Efficient String Mining under Constraints Via the Deferred Frequency Index. - David Weese; Marcel H. Schulz (ICDM, 2008)

Fast and Adaptive Variable Order Markov Chain Construction. - Marcel H. Schulz; David Weese; Tobias Rausch; Andreas Döring 001; Knut Reinert; Martin Vingron (WABI, 2008)

The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences. - Marcel H. Schulz; Sebastian Bauer 002; Peter N. Robinson (Int. J. Bioinform. Res. Appl., 2008)

Exact Score Distribution Computation for Similarity Searches in Ontologies. - Marcel H. Schulz; Sebastian Köhler 001; Sebastian Bauer 002; Martin Vingron; Peter N. Robinson (WABI, 2009)

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. - Kai Ye 001; Marcel H. Schulz; Quan Long; Rolf Apweiler; Zemin Ning (Bioinform., 2009)

DECOD: fast and accurate discriminative DNA motif finding. - Peter Huggins; Shan Zhong; Idit Shiff; Rachel Beckerman; Oleg Laptenko; Carol Prives; Marcel H. Schulz; Itamar Simon; Ziv Bar-Joseph (Bioinform., 2011)

Exact score distribution computation for ontological similarity searches. - Marcel H. Schulz; Sebastian Köhler 001; Sebastian Bauer 002; Peter N. Robinson (BMC Bioinform., 2011)

Bayesian ontology querying for accurate and noise-tolerant semantic searches. - Sebastian Bauer 002; Sebastian Köhler 001; Marcel H. Schulz; Peter N. Robinson (Bioinform., 2012)

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. - Anne-Katrin Emde; Marcel H. Schulz; David Weese; Ruping Sun; Martin Vingron; Vera M. Kalscheuer; Stefan A. Haas; Knut Reinert (Bioinform., 2012)

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. - Jonathan Göke; Marcel H. Schulz; Julia Lasserre; Martin Vingron (Bioinform., 2012)

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. - Marcel H. Schulz; Daniel R. Zerbino; Martin Vingron; Ewan Birney (Bioinform., 2012)

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. - Marcel H. Schulz; William E. Devanny; Anthony Gitter; Shan Zhong; Jason Ernst; Ziv Bar-Joseph (BMC Syst. Biol., 2012)

Fiona: a parallel and automatic strategy for read error correction. - Marcel H. Schulz; David Weese; Manuel Holtgrewe; Viktoria Dimitrova; Sijia Niu; Knut Reinert; Hugues Richard (Bioinform., 2014)

A general concept for consistent documentation of computational analyses. - Peter Ebert; Fabian Müller 001; Karl Nordström; Thomas Lengauer; Marcel H. Schulz (Database J. Biol. Databases Curation, 2015)

Informed kmer selection for de novo transcriptome assembly. - Dilip A. Durai; Marcel H. Schulz (Bioinform., 2016)

Multitask regression for condition-specific prioritization of miRNA targets in transcripts. - Azim Dehghani Amirabad; Marcel H. Schulz (PeerJ Prepr., 2016)

Probabilistic Models for Error Correction of Nonuniform Sequencing Data. - Marcel H. Schulz; Ziv Bar-Joseph (Algorithms for Next-Generation Sequencing Data, 2017)

DNA-Seq Error Correction Based on Substring Indices. - David Weese; Marcel H. Schulz; Hugues Richard (Algorithms for Next-Generation Sequencing Data, 2017)

RegulatorTrail: a web service for the identification of key transcriptional regulators. - Tim Kehl; Lara Schneider; Florian Schmidt 003; Daniel Stöckel; Nico Gerstner; Christina Backes; Eckart Meese; Andreas Keller; Marcel H. Schulz; Hans-Peter Lenhof (Nucleic Acids Res., 2017)

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets. - Florian Schmidt 003; Markus List; Engin Cukuroglu; Sebastian Köhler 001; Jonathan Göke; Marcel H. Schulz (Bioinform., 2018)

