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ORCIDMarcel H. Schulz
Person information
- affiliation: Max Planck Institute for Informatics
- affiliation: Carnegie Mellon University, Lane Center for Computational Biology
- affiliation: Max Planck Institute for Molecular Genetics
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Journal Articles
- 2023
[j28]Dennis Hecker
, Fatemeh Behjati-Ardakani, Alexander Karollus, Julien Gagneur, Marcel H. Schulz:
The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data. Bioinform. 39(2) (2023)- 2022
- [j27]Nikoletta Katsaouni, Florian Aul, Lukas Krischker, Sascha Schmalhofer, Lars Hedrich, Marcel H. Schulz:
Energy efficient convolutional neural networks for arrhythmia detection. Array 13: 100127 (2022) - [j26]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:
A universal model of RNA.DNA: DNA triplex formation accurately predicts genome-wide RNA-DNA interactions. Briefings Bioinform. 23(6) (2022) - 2021
- [j25]Peter Ebert, Marcel H. Schulz:
Fast detection of differential chromatin domains with SCIDDO. Bioinform. 37(9): 1198-1205 (2021) - [j24]Michael Scherer, Florian Schmidt, Olga Lazareva, Jörn Walter, Jan Baumbach, Marcel H. Schulz, Markus List:
Machine learning for deciphering cell heterogeneity and gene regulation. Nat. Comput. Sci. 1(3): 183-191 (2021) - [j23]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:
Fostering accessible online education using Galaxy as an e-learning platform. PLoS Comput. Biol. 17(5) (2021) - 2020
- [j22]Nina Baumgarten, Florian Schmidt, Marcel H. Schulz:
Improved linking of motifs to their TFs using domain information. Bioinform. 36(6): 1655-1662 (2020) - [j21]Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz:
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. J. Comput. Biol. 27(3): 330-341 (2020) - [j20]Nina Baumgarten, Dennis Hecker, Sivarajan Karunanithi, Florian Schmidt, Markus List, Marcel H. Schulz:
EpiRegio: analysis and retrieval of regulatory elements linked to genes. Nucleic Acids Res. 48(Webserver-Issue): W193-W199 (2020) - 2019
- [j19]Florian Schmidt, Marcel H. Schulz:
On the problem of confounders in modeling gene expression. Bioinform. 35(4): 711-719 (2019) - [j18]Florian Schmidt, Fabian Kern, Peter Ebert, Nina Baumgarten, Marcel H. Schulz:
TEPIC 2 - an extended framework for transcription factor binding prediction and integrative epigenomic analysis. Bioinform. 35(9): 1608-1609 (2019) - [j17]Markus List, Azim Dehghani Amirabad, Dennis Kostka, Marcel H. Schulz:
Large-scale inference of competing endogenous RNA networks with sparse partial correlation. Bioinform. 35(14): i596-i604 (2019) - 2018
- [j16]Andrea Hornáková, Markus List, Jilles Vreeken, Marcel H. Schulz:
JAMI: fast computation of conditional mutual information for ceRNA network analysis. Bioinform. 34(17): 3050-3051 (2018) - [j15]Florian Schmidt, Markus List, Engin Cukuroglu, Sebastian Köhler, Jonathan Göke, Marcel H. Schulz:
An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets. Bioinform. 34(17): i908-i916 (2018) - [j14]Dilip A. Durai, Marcel H. Schulz:
In silico read normalization using set multi-cover optimization. Bioinform. 34(19): 3273-3280 (2018) - 2017
- [j13]Tim Kehl, Lara Schneider, Florian Schmidt, Daniel Stöckel, Nico Gerstner, Christina Backes, Eckart Meese, Andreas Keller, Marcel H. Schulz, Hans-Peter Lenhof:
RegulatorTrail: a web service for the identification of key transcriptional regulators. Nucleic Acids Res. 45(Webserver-Issue): W146-W153 (2017) - 2016
- [j12]Dilip A. Durai, Marcel H. Schulz:
Informed kmer selection for de novo transcriptome assembly. Bioinform. 32(11): 1670-1677 (2016) - 2015
- [j11]Peter Ebert, Fabian Müller, Karl Nordström, Thomas Lengauer, Marcel H. Schulz:
