@article{Alka2022, abstract = {AbstractThe extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. For targeted approaches in metabolomics a main challenge is the detection of false positive metabolic features in the low signal-to-noise ranges of data-independent acquisition results and their filtering. Another factor is that the creation of assay libraries for data-independent acquisition analysis and the processing of extracted ion chromatograms have not been automated in metabolomics. Here we present a fully automated open-source workflow for high-throughput metabolomics that combines data-dependent and data-independent acquisition for library generation, analysis, and statistical validation, with rigorous control of the false-discovery rate while matching manual analysis regarding quantification accuracy. Using an experimentally specific data-dependent acquisition library based on reference substances allows for accurate identification of compounds and markers from data-independent acquisition data in low concentrations, facilitating biomarker quantification.}, author = {Alka, Oliver and Shanthamoorthy, Premy and Witting, Michael and Kleigrewe, Karin and Kohlbacher, Oliver and Röst, Hannes L.}, doi = {10.1038/s41467-022-29006-z}, journal = {Nature Communications}, month = {mar}, title = {DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics}, url = {https://doi.org/10.1038/s41467-022-29006-z}, volume = {13}, year = {2022} } @article{Beck2013, abstract = {One of the most important physiological platelet inhibitors is endothelium-derived prostacyclin which stimulates the platelet cyclic adenosine monophosphate/protein kinase A (cAMP/PKA)-signaling cascade and inhibits virtually all platelet-activating key mechanisms. Using quantitative mass spectrometry, we analyzed time-resolved phosphorylation patterns in human platelets after treatment with iloprost, a stable prostacyclin analog, for 0, 10, 30, and 60 seconds to characterize key mediators of platelet inhibition and activation in 3 independent biological replicates. We quantified over 2700 different phosphorylated peptides of which 360 were significantly regulated upon stimulation. This comprehensive and time-resolved analysis indicates that platelet inhibition is a multi-pronged process involving different kinases and phosphatases as well as many previously unanticipated proteins and pathways.}, author = {Beck, Florian and Geiger, Jörg and Zahedi, René P. and Gambaryan, Stepan and Veit, Johannes and Vaudel, Marc and Nollau, Peter and Kohlbacher, Oliver and Martens, Lennart and Walter, Ulrich and Sickmann, Albert and Rp, Zahedi}, doi = {10.1182/blood-2013-07-512384}, journal = {Blood}, month = {dec}, pages = {e1-e10}, title = {Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways}, url = {http://www.bloodjournal.org/content/123/5/e1.full.pdf}, volume = {123}, year = {2013} } @article{Bichmann2019, author = {Bichmann, Leon and Nelde, Annika and Ghosh, Michael and Heumos, Lukas and Mohr, Christopher and Peltzer, Alexander and Kuchenbecker, Leon and Sachsenberg, Timo and Walz, Juliane S. and Stevanović, Stefan and Rammensee, Hans-Georg and Kohlbacher, Oliver}, doi = {10.1021/acs.jproteome.9b00313}, journal = {Journal of Proteome Research}, month = {oct}, pages = {3876-3884}, title = {MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics}, url = {https://oadoi.org/10.1021/acs.jproteome.9b00313}, volume = {18}, year = {2019} } @article{Bichmann2021, author = {Bichmann, Leon and Gupta, Shubham and Rosenberger, George and Kuchenbecker, Leon and Sachsenberg, Timo and Ewels, Phil and Alka, Oliver and Pfeuffer, Julianus and Kohlbacher, Oliver and Röst, Hannes}, doi = {10.1021/acs.jproteome.1c00123}, journal = {Journal of Proteome Research}, month = {jun}, pages = {3758-3766}, title = {DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics}, url = {https://oadoi.org/10.1021/acs.jproteome.1c00123}, volume = {20}, year = {2021} } @article{Bilich2018, abstract = {Abstract Chronic myeloid leukemia (CML) is characterized by the translocation t(9;22), which leads to the formation of the BCR-ABL fusion transcript. Several approved tyrosine kinase inhibitors (TKIs) target the resulting fusion protein, leading to an improved prognosis of CML patients. Currently, the main treatment goal is the achievement of a deep molecular response (MR), in which TKI therapy can be terminated. Several studies provide evidence that immunological control plays a major role for the course of CML and contributes to the achievement of deep MR in CML patients under TKI treatment (CMLTKI). This implies that reinforcing these immune responses might sustain long-term TKI-free survival or even cure for CML patients. Besides unspecific immunotherapy, such as interferon or immune checkpoint blocking antibodies, a more specific and minor side effect targeting of CML cells might be achieved by antigen-specific immunotherapy approaches. The prerequisite for such strategies is the identification of T-cell targets represented by tumor-associated human leukocyte antigen (HLA)-presented peptides on malignant cells. In this study, we used a mass spectrometry-based approach to identify naturally presented, CML-associated peptides in primary CML samples (HLA class I, n=21, 11,945 peptides, 5,478 source proteins; class II, n=20, 5,991 peptides, 1,302 proteins). Comparative HLA peptidome profiling using a comprehensive dataset of various benign tissues (e.g. blood, bone marrow, spleen, and lung) revealed frequently presented and strictly CML-associated antigens. In detail, the benign tissue dataset comprises hematological benign samples (class I, n=108, 51,233 peptides, 11,437 proteins; class II, n=88, 42,753 peptides, 4,877 proteins) and non-hematological benign tissues (28 tissues, n=166; class I, 128,590 peptides, 16,405 proteins; class II, 143,652 peptides, 13,410 proteins). We identified 50 CML-associated, HLA class I-restricted peptides with HLA allotype adjusted representation frequencies of ≥38% presented on HLA-A*02, -A*03, -A*11, and -B*07. HLA class II comparative profiling delineated 36 peptides exclusively and frequently presented in the HLA peptidome of ≥20% analyzed CML patients. For immunological characterization, we selected 8 HLA class I- and 6 class II-restricted highly CML-associated antigens. These peptides were analyzed in IFNγ ELISPOT assays using PBMCs from CMLTKI patients and healthy volunteers (HVs). Peptide-specific immune recognition was detected for 1/8 (13%) HLA class I peptides in 2/17 (12%) of CMLTKI patients. We hypothesized that this weak immune response might be due to an impaired CD8+ T cell function that reportedly is caused by TKI treatment. Thus, we compared T-cell responses against viral epitopes in IFNγ ELISPOT assays of CMLTKI patients with that of HVs and chronic lymphocytic leukemia (CLL) patients: in line with our hypothesis, we observed significantly reduced IFNγ release of T cells from CMLTKI patients compared to HVs and CLL patients (p<0.001), whereas CD8+ T-cell counts were not reduced. In contrast, no reduced IFNγ production was observed for HLA class II-restricted viral epitopes. These results were confirmed by memory T-cell responses detected for 6/6 (100%) HLA class II CML-associated peptides with frequencies up to 24% (4/17) of analyzed CMLTKI patients. To assess the immunogenicity of all HLA class I peptides, we performed in vitro artificial antigen presenting cell-based priming experiments using CD8+ T cells of HVs and CML patients. Effective priming of T cells was observed for 8/8 CML-associated peptides in ≥70% of analyzed HVs with frequencies of 0.1-33.9% (mean 2.2%) of CD8+ peptide-specific T cells. Notably, peptide-specific CD8+ T cells with frequencies of 0.1-2.2% (mean 0.4%) could also be