Publications

Zlatka Fischer, Katharina Imkeller, Marcel H. Schulz, Nina Baumgarten (2026). A categorization of spatial transcriptomics methods for cell–cell communication analysis. Trends in Genetics.

Fatemeh Behjati Ardakani, Shamim Ashrafiyan, Laura Rumpf, Dennis Hecker, Marcel H Schulz (2026). Comparing machine learning methods predicting transcriptome from epigenome with applications to association studies. Genome Biology.

Shamim Ashrafiyan, Iaroslav Kosaretskii, Marcel H. Schulz (2026). AtlasLens: Metadata-centric exploration and analysis of single-cell atlases. Preprint (BioRxiv).

Simonida Zehr, Sandra Seredinski, Katalin Pálfi, James A. Oo, Emma C. Walsh, Alessandro Bonetti, Matthias S. Leisegang, Ralf P. Brandes, Marcel H. Schulz, Dr. Timothy Warwick (2026). Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions. Nucleic Acids Research.

Nikoletta Katsaouni, Marcel H. Schulz (2026). RANKOR: Direct Drug Prioritization from Bulk and Single-Cell Transcriptomic Signatures. Preprint (BioRxiv).

Jana Hahn, Pooja Gune, Sascha Hein, Wolf Holtkamp, Marcel H. Schulz, Walter Matheis, Volker Öppling, Christel Kamp (2026). Quantifying Components in a Model Vaccine with Machine-Learning-Augmented Raman Spectroscopy. Analytical Chemistry.

Lukas Geis, Dennis Hecker, Martin Hoefer, Ulrich Meyer, Marcel H. Schulz (2026). Probing transcription factor subsets in gene regulatory networks. Algorithms for molecular biology: AMB.

Christina Wrobel (formerly Kalk), Justin Murtagh, Vladimir Despic, Michaela Müller-McNicoll, Marcel H. Schulz (2026). Prediction and evaluation of Split-ORFs using Ribo-seq data. Preprint (BioRxiv).

Laura Rumpf, Fatemeh Behjati Ardakani, Dennis Hecker, Marcel H. Schulz (2026). Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data. Bioinformatics.

Eric Schoger, Rosa Kim, Federico Bleckwedel, Tomás M. Peralta, Laura Priesmeier, Janek A. Fischer, Laura Stengel, Cheila Rocha, Gabriela L. Santos, Susanne Lutz, Etienne Boileau, Nina Baumgarten, Marcel H. Schulz, Christoph Dieterich, Oliver J. Müller, Lukas Cyganek, Alfredo Cabrera-Orefice, Hanna Eberl, Christoph Maack, Katrin Streckfuss-Bömeke, Mario G. Pavez-Giani, Shirin Doroudgar, Samuel Sossalla, Laura C. Zelarayán (2026). Enhancing KLF15 activity in cardiomyocytes: a novel approach to prevent pathological reprogramming and fibrosis via nuclease-deficient dCas9VPR. Signal Transduction and Targeted Therapy.

Dennis Hecker, Xiaoning Song, Nina Baumgarten, Anastasiia Diagel, Nikoletta Katsaouni, Ling Li, Shuangyue Li, Ranjan Kumar Maji, Fatemeh Behjati Ardakani, Lijiang Ma, Zhaolong Li, Aldo Moggio, Daniel Tews, Hendrik Sager, Lars Maegdefessel, Martin Wabitsch, Johan L. M. Björkegren, Heribert Schunkert, Zhifen Chen, Marcel H. Schulz (2026). Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci. Nature Communications.

Ranjan Kumar Maji, Giulia Cantini, Hui Cheng, Annalisa Marsico, Marcel H Schulz (2026). miRXplain: explainable isomiR-aware microRNA target prediction using CLIP-L experiments and hybrid attention transformers. Preprint (BioRxiv).

Nikoletta Katsaouni, Marcel H. Schulz (2026). Hierarchical Representation Learning for Drug Mechanism-of-Action Prediction from Gene Expression Data. Preprint (BioRxiv).

Pinar Cakmak, Jennifer H. Lun, Miriam Köhler, Michael C. Burger, Jadranka Macas, Tatjana Starzetz, Marcel H. Schulz, Yvonne Reiss, Karl H. Plate, Katharina J. Weber (2026). Comparative cross-methodological analysis of the IDH-wildtype glioblastoma tumor microenvironment. Journal of Cancer Research and Clinical Oncology.

Dr. Timothy Warwick, Christina Wrobel (formerly Kalk), Ralf P. Brandes, Marcel H. Schulz (2025). TripLexicon: prediction and analysis of gene regulatory RNA-DNA interactions. Bioinformatics (Oxford, England).

