Marcel H. Schulz

40 papers A* 1A 1B 1C 2Journal 33

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Decoding heart failure subtypes with neural networks via differential explanation analysis. Briefings Bioinform. Mariano Ruz Jurado, David Rodriguez Morales, Elijah Genetzakis, Fatemeh Behjati-Ardakani, Lukas Zanders, Ariane Fischer, Florian Buettner, Marcel H. Schulz, Stefanie Dimmeler, David John
2025	J	`jnl`	GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data. PLoS Comput. Biol. Simonida Zehr, Sebastian Wolf, Thomas Oellerich, Matthias S. Leisegang, Ralf P. Brandes, Marcel H. Schulz, Timothy Warwick
2025	J	`jnl`	TripLexicon: prediction and analysis of gene regulatory RNA-DNA interactions. Bioinform. Timothy Warwick, Christina Kalk, Ralf P. Brandes, Marcel H. Schulz
2023	A	`conf`	Debugging Low Power Analog Neural Networks for Edge Computing. DATE Sascha Schmalhofer, Marwin Möller, Nikoletta Katsaouni, Marcel H. Schulz, Lars Hedrich
2023	J	`jnl`	Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data. Bioinform. Jonas Fischer, Marcel H. Schulz
2023	J	`jnl`	The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data. Bioinform. Dennis Hecker, Fatemeh Behjati-Ardakani, Alexander Karollus, Julien Gagneur, Marcel H. Schulz
2022	J	`jnl`	A universal model of RNA.DNA: DNA triplex formation accurately predicts genome-wide RNA-DNA interactions. Briefings Bioinform. 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, Ralf P. Brandes
2022	J	`jnl`	Energy efficient convolutional neural networks for arrhythmia detection. Array Nikoletta Katsaouni, Florian Aul, Lukas Krischker, Sascha Schmalhofer, Lars Hedrich, Marcel H. Schulz
2021	J	`jnl`	Fast detection of differential chromatin domains with SCIDDO. Bioinform. Peter Ebert, Marcel H. Schulz
2021	J	`jnl`	Fostering accessible online education using Galaxy as an e-learning platform. PLoS Comput. Biol. 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, Bérénice Batut, Björn A. Grüning
2021	J	`jnl`	Machine learning for deciphering cell heterogeneity and gene regulation. Nat. Comput. Sci. Michael Scherer, Florian Schmidt, Olga Lazareva, Jörn Walter, Jan Baumbach, Marcel H. Schulz, Markus List
2020	J	`jnl`	Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. J. Comput. Biol. Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz
2020	J	`jnl`	EpiRegio: analysis and retrieval of regulatory elements linked to genes. Nucleic Acids Res. Nina Baumgarten, Dennis Hecker, Sivarajan Karunanithi, Florian Schmidt, Markus List, Marcel H. Schulz
2020	J	`jnl`	Improved linking of motifs to their TFs using domain information. Bioinform. Nina Baumgarten, Florian Schmidt, Marcel H. Schulz
2019	J	`jnl`	Large-scale inference of competing endogenous RNA networks with sparse partial correlation. Bioinform. Markus List, Azim Dehghani Amirabad, Dennis Kostka, Marcel H. Schulz
2019	J	`jnl`	On the problem of confounders in modeling gene expression. Bioinform. Florian Schmidt, Marcel H. Schulz
2019	J	`jnl`	TEPIC 2 - an extended framework for transcription factor binding prediction and integrative epigenomic analysis. Bioinform. Florian Schmidt, Fabian Kern, Peter Ebert, Nina Baumgarten, Marcel H. Schulz
2018	J	`jnl`	An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets. Bioinform. Florian Schmidt, Markus List, Engin Cukuroglu, Sebastian Köhler, Jonathan Göke, Marcel H. Schulz
2018	B	`conf`	Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. RECOMB Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz
2018	J	`jnl`	In silico read normalization using set multi-cover optimization. Bioinform. Dilip A. Durai, Marcel H. Schulz
2018	J	`jnl`	JAMI: fast computation of conditional mutual information for ceRNA network analysis. Bioinform. Andrea Hornáková, Markus List, Jilles Vreeken, Marcel H. Schulz
2018	J	`jnl`	Predicting transcription factor binding using ensemble random forest models. F1000Research Fatemeh Behjati-Ardakani, Florian Schmidt, Marcel H. Schulz
2017	—	`ch.`	DNA-Seq Error Correction Based on Substring Indices. Algorithms for Next-Generation Sequencing Data David Weese, Marcel H. Schulz, Hugues Richard
2017	—	`ch.`	Probabilistic Models for Error Correction of Nonuniform Sequencing Data. Algorithms for Next-Generation Sequencing Data Marcel H. Schulz, Ziv Bar-Joseph
2017	J	`jnl`	RegulatorTrail: a web service for the identification of key transcriptional regulators. Nucleic Acids Res. Tim Kehl, Lara Schneider, Florian Schmidt, Daniel Stöckel, Nico Gerstner, Christina Backes, Eckart Meese, Andreas Keller, Marcel H. Schulz, Hans-Peter Lenhof
2016	J	`jnl`	Informed Bioinform. Dilip A. Durai, Marcel H. Schulz
2016	J	`jnl`	Multitask regression for condition-specific prioritization of miRNA targets in transcripts. PeerJ Prepr. Azim Dehghani Amirabad, Marcel H. Schulz
2015	J	`jnl`	A general concept for consistent documentation of computational analyses. Database J. Biol. Databases Curation Peter Ebert, Fabian Müller, Karl Nordström, Thomas Lengauer, Marcel H. Schulz
2014	J	`jnl`	Fiona: a parallel and automatic strategy for read error correction. Bioinform. Marcel H. Schulz, David Weese, Manuel Holtgrewe, Viktoria Dimitrova, Sijia Niu, Knut Reinert, Hugues Richard
2012	J	`jnl`	Bayesian ontology querying for accurate and noise-tolerant semantic searches. Bioinform. Sebastian Bauer, Sebastian Köhler, Marcel H. Schulz, Peter N. Robinson
2012	J	`jnl`	DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst. Biol. Marcel H. Schulz, William E. Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph
2012	J	`jnl`	Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinform. Anne-Katrin Emde, Marcel H. Schulz, David Weese, Ruping Sun, Martin Vingron, Vera M. Kalscheuer, Stefan A. Haas, Knut Reinert
2012	J	`jnl`	Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinform. Jonathan Göke, Marcel H. Schulz, Julia Lasserre, Martin Vingron
2011	J	`jnl`	DECOD: fast and accurate discriminative DNA motif finding. Bioinform. Peter Huggins, Shan Zhong, Idit Shiff, Rachel Beckerman, Oleg Laptenko, Carol Prives, Marcel H. Schulz, Itamar Simon, Ziv Bar-Joseph
2011	J	`jnl`	Exact score distribution computation for ontological similarity searches. BMC Bioinform. Marcel H. Schulz, Sebastian Köhler, Sebastian Bauer, Peter N. Robinson
2009	C	`conf`	Exact Score Distribution Computation for Similarity Searches in Ontologies. WABI Marcel H. Schulz, Sebastian Köhler, Sebastian Bauer, Martin Vingron, Peter N. Robinson
2009	J	`jnl`	Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinform. Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, Zemin Ning
2008	A*	`conf`	Efficient String Mining under Constraints Via the Deferred Frequency Index. ICDM David Weese, Marcel H. Schulz
2008	C	`conf`	Fast and Adaptive Variable Order Markov Chain Construction. WABI Marcel H. Schulz, David Weese, Tobias Rausch, Andreas Döring, Knut Reinert, Martin Vingron
2008	J	`jnl`	The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences. Int. J. Bioinform. Res. Appl. Marcel H. Schulz, Sebastian Bauer, Peter N. Robinson