Applied Bioinformatics Group

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Timo Sachsenberg

Location: Sand 14 Tübingen 72076


Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana (PNAS)
Laubinger S., Sachsenberg T., Zeller G., Busch W., Lohmann J. U., Rätsch G., Weigel D.

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana (Genome Biology)
Laubinger S., Zeller G., Henz S.R., Sachsenberg T., Widmer C.K., Naouar N., Vuylsteke M., Schölkopf B., Rätsch G. and Weigel D. (2008)

Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays (Plant Journal)
Zeller G., Henz S.R., Widmer C.K., Sachsenberg T., Rätsch G. and Weigel D. and Laubinger S. (2009)

Global effects of the small RNA biogenesis machinery on the Arabidopsis transcriptome, (PNAS).
Laubinger S., Zeller G., Henz S.R., Buechel S., Sachsenberg T., Rätsch G. and Weigel D. (2010)

PTMeta: Increasing identification rates of modified peptides using modification pre-scanning and meta-analysis (Proteomics)
Sven Nahnsen, Timo Sachsenberg, Oliver Kohlbacher (2013)

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. (Mol. Cell. Prot.)
Walzer, M, Qi, D, Mayer, G, Uszkoreit, J, Eisenacher, M, Sachsenberg, T, Gonzalez-Galarza, FF, Fan, J, Bessant, C, Deutsch, EW, Reisinger, F, Vizcaíno, JA, Medina-Aunon, JA, Albar, JP, Kohlbacher, O, and Jones, AR (2013)

A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools
Novák J, Sachsenberg T, Hoksza D, Skopal, T, Kohlbacher, O - 7th International Conference on Practical Applications of Computational Biology & Bioinformatics (2013)

On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications
J Novák, T Sachsenberg, D Hoksza, T Skopal, O Kohlbacher - Journal of Integrative Bioinformatics 10 (3), 228 (2013)

The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience
Griss, Johannes and Jones, Andrew R and Sachsenberg, Timo and Walzer, Mathias and Gatto, Laurent and Hartler, Jurgen and Thallinger, Gerhard G and Salek, Reza M and Steinbeck, Christoph and Neuhauser, Nadin and others - Molecular & Cellular Proteomics (2014)

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins
Katharina Kramer, Timo Sachsenberg, Benedikt M Beckmann, Saadia Qamar, Kum-Loong Boon, Matthias W Hentze, Oliver Kohlbacher, Henning Urlaub - Nature Methods (2014)

Analysis of protein-RNA interactions by UV-induced cross-linking and mass spectrometry. Methods. (2015)
Sharma, K, Hrle, A, Kramer, K, Sachsenberg, T, Staals, RH, Randau, L, Marchfelder, A, van der Oost, J, Kohlbacher, O, Conti, E, and Urlaub, H (accepted).

Dithiothreitol (DTT) Acts as a Specific, UV-inducible Cross-linker in Elucidation of Protein–RNA Interactions. (Moll. Cell. Prot., 2015)
Uzma Zaman, Florian M Richter, Romina Hofele, Katharina Kramer, Timo Sachsenberg, Oliver Kohlbacher, Christof Lenz, Henning Urlaub

Ten Simple Rules for Taking Advantage of git and GitHub. (PLOS ONE, 2016)
Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J Eglen, Daniel S Katz, Tom J Pollard, Alexander Konovalov, Robert M Flight, Kai Blin, Juan Antonio Vizcaino

LFQProfiler and RNP (xl)-Open-source tools for label-free quantification and protein-RNA cross-linking integrated into Proteome Discoverer. (Journal of proteome research, 2016)
J Veit, T Sachsenberg, A Chernev, F Aicheler, H Urlaub, O Kohlbacher

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics (Journal of Proteomics, 2016)
Enrique Audain, Julian Uszkoreit, Timo Sachsenberg, Julianus Pfeuffer, Xiao Liang, Henning Hermjakob, Aniel Sanchez, Martin Eisenacher, Knut Reinert, David L Tabb, Oliver Kohlbacher, Yasset Perez-Riverol

OpenMS: a flexible open-source software platform for mass spectrometry data analysis (Nature Methods, 2016)
Hannes L Röst, Timo Sachsenberg, Stephan Aiche, Chris Bielow, Hendrik Weisser, Fabian Aicheler, Sandro Andreotti, Hans-Christian Ehrlich, Petra Gutenbrunner, Erhan Kenar, Xiao Liang, Sven Nahnsen, Lars Nilse, Julianus Pfeuffer, George Rosenberger, Marc Rurik, Uwe Schmitt, Johannes Veit, Mathias Walzer, David Wojnar, Witold E Wolski, Oliver Schilling, Jyoti S Choudhary, Lars Malmström, Ruedi Aebersold et al.

BioContainers: an open-source and community-driven framework for software standardization (Bioinformatics)
F da Veiga Leprevost, BA Grüning, S Alves Aflitos, HL Röst, J Uszkoreit, ...

OpenMS–A platform for reproducible analysis of mass spectrometry data (Journal of biotechnology 2017)
J Pfeuffer, T Sachsenberg, O Alka, M Walzer, A Fillbrunn, L Nilse, ...