Niklas Herrle, Pedro F. Malacarne, Dr. Timothy Warwick, Alfredo Cabrera-Orefice, Yiheng Chen, Maedeh Gheisari, Souradeep Chatterjee, Matthias S. Leisegang, Tamim Sarakpi, Sarah Wionski, Melina Lopez, Carine Kader, Tom Teichmann, Maria-Kyriaki Drekolia, Ina Koch, Marcus Keßler, Sabine Klein, Frank Erhard Uschner, Jonel Trebicka, Steffen Brunst, Ewgenij Proschak, Stefan Günther, Mónica Rosas-Lemus, Nina Baumgarten, Stephan Klatt, Thimoteus Speer, Sofia-Iris Bibli, Marta Segarra, Amparo Acker-Palmer, Julian U. G. Wagner, Ilka Wittig, Stefanie Dimmeler, Marcel H. Schulz, J. B. Richards, Ralf Gilsbach, Travis T Denton, Ingrid Fleming, Luciana Hannibal, Ralf P. Brandes, Flávia Rezende (2025). The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cells. The EMBO journal.

Maria Pires Pacheco, Déborah Gerard, Riley J. Mangan, Alec R. Chapman, Dennis Hecker, Manolis Kellis, Marcel H. Schulz, Lasse Sinkkonen, Thomas Sauter (2025). Epigenetic control of metabolic identity across cell types. BMC genomics.

Davíd Rodriguez Morales, Veronica Larcher, Mariano Ruz Jurado, Denada Arifaj, Lukas S. Tombor, Lukas Zanders, Andreas M. Zeiher, Christoph Kuppe, David John, Julian U. G. Wagner, Marcel H. Schulz, Stefanie Dimmeler (2025). Vascular Niches Are the Primary Hotspots in Cardiac Aging. Circulation Research.

Mariano Ruz Jurado, Davíd Rodriguez Morales, Elijah Genetzakis, Fatemeh Behjati Ardakani, Lukas Zanders, Ariane Fischer, Florian Buettner, Marcel H. Schulz, Stefanie Dimmeler, David John (2025). Decoding heart failure subtypes with neural networks via differential explanation analysis. Briefings in Bioinformatics.

Yu-Yu Lin, Kersten Breuer, Dieter Weichenhan, Pascal Lafrenz, Antonella Sarnataro, Agata Wilk, Maryna Chepeleva, Oliver Mücke, Maximilian Schönung, Franziska Petermann, Philip Reiner Kensche, Lena Weiser, Frank Thommen, Gideon Giacomelli, Karl Nordstroem, Edahi Gonzalez-Avalos, Angelika Merkel, Helene Kretzmer, Jonas Fischer, Stephen Krämer, Murat Iskar, Stephan Wolf, Ivo Buchhalter, Manel Esteller, Christian Lawerenz, Sven Twardziok, Marc Zapatka, Volker Hovestadt, Matthias Schlesner, Marcel H. Schulz, Steve Hoffmann, Clarissa Gerhauser, Jörn Walter, Mark Hartmann, Daniel B. Lipka, Yassen Assenov, Christoph Bock, Christoph Plass, Reka Toth, Pavlo Lutsik (2025). Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard. Nucleic Acids Research.

Leah Rebecca Vanicek, Ariane Fischer, Mariano Ruz Jurado, Anita Tamiato, Tara Procida-Kowalski, Jochen Wilhelm, Dennis Hecker, Maximilian Merten, Felicitas Escher, Badder Kattih, Valentina Puntmann, David John, Marcel H. Schulz, Eike Nagel, Stefanie Dimmeler, Guillermo Luxán (2025). STAT3 expression is reduced in cardiac pericytes in HFpEF and its loss reduces cellular adhesion and induces pericyte senescence. FEBS letters.

Ranjan K. Maji, Matthias S. Leisegang, Reinier A. Boon, Marcel H. Schulz (2025). Revealing microRNA regulation in single cells. Trends in genetics: TIG.

Ranjan Kumar Maji, Ariane Fischer, Eva-Maria Rogg, Melanie Möller, Gilles Gasparoni, Martin Simon, Stefanie Dimmeler, Marcel H. Schulz (2025). A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarction. Scientific Data.

Ranjan Kumar Maji, Marcel H. Schulz (2025). Temporal Expression Analysis to Unravel Gene Regulatory Dynamics by microRNAs. Methods in Molecular Biology (Clifton, N.J.).

Dennis Hecker, Marcel H. Schulz (2025). Prediction of Enhancer-Gene Interactions Using Chromatin-Conformation Capture and Epigenome Data Using STARE. Methods in Molecular Biology (Clifton, N.J.).

James A. Oo, Dr. Timothy Warwick, Katalin Pálfi, Frederike Lam, Francois McNicoll, Cristian Prieto-Garcia, Stefan Günther, Can Cao, Yinuo Zhou, Alexey A. Gavrilov, Sergey V. Razin, Alfredo Cabrera-Orefice, Ilka Wittig, Soni Savai Pullamsetti, Leo Kurian, Ralf Gilsbach, Marcel H. Schulz, Ivan Dikic, Michaela Müller-McNicoll, Ralf P. Brandes, Matthias S. Leisegang (2025). Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers. Nature Communications.