induced in samples of CMLTKI patients that had not displayed preexisting immune responses. For 6/8 peptides, we observed multifunctionality of peptide-specific T cells by IFNγ and TNF production as well as upregulation of the degranulation marker CD107a. Cytotoxicity assays with polyclonal peptide-specific effector T cells confirmed the capacity to induce antigen-specific lysis for 3/4 analyzed peptides. Taken together, we here identified novel, naturally presented, CML-associated antigens and validated them as promising targets for tailored T cell-based immunotherapeutic approaches for CML patients. Disclosures Salih: Several patent applications: Patents & Royalties: e.g. EP3064507A1. Kowalewski:Immatics Biotechnologies GmbH: Employment. Schuster:Immatics Biotechnologies GmbH: Employment. Brümmendorf:Pfizer: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Janssen: Consultancy; Merck: Consultancy; Takeda: Consultancy. Niederwieser:Miltenyi: Speakers Bureau; Novartis: Research Funding. }, author = {Bilich, Tatjana and Nelde, Annika and Bichmann, Leon and Salih, Helmut R. and Kowalewski, Daniel Johannes and Schuster, Heiko and Tsou, Chih-Chiang and Marcu, Ana and Luebke, Maren and Neidert, Marian C. and Lübke, Maren and Roerden, Malte and Rieth, Jonas and Schemionek, Mirle and Brümmendorf, Tim H. and Bruemmendorf, Tim H. and Vucinic, Vladan and Niederwieser, Dietger and Maerklin, Melanie and Bauer, Jens and Märklin, Melanie and Peper, Janet K. and Klein, Reinhild and Kohlbacher, Oliver and Kanz, Lothar and Rammensee, Hans-Georg and Stevanovic, Stefan and Walz, Juliane S.}, doi = {10.1182/blood-2018-07-866830}, journal = {Blood}, month = {nov}, pages = {4243-4243}, title = {The HLA Ligandome Landscape of Chronic Myeloid Leukemia Delineates Novel T-Cell Epitopes for Immunotherapy}, url = {https://oadoi.org/10.1182/blood-2018-07-866830}, volume = {132}, year = {2018} } @article{Buchert2022, abstract = {To identify potential genetic causes for Mayer-Rokitansky-Küster-Hauser syndrome (MRKH), we analyzed blood and rudimentary uterine tissue of 5 MRKH discordant monozygotic twin pairs. Assuming that a variant solely identified in the affected twin or affected tissue could cause the phenotype, we identified a mosaic variant in ACTR3B with high allele frequency in the affected tissue, low allele frequency in the blood of the affected twin, and almost absent in blood of the unaffected twin. Focusing on MRKH candidate genes, we detected a pathogenic variant in GREB1L in one twin pair and their unaffected mother showing a reduced phenotypic penetrance. Furthermore, two variants of unknown clinical significance in PAX8 and WNT9B were identified. In addition, we conducted transcriptome analysis of affected tissue and observed perturbations largely similar to those in sporadic cases. These shared transcriptional changes were enriched for terms associated with estrogen and its receptors pointing at a role of estrogen in MRKH pathology. Our genome sequencing approach of blood and uterine tissue of discordant twins is the most extensive study performed on twins discordant for MRKH so far. As no clear pathogenic differences were detected, research to evaluate other regulatory layers are required to better understand the complex etiology of MRKH.}, author = {Buchert, Rebecca and Schenk, Elisabeth and Hentrich, Thomas and Weber, Nico and Rall, Katharina and Sturm, Marc and Kohlbacher, Oliver and Koch, André and Riess, Olaf and Brucker, Sara Y. and Schulze-Hentrich, Julia M.}, doi = {10.3390/jcm11195598}, journal = {Journal of Clinical Medicine}, month = {sep}, pages = {5598}, title = {Genome Sequencing and Transcriptome Profiling in Twins Discordant for Mayer-Rokitansky-Küster-Hauser Syndrome}, url = {https://doi.org/10.3390/jcm11195598}, volume = {11}, year = {2022} } @article{Dai2021, abstract = {AbstractThe amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.