Differential Enzymatic 16O/18O Labeling for the Detection of Cross-Linked Nucleic Acid–Protein Heteroconjugates (Analytical chemistry 2017)
FJ Flett, T Sachsenberg, O Kohlbacher, CL Mackay, H Interthal

Posters / Presentations:


OpenMS/TOPP - preprogrammed building blocks for the analysis of large-scale proteomics and metabolomics data (ASMS conference, 2011)

Erhan Kenar, Sven Nahnsen, Lars Nilse, Timo Sachsenberg, Mathias Walzer, Oliver Kohlbacher


UV-induced protein–RNA cross-linking: Identification of RNA-binding domains, peptides, and amino acids (ASMS conference, 2012)

Katharina Kramer; Timo Sachsenberg; Oliver Kohlbacher; Henning Urlaub


High-throughput analysis of stable isotope probing experiments in metaproteomic studies

FA Herbst, T Sachsenberg, M Taubert, M von Bergen, O Kohlbacher, J Seiffert


Protein-RNA interactions: Large-scale identification of peptides crosslinked to RNA through database searches against entire proteomes (ASMS conference, 2013, oral presentation)
Katharina Kramer, Timo Sachsenberg, Saadia Qamar, Oliver Kohlbacher, Henning Urlaub

Analyses of yeast mRNPs by the use of the  photo-reactive nucleobase 4-thio-uracil and mass spectrometry (ASMS conference, 2013)
Uzma Zaman, Kum-Loong Boon, Katharina Kramer, Timo Sachsenberg, Oliver Kohlbacher, Reinhard Lührmann, Henning Urlaub

Unbiased identification of protein–RNA contact sites in vivo at amino acid and nucleotide resolution after UV cross-linking (ASMS conference, 2014)
Katharina Kramer, Timo Sachsenberg, Benedikt Beckmann, Saadia Qamar, Matthias W. Hentze, Oliver Kohlbacher, Henning Urlaub1

Protein–RNA contacts in CRISPR-Cas protein complexes of the prokaryotic adaptive immune systems (ASMS conference, 2014)
Kundan Sharma, Katharina Kramer, Timo Sachsenberg, Oliver Kohlbacher, Raymond Staals, Tim Künne, Stan J. J. Brouns, John Van der Oost, Henning Urlaub

Mass-spectrometry-based quantitative protein–RNA cross-linking study (ASMS conference, 2014)
Saadia Qamar, Katharina Kramer, Timo Sachsenberg, Oliver Kohlbacher, Henning Urlaub

Large-scale analysis of non-targeted LC-MS metabolomics data with OpenMS in the Compound Discoverer platform (ASMS conference, 2014)
Fabian Aicheler, Timo Sachsenberg, Erhan Kenar, Sebastian Kusch, Hans Grensemann, Oliver Kohlbacher

DTT Mediates Site-Specific Protein/RNA Crosslinking upon UV Irradiation (ASMS conference, 2014)
Uzma Zaman, Katharina Kramer, Timo Sachsenberg, Oliver Kohlbacher, Christof Lenz, Henning Urlaub

LFQProfiler and RNPxl – two free plugins for Proteome DiscovererTM based on OpenMS (HUPO conference, 2015)
Johannes Veit , Fabian Aicheler, Julianus Pfeuffer, Hendrik Weisser, Timo Sachsenberg, Knut Reinert and Oliver Kohlbacher

An automated software pipeline for protein-RNA and protein-DNA cross-link identification in Proteome Discoverer 2.0 (HUPO conference, 2015)
Timo Sachsenberg, Aleksandar Chernev, Romina Hofele, Saadia Qamar, Uzma Zaman, Kundan Sharma, Christin Kappert, Katharina Kramer, Julianus Pfeuffer, Xiao Liang, Johannes Veit, Knut Reinert, Christof Lenz, Henning Urlaub, Oliver Kohlbacher
RNPxl 2 - Protein-RNA interaction site localization from UV cross-linked peptide-RNA oligonucleotides in Proteome DiscovererTM 2.1 (ASMS conference, 2016)

Timo Sachsenberg; Johannes Veit, Aleksandar Chernev, Kundan Sharma, Romina Hofele, Saadia Qamar, Uzma Zaman, Christin Kappert, Katharina Kramer, Julianus Pfeuffer, Xiao Liang, Knut Reinert, Christof Lenz, Henning Urlaub and Oliver Kohlbacher

Mass spectrometric analysis of UV and chemical protein-DNA cross-links in a chromatin model (ASMS Conference, 2017)
Alexandra Stützer, Christin Kappert, Aleksandar Chernev, Katharina Mucek, Timo Sachsenberg, Oliver Kohlbacher, Wolfgang Fischle, Henning Urlaub

OpenProXL: a fast and versatile XL-MS identification tool (ASMS Conference, 2017)
Eugen Netz, Timo Sachsenberg, Christian Johannes Gloeckner, Oliver Kohlbacher

Imputation of Missing Data in Quantitative Proteomics using Singular Value Thresholding
Tjeerd Dijkstra, Timo Sachsenberg, Oliver Kohlbacher

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