Laura Rumpf, Marcel H. Schulz (2025). Learning Enhancer-Gene associations from Bulk Transcriptomic and Epigenetic Sequencing Data with STITCHIT. Methods in Molecular Biology (Clifton, N.J.).

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

Nina Baumgarten, Laura Rumpf, Thorsten Kessler, Marcel H. Schulz (2024). A statistical approach for identifying single nucleotide variants that affect transcription factor binding. iScience.

Lucia Alcober-Boquet, Nico Kraus, Lisa Sophie Huber, Rajkumar Vutukuri, Dominik C. Fuhrmann, Claudia Stross, Liliana Schaefer, Klaus Scholich, Stefan Zeuzem, Albrecht Piiper, Marcel H. Schulz, Jonel Trebicka, Christoph Welsch, Cristina Ortiz (2024). BI-3231, an enzymatic inhibitor of HSD17B13, reduces lipotoxic effects induced by palmitic acid in murine and human hepatocytes. American Journal of Physiology. Cell Physiology.

Borja Gomez Ramos, Jochen Ohnmacht, Nikola de Lange, Elena Valceschini, Aurélien Ginolhac, Marie Catillon, Daniele Ferrante, Aleksandar Rakovic, Rashi Halder, François Massart, Giuseppe Arena, Paul Antony, Silvia Bolognin, Christine Klein, Roland Krause, Marcel H. Schulz, Thomas Sauter, Rejko Krüger, Lasse Sinkkonen (2024). Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation. EMBO reports.

Mariano Ruz Jurado, Lukas S. Tombor, Mani Arsalan, Tomas Holubec, Fabian Emrich, Thomas Walther, Wesley Abplanalp, Ariane Fischer, Andreas M. Zeiher, Marcel H. Schulz, Stefanie Dimmeler, David John (2024). Improved integration of single-cell transcriptome data demonstrates common and unique signatures of heart failure in mice and humans. GigaScience.

Miriam Köhler, Yvonne Reiss, Jadranka Macas, Pinar Cakmak, Nadine Flinner, Katharina Imkeller, Jennifer H. Lun, Jonathan Schupp, Tatjana Starzetz, Nivetha Krishna Moorthy, Karl H. Plate, Marcel H. Schulz (2024). An AI-based cell segmentation pipeline for studying immune markers from brightfield microscopy images.

Andre Brezski, Justin Murtagh, Marcel H. Schulz, Kathi Zarnack (2024). A systematic analysis of circRNAs in subnuclear compartments. RNA biology.

Dennis Hecker, Michael Lauber, Fatemeh Behjati Ardakani, Shamim Ashrafiyan, Quirin Manz, Johannes Kersting, Markus Hoffmann, Marcel H. Schulz, Markus List (2023). Computational tools for inferring transcription factor activity. Proteomics.

Jan Grau, Florian Schmidt, Marcel H. Schulz (2023). Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models. Nucleic Acids Research.

Sabine Steffens, Katrin Schröder, Martina Krüger, Christoph Maack, Katrin Streckfuss-Bömeke, Johannes Backs, Rolf Backofen, Bettina Baeßler, Yvan Devaux, Ralf Gilsbach, Jordi Heijman, Jochen Knaus, Rafael Kramann, Dominik Linz, Allyson L. Lister, Henrike Maatz, Lars Maegdefessel, Manuel Mayr, Benjamin Meder, Sara Y. Nussbeck, Eva A. Rog-Zielinska, Marcel H. Schulz, Albert Sickmann, Gökhan Yigit, Peter Kohl (2023). The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary. Clinical Research in Cardiology: Official Journal of the German Cardiac Society.

Robert Schierwagen, Wenyi Gu, Angela Brieger, Bernhard Brüne, Sandra Ciesek, Ivan Đikić, Stefanie Dimmeler, Gerd Geisslinger, Florian R. Greten, Eva Hermann, Eberhard Hildt, Volkhard A. J. Kempf, Sabine Klein, Ina Koch, Heiko Mühl, Volker Müller, Kai-Henrik Peiffer, Roxane-Isabelle Kestner, Albrecht Piiper, Gernot Rohde, Klaus Scholich, Marcel H. Schulz, Holger Storf, Tuna Toptan, Mariuca Vasa-Nicotera, Maria J. G. T. Vehreschild, Andreas Weigert, Peter J. Wild, Stefan Zeuzem, Cornelius Engelmann, ACLF-I Investigators, Liliana Schaefer, Christoph Welsch, Jonel Trebicka (2023). Pathogenetic mechanisms and therapeutic approaches of acute-to-chronic liver failure. American Journal of Physiology. Cell Physiology.

Chaonan Zhu, Nina Baumgarten, Meiqian Wu, Yue Wang, Arka Provo Das, Jaskiran Kaur, Fatemeh Behjati Ardakani, Thanh Thuy Duong, Minh Duc Pham, Maria Duda, Stefanie Dimmeler, Ting Yuan, Marcel H. Schulz, Jaya Krishnan (2023). CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes. Human Genomics.

