Timo Sachsenberg

发表

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

Lennart Martens, Harald Barsnes, Yasset Perez-Riverol, 2019, bioRxiv.

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

Knut Reinert, Erhan Kenar, Timo Sachsenberg, 2015, Proteomics.

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

Timo Sachsenberg, Samuel Wein, Byron Andrews, 2020, Nature Communications.

Ten Simple Rules for Taking Advantage of Git and GitHub

Kai Blin, Juan Antonio Vizcaíno, Daniel S. Katz, 2014, bioRxiv.

SmartPeak automates targeted and quantitative metabolomics data processing

Timo Sachsenberg, Oliver Kohlbacher, Svetlana Kutuzova, 2020, bioRxiv.

Expanding the Use of Spectral Libraries in Proteomics.

Johannes Griss, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2018, Journal of proteome research.

CHAPTER 6:OpenMS and KNIME for Mass Spectrometry Data Processing

Timo Sachsenberg, Samuel Wein, Marc Rurik, 2020 .

Recommendations for the packaging and containerizing of bioinformatics software

Olivier Sallou, Yasset Perez-Riverol, Daniel Blankenberg, 2018, F1000Research.

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

Harald Barsnes, Johannes Griss, Rafael C. Jimenez, 2017, Bioinform..

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion.

Lennart Martens, Harald Barsnes, Yasset Perez-Riverol, 2019, Journal of proteome research.

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

Oliver Kohlbacher, Benjamin A. Garcia, Timo Sachsenberg, 2018, Nature Communications.

EPIFANY – A method for efficient high-confidence protein inference

Oliver Serang, Knut Reinert, Timo Sachsenberg, 2019, bioRxiv.

MHCquant: Automated and reproducible data analysis for immunopeptidomics.

Timo Sachsenberg, Oliver Kohlbacher, Alexander Peltzer, 2019, Journal of proteome research.

OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS

Oliver Kohlbacher, Timo Sachsenberg, Mathias Walzer, 2020, Molecular & Cellular Proteomics.

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

Martin Eisenacher, Yasset Perez-Riverol, Knut Reinert, 2017, Journal of proteomics.

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

Jun Fan, Christoph Steinbeck, Johannes Griss, 2014, Molecular & Cellular Proteomics.

DIAproteomics: A multi-functional data analysis pipeline for data-independent-acquisition proteomics and peptidomics

Timo Sachsenberg, Oliver Kohlbacher, George Rosenberger, 2020, bioRxiv.

Proceedings of the EuBIC-MS 2020 Developers’ Meeting

Wout Bittremieux, Yasset Perez-Riverol, Eric W. Deutsch, 2020, EuPA Open Proteomics.

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

Oliver Kohlbacher, Timo Sachsenberg, Henning Urlaub, 2016, Journal of proteome research.

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

Martin Eisenacher, Johannes Griss, Juan Antonio Vizcaíno, 2018, Nucleic Acids Res..

EPIFANY - A method for efficient high-confidence protein inference.

Oliver Serang, Knut Reinert, Oliver Kohlbacher, 2020, Journal of proteome research.

Computational methods for mass spectrometry-based study of protein-RNA or protein-DNA complexes and quantitative metaproteomics

Timo Sachsenberg, Timo Sachsenberg, 2017 .

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

Knut Reinert, Oliver Kohlbacher, Timo Sachsenberg, 2017, Journal of biotechnology.

On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications

Tomás Skopal, Oliver Kohlbacher, David Hoksza, 2013, J. Integr. Bioinform..

A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools

Tomás Skopal, Oliver Kohlbacher, David Hoksza, 2013, PACBB.

The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics

Martin Eisenacher, Jun Fan, Juan Antonio Vizcaíno, 2013, Molecular & Cellular Proteomics.

Ten Simple Rules for Taking Advantage of git and GitHub

Kai Blin, Yasset Perez-Riverol, Daniel S. Katz, 2016 .

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

Martin Eisenacher, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2019, Analytical chemistry.

Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays.

Gunnar Rätsch, Timo Sachsenberg, Detlef Weigel, 2009, The Plant journal : for cell and molecular biology.

OpenMS for open source analysis of mass spectrometric data

Oliver Kohlbacher, Timo Sachsenberg, Hendrik Weisser, 2019 .

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

Oliver Kohlbacher, Timo Sachsenberg, Henning Urlaub, 2014, Nature Methods.

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

Gunnar Rätsch, Wolfgang Busch, Timo Sachsenberg, 2008, Proceedings of the National Academy of Sciences.

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

Martin Taubert, Jana Seifert, Oliver Kohlbacher, 2015, Journal of proteome research.

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana

Gunnar Rätsch, Bernhard Schölkopf, Timo Sachsenberg, 2008, Genome Biology.