}, author = {Dai, Chengxin and Füllgrabe, Anja and Pfeuffer, Julianus and Solovyeva, Elizaveta M. and Deng, Jingwen and Moreno, Pablo and Kamatchinathan, Selvakumar and Kundu, Deepti Jaiswal and George, Nancy and Fexova, Silvie and Grüning, Björn and Föll, Melanie Christine and Griss, Johannes and Vaudel, Marc and Audain, Enrique and Locard-Paulet, Marie and Turewicz, Michael and Eisenacher, Martin and Uszkoreit, Julian and Van Den Bossche, Tim and Schwämmle, Veit and Webel, Henry and Schulze, Stefan and Bouyssié, David and Jayaram, Savita and Duggineni, Vinay Kumar and Samaras, Patroklos and Wilhelm, Mathias and Choi, Meena and Wang, Mingxun and Kohlbacher, Oliver and Brazma, Alvis and Papatheodorou, Irene and Bandeira, Nuno and Deutsch, Eric W. and Vizcaíno, Juan Antonio and Bai, Mingze and Sachsenberg, Timo and Levitsky, Lev I. and Perez-Riverol, Yasset}, doi = {10.1038/s41467-021-26111-3}, journal = {Nature Communications}, month = {oct}, title = {A proteomics sample metadata representation for multiomics integration and big data analysis}, url = {https://doi.org/10.1038/s41467-021-26111-3}, volume = {12}, year = {2021} } @article{Friedrich2015, abstract = {Big data bioinformatics aims at drawing biological conclusions from huge and complex biological datasets. Added value from the analysis of big data, however, is only possible if the data is accompanied by accurate metadata annotation. Particularly in high-throughput experiments intelligent approaches are needed to keep track of the experimental design, including the conditions that are studied as well as information that might be interesting for failure analysis or further experiments in the future. In addition to the management of this information, means for an integrated design and interfaces for structured data annotation are urgently needed by researchers. Here, we propose a factor-based experimental design approach that enables scientists to easily create large-scale experiments with the help of a web-based system. We present a novel implementation of a web-based interface allowing the collection of arbitrary metadata. To exchange and edit information we provide a spreadsheet-based, humanly readable format. Subsequently, sample sheets with identifiers and metainformation for data generation facilities can be created. Data files created after measurement of the samples can be uploaded to a datastore, where they are automatically linked to the previously created experimental design model.}, author = {Friedrich, Andreas and Kenar, Erhan and Kohlbacher, Oliver and Nahnsen, Sven}, doi = {10.1155/2015/958302}, journal = {BioMed Research International}, month = {jan}, pages = {1-8}, title = {Intuitive Web-Based Experimental Design for High-Throughput Biomedical Data}, url = {https://doi.org/10.1155/2015/958302}, volume = {2015}, year = {2015} } @article{Gerasch2014, abstract = {Interactive visual analysis of biological high-throughput data in the context of the underlying networks is an essential task in modern biomedicine with applications ranging from metabolic engineering to personalized medicine. The complexity and heterogeneity of data sets require flexible software architectures for data analysis. Concise and easily readable graphical representation of data and interactive navigation of large data sets are essential in this context. We present BiNA - the Biological Network Analyzer - a flexible open-source software for analyzing and visualizing biological networks. Highly configurable visualization styles for regulatory and metabolic network data offer sophisticated drawings and intuitive navigation and exploration techniques using hierarchical graph concepts. The generic projection and analysis framework provides powerful functionalities for visual analyses of high-throughput omics data in the context of networks, in particular for the differential analysis and the analysis of time series data. A direct interface to an underlying data warehouse provides fast access to a wide range of semantically integrated biological network databases. A plugin system allows simple customization and integration of new analysis algorithms or visual representations. BiNA is available under the 3-clause BSD license at http://bina.unipax.info/.