Simone Franziska Glaser, Andre Brezski, Nina Baumgarten, Marius Klangwart, Andreas W. Heumüller, Ranjan Kumar Maji, Matthias S. Leisegang, Stefan Guenther, Christoph M. Zehendner, David John, Marcel H. Schulz, Kathi Zarnack, Stefanie Dimmeler (2023). Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4. Cell Reports.

Ranjan Kumar Maji, Beate Czepukojc, Michael Scherer, Sascha Tierling, Cristina Cadenas, Kathrin Gianmoena, Nina Gasparoni, Karl Nordström, Gilles Gasparoni, Stephan Laggai, Xinyi Yang, Anupam Sinha, Peter Ebert, Maren Falk-Paulsen, Sarah Kinkley, Jessica Hoppstädter, Ho-Ryun Chung, Philip Rosenstiel, Jan G. Hengstler, Jörn Walter, Marcel H. Schulz, Sonja M. Kessler, Alexandra K. Kiemer (2023). Alterations in the hepatocyte epigenetic landscape in steatosis. Epigenetics & Chromatin.

Jonas Fischer, Marcel H. Schulz (2023). Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data. Bioinformatics (Oxford, England).

Markus Hoffmann, Nico Trummer, Leon Schwartz, Jakub Jankowski, Hye Kyung Lee, Lina-Liv Willruth, Olga Lazareva, Kevin Yuan, Nina Baumgarten, Florian Schmidt, Jan Baumbach, Marcel H Schulz, David B Blumenthal, Lothar Hennighausen, Markus List (2023). TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors. GigaScience.

Sebastian Cremer, Nikoletta Katsaouni, Wesley Tyler Abplanalp, Alexander Berkowitsch, Klara Kirschbaum, Michael A. Rieger, Steffen Rapp, Philipp S. Wild, Stefanie Dimmeler, Marcel H. Schulz, Andreas M. Zeiher (2023). Interaction of inherited genetic variants in the NLRP3 inflammasome/IL-6 pathway with acquired clonal hematopoiesis to modulate mortality risk in patients with HFrEF.

Frederike Boos, James A. Oo, Dr. Timothy Warwick, Stefan Günther, Judit Izquierdo Ponce, Melina Lopez, Diba Rafii, Giulia Buchmann, Minh Duc Pham, Zahraa S. Msheik, Tianfu Li, Sandra Seredinski, Shaza Haydar, Sepide Kashefiolasl, Karl H. Plate, Rüdiger Behr, Matthias Mietsch, Jaya Krishnan, Soni S. Pullamsetti, Sofia-Iris Bibli, Rabea Hinkel, Andrew H. Baker, Reinier A. Boon, Marcel H. Schulz, Ilka Wittig, Francis J. Miller, Ralf P. Brandes, Matthias S. Leisegang (2023). The endothelial-enriched lncRNA LINC00607 mediates angiogenic function. Basic Research in Cardiology.

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

Arber Qoku, Nikoletta Katsaouni, Nadine Flinner, Florian Buettner, Marcel H. Schulz (2023). Multimodal analysis methods in predictive biomedicine. Computational and Structural Biotechnology Journal.

Nikoletta Katsaouni, Pablo Llavona, Yascha Khodamoradi, Ann-Kathrin Otto, Stephanie Körber, Christof Geisen, Christian Seidl, Maria J. G. T. Vehreschild, Sandra Ciesek, Jörg Ackermann, Ina Koch, Marcel H. Schulz, Daniela S. Krause (2023). Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV-2 infection. PloS One.

Matthias S. Leisegang, Jasleen Kaur Bains, Sandra Seredinski, James A. Oo, Nina M. Krause, Chao-Chung Kuo, Stefan Günther, Nevcin Sentürk Cetin, Dr. Timothy Warwick, Can Cao, Frederike Boos, Judit Izquierdo Ponce, Shaza Haydar, Rebecca Bednarz, Chanil Valasarajan, Dominik C. Fuhrmann, Jens Preussner, Mario Looso, Soni S. Pullamsetti, Marcel H. Schulz, Hendrik R. A. Jonker, Christian Richter, Flávia Rezende, Ralf Gilsbach, Beatrice Pflüger-Müller, Ilka Wittig, Ingrid Grummt, Teodora Ribarska, Ivan G. Costa, Harald Schwalbe, Ralf P. Brandes (2022). HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex. Nature Communications.

Dr. 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). A universal model of RNA.DNA:DNA triplex formation accurately predicts genome-wide RNA-DNA interactions. Briefings in Bioinformatics.

Dr. Timothy Warwick, Marcel H. Schulz, Ralf Gilsbach, Ralf P. Brandes, Sabine Seuter (2022). Nuclear receptor activation shapes spatial genome organization essential for gene expression control: lessons learned from the vitamin D receptor. Nucleic Acids Research.

