon-Dschun, Behrens, Thomas, Brüning, Thomas, Fassunke, Jana, Buettner, Reinhard, Uszkoreit, Julian, Adamzik, Michael, Eisenacher, Martin, Sitek, Barbara
Publicado 2022

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

Toward an Integrated Machine Learning Model of a Proteomics Experiment

por Neely, Benjamin A., Dorfer, Viktoria, Martens, Lennart, Bludau, Isabell, Bouwmeester, Robbin, Degroeve, Sven, Deutsch, Eric W., Gessulat, Siegfried, Käll, Lukas, Palczynski, Pawel, Payne, Samuel H., Rehfeldt, Tobias Greisager, Schmidt, Tobias, Schwämmle, Veit, Uszkoreit, Julian, Vizcaíno, Juan Antonio, Wilhelm, Mathias, Palmblad, Magnus
Publicado 2023

BioContainers: an open-source and community-driven framework for software standardization

por da Veiga Leprevost, Felipe, Grüning, Björn A, Alves Aflitos, Saulo, Röst, Hannes L, Uszkoreit, Julian, Barsnes, Harald, Vaudel, Marc, Moreno, Pablo, Gatto, Laurent, Weber, Jonas, Bai, Mingze, Jimenez, Rafael C, Sachsenberg, Timo, Pfeuffer, Julianus, Vera Alvarez, Roberto, Griss, Johannes, Nesvizhskii, Alexey I, Perez-Riverol, Yasset
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

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases

por Mayer, Gerhard, Müller, Wolfgang, Schork, Karin, Uszkoreit, Julian, Weidemann, Andreas, Wittig, Ulrike, Rey, Maja, Quast, Christian, Felden, Janine, Glöckner, Frank Oliver, Lange, Matthias, Arend, Daniel, Beier, Sebastian, Junker, Astrid, Scholz, Uwe, Schüler, Danuta, Kestler, Hans A, Wibberg, Daniel, Pühler, Alfred, Twardziok, Sven, Eils, Jürgen, Eils, Roland, Hoffmann, Steve, Eisenacher, Martin, Turewicz, Michael
Publicado 2021

A proteomics sample metadata representation for multiomics integration and big data analysis

por Dai, Chengxin, Füllgrabe, Anja, Pfeuffer, Julianus, Solovyeva, Elizaveta M., Deng, Jingwen, Moreno, Pablo, Kamatchinathan, Selvakumar, Kundu, Deepti Jaiswal, George, Nancy, Fexova, Silvie, Grüning, Björn, Föll, Melanie Christine, Griss, Johannes, Vaudel, Marc, Audain, Enrique, Locard-Paulet, Marie, Turewicz, Michael, Eisenacher, Martin, Uszkoreit, Julian, Van Den Bossche, Tim, Schwämmle, Veit, Webel, Henry, Schulze, Stefan, Bouyssié, David, Jayaram, Savita, Duggineni, Vinay Kumar, Samaras, Patroklos, Wilhelm, Mathias, Choi, Meena, Wang, Mingxun, Kohlbacher, Oliver, Brazma, Alvis, Papatheodorou, Irene, Bandeira, Nuno, Deutsch, Eric W., Vizcaíno, Juan Antonio, Bai, Mingze, Sachsenberg, Timo, Levitsky, Lev I., Perez-Riverol, Yasset
Publicado 2021