}, author = {Gerasch, Andreas and Faber, Daniel and Küntzer, Jan and Niermann, Peter and Kohlbacher, Oliver and Lenhof, Hans-Peter and Kaufmann, Michael}, doi = {10.1371/journal.pone.0087397}, journal = {PLoS ONE}, month = {feb}, pages = {e87397}, title = {BiNA: A Visual Analytics Tool for Biological Network Data}, url = {https://doi.org/10.1371/journal.pone.0087397}, volume = {9}, year = {2014} } @article{Hoffmann2023, abstract = {In recent years, modern life sciences research underwent a rapid development driven mainly by the technical improvements in analytical areas leading to miniaturization, parallelization, and high throughput processing of biological samples. This has led to the generation of huge amounts of experimental data. To meet these rising demands, the German Network for Bioinformatics Infrastructure (de.NBI) was established in 2015 as a national bioinformatics consortium aiming to provide high quality bioinformatics services, comprehensive training, powerful computing capacities (de.NBI Cloud) as well as connections to the European Life Science Infrastructure ELIXIR, with the goal to assist researchers in exploring and exploiting data more effectively. Since its foundation, de.NBI Cloud has formed the scientific and collaborative backbone for new major German initiatives like NFDI or EOSC-Life in the European sector of computational biosciences. Above all, the cooperation with various NFDI consortia such as NFDI4Biodiversity, DataPLANT, GHGA, FAIRagro or NFDI4Microbiota showcases the power, range and flexibility of the de.NBI Cloud, especially for the national life science community. In conclusion, the de.NBI Cloud provides the ability to unlock the full potential of research data and enables easier collaboration across different ecosystems and research areas, which in turn enables scientists to innovate and scale-up their data-driven research, not only in the life and computational biosciences, but across the different science domains addressed by the NFDI. }, author = {Hoffmann, Nils and Maus, Irena and Beier, Sebastian and Belmann, Peter and Krüger, Jan and Tauch, Andreas and Goesmann, Alexander and Eils, Roland and Bork, Peer and Kohlbacher, Oliver and Kummer, Ursula and Backofen, Rolf and Buchhalter, Ivo and Sczyrba, Alexander}, doi = {10.52825/cordi.v1i.387}, journal = {Proceedings of the Conference on Research Data Infrastructure}, month = {sep}, title = {Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities}, url = {https://doi.org/10.52825/cordi.v1i.387}, volume = {1}, year = {2023} } @article{Immel2021, abstract = {AbstractThe Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34–58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections.}, author = {Immel, Alexander and Pierini, Federica and Rinne, Christoph and Meadows, John and Barquera, Rodrigo and Szolek, András and Susat, Julian and Böhme, Lisa and Dose, Janina and Bonczarowska, Joanna and Drummer, Clara and Fuchs, Katharina and Ellinghaus, David and Kässens, Jan Christian and Furholt, Martin and Kohlbacher, Oliver and Schade-Lindig, Sabine and Franke, Andre and Schreiber, Stefan and Krause, Johannes and Müller, Johannes and Lenz, Tobias L. and Nebel, Almut and Krause-Kyora, Ben}, doi = {10.1038/s42003-020-01627-4}, journal = {Communications Biology}, month = {jan}, title = {Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry}, url = {https://doi.org/10.1038/s42003-020-01627-4}, volume = {4}, year = {2021} } @article{Licha2019, author = {Licha, David and Aminzadeh-Gohari, Sepideh and Alka, Oliver and Breitkreuz, Leander and Kohlbacher, Oliver and Vidali, Silvia and Reischl, Roland J. and Feichtinger, René G. and Kofler, Barbara and Huber, Christian G.