In silico read normalization using set multi-cover optimization. - Dilip A. Durai; Marcel H. Schulz (Bioinform., 2018)

JAMI: fast computation of conditional mutual information for ceRNA network analysis. - Andrea Hornáková; Markus List; Jilles Vreeken; Marcel H. Schulz (Bioinform., 2018)

Predicting transcription factor binding using ensemble random forest models. - Fatemeh Behjati-Ardakani; Florian Schmidt 003; Marcel H. Schulz (F1000Research, 2018)

Large-scale inference of competing endogenous RNA networks with sparse partial correlation. - Markus List; Azim Dehghani Amirabad; Dennis Kostka; Marcel H. Schulz (Bioinform., 2019)

TEPIC 2 - an extended framework for transcription factor binding prediction and integrative epigenomic analysis. - Florian Schmidt 003; Fabian Kern; Peter Ebert; Nina Baumgarten; Marcel H. Schulz (Bioinform., 2019)

On the problem of confounders in modeling gene expression. - Florian Schmidt 003; Marcel H. Schulz (Bioinform., 2019)

Improved linking of motifs to their TFs using domain information. - Nina Baumgarten; Florian Schmidt 003; Marcel H. Schulz (Bioinform., 2020)

Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. - Shounak Chakraborty 003; Stefan Canzar; Tobias Marschall; Marcel H. Schulz (J. Comput. Biol., 2020)

EpiRegio: analysis and retrieval of regulatory elements linked to genes. - Nina Baumgarten; Dennis Hecker; Sivarajan Karunanithi; Florian Schmidt 003; Markus List; Marcel H. Schulz (Nucleic Acids Res., 2020)

Fast detection of differential chromatin domains with SCIDDO. - Peter Ebert; Marcel H. Schulz (Bioinform., 2021)

Machine learning for deciphering cell heterogeneity and gene regulation. - Michael Scherer; Florian Schmidt 003; Olga Lazareva; Jörn Walter; Jan Baumbach; Marcel H. Schulz; Markus List (Nat. Comput. Sci., 2021)

Fostering accessible online education using Galaxy as an e-learning platform. - Beatriz Serrano-Solano; Melanie Christine Föll; Cristóbal Gallardo-Alba; Anika Erxleben; Helena Rasche; Saskia D. Hiltemann; Matthias Fahrner; Mark J. Dunning; Marcel H. Schulz; Beáta Scholtz; Dave Clements; Anton Nekrutenko; et al. (PLoS Comput. Biol., 2021)

Energy efficient convolutional neural networks for arrhythmia detection. - Nikoletta Katsaouni; Florian Aul; Lukas Krischker; Sascha Schmalhofer; Lars Hedrich; Marcel H. Schulz (Array, 2022)

A universal model of RNA.DNA: DNA triplex formation accurately predicts genome-wide RNA-DNA interactions. - Timothy Warwick; Sandra Seredinski; Nina M. Krause; Jasleen Kaur Bains; Lara Althaus; James A Oo; Alessandro Bonetti; Anne Dueck; Stefan Engelhardt; Harald Schwalbe; Matthias S. Leisegang; Marcel H. Schulz; et al. (Briefings Bioinform., 2022)

Debugging Low Power Analog Neural Networks for Edge Computing. - Sascha Schmalhofer; Marwin Möller; Nikoletta Katsaouni; Marcel H. Schulz; Lars Hedrich (DATE, 2023)

The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data. - Dennis Hecker; Fatemeh Behjati-Ardakani; Alexander Karollus; Julien Gagneur; Marcel H. Schulz (Bioinform., 2023)

GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data. - Simonida Zehr; Sebastian Wolf; Thomas Oellerich; Matthias S. Leisegang; Ralf P. Brandes; Marcel H. Schulz; Timothy Warwick (PLoS Comput. Biol., 2025)