Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides von Umer, Husen M, Audain, Enrique, Zhu, Yafeng, Pfeuffer, Julianus, Sachsenberg, Timo, Lehtiö, Janne, Branca, Rui M, Perez-Riverol, Yasset

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Comprehensive analysis of alternative splicing across tumors from 8,705 patients von Kahles, A, Lehmann, K-V, Toussaint, NC, Huser, M, Stark, SG, Sachsenberg, T, Stegle, O, Kohlbacher, O, Sander, C, Ratsch, G

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Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry von Stützer, A, Welp, LM, Raabe, M, Sachsenberg, T, Kappert, C, Wulf, A, Lau, AM, David, S-S, Chernev, A, Kramer, K, Politis, A, Kohlbacher, O, Fischle, W, Urlaub, H

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

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Aus der Tannenwalds Kinderstube

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A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry von Wein, Samuel, Andrews, Byron, Sachsenberg, Timo, Santos-Rosa, Helena, Kohlbacher, Oliver, Kouzarides, Tony, Garcia, Benjamin A., Weisser, Hendrik

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

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Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana von Laubinger, Sascha, Sachsenberg, Timo, Zeller, Georg, Busch, Wolfgang, Lohmann, Jan U, Rätsch, Gunnar, Weigel, Detlef

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ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion von Hulstaert, Niels, Shofstahl, Jim, Sachsenberg, Timo, Walzer, Mathias, Barsnes, Harald, Martens, Lennart, Perez-Riverol, Yasset

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

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Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins von Kramer, Katharina, Sachsenberg, Timo, Beckmann, Benedikt M, Qamar, Saadia, Boon, Kum-Loong, Hentze, Matthias W, Kohlbacher, Oliver, Urlaub, Henning

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Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays von Zeller, Georg, Henz, Stefan R, Widmer, Christian K, Sachsenberg, Timo, Rätsch, Gunnar, Weigel, Detlef, Laubinger, Sascha

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

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Ten Simple Rules for Taking Advantage of Git and GitHub von 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

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Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry von Stützer, Alexandra, Welp, Luisa M., Raabe, Monika, Sachsenberg, Timo, Kappert, Christin, Wulf, Alexander, Lau, Andy M., David, Stefan-Sebastian, Chernev, Aleksandar, Kramer, Katharina, Politis, Argyris, Kohlbacher, Oliver, Fischle, Wolfgang, Urlaub, Henning

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LFQ-Based Peptide and Protein Intensity Differential Expression Analysis von Bai, Mingze, Deng, Jingwen, Dai, Chengxin, Pfeuffer, Julianus, Sachsenberg, Timo, Perez-Riverol, Yasset

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mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics von Hoffmann, Nils, Rein, Joel, Sachsenberg, Timo, Hartler, Jürgen, Haug, Kenneth, Mayer, Gerhard, Alka, Oliver, Dayalan, Saravanan, Pearce, Jake T. M, Rocca-Serra, Philippe, Qi, Da, Eisenacher, Martin, Perez-Riverol, Yasset, Vizcaíno, Juan Antonio, Salek, Reza M, Neumann, Steffen, Jones, Andrew R

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OpenMS: a flexible open-source software platform for mass spectrometry data analysis von Röst, Hannes L, Sachsenberg, Timo, Aiche, Stephan, Bielow, Chris, Weisser, Hendrik, Aicheler, Fabian, Andreotti, Sandro, Ehrlich, Hans-Christian, Gutenbrunner, Petra, Kenar, Erhan, Liang, Xiao, Nahnsen, Sven, Nilse, Lars, Pfeuffer, Julianus, Rosenberger, George, Rurik, Marc, Schmitt, Uwe, Veit, Johannes, Walzer, Mathias, Wojnar, David, Wolski, Witold E, Schilling, Oliver, Choudhary, Jyoti S, Malmström, Lars, Aebersold, Ruedi, Reinert, Knut, Kohlbacher, Oliver

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

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Expanding the Use of Spectral Libraries in Proteomics von Deutsch, Eric W, Perez-Riverol, Yasset, Chalkley, Robert J, Wilhelm, Mathias, Tate, Stephen, Sachsenberg, Timo, Walzer, Mathias, Käll, Lukas, Delanghe, Bernard, Böcker, Sebastian, Schymanski, Emma L, Wilmes, Paul, Dorfer, Viktoria, Kuster, Bernhard, Volders, Pieter-Jan, Jehmlich, Nico, Vissers, Johannes P. C, Wolan, Dennis W, Wang, Ana Y, Mendoza, Luis, Shofstahl, Jim, Dowsey, Andrew W, Griss, Johannes, Salek, Reza M, Neumann, Steffen, Binz, Pierre-Alain, Lam, Henry, Vizcaíno, Juan Antonio, Bandeira, Nuno, Röst, Hannes

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