A general concept for consistent documentation of computational analyses. Database J. Biol. Databases Curation 2015 (2015) - 2014
- [j10]Marcel H. Schulz, David Weese, Manuel Holtgrewe, Viktoria Dimitrova, Sijia Niu, Knut Reinert, Hugues Richard:
Fiona: a parallel and automatic strategy for read error correction. Bioinform. 30(17): 356-363 (2014) - 2012
- [j9]Anne-Katrin Emde, Marcel H. Schulz, David Weese, Ruping Sun, Martin Vingron, Vera M. Kalscheuer, Stefan A. Haas, Knut Reinert:
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinform. 28(5): 619-627 (2012) - [j8]Jonathan Göke, Marcel H. Schulz, Julia Lasserre, Martin Vingron:
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinform. 28(5): 656-663 (2012) - [j7]Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron, Ewan Birney:
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinform. 28(8): 1086-1092 (2012) - [j6]Sebastian Bauer, Sebastian Köhler, Marcel H. Schulz, Peter N. Robinson:
Bayesian ontology querying for accurate and noise-tolerant semantic searches. Bioinform. 28(19): 2502-2508 (2012) - [j5]Marcel H. Schulz, William E. Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph:
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst. Biol. 6: 104 (2012) - 2011
- [j4]Peter Huggins, Shan Zhong, Idit Shiff, Rachel Beckerman, Oleg Laptenko, Carol Prives, Marcel H. Schulz, Itamar Simon, Ziv Bar-Joseph:
DECOD: fast and accurate discriminative DNA motif finding. Bioinform. 27(17): 2361-2367 (2011) - [j3]Marcel H. Schulz, Sebastian Köhler, Sebastian Bauer, Peter N. Robinson:
Exact score distribution computation for ontological similarity searches. BMC Bioinform. 12: 441 (2011) - 2009
- [j2]Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, Zemin Ning:
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinform. 25(21): 2865-2871 (2009) - 2008
- [j1]Marcel H. Schulz, Sebastian Bauer, Peter N. Robinson:
The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences. Int. J. Bioinform. Res. Appl. 4(1): 81-95 (2008)
Conference and Workshop Papers
- 2023
- [c5]Sascha Schmalhofer, Marwin Möller, Nikoletta Katsaouni, Marcel H. Schulz, Lars Hedrich:
Debugging Low Power Analog Neural Networks for Edge Computing. DATE 2023: 1-2 - 2018
- [c4]Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz:
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. RECOMB 2018: 21-36 - 2009
- [c3]Marcel H. Schulz, Sebastian Köhler, Sebastian Bauer, Martin Vingron, Peter N. Robinson:
Exact Score Distribution Computation for Similarity Searches in Ontologies. WABI 2009: 298-309 - 2008
- [c2]David Weese, Marcel H. Schulz:
Efficient String Mining under Constraints Via the Deferred Frequency Index. ICDM 2008: 374-388 - [c1]Marcel H. Schulz, David Weese, Tobias Rausch, Andreas Döring, Knut Reinert, Martin Vingron:
Fast and Adaptive Variable Order Markov Chain Construction. WABI 2008: 306-317
Parts in Books or Collections
- 2017
- [p2]Marcel H. Schulz, Ziv Bar-Joseph:
Probabilistic Models for Error Correction of Nonuniform Sequencing Data. Algorithms for Next-Generation Sequencing Data 2017: 131-145 - [p1]David Weese, Marcel H. Schulz, Hugues Richard:
DNA-Seq Error Correction Based on Substring Indices. Algorithms for Next-Generation Sequencing Data 2017: 147-166
Informal and Other Publications
- 2018
- [i2]Fatemeh Behjati-Ardakani, Florian Schmidt, Marcel H. Schulz:
Predicting transcription factor binding using ensemble random forest models. F1000Research 7: 1603 (2018) - 2016
- [i1]Azim Dehghani Amirabad, Marcel H. Schulz:
Multitask regression for condition-specific prioritization of miRNA targets in transcripts. PeerJ Prepr. 4: e2377 (2016)
Coauthor Index
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