Publications by authors named "Oliver Kohlbacher"

100Publications

Determination of the Geographical Origin of L. by H NMR Spectroscopy.

J Agric Food Chem 2020 Oct 26. Epub 2020 Oct 26.

Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jafc.0c05642DOI Listing
October 2020

Identifying Disease-Causing Mutations with Privacy Protection.

Bioinformatics 2020 Jul 19. Epub 2020 Jul 19.

Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btaa641DOI Listing
July 2020

Enabling ad-hoc reuse of private data repositories through schema extraction.

J Biomed Semantics 2020 Jul 8;11(1). Epub 2020 Jul 8.

Informatik 5, RWTH Aachen University, Ahornstr. 55, Aachen, 52062, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13326-020-00223-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341611PMC
July 2020

Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells.

Cell Commun Signal 2020 Jun 23;18(1):99. Epub 2020 Jun 23.

Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12964-020-00591-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310537PMC
June 2020

Proteins and Molecular Pathways Relevant for the Malignant Properties of Tumor-Initiating Pancreatic Cancer Cells.

Cells 2020 Jun 3;9(6). Epub 2020 Jun 3.

Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, A-5020 Salzburg, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3390/cells9061397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7349116PMC
June 2020

Corrigendum to Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities.

J Proteomics 2020 Jul 25;224:103829. Epub 2020 May 25.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jprot.2020.103829DOI Listing
July 2020

Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities.

J Proteomics 2020 Jun 23;222:103791. Epub 2020 Apr 23.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jprot.2020.103791DOI Listing
June 2020

FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics.

Cell Syst 2020 02 19;10(2):213-218.e6. Epub 2020 Feb 19.

Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany; Center for Quantitative Biology, University of Tübingen, Sand 14, 72076 Tübingen, Germany; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 4, 72076 Tübingen, Germany; Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Str. 9, 72076 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2020.01.003DOI Listing
February 2020

EPIFANY: A Method for Efficient High-Confidence Protein Inference.

J Proteome Res 2020 03 13;19(3):1060-1072. Epub 2020 Feb 13.

Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.9b00566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7583457PMC
March 2020

Metabolomics Data Processing Using OpenMS.

Methods Mol Biol 2020 ;2104:49-60

Applied Bioinformatics Group, University of Tübingen, Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-0716-0239-3_4DOI Listing
January 2020

Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast.

Front Cell Dev Biol 2019 17;7:338. Epub 2019 Dec 17.

Molecular Cell Biology, Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcell.2019.00338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927922PMC
December 2019

Identification of Ppar-modulated miRNA hubs that target the fibrotic tumor microenvironment.

Proc Natl Acad Sci U S A 2020 01 23;117(1):454-463. Epub 2019 Dec 23.

Department for Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1909145117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6955372PMC
January 2020

MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics.

J Proteome Res 2019 11 22;18(11):3876-3884. Epub 2019 Oct 22.

Biomolecular Interactions , Max Planck Institute for Developmental Biology , Tübingen 72076 , Germany.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00313
Publisher Site
http://dx.doi.org/10.1021/acs.jproteome.9b00313DOI Listing
November 2019

Challenges of big data integration in the life sciences.

Anal Bioanal Chem 2019 Oct 28;411(26):6791-6800. Epub 2019 Aug 28.

Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00216-019-02074-9DOI Listing
October 2019

Untargeted Metabolomics Reveals Molecular Effects of Ketogenic Diet on Healthy and Tumor Xenograft Mouse Models.

Int J Mol Sci 2019 Aug 8;20(16). Epub 2019 Aug 8.

Bioanalytical Research Laboratories, Department of Biosciences and Cancer Cluster Salzburg, University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms20163873DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6719192PMC
August 2019

Food fingerprinting: Mass spectrometric determination of the cocoa shell content (Theobroma cacao L.) in cocoa products by HPLC-QTOF-MS.

Food Chem 2019 Nov 24;298:125013. Epub 2019 Jun 24.

Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.foodchem.2019.125013DOI Listing
November 2019

Induction of neoantigen-reactive T cells from healthy donors.

Nat Protoc 2019 06 17;14(6):1926-1943. Epub 2019 May 17.

Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41596-019-0170-6DOI Listing
June 2019

Food Authentication: Small-Molecule Profiling as a Tool for the Geographic Discrimination of German White Asparagus.

J Agric Food Chem 2018 Dec 4;66(50):13328-13339. Epub 2018 Dec 4.