}, doi = {10.3390/ijms20163873}, journal = {International Journal of Molecular Sciences}, month = {aug}, pages = {3873}, title = {Untargeted Metabolomics Reveals Molecular Effects of Ketogenic Diet on Healthy and Tumor Xenograft Mouse Models}, url = {https://doi.org/10.3390/ijms20163873}, volume = {20}, year = {2019} } @article{Meckbach2014, author = {Meckbach, D. and Menzel, M. and Weide, B. and Toussaint, N. C. and Schilbach, K. and Noor, S. and Eigentler, T. and Ikenberg, K. and Busch, C. and Quintanilla-Martinez, L. and Kohlhofer, U. and Goeke, A. and Goeke, F. and Handgretinger, R. and Ottmann, C. and Bastian, B. C. and Garbe, C. and Roecken, M. and Perner, S. and Kohlbacher, O. and Bauer, J.}, month = {jan}, title = {In melanoma, YAP1 signaling is affected by copy number alterations and its overexpression impairs patient survival}, year = {2014} } @article{Mühlenbruch2023, abstract = {Abstract Background The immune peptidome of OPSCC has not previously been studied. Cancer-antigen specific vaccination may improve clinical outcome and efficacy of immune checkpoint inhibitors such as PD1/PD-L1 antibodies. Methods Mapping of the OPSCC HLA ligandome was performed by mass spectrometry (MS) based analysis of naturally presented HLA ligands isolated from tumour tissue samples (n = 40) using immunoaffinity purification. The cohort included 22 HPV-positive (primarily HPV-16) and 18 HPV-negative samples. A benign reference dataset comprised of the HLA ligandomes of benign haematological and tissue datasets was used to identify tumour-associated antigens. Results MS analysis led to the identification of naturally HLA-presented peptides in OPSCC tumour tissue. In total, 22,769 peptides from 9485 source proteins were detected on HLA class I. For HLA class II, 15,203 peptides from 4634 source proteins were discovered. By comparative profiling against the benign HLA ligandomic datasets, 29 OPSCC-associated HLA class I ligands covering 11 different HLA allotypes and nine HLA class II ligands were selected to create a peptide warehouse. Conclusion Tumour-associated peptides are HLA-presented on the cell surfaces of OPSCCs. The established warehouse of OPSCC-associated peptides can be used for downstream immunogenicity testing and peptide-based immunotherapy in (semi)personalised strategies. }, author = {Mühlenbruch, Lena and Abou-Kors, Tsima and Dubbelaar, Marissa L. and Bichmann, Leon and Kohlbacher, Oliver and Bens, Martin and Thomas, Jaya and Ezić, Jasmin and Kraus, Johann M. and Kestler, Hans A. and von Witzleben, Adrian and Mytilineos, Joannis and Fürst, Daniel and Engelhardt, Daphne and Doescher, Johannes and Greve, Jens and Schuler, Patrick J. and Theodoraki, Marie-Nicole and Brunner, Cornelia and Hoffmann, Thomas K. and Rammensee, Hans-Georg and Walz, Juliane S. and Laban, Simon}, doi = {10.1038/s41416-023-02197-y}, journal = {British Journal of Cancer}, month = {feb}, pages = {1777-1787}, title = {The HLA ligandome of oropharyngeal squamous cell carcinomas reveals shared tumour-exclusive peptides for semi-personalised vaccination}, url = {https://oadoi.org/10.1038/s41416-023-02197-y}, volume = {128}, year = {2023} } @article{Nothias2020, author = {Nothias, Louis-Félix and van der Hooft, Justin J. J. and Vargas, Fernando and Weldon, Kelly C. and Witting, Michael and Yang, Heejung and Zhang, Zheng and Zubeil, Florian and Wang, Mingxun and Lf, Nothias and Petras, Daniel and Schmid, Robin and Dührkop, Kai and Dang, Tam and Garg, Neha and Gauglitz, Julia M. and Rainer, Johannes and Gurevich, Alexey and Isaac, Giorgis and Jarmusch, Alan K. and Sarvepalli, Abinesh and Kameník, Zdeněk and Kang, Kyo Bin and Kessler, Nikolas and Protsyuk, Ivan and Koester, Irina and