Franziska Drews, Abdulrahman Salhab, Sivarajan Karunanithi, Miriam Cheaib, Martin Jung, Marcel H. Schulz, Martin Simon (2022). Broad domains of histone marks in the highly compact Paramecium macronuclear genome. Genome Research.

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

Ralf Schulze Brüning, Lukas Tombor, Marcel H. Schulz, Stefanie Dimmeler, David John (2022). Comparative analysis of common alignment tools for single-cell RNA sequencing. GigaScience.

Franziska Drews, Sivarajan Karunanithi, Ulrike Götz, Simone Marker, Raphael deWijn, Marcello Pirritano, Angela M. Rodrigues-Viana, Martin Jung, Gilles Gasparoni, Marcel H. Schulz, Martin Simon (2021). Two Piwis with Ago-like functions silence somatic genes at the chromatin level. RNA biology.

Florian Schmidt, Alexander Marx, Nina Baumgarten, Marie Hebel, Martin Wegner, Manuel Kaulich, Matthias S. Leisegang, Ralf P. Brandes, Jonathan Göke, Jilles Vreeken, Marcel H. Schulz (2021). Integrative analysis of epigenetics data identifies gene-specific regulatory elements. Nucleic Acids Research.

Jessica Hoppstädter, Anna Dembek, Marcus Höring, Hanna S. Schymik, Charlotte Dahlem, Afnan Sultan, Natalie Wirth, Salma Al-Fityan, Britta Diesel, Gilles Gasparoni, Jörn Walter, Volkhard Helms, Hanno Huwer, Martin Simon, Gerhard Liebisch, Marcel H. Schulz, Alexandra K. Kiemer (2021). Dysregulation of cholesterol homeostasis in human lung cancer tissue and tumour-associated macrophages. EBioMedicine.

Nikoletta Katsaouni, Araek Tashkandi, Lena Wiese, Marcel H. Schulz (2021). Machine learning based disease prediction from genotype data. Biological Chemistry.

Nina Baumgarten, Florian Schmidt, Martin Wegner, Marie Hebel, Manuel Kaulich, Marcel H. Schulz (2021). Computational prediction of CRISPR-impaired non-coding regulatory regions. Biological Chemistry.

Peter Ebert, Marcel H. Schulz (2021). Fast detection of differential chromatin domains with SCIDDO. Bioinformatics (Oxford, England).

Beatriz Serrano-Solano, Melanie C. Föll, Cristóbal Gallardo-Alba, Anika Erxleben, Helena Rasche, Saskia Hiltemann, Matthias Fahrner, Mark J. Dunning, Marcel H. Schulz, Beáta Scholtz, Dave Clements, Anton Nekrutenko, Bérénice Batut, Björn A. Grüning (2021). Fostering accessible online education using Galaxy as an e-learning platform. PLoS computational biology.

Markus Hoffmann, Elisabeth Pachl, Michael Hartung, Veronika Stiegler, Jan Baumbach, Marcel H. Schulz, Markus List (2021). SPONGEdb: a pan-cancer resource for competing endogenous RNA interactions. NAR cancer.

Michael Scherer, Florian Schmidt, Olga Lazareva, Jörn Walter, Jan Baumbach, Marcel H. Schulz, Markus List (2021). Machine learning for deciphering cell heterogeneity and gene regulation. Nature Computational Science.

Dr. Timothy Warwick, Marcel H. Schulz, Stefan Günther, Ralf Gilsbach, Antonio Neme, Carsten Carlberg, Ralf P. Brandes, Sabine Seuter (2021). A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes. Scientific Reports.

Jonas Fischer, Fatemeh Behjati Ardakani, Kathrin Kattler, Jörn Walter, Marcel H. Schulz (2021). CpG content-dependent associations between transcription factors and histone modifications. PloS One.

Florian Aul, Nikoletta Katsaouni, Marcel H. Schulz, Lars Hedrich (2020). Synthesis of Power-Efficient Analog Neural Networks for Signal Processing. IEEE Xplore.

Fatemeh Behjati Ardakani, Kathrin Kattler, Tobias Heinen, Florian Schmidt, David Feuerborn, Gilles Gasparoni, Konstantin Lepikhov, Patrick Nell, Jan Hengstler, Jörn Walter, Marcel H. Schulz (2020). Prediction of single-cell gene expression for transcription factor analysis. GigaScience.

Giulia K. Buchmann, Christoph Schürmann, Tim Warwick, Marcel H. Schulz, Manuela Spaeth, Oliver J. Müller, Katrin Schröder, Hanjoong Jo, Norbert Weissmann, Ralf P. Brandes (2020). Deletion of NoxO1 limits atherosclerosis development in female mice. Redox Biology.

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

Jenny Vanessa Valbuena Perez, Rebecca Linnenberger, Anna Dembek, Stefano Bruscoli, Carlo Riccardi, Marcel H. Schulz, Markus R. Meyer, Alexandra K. Kiemer, Jessica Hoppstädter (2020). Altered glucocorticoid metabolism represents a feature of macroph-aging. Aging Cell.

