Publications

Sedaghat-Hamedani F, Haas J, Zhu F, Geier C, Kayvanpour E, Liss M, Lai A1, Frese K, Pribe-Wolferts R, Amr A, Li DT, Samani OS, Carstensen A, Bordalo DM, Müller M, Fischer C, Shao J, Wang J, Nie M, Yuan L, Haßfeld S, Schwartz C, Zhou M, Zhou Z, Shu Y, Wang M, Huang K, Zeng Q, Cheng L, Fehlmann T, Ehlermann P, Keller A, Dieterich C, Streckfuß-Bömeke K, Liao Y, Gotthardt M, Katus HA, Meder B (2017) Clinical genetics and outcome of left ventricular non-compaction cardiomyopathy.PMID: 29029073

Ingmar Sören Meyer, Andreas Jungmann, Christoph Dieterich, Min Zhang, Felix Lasitschka, Susann Werkmeister, Jan Haas, Oliver J Müller, Michael Boutros, Matthias Nahrendorf, Hugo A Katus, Stefan E HardtFlorian Leuschner (2017)The cardiac microenvironment uses non‐canonical WNT signaling to activate monocytes after myocardial infarction.” EMBO Molecular Medicine (2017): e201707565.

Uvarovskii A. and Dieterich C. (2017), pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments., Bioinformatics, accepted.

Siede D., Rapti K. , Gorska AA., Katus HA., Altmüller J., Boeckel JN, Meder B., Maack C., Völkers M., Müller OJ., Backs J., Dieterich C. (2017), Identification of circular RNAs with host gene-independent expression in human model systems for cardiac differentiation and disease., Journal of Molecular and Cellular Cardiology.

Metge, F.; Czaja-Hasse, L. F.; Reinhardt, R. & Dieterich, C. (2017), ‘FUCHS-towards full circular RNA characterization using RNAseq.’, PeerJ 5, e2934.

Rajman, M.; Metge, F.; Fiore, R.; Khudayberdiev, S.; Aksoy-Aksel, A.; Bicker, S.; Ruedell Reschke, C.; Raoof, R.; Brennan, G. P.; Delanty, N.; Farrell, M. A.; O’Brien, D. F.; Bauer, S.; Norwood, B.; Veno, M. T.; Krüger, M.; Braun, T.; Kjems, J.; Rosenow, F.; Henshall, D. C.; Dieterich, C. & Schratt, G. (2017), ‘A microRNA-129-5p/Rbfox crosstalk coordinates homeostatic downscaling of excitatory synapses.’, The EMBO journal 36, 1770–1787.

Roehr, J. T.; Dieterich, C. & Reinert, K. (2017), ‘Flexbar 3.0 – SIMD and multicore parallelization.’, Bioinformatics (Oxford, England).

Schulze Heuling, E.; Knab, F.; Radke, J.; Eskilsson, E.; Martinez-Ledesma, E.; Koch, A.; Czabanka, M.; Dieterich, C.; Verhaak, R. G.; Harms, C. & Euskirchen, P. (2017), ‘Prognostic Relevance of Tumor Purity and Interaction with MGMT Methylation in Glioblastoma.’, Molecular cancer research : MCR 15, 532–540.

Malone, B.; Atanassov, I.; Aeschimann, F.; Li, X.; Grosshans, H. & Dieterich, C. (2017), ‘Bayesian prediction of RNA translation from ribosome profiling.‘, Nucleic acids research.

Piechotta, M.; Wyler, E.; Ohler, U.; Landthaler, M. & Dieterich, C. (2017), ‘JACUSA: site-specific identification of RNA editing events from replicate sequencing data.‘, BMC bioinformatics 18, 7.

Hinze, F.; Dieterich, C.; Radke, M. H.; Granzier, H. & Gotthardt, M. (2016), ‘Reducing RBM20 activity improves diastolic dysfunction and cardiac atrophy.’, Journal of molecular medicine (Berlin, Germany) 94, 1349-1358.

Noormohammadi, A.; Khodakarami, A.; Gutierrez-Garcia, R.; Lee, H. J.; Koyuncu, S.; Konig, T.; Schindler, C.; Saez, I.; Fatima, A.; Dieterich, C. & Vilchez, D. (2016), ‘Somatic increase of CCT8 mimics proteostasis of human pluripotent stem cells and extends C. elegans lifespan.‘, Nature communications 7, 13649.

Kel, I.; Chang, Z.; Galluccio, N.; Romeo, M.; Beretta, S.; Diomede, L.; Mezzelani, A.; Milanesi, L.; Dieterich, C. & Merelli, I. (2016), ‘SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans.’, Molecular bioSystems 12, 3447-3458.

Jakobi, T.; Czaja-Hasse, L. F.; Reinhardt, R. & Dieterich, C. (2016), ‘Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts.‘, Genomics, proteomics & bioinformatics 14, China, 216-23.

Le, H. Q.; Ghatak, S.; Yeung, C.-Y. C.; Tellkamp, F.; Gunschmann, C.; Dieterich, C.; Yeroslaviz, A.; Habermann, B.; Pombo, A.; Niessen, C. M. & Wickstrom, S. A. (2016), ‘Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment.‘, Nature cell biology 18, 864-75.