Hamburg School of Food Science, Institute of Food Chemistry , University of Hamburg , Grindelallee 117 , 20146 Hamburg , Germany.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/acs.jafc.8b05791
Publisher Site
http://dx.doi.org/10.1021/acs.jafc.8b05791DOI Listing
December 2018

An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides.

PLoS Pathog 2018 10 18;14(10):e1007368. Epub 2018 Oct 18.

Plateforme GENOMAX, Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1007368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207329PMC
October 2018

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Cancer Cell 2018 08 2;34(2):211-224.e6. Epub 2018 Aug 2.

ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; ETH Zurich, Department of Biology, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ccell.2018.07.001DOI Listing
August 2018

Population-specific design of de-immunized protein biotherapeutics.

PLoS Comput Biol 2018 03 2;14(3):e1005983. Epub 2018 Mar 2.

Center for Bioinformatics, University of Tübingen, Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1005983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5851651PMC
March 2018

qPortal: A platform for data-driven biomedical research.

PLoS One 2018 19;13(1):e0191603. Epub 2018 Jan 19.

Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0191603PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5774839PMC
February 2018

Favorable immune signature in CLL patients, defined by antigen-specific T-cell responses, might prevent second skin cancers.

Leuk Lymphoma 2018 08 3;59(8):1949-1958. Epub 2018 Jan 3.

b Department of Immunology , Institute for Cell Biology, University of Tübingen , Tübingen , Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/10428194.2017.1403022DOI Listing
August 2018

Genetic variation in human drug-related genes.

Genome Med 2017 12 22;9(1):117. Epub 2017 Dec 22.

Department of Systems Biology, Harvard Medical School, Boston, 02115, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13073-017-0502-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5740940PMC
December 2017

Differential Enzymatic O/O Labeling for the Detection of Cross-Linked Nucleic Acid-Protein Heteroconjugates.

Anal Chem 2017 11 13;89(21):11208-11213. Epub 2017 Oct 13.

Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3FF, Scotland, U.K.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.analchem.7b01625DOI Listing
November 2017

OpenMS - A platform for reproducible analysis of mass spectrometry data.

J Biotechnol 2017 Nov 27;261:142-148. Epub 2017 May 27.

Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Center for Quantitative Biology, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tuebingen, Germany. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jbiotec.2017.05.016DOI Listing
November 2017

ImmunoNodes - graphical development of complex immunoinformatics workflows.

BMC Bioinformatics 2017 May 8;18(1):242. Epub 2017 May 8.

Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-017-1667-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422934PMC
May 2017

Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus.

PLoS Pathog 2016 Dec 15;12(12):e1006071. Epub 2016 Dec 15.

University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1006071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5158082PMC
December 2016

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

J Proteomics 2017 01 4;150:170-182. Epub 2016 Aug 4.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jprot.2016.08.002DOI Listing
January 2017

Copper oxide nanoparticle toxicity profiling using untargeted metabolomics.

Part Fibre Toxicol 2016 09 8;13(1):49. Epub 2016 Sep 8.

Department of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12989-016-0160-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5017021PMC
September 2016

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

Nat Methods 2016 Aug 27;13(8):651-656. Epub 2016 Jun 27.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.3902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968634PMC
August 2016

LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer.

J Proteome Res 2016 09 10;15(9):3441-8. Epub 2016 Aug 10.

Center for Bioinformatics, University of Tübingen , 72074 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.6b00407DOI Listing
September 2016

Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry.

Anal Chim Acta 2016 Aug 25;930:13-22. Epub 2016 May 25.

Department of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Salzburg, Austria. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.aca.2016.05.017DOI Listing
August 2016

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.

PLoS Comput Biol 2016 05 13;12(5):e1004920. Epub 2016 May 13.

Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866734PMC
May 2016

FRED 2: an immunoinformatics framework for Python.

Bioinformatics 2016 07 26;32(13):2044-6. Epub 2016 Feb 26.

Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany Quantitative Biology Center, Tübingen 72076, Germany Faculty of Medicine, University of Tübingen, Tübingen 72076, Germany Max Planck Institute for Developmental Biology, Biomolecular Interactions, Tübingen 72076, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920123PMC
July 2016

BALL-SNPgp-from genetic variants toward computational diagnostics.

Bioinformatics 2016 06 15;32(12):1888-90. Epub 2016 Feb 15.

Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw084DOI Listing
June 2016

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

Authors:
Uli Fechner Chris de Graaf Andrew E Torda Stefan Güssregen Andreas Evers Hans Matter Gerhard Hessler Nicola J Richmond Peter Schmidtke Marwin H S Segler Mark P Waller Stefanie Pleik Joan-Emma Shea Zachary Levine Ryan Mullen Karina van den Broek Matthias Epple Hubert Kuhn Andreas Truszkowski Achim Zielesny Johannes Hans Fraaije Ruben Serral Gracia Stefan M Kast Krishna C Bulusu Andreas Bender Abraham Yosipof Oren Nahum Hanoch Senderowitz Timo Krotzky Robert Schulz Gerhard Wolber Stefan Bietz Matthias Rarey Markus O Zimmermann Andreas Lange Manuel Ruff Johannes Heidrich Ionut Onlia Thomas E Exner Frank M Boeckler Marcel Bermudez Dzmitry S Firaha Oldamur Hollóczki Barbara Kirchner Christofer S Tautermann Andrea Volkamer Sameh Eid Samo Turk Friedrich Rippmann Simone Fulle Noureldin Saleh Giorgio Saladino Francesco L Gervasio Elke Haensele Lee Banting David C Whitley Jana Sopkova-de Oliveira Santos Ronan Bureau Timothy Clark Achim Sandmann Harald Lanig Patrick Kibies Jochen Heil Franziska Hoffgaard Roland Frach Julian Engel Steven Smith Debjit Basu Daniel Rauh Oliver Kohlbacher Frank M Boeckler Jonathan W Essex Michael S Bodnarchuk Gregory A Ross Arndt R Finkelmann Andreas H Göller Gisbert Schneider Tamara Husch Christoph Schütter Andrea Balducci Martin Korth Fidele Ntie-Kang Stefan Günther Wolfgang Sippl Luc Meva'a Mbaze Fidele Ntie-Kang Conrad V Simoben Lydia L Lifongo Fidele Ntie-Kang Philip Judson Jiří Barilla Miloš V Lokajíček Hana Pisaková Pavel Simr Natalia Kireeva Alexandre Petrov Denis Ostroumov Vitaly P Solovev Vladislav S Pervov Nils-Ole Friedrich Kai Sommer Matthias Rarey Johannes Kirchmair Eugen Proschak Julia Weber Daniel Moser Lena Kalinowski Janosch Achenbach Mark Mackey Tim Cheeseright Gerrit Renner Gerrit Renner Torsten C Schmidt Jürgen Schram Marion Egelkraut-Holtus Albert van Oeyen Tuomo Kalliokoski Denis Fourches Akachukwu Ibezim Chika J Mbah Umale M Adikwu Ngozi J Nwodo Alexander Steudle Brian B Masek Stephan Nagy David Baker Fred Soltanshahi Roman Dorfman Karen Dubrucq Hitesh Patel Oliver Koch Florian Mrugalla Stefan M Kast Qurrat U Ain Julian E Fuchs Robert M Owen Kiyoyuki Omoto Rubben Torella David C Pryde Robert Glen Andreas Bender Petr Hošek Vojtěch Spiwok Lewis H Mervin Ian Barrett Mike Firth David C Murray Lisa McWilliams Qing Cao Ola Engkvist Dawid Warszycki Marek Śmieja Andrzej J Bojarski Natalia Aniceto Alex Freitas Taravat Ghafourian Guido Herrmann Valentina Eigner-Pitto Alexandra Naß Rafał Kurczab Andrzej J Bojarski Andreas Lange Marcel B Günther Susanne Hennig Felix M Büttner Christoph Schall Adrian Sievers-Engler Francesco Ansideri Pierre Koch Thilo Stehle Stefan Laufer Frank M Böckler Barbara Zdrazil Floriane Montanari Gerhard F Ecker Christoph Grebner Anders Hogner Johan Ulander Karl Edman Victor Guallar Christian Tyrchan Johan Ulander Christian Tyrchan Wolfgang Klute Fredrik Bergström Christian Kramer Quoc Dat Nguyen Roland Frach Patrick Kibies Steven Strohfeldt Saraphina Böttcher Tim Pongratz Dominik Horinek Stefan M Kast Bernd Rupp Raed Al-Yamori Michael Lisurek Ronald Kühne Filipe Furtado Karina van den Broek Ludger Wessjohann Miriam Mathea Knut Baumann Siti Zuraidah Mohamad-Zobir Xianjun Fu Tai-Ping Fan Andreas Bender Maximilian A Kuhn Christoph A Sotriffer Azedine Zoufir Xitong Li Lewis Mervin Ellen Berg Mark Polokoff Wolf D Ihlenfeldt Wolf D Ihlenfeldt Jette Pretzel Zayan Alhalabi Robert Fraczkiewicz Marvin Waldman Robert D Clark Neem Shaikh Prabha Garg Alexander Kos Hans-Jürgen Himmler Achim Sandmann Christophe Jardin Heinrich Sticht Thomas B Steinbrecher Markus Dahlgren Daniel Cappel Teng Lin Lingle Wang Goran Krilov Robert Abel Richard Friesner Woody Sherman Ina A Pöhner Joanna Panecka Rebecca C Wade Stefan Bietz Karen T Schomburg Matthias Hilbig Matthias Rarey Christian Jäger Vivien Wieczorek Lance M Westerhoff Oleg Y Borbulevych Hans-Ulrich Demuth Mirko Buchholz Denis Schmidt Thomas Rickmeyer Timo Krotzky Peter Kolb Sumit Mittal Elsa Sánchez-García Mauro S Nogueira Tiago B Oliveira Fernando B da Costa Thomas J Schmidt

