Software platforms for quantitative proteomics. - Ole Schulz-Trieglaff (Computational Proteomics, 2005)

Stochastic Petri Nets in Systems Biology. - Ole Schulz-Trieglaff (BMC Bioinform., 2005)

A geometric approach for the alignment of liquid chromatography - mass spectrometry data. - Eva Lange; Clemens Gröpl; Ole Schulz-Trieglaff; Andreas Leinenbach; Christian G. Huber; Knut Reinert (ISMB/ECCB (Supplement of Bioinformatics), 2007)

A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data. - Ole Schulz-Trieglaff; Rene Hussong; Clemens Gröpl; Andreas Hildebrandt 001; Knut Reinert (RECOMB, 2007)

TOPP - the OpenMS proteomics pipeline. - Oliver Kohlbacher; Knut Reinert; Clemens Gröpl; Eva Lange; Nico Pfeifer; Ole Schulz-Trieglaff; Marc Sturm (Bioinform., 2007)

LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. - Ole Schulz-Trieglaff; Nico Pfeifer; Clemens Gröpl; Oliver Kohlbacher; Knut Reinert (BMC Bioinform., 2008)

OpenMS - An open-source software framework for mass spectrometry. - Marc Sturm; Andreas Bertsch; Clemens Gröpl; Andreas Hildebrandt 001; Rene Hussong; Eva Lange; Nico Pfeifer; Ole Schulz-Trieglaff; Alexandra Zerck; Knut Reinert; Oliver Kohlbacher (BMC Bioinform., 2008)

Computational Quantification of Peptides from LC-MS Data. - Ole Schulz-Trieglaff; Rene Hussong; Clemens Gröpl; Andreas Leinenbach; Andreas Hildebrandt 001; Christian G. Huber; Knut Reinert (J. Comput. Biol., 2008)

Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. - Ole Schulz-Trieglaff; Egidijus Machtejevas; Knut Reinert; Hartmut Schlüter; Joachim Thiemann; Klaus Unger (BioData Min., 2009)

Computational methods for Quantitative Peptide Mass Spectrometry (Rechnergestützte Methoden für die Quantitative Massenspektrometrie von Peptiden) - Ole Schulz-Trieglaff (2009)

Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes. - Anthony J. Cox; Tobias Jakobi; Giovanna Rosone; Ole Schulz-Trieglaff (WABI, 2012)

metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. - Christina Ander; Ole Schulz-Trieglaff; Jens Stoye; Anthony J. Cox (BMC Bioinform., 2013)

BEETL-fastq: a searchable compressed archive for DNA reads. - Lilian Janin; Ole Schulz-Trieglaff; Anthony J. Cox (Bioinform., 2014)

NxTrim: optimized trimming of Illumina mate pair reads. - Jared O'Connell; Ole Schulz-Trieglaff; Emma Carlson; Matthew M. Hims; Niall A. Gormley; Anthony J. Cox (Bioinform., 2015)

Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions. - Rudy Arthur; Jared O'Connell; Ole Schulz-Trieglaff; Anthony J. Cox (Bioinform., 2016)

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. - Xiaoyu Chen; Ole Schulz-Trieglaff; Richard Shaw; Bret Barnes; Felix Schlesinger; Morten Källberg; Anthony J. Cox; Semyon Kruglyak; Christopher T. Saunders (Bioinform., 2016)

AKT: ancestry and kinship toolkit. - Rudy Arthur; Ole Schulz-Trieglaff; Anthony J. Cox; Jared O'Connell (Bioinform., 2017)