Marcel H Schulz

Marcel H Schulz

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Marcel H Schulz

Marcel H Schulz

Publications by authors named "Marcel H Schulz"

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Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium.

Nucleic Acids Res 2019 Sep;47(15):8036-8049

Cluster of Excellence, Multimodal Computing and Interaction, Saarland University and Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/nar/gkz553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735861PMC
September 2019

The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development.

Dev Cell 2019 Sep 15;50(5):644-657.e8. Epub 2019 Aug 15.

Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2019.07.013DOI Listing
September 2019

Phenotypic Plasticity of Fibroblasts during Mammary Carcinoma Development.

Int J Mol Sci 2019 Sep 9;20(18). Epub 2019 Sep 9.

Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany.

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http://dx.doi.org/10.3390/ijms20184438DOI Listing
September 2019

Transcriptomics of a KDELR1 knockout cell line reveals modulated cell adhesion properties.

Sci Rep 2019 Jul 23;9(1):10611. Epub 2019 Jul 23.

Molecular and Cell Biology, Department of Biosciences (FR 8.3) and Center of Human and Molecular Biology (ZHMB), Saarland University, D-66123, Saarbrücken, Germany.

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http://dx.doi.org/10.1038/s41598-019-47027-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650600PMC
July 2019

Large-scale inference of competing endogenous RNA networks with sparse partial correlation.

Bioinformatics 2019 Jul;35(14):i596-i604

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btz314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612827PMC
July 2019

TEPIC 2-an extended framework for transcription factor binding prediction and integrative epigenomic analysis.

Bioinformatics 2019 May;35(9):1608-1609

High throughput Genomics and Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, Saarbrücken, Germany.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499243PMC
May 2019

Transcriptome Kinetics of in Response to Viral Killer Toxin K1.

Front Microbiol 2019 16;10:1102. Epub 2019 May 16.

Department of Molecular and Cell Biology, Saarland University, Saarbrücken, Germany.

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http://dx.doi.org/10.3389/fmicb.2019.01102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6531845PMC
May 2019

Automated analysis of small RNA datasets with RAPID.

PeerJ 2019 10;7:e6710. Epub 2019 Apr 10.

Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.

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https://peerj.com/articles/6710
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http://dx.doi.org/10.7717/peerj.6710DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462184PMC
April 2019

Improving in-silico normalization using read weights.

Sci Rep 2019 Mar 26;9(1):5133. Epub 2019 Mar 26.

Cluster of Excellence on Multimodal Computing and Interaction (MMCI) and Max Planck Insitute for Informatics (MPII), Saarland University, Saarbrücken, Germany.

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http://dx.doi.org/10.1038/s41598-019-41502-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6435659PMC
March 2019

On the problem of confounders in modeling gene expression.

Bioinformatics 2019 Feb;35(4):711-719

High-througput Genomics and Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty674DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6530814PMC
February 2019

Identification of transcription factor binding sites using ATAC-seq.

Genome Biol 2019 02 26;20(1):45. Epub 2019 Feb 26.

Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, 52074, Germany.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1642-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391789PMC
February 2019

Analysis of Cell Type-Specific Effects of MicroRNA-92a Provides Novel Insights Into Target Regulation and Mechanism of Action.

Circulation 2018 11;138(22):2545-2558

Institute of Cardiovascular Regeneration, Goethe University, Frankfurt, Germany (E.-M.R., W.T.A., C.B., D.J., M.H.S., J.K., A.F., A.B., S.D.).

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http://dx.doi.org/10.1161/CIRCULATIONAHA.118.034598DOI Listing
November 2018

Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosis.

Biochim Biophys Acta Mol Basis Dis 2018 10 30;1864(10):3099-3108. Epub 2018 May 30.

Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bbadis.2018.05.024DOI Listing
October 2018

In silico read normalization using set multi-cover optimization.

Bioinformatics 2018 10;34(19):3273-3280

Cluster of Excellence on Multimodal Computing and Interaction, Saarland University, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157080PMC
October 2018

JAMI: fast computation of conditional mutual information for ceRNA network analysis.

Bioinformatics 2018 09;34(17):3050-3051

Max Planck Institute for Informatics, Saarland University, Saarland Informatics Campus, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129307PMC
September 2018

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets.

Bioinformatics 2018 09;34(17):i908-i916

Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129283PMC
September 2018

Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation.

Genes (Basel) 2018 Feb 21;9(2). Epub 2018 Feb 21.

Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.3390/genes9020117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5852613PMC
February 2018

RegulatorTrail: a web service for the identification of key transcriptional regulators.

Nucleic Acids Res 2017 07;45(W1):W146-W153

Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/nar/gkx350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570139PMC
July 2017

Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes.

Nucleic Acids Res 2016 07 16;44(12):5908-23. Epub 2016 Apr 16.

Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany

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http://dx.doi.org/10.1093/nar/gkw267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937312PMC
July 2016

Informed kmer selection for de novo transcriptome assembly.

Bioinformatics 2016 06 28;32(11):1670-7. Epub 2016 Apr 28.

Cluster of Excellence on Multimodal Computing and Interaction, Saarland University, Saarbrücken, 66123, Germany Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btw217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892416PMC
June 2016

A general concept for consistent documentation of computational analyses.