Gerchen, J. F.; Reichert, S. J.; Rohr, J. T.; Dieterich, C.; Kloas, W. & Stock, M. (2016), ‘A Single Transcriptome of a Green Toad (Bufo viridis) Yields Candidate Genes for Sex Determination and -Differentiation and Non-Anonymous Population Genetic Markers.’, PloS one 11, e0156419.

Cheng, J.; Metge, F. & Dieterich, C. (2016), ‘Specific identification and quantification of circular RNAs from sequencing data.’, Bioinformatics (Oxford, England) 32, 1094-6.

Nakamura, S.; Karalay, O.; Jager, P. S.; Horikawa, M.; Klein, C.; Nakamura, K.; Latza, C.; Templer, S. E.; Dieterich, C. & Antebi, A. (2016), ‘Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals.‘, Nature communications 7, 10944.

Guo, L.; Chang, Z.; Dieterich, C. & Streit, A. (2015), ‘A protocol for chemical mutagenesis in Strongyloides ratti.’, Experimental parasitology 158, 2-7.

Baskaran, P.; Rodelsperger, C.; Prabh, N.; Serobyan, V.; Markov, G. V.; Hirsekorn, A. & Dieterich, C. (2015), ‘Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus.’, BMC evolutionary biology 15, 185.

Morgner, J.; Ghatak, S.; Jakobi, T.; Dieterich, C.; Aumailley, M. & Wickstrom, S. A. (2015), ‘Integrin-linked kinase regulates the niche of quiescent epidermal stem cells.‘, Nature communications 6, 8198.

Lamanna, F.; Kirschbaum, F.; Waurick, I.; Dieterich, C. & Tiedemann, R. (2015), ‘Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae).‘, BMC genomics 16, 668.

Aeschimann, F.; Xiong, J.; Arnold, A.; Dieterich, C. & Grosshans, H. (2015), ‘Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling.’, Methods (San Diego, Calif.) 85, 75-89.

Boucas, J.; Fritz, C.; Schmitt, A.; Riabinska, A.; Thelen, L.; Peifer, M.; Leeser, U.; Nuernberg, P.; Altmueller, J.; Gaestel, M.; Dieterich, C. & Reinhardt, H. C. (2015), ‘Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression.’, PloS one 10, e0125745. (co-shared last author)

Steckelberg, A.-L.; Altmueller, J.; Dieterich, C. & Gehring, N. H. (2015), ‘CWC22-dependent pre-mRNA splicing and eIF4A3 binding enables global deposition of exon junction complexes.’, Nucleic acids research 43, 4687-700.

Valluy, J.; Bicker, S.; Aksoy-Aksel, A.; Lackinger, M.; Sumer, S.; Fiore, R.; Wust, T.; Seffer, D.; Metge, F.; Dieterich, C.; Wohr, M.; Schwarting, R. & Schratt, G. (2015), ‘A coding-independent function of an alternative Ube3a transcript during neuronal development.‘, Nature neuroscience 18, 666-73.

Walentin, K.; Hinze, C.; Werth, M.; Haase, N.; Varma, S.; Morell, R.; Aue, A.; Potschke, E.; Warburton, D.; Qiu, A.; Barasch, J.; Purfurst, B.; Dieterich, C.; Popova, E.; Bader, M.; Dechend, R.; Staff, A. C.; Yurtdas, Z. Y.; Kilic, E. & Schmidt-Ott, K. M. (2015), ‘A Grhl2-dependent gene network controls trophoblast branching morphogenesis.’, Development (Cambridge, England) 142, 1125-36.

Mourier, A.; Motori, E.; Brandt, T.; Lagouge, M.; Atanassov, I.; Galinier, A.; Rappl, G.; Brodesser, S.; Hultenby, K.; Dieterich, C. & Larsson, N.-G. (2015), ‘Mitofusin 2 is required to maintain mitochondrial coenzyme Q levels.’, The Journal of cell biology 208, 429-42.

Ivanov, A.; Memczak, S.; Wyler, E.; Torti, F.; Porath, H. T.; Orejuela, M. R.; Piechotta, M.; Levanon, E. Y.; Landthaler, M.; Dieterich, C. & Rajewsky, N. (2015), ‘Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals.‘, Cell reports 10, 170-7.

Blin, K.; Dieterich, C.; Wurmus, R.; Rajewsky, N.; Landthaler, M. & Akalin, A. (2015), ‘DoRiNA 2.0–upgrading the doRiNA database of RNA interactions in post-transcriptional regulation.‘, Nucleic acids research 43, D160-7.

Borcherds, W.; Theillet, F.-X.; Katzer, A.; Finzel, A.; Mishall, K. M.; Powell, A. T.; Wu, H.; Manieri, W.; Dieterich, C.; Selenko, P.; Loewer, A. & Daughdrill, G. W. (2014), ‘Disorder and residual helicity alter p53-Mdm2 binding affinity and signaling in cells.’, Nature chemical biology 10, 1000-2.

Gusmao, E. G.; Dieterich, C.; Zenke