Beatrice Pflüger-Müller, James A. Oo, Jan Heering, Dr. Timothy Warwick, Ewgenij Proschak, Stefan Günther, Mario Looso, Flávia Rezende, Christian Fork, Gerd Geisslinger, Dominique Thomas, Robert Gurke, Dieter Steinhilber, Marcel H. Schulz, PhD, Matthias S. Leisegang, Ralf P. Brandes (2020). The endocannabinoid anandamide has an anti-inflammatory effect on CCL2 expression in vascular smooth muscle cells. Basic Research in Cardiology.

Vanessa Königs, Camila de Oliveira Freitas Machado, Benjamin Arnold, Nicole Blümel, Anfisa Solovyeva, Sinah Löbbert, Michal Schafranek, Igor Ruiz De Los Mozos, Ilka Wittig, Francois McNicoll, Marcel H. Schulz, Michaela Müller-McNicoll (2020). SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly. Nature Structural & Molecular Biology.

Nina Baumgarten, Florian Schmidt, Marcel H. Schulz (2020). Improved linking of motifs to their TFs using domain information. Bioinformatics (Oxford, England).

Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz (2020). Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology.

Stefanie Gier, Martin Simon, Gilles Gasparoni, Salem Khalifa, Marcel H. Schulz, Manfred J. Schmitt, Frank Breinig (2020). Yeast Viral Killer Toxin K1 Induces Specific Host Cell Adaptions via Intrinsic Selection Pressure. Applied and Environmental Microbiology.

Florian Schmidt, Fabian Kern, Marcel H. Schulz (2020). Integrative prediction of gene expression with chromatin accessibility and conformation data. Epigenetics & Chromatin.

Sivarajan Karunanithi, Vidya Oruganti, Raphael de Wijn, Franziska Drews, Miriam Cheaib, Karl Nordström, Martin Simon, Marcel H. Schulz (2020). Feeding exogenous dsRNA interferes with endogenous sRNA accumulation in Paramecium. DNA research: an international journal for rapid publication of reports on genes and genomes.

Mikko Rautiainen, Dilip A Durai, Ying Chen, Lixia Xin, Hwee Meng Low, Jonathan Göke, Tobias Marschall, Marcel H. Schulz (2020). AERON: Transcript quantification and gene-fusion detection using long reads. Preprint.

Karl J. V. Nordström, Florian Schmidt, Nina Gasparoni, Abdulrahman Salhab, Gilles Gasparoni, Kathrin Kattler, Fabian Müller, Peter Ebert, Ivan G. Costa, DEEP consortium, Nico Pfeifer, Thomas Lengauer, Marcel H. Schulz, Jörn Walter (2019). Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data. Nucleic Acids Research.

Tarek Kröhler, Sonja M. Kessler, Kevan Hosseini, Markus List, Ahmad Barghash, Sonika Patial, Stephan Laggai, Katja Gemperlein, Johannes Haybaeck, Rolf Müller, Volkhard Helms, Marcel H. Schulz, Jessica Hoppstädter, Perry J. Blackshear, Alexandra K. Kiemer (2019). The mRNA-binding Protein TTP/ZFP36 in Hepatocarcinogenesis and Hepatocellular Carcinoma. Cancers.

Nicole Ritter, Tamer Ali, Nina Kopitchinski, Peggy Schuster, Arica Beisaw, David A. Hendrix, Marcel H. Schulz, Michaela Müller-McNicoll, Stefanie Dimmeler, Phillip Grote (2019). The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development. Developmental Cell.

Eiman Elwakeel, Mirko Brüggemann, Annika F. Fink, Marcel H. Schulz, Tobias Schmid, Rajkumar Savai, Bernhard Brüne, Kathi Zarnack, Andreas Weigert (2019). Phenotypic Plasticity of Fibroblasts during Mammary Carcinoma Development. International Journal of Molecular Sciences.

Sivarajan Karunanithi, Vidya Oruganti, Simone Marker, Angela M. Rodriguez-Viana, Franziska Drews, Marcello Pirritano, Karl Nordström, Martin Simon, Marcel H. Schulz (2019). Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium. Nucleic Acids Research.

Andrea Blum, Saleem Khalifa, Karl Nordström, Martin Simon, Marcel H. Schulz, Manfred J. Schmitt (2019). Transcriptomics of a KDELR1 knockout cell line reveals modulated cell adhesion properties. Scientific Reports.

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

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

Dilip A. Durai, Marcel H. Schulz (2019). Improving in-silico normalization using read weights. Scientific Reports.

Deborah Gérard, Florian Schmidt, Aurélien Ginolhac, Martine Schmitz, Rashi Halder, Peter Ebert, Marcel H. Schulz, Thomas Sauter, Lasse Sinkkonen (2019). Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency. Nucleic Acids Research.

Florian Schmidt, Marcel H. Schulz (2019). On the problem of confounders in modeling gene expression. Bioinformatics (Oxford, England).

Zhijian Li, Marcel H. Schulz, Thomas Look, Matthias Begemann, Martin Zenke, Ivan G. Costa (2019). Identification of transcription factor binding sites using ATAC-seq. Genome Biology.

Stefanie Gier, Martin Simon, Karl Nordström, Salem Khalifa, Marcel H. Schulz, Manfred J. Schmitt, Frank Breinig (2019). Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1. Frontiers in Microbiology.

Sonja M. Kessler, Kevan Hosseini, Usama Khamis Hussein, Kyoung Min Kim, Markus List, Christina S. Schultheiß, Marcel H. Schulz, Stephan Laggai, Kyu Yun Jang, Alexandra K. Kiemer (2019). Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survival. Cellular Physiology and Biochemistry: International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology.

Sivarajan Karunanithi, Martin Simon, Marcel H. Schulz (2019). Automated analysis of small RNA datasets with RAPID. PeerJ.

Fatemeh Behjati Ardakani, Kathrin Kattler, Karl Nordström, Nina Gasparoni, Gilles Gasparoni, Sarah Fuchs, Anupam Sinha, Matthias Barann, Peter Ebert, Jonas Fischer, Barbara Hutter, Gideon Zipprich, Charles D. Imbusch, Bärbel Felder, Jürgen Eils, Benedikt Brors, Thomas Lengauer, Thomas Manke, Philip Rosenstiel, Jörn Walter, Marcel H. Schulz (2018). Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters. Epigenetics & Chromatin.

Eva-Maria Rogg, Wesley T. Abplanalp, Corinne Bischof, David John, Marcel H. Schulz, Jaya Krishnan, Ariane Fischer, Chiara Poluzzi, Liliana Schaefer, Angelika Bonauer, Andreas M. Zeiher, Stefanie Dimmeler (2018). Analysis of Cell Type-Specific Effects of MicroRNA-92a Provides Novel Insights Into Target Regulation and Mechanism of Action. Circulation.

Azim Dehghani Amirabad, Pathmanaban Ramasamy, Marina Wierz, Karl Nordström, Sonja M. Kessler, Marcel H. Schulz, Martin Simon (2018). Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosis. Biochimica Et Biophysica Acta. Molecular Basis of Disease.

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

Andrea Hornakova, Markus List, Jilles Vreeken, Marcel H. Schulz (2018). JAMI: fast computation of conditional mutual information for ceRNA network analysis. Bioinformatics (Oxford, England).

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

Katrin Grosser, Pathmanaban Ramasamy, Azim Dehghani Amirabad, Marcel H. Schulz, Gilles Gasparoni, Martin Simon, Martina Schrallhammer (2018). More than the \"Killer Trait\": Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host. Genome Biology and Evolution.

Marcello Pirritano, Ulrike Götz, Sivarajan Karunanithi, Karl Nordström, Marcel H. Schulz, Martin Simon (2018). Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation. Genes.

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

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

Florian Schmidt, Nina Gasparoni, Gilles Gasparoni, Kathrin Gianmoena, Cristina Cadenas, Julia K. Polansky, Peter Ebert, Karl Nordström, Matthias Barann, Anupam Sinha, Sebastian Fröhler, Jieyi Xiong, Azim Dehghani Amirabad, Fatemeh Behjati Ardakani, Barbara Hutter, Gideon Zipprich, Bärbel Felder, Jürgen Eils, Benedikt Brors, Wei Chen, Jan G. Hengstler, Alf Hamann, Thomas Lengauer, Philip Rosenstiel, Jörn Walter, Marcel H. Schulz (2017). Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction. Nucleic Acids Research.

Hendrik G. Stunnenberg, International Human Epigenome Consortium, Martin Hirst (2016). The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell.

Pawel Durek, Karl Nordström, Gilles Gasparoni, Abdulrahman Salhab, Christopher Kressler, Melanie de Almeida, Kevin Bassler, Thomas Ulas, Florian Schmidt, Jieyi Xiong, Petar Glažar, Filippos Klironomos, Anupam Sinha, Sarah Kinkley, Xinyi Yang, Laura Arrigoni, Azim Dehghani Amirabad, Fatemeh Behjati Ardakani, Lars Feuerbach, Oliver Gorka, Peter Ebert, Fabian Müller, Na Li, Stefan Frischbutter, Stephan Schlickeiser, Carla Cendon, Sebastian Fröhler, Bärbel Felder, Nina Gasparoni, Charles D. Imbusch, Barbara Hutter, Gideon Zipprich, Yvonne Tauchmann, Simon Reinke, Georgi Wassilew, Ute Hoffmann, Andreas S. Richter, Lina Sieverling, DEEP Consortium, Hyun-Dong Chang, Uta Syrbe, Ulrich Kalus, Jürgen Eils, Benedikt Brors, Thomas Manke, Jürgen Ruland, Thomas Lengauer, Nikolaus Rajewsky, Wei Chen, Jun Dong, Birgit Sawitzki, Ho-Ryun Chung, Philip Rosenstiel, Marcel H. Schulz, Joachim L. Schultze, Andreas Radbruch, Jörn Walter, Alf Hamann, Julia K. Polansky (2016). Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development. Immunity.