Database (Oxford) 2015 8;2015:bav050. Epub 2015 Jun 8.

Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany Graduate School of Computer Science, Saarland University, Saarbrücken, Germany Department of Genetics, Saarland University, Saarbrücken, Germany and Cluster of Excellence on Multimodal Computing and Interaction, Saarland University, Saarbrücken, Germany Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany Graduate School of Computer Science, Saarland University, Saarbrücken, Germany Department of Genetics, Saarland University, Saarbrücken, Germany and Cluster of Excellence on Multimodal Computing and Interaction, Saarland University, Saarbrücken, Germany

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http://dx.doi.org/10.1093/database/bav050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460408PMC
March 2016

Letting the data speak for themselves: a fully Bayesian approach to transcriptome assembly.

Authors:
Marcel H Schulz

Genome Biol 2014 ;15(10):498

Excellence Cluster for Multimodal Computing and Interaction, Saarland 66123, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4318165PMC
http://dx.doi.org/10.1186/s13059-014-0498-8DOI Listing
October 2015

De novo ChIP-seq analysis.

Genome Biol 2015 Sep 23;16:205. Epub 2015 Sep 23.

Computational Biology Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, 15213, USA.

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http://dx.doi.org/10.1186/s13059-015-0756-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579611PMC
September 2015

Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia.

DNA Res 2015 Aug 31;22(4):293-305. Epub 2015 Jul 31.

Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany

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http://dx.doi.org/10.1093/dnares/dsv014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535620PMC
August 2015

Fiona: a parallel and automatic strategy for read error correction.

Bioinformatics 2014 Sep;30(17):i356-63

'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France.

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http://dx.doi.org/10.1093/bioinformatics/btu440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147893PMC
September 2014

Reconstructing dynamic microRNA-regulated interaction networks.

Proc Natl Acad Sci U S A 2013 Sep 28;110(39):15686-91. Epub 2013 Aug 28.

Ray and Stephanie Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213.

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http://dx.doi.org/10.1073/pnas.1303236110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785769PMC
September 2013

Probabilistic error correction for RNA sequencing.

Nucleic Acids Res 2013 May 4;41(10):e109. Epub 2013 Apr 4.

Machine Learning Department, Carnegie Mellon University, 5000 Forbes Avenue Pittsburgh, PA 15217, USA.

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http://dx.doi.org/10.1093/nar/gkt215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664804PMC
May 2013

Bayesian ontology querying for accurate and noise-tolerant semantic searches.

Bioinformatics 2012 Oct 26;28(19):2502-8. Epub 2012 Jul 26.

Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463114PMC
October 2012

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.

BMC Syst Biol 2012 Aug 16;6:104. Epub 2012 Aug 16.

Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1752-0509-6-104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464930PMC
August 2012

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.

Bioinformatics 2012 Apr 24;28(8):1086-92. Epub 2012 Feb 24.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324515PMC
April 2012

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.

Bioinformatics 2012 Mar 11;28(5):619-27. Epub 2012 Jan 11.

Department of Computer Science, Freie Universität Berlin, Takustrasse 9, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts019DOI Listing
March 2012

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.

Bioinformatics 2012 Mar 12;28(5):656-63. Epub 2012 Jan 12.

Department for Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289921PMC
March 2012

Exact score distribution computation for ontological similarity searches.

BMC Bioinformatics 2011 Nov 12;12:441. Epub 2011 Nov 12.

Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1186/1471-2105-12-441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240574PMC
November 2011

DECOD: fast and accurate discriminative DNA motif finding.

Bioinformatics 2011 Sep 12;27(17):2361-7. Epub 2011 Jul 12.

Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157928PMC
September 2011

Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions.

Nucleic Acids Res 2011 Apr 24;39(7):2492-502. Epub 2010 Nov 24.

Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkq1081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074119PMC
April 2011

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.

Nucleic Acids Res 2010 Jun 11;38(10):e112. Epub 2010 Feb 11.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkq041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879520PMC
June 2010

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

Bioinformatics 2009 Nov 26;25(21):2865-71. Epub 2009 Jun 26.

EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btp394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781750PMC
November 2009

Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts.

Genomics 2009 Nov 4;94(5):308-16. Epub 2009 Aug 4.

Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S088875430900161
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http://dx.doi.org/10.1016/j.ygeno.2009.07.005DOI Listing
November 2009

Clinical diagnostics in human genetics with semantic similarity searches in ontologies.

Am J Hum Genet 2009 Oct;85(4):457-64

Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

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http://dx.doi.org/10.1016/j.ajhg.2009.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756558PMC
October 2009

A short ultraconserved sequence drives transcription from an alternate FBN1 promoter.

Int J Biochem Cell Biol 2008 2;40(4):638-50. Epub 2007 Oct 2.

Institute for Medical Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

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http://dx.doi.org/10.1016/j.biocel.2007.09.004DOI Listing
July 2008

The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences.

Int J Bioinform Res Appl 2008 ;4(1):81-95

Institute fur Medizinische Genetik, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin,

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http://www.inderscience.com/link.php?id=17165
Publisher Site
http://dx.doi.org/10.1504/IJBRA.2008.017165DOI Listing
May 2008