J Cheminform 2016 Apr 26;8(Suppl 1):18. Epub 2016 Apr 26.

Central Institute for Scientific Computing (ZISC), FAU-Erlangen-Nürnberg, Martensstr. 5a, 91058, Erlangen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13321-016-0119-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896257PMC
April 2016

From the desktop to the grid: scalable bioinformatics via workflow conversion.

BMC Bioinformatics 2016 Mar 12;17:127. Epub 2016 Mar 12.

Center for Bioinformatics and Dept. of Computer Science, University of Tübingen, Sand 14, Tübingen, 72070, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-016-0978-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4788856PMC
March 2016

Challenges in Large-Scale Computational Mass Spectrometry and Multiomics.

J Proteome Res 2016 Mar;15(3):681-2

Department of Biochemistry, The University of Texas Health Science Center at San Antonio.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.6b00067DOI Listing
March 2016

Designing string-of-beads vaccines with optimal spacers.

Genome Med 2016 Jan 26;8(1). Epub 2016 Jan 26.

Center for Bioinformatics, University of Tübingen, 72076, Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13073-016-0263-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728757PMC
January 2016

Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence.

J Proteome Res 2016 Jan 8;15(1):182-92. Epub 2015 Dec 8.

Quantitative Biology Center, Eberhard Karls University of Tuebingen , Auf der Morgenstelle 10, 72076 Tuebingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.5b00704DOI Listing
January 2016

Immunoinformatics and epitope prediction in the age of genomic medicine.

Genome Med 2015 Nov 20;7:119. Epub 2015 Nov 20.

Applied Bioinformatics, Center of Bioinformatics and Department of Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13073-015-0245-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654883PMC
November 2015

Testing and Validation of Computational Methods for Mass Spectrometry.

J Proteome Res 2016 Mar 17;15(3):809-14. Epub 2015 Nov 17.

CECAD, University of Cologne , 50931 Cologne, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.5b00852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804830PMC
March 2016

DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats.

Nucleic Acids Res 2015 Nov 19;43(20):10065-80. Epub 2015 Oct 19.

Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv1053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787788PMC
November 2015

Dithiothreitol (DTT) Acts as a Specific, UV-inducible Cross-linker in Elucidation of Protein-RNA Interactions.

Mol Cell Proteomics 2015 Dec 8;14(12):3196-210. Epub 2015 Oct 8.

From the ‡Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany; §Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/mcp.M115.052795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762631PMC
December 2015

Retention Time Prediction Improves Identification in Nontargeted Lipidomics Approaches.

Anal Chem 2015 Aug 22;87(15):7698-704. Epub 2015 Jul 22.

†Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen, Baden-Württemberg, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.analchem.5b01139DOI Listing
August 2015

The antigenic landscape of multiple myeloma: mass spectrometry (re)defines targets for T-cell-based immunotherapy.

Blood 2015 Sep 2;126(10):1203-13. Epub 2015 Jul 2.

Institute for Cell Biology, Department of Immunology, and Cancer Immunotherapy Unit, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1182/blood-2015-04-640532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608392PMC
September 2015

Protein (multi-)location prediction: utilizing interdependencies via a generative model.

Bioinformatics 2015 Jun;31(12):i365-74

Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA, Applied Bioinformatics, Center for Bioinformatics, University of Tuebingen, Germany, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA and School of Computing, Queen's University, Kingston, ON, Canada Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA, Applied Bioinformatics, Center for Bioinformatics, University of Tuebingen, Germany, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA and School of Computing, Queen's University, Kingston, ON, Canada Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA, Applied Bioinformatics, Center for Bioinformatics, University of Tuebingen, Germany, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA and School of Computing, Queen's University, Kingston, ON, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765880PMC
June 2015

Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry.

Methods 2015 Nov 10;89:138-48. Epub 2015 Jun 10.

Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Center, Göttingen, Germany.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S10462023150024
Publisher Site
http://dx.doi.org/10.1016/j.ymeth.2015.06.005DOI Listing
November 2015

Intuitive web-based experimental design for high-throughput biomedical data.

Biomed Res Int 2015 14;2015:958302. Epub 2015 Apr 14.

Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://www.hindawi.com/journals/bmri/2015/958302/
Publisher Site
http://dx.doi.org/10.1155/2015/958302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411450PMC
February 2016

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

J Proteome Res 2015 Jul 10;14(7):2988-97. Epub 2015 Jun 10.

Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/acs.jproteome.5b00121
Publisher Site
http://dx.doi.org/10.1021/acs.jproteome.5b00121DOI Listing
July 2015

Managing expectations when publishing tools and methods for computational proteomics.

J Proteome Res 2015 May 22;14(5):2002-4. Epub 2015 Apr 22.

∥Department of Biochemistry, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio 78229, Texas, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr501318dDOI Listing
May 2015

EpiToolKit--a web-based workbench for vaccine design.

Bioinformatics 2015 Jul 20;31(13):2211-3. Epub 2015 Feb 20.

Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481845PMC
July 2015

WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome.

J Cell Sci 2015 Jan;128(2):207-17

International Max Planck Research School 'From Molecules to Organisms', Max Planck Institute for Developmental Biology and Eberhard Karls University Tuebingen, Spemannstr. 35 - 39, 72076 Tuebingen, Germany Applied Bioinformatics Group, Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, Eberhard Karls University Tuebingen, Sand 14, 72076 Tuebingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1242/jcs.146258DOI Listing
January 2015

Fluorescence-based imaging of autophagy progression by human WIPI protein detection.

Methods 2015 Mar 22;75:69-78. Epub 2014 Nov 22.

Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany; International Max Planck Research School 'From Molecules to Organisms', Max Planck Institute for Developmental Biology and Eberhard Karls University Tuebingen, Spemannstr. 35-39, 72076 Tuebingen, Germany. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymeth.2014.11.011DOI Listing
March 2015

MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics.

J Proteome Res 2015 Feb 1;14(2):619-27. Epub 2014 Dec 1.

Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen , 72074 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr500245wDOI Listing
February 2015

Activation of lymphoma-associated MyD88 mutations via allostery-induced TIR-domain oligomerization.

Blood 2014 Dec 30;124(26):3896-904. Epub 2014 Oct 30.

Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia; Centre of Excellence EN-FIST, Ljubljana, Slovenia;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1182/blood-2014-05-573188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4282153PMC
December 2014

ballaxy: web services for structural bioinformatics.

Bioinformatics 2015 Jan 2;31(1):121-2. Epub 2014 Sep 2.

Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btu574DOI Listing
January 2015

Competing salt effects on phase behavior of protein solutions: tailoring of protein interaction by the binding of multivalent ions and charge screening.

J Phys Chem B 2014 Sep 15;118(38):11365-74. Epub 2014 Sep 15.

Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp5058622DOI Listing
September 2014

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins.

Nat Methods 2014 Oct 31;11(10):1064-70. Epub 2014 Aug 31.

1] Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [2] Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Center, Göttingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.3092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485471PMC
October 2014

OptiType: precision HLA typing from next-generation sequencing data.

Bioinformatics 2014 Dec 20;30(23):3310-6. Epub 2014 Aug 20.

Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Institute of Medical Genetics and Applied Genomics, University of Tübingen, and CeGaT GmbH, 72076 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btu548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441069PMC
December 2014

Blocked inverted indices for exact clustering of large chemical spaces.

J Chem Inf Model 2014 Sep 2;54(9):2395-401. Epub 2014 Sep 2.

Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center and Dept. of Computer Science, University of Tübingen , Sand 14, 72076 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci500150tDOI Listing
September 2014

Performance studies on distributed virtual screening.

Biomed Res Int 2014 17;2014:624024. Epub 2014 Jun 17.

Center for Research Computing, University of Notre Dame, P.O. Box 539, Notre Dame, IN 46556, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1155/2014/624024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083208PMC
March 2015

Clinical and non-targeted metabolomic profiling of homozygous carriers of Transcription Factor 7-like 2 variant rs7903146.

Sci Rep 2014 Jun 13;4:5296. Epub 2014 Jun 13.

1] Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany [2] German Center for Diabetes Research (DZD), Tübingen [3] Division of Clinical Chemistry and Pathobiochemistry, Department of Internal Medicine 4, University Hospital Tuebingen, Tuebingen, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep05296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055885PMC
June 2014