Ulrike Götz, Simone Marker, Miriam Cheaib, Karsten Andresen, Simon Shrestha, Dilip A. Durai, Karl J. Nordström, Marcel H. Schulz, Martin Simon (2016). Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes. Nucleic Acids Research.

Dilip A. Durai, Marcel H. Schulz (2016). Informed kmer selection for de novo transcriptome assembly. Bioinformatics (Oxford, England).

Xin He, A. Ercument Cicek, Yuhao Wang, Marcel H. Schulz, Hai-Son Le, Ziv Bar-Joseph (2015). De novo ChIP-seq analysis. Genome Biology.

Miriam Cheaib, Azim Dehghani Amirabad, Karl J. V. Nordström, Marcel H. Schulz, Martin Simon (2015). Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia. DNA research: an international journal for rapid publication of reports on genes and genomes.

Peter Ebert, Fabian Müller, Karl Nordström, Thomas Lengauer, Marcel H. Schulz (2015). A general concept for consistent documentation of computational analyses. Database: The Journal of Biological Databases and Curation.

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

Marcel H. Schulz (2014). Letting the data speak for themselves: a fully Bayesian approach to transcriptome assembly. Genome Biology.

Tamara Steijger, Josep F. Abril, Pär G. Engström, Felix Kokocinski, RGASP Consortium, Tim J. Hubbard, Roderic Guigó, Jennifer Harrow, Paul Bertone (2013). Assessment of transcript reconstruction methods for RNA-seq. Nature Methods.

Marcel H. Schulz, Kusum V. Pandit, Christian L. Lino Cardenas, Namasivayam Ambalavanan, Naftali Kaminski, Ziv Bar-Joseph (2013). Reconstructing dynamic microRNA-regulated interaction networks. Proceedings of the National Academy of Sciences of the United States of America.

Hai-Son Le, Marcel H. Schulz, Brenna M. McCauley, Veronica F. Hinman, Ziv Bar-Joseph (2013). Probabilistic error correction for RNA sequencing. Nucleic Acids Research.

Sebastian Bauer, Sebastian Köhler, Marcel H. Schulz, Peter N. Robinson (2012). Bayesian ontology querying for accurate and noise-tolerant semantic searches. Bioinformatics (Oxford, England).

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

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

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

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

Stefan Roepcke, Silke Stahlberg, Holger Klein, Marcel H. Schulz, Lars Theobald, Sabrina Gohlke, Martin Vingron, Diego J. Walther (2011). A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ. BMC genomics.

Marcel H. Schulz, Sebastian Köhler, Sebastian Bauer, Peter N. Robinson (2011). Exact score distribution computation for ontological similarity searches. BMC bioinformatics.

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

Christian Rödelsperger, Gao Guo, Mateusz Kolanczyk, Angelika Pletschacher, Sebastian Köhler, Sebastian Bauer, Marcel H. Schulz, Peter N. Robinson (2011). Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions. Nucleic Acids Research.

Hugues Richard, Marcel H. Schulz, Marc Sultan, Asja Nürnberger, Sabine Schrinner, Daniela Balzereit, Emilie Dagand, Axel Rasche, Hans Lehrach, Martin Vingron, Stefan A. Haas, Marie-Laure Yaspo (2010). Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Research.

Christian Rödelsperger, Sebastian Köhler, Marcel H. Schulz, Thomas Manke, Sebastian Bauer, Peter N. Robinson (2009). Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts. Genomics.

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

Sebastian Köhler, Marcel H. Schulz, Peter Krawitz, Sebastian Bauer, Sandra Dölken, Claus E. Ott, Christine Mundlos, Denise Horn, Stefan Mundlos, Peter N. Robinson (2009). Clinical diagnostics in human genetics with semantic similarity searches in ontologies. American Journal of Human Genetics.

Marc Sultan, Marcel H. Schulz, Hugues Richard, Alon Magen, Andreas Klingenhoff, Matthias Scherf, Martin Seifert, Tatjana Borodina, Aleksey Soldatov, Dmitri Parkhomchuk, Dominic Schmidt, Sean O'Keeffe, Stefan Haas, Martin Vingron, Hans Lehrach, Marie-Laure Yaspo (2008). A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (New York, N.Y.).

Marcel H. Schulz, Sebastian Bauer, Peter N. Robinson (2008). The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences. International Journal of Bioinformatics Research and Applications.

Gao Guo, Sebastian Bauer, Jochen Hecht, Marcel H. Schulz, Andreas Busche, Peter N. Robinson (2008). A short ultraconserved sequence drives transcription from an alternate FBN1 promoter. The International Journal of Biochemistry & Cell Biology.