Korf, Ansgar and Ernst, Madeleine and Le Gouellec, Audrey and Ludwig, Marcus and Martin H., Christian and Tsugawa, Hiroshi and McCall, Laura-Isobel and McSayles, Jonathan and Meyer, Sven W. and Fleischauer, Markus and Mohimani, Hosein and Morsy, Mustafa and Moyne, Oriane and Allard, Pierre-Marie and Neumann, Steffen and Barsch, Aiko and Neuweger, Heiko and Cachet, Xavier and Aicheler, Fabian and Nguyen, Ngoc Hung and Caraballo-Rodriguez, Andres Mauricio and Nothias-Esposito, Melissa and Aksenov, Alexander A. and Da Silva, Ricardo R. and Paolini, Julien and Phelan, Vanessa V. and Alka, Oliver and Pluskal, Tomáš and Quinn, Robert A. and Rogers, Simon and Shrestha, Bindesh and Tripathi, Anupriya and Kohlbacher, Oliver and Dorrestein, Pieter C. and Böcker, Sebastian and Alexandrov, Theodore and Bandeira, Nuno and Pc, Dorrestein}, doi = {10.1038/s41592-020-0933-6}, journal = {Nature Methods}, month = {aug}, pages = {905-908}, title = {Feature-based molecular networking in the GNPS analysis environment}, url = {https://oadoi.org/10.1038/s41592-020-0933-6}, volume = {17}, year = {2020} } @article{Perez-Riverol2016, author = {Perez-Riverol, Yasset and Griss, Johannes and Lewis, Steve and Tabb, David L. and del-Toro, Noemi and Dianes, José A. and Walzer, Mathias and Rurik, Marc and Kohlbacher, Oliver and Hermjakob, Henning and Wang, Rui and Vizcaíno, Juan Antonio}, doi = {10.1038/nmeth.3902}, journal = {Nature Methods}, month = {jun}, pages = {651-656}, title = {Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.}, url = {http://europepmc.org/articles/pmc4968634?pdf=render}, volume = {13}, year = {2016} } @article{Röst2016, author = {Röst, Hannes L. and Sachsenberg, Timo and Aiche, Stephan and Bielow, Chris and Weisser, Hendrik and Aicheler, Fabian and Andreotti, Sandro and Ehrlich, Hans-Christian and Gutenbrunner, Petra and Kenar, Erhan and Liang, Xiao and Nahnsen, Sven and Nilse, Lars and Pfeuffer, Julianus and Rosenberger, George and Rurik, Marc and Schmitt, Uwe and Veit, Johannes and Walzer, Mathias and Wojnar, David and Wolski, Witold E. and Schilling, Oliver and Choudhary, Jyoti S. and Malmström, Lars and Aebersold, Ruedi and Reinert, Knut and Kohlbacher, Oliver}, doi = {10.1038/nmeth.3959}, journal = {Nature Methods}, month = {aug}, pages = {741-748}, title = {OpenMS: a flexible open-source software platform for mass spectrometry data analysis}, url = {http://edoc.mdc-berlin.de/15966/7/15966suppl.pdf}, volume = {13}, year = {2016} } @article{van Rijswijk2017, abstract = {Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the “Future of metabolomics in ELIXIR” was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.}, author = {van Rijswijk, Merlijn and Beirnaert, Charlie and Caron, Christophe and Cascante, Marta and Dominguez, Victoria and Dunn, Warwick B. and Ebbels, Timothy M. D. and Giacomoni, Franck and Gonzalez-Beltran, Alejandra and Hankemeier, Thomas and Haug, Kenneth and Izquierdo-Garcia, Jose L. and Jimenez, Rafael C. and Jourdan, Fabien and Kale, Namrata and Klapa, Maria I. and Kohlbacher, Oliver and Koort, Kairi and Kultima, Kim and Le Corguillé, Gildas and Moreno, Pablo and Moschonas, Nicholas K. and Neumann, Steffen and O’Donovan, Claire and Reczko, Martin and Rocca-Serra, Philippe and Rosato, Antonio and Salek, Reza M. and Sansone, Susanna-Assunta and Satagopam, Venkata and Schober, Daniel and Shimmo, Ruth and Spicer, Rachel A. and Spjuth, Ola and Thévenot, Etienne A. and Viant, Mark R. and Weber, Ralf J. M. and Willighagen, Egon L. and Zanetti, Gianluigi and Steinbeck, Christoph}, doi = {10.12688/f1000research.12342.2}, journal = {F1000Research}, month = {oct}, pages = {1649}, title = {The future of metabolomics in ELIXIR}, url = {https://f1000research.com/articles/6-1649/v2/pdf}, volume = {6}, year = {2017} } @article{Völkel2021, abstract = { Background Overcoming the COVID-19 crisis requires new ideas and strategies for online communication of personal medical information and patient empowerment. Rapid testing of a large number of subjects is essential for monitoring and delaying the spread of SARS-CoV-2 in order to mitigate the pandemic’s consequences. People who do not know that they are infected may not stay in quarantine and, thus, risk infecting others. Unfortunately, the massive number of COVID-19 tests performed is challenging for both laboratories and the units that conduct throat swabs and communicate the results. Objective The goal of this study was to reduce the communication burden for health care professionals. We developed a secure and easy-to-use tracking system to report COVID-19 test results online that is simple to understand for the tested subjects as soon as these results become available. Instead of personal calls, the system updates the status and the results of the tests automatically. This aims to reduce the delay when informing testees about their results and, consequently, to slow down the virus spread. Methods The application in this study draws on an existing tracking tool. With this open-source and browser-based online tracking system, we aim to minimize the time required to inform the tested person and the testing units (eg, hospitals or the public health care system). The system can be integrated into the clinical workflow with very modest effort and avoids excessive load to telephone hotlines. Results The test statuses and results are published on a secured webpage, enabling regular status checks by patients; status checks are performed without the use of smartphones, which has some importance, as smartphone usage diminishes with age. Stress tests and statistics show the performance of our software. CTest is currently running at two university hospitals in Germany—University Hospital Ulm and University Hospital Tübingen—with thousands of tests being performed each week. Results show a mean number of 10 (SD 2.8) views per testee. Conclusions CTest runs independently of existing infrastructures, aims at straightforward integration, and aims for the safe transmission of information. The system is easy to use for testees. QR (Quick Response) code links allow for quick access to the test results. The mean number of views per entry indicates a reduced amount of time for both health care professionals and testees. The system is quite generic and can be extended and adapted to other communication tasks. }, author = {Völkel, Gunnar and Fürstberger, Axel and Schwab, Julian D. and Werle, Silke D. and Ikonomi, Nensi and Gscheidmeier, Thomas and Kraus, Johann M. and Groß, Alexander and Holderried, Martin and Balig, Julien and Jobst, Franz and Kuhn, Peter and Kuhn, Klaus A. and Kohlbacher, Oliver and Kaisers, Udo X. and Seufferlein, Thomas and Kestler, Hans A.}, doi = {10.2196/27348}, journal = {Journal of Medical Internet Research}, month = {jun}, pages = {e27348}, title = {Patient Empowerment During the COVID-19 Pandemic by Ensuring Safe and Fast Communication of Test Results: Implementation and Performance of a Tracking System}, url = {https://doi.org/10.2196/27348}, volume = {23}, year = {2021} } @article{Völkel2021_2, author = {Völkel, Gunnar and Fürstberger, Axel and Schwab, Julian D. and Werle, Silke D. and Ikonomi, Nensi and Gscheidmeier, Thomas and Kraus, Johann M. and Groß, Alexander and Holderried, Martin and Balig, Julien and Jobst, Franz and Kuhn, Peter and Kuhn, Klaus A. and Kohlbacher, Oliver and Kaisers, Udo X. and Seufferlein, Thomas and Kestler, Hans A.}, doi = {10.2196/31253}, journal = {Journal of Medical Internet Research}, month = {jun}, pages = {e31253}, title = {Metadata Correction: Patient Empowerment During the COVID-19 Pandemic by Ensuring Safe and Fast Communication of Test Results: Implementation and Performance of a Tracking System}, url = {https://doi.org/10.2196/31253}, volume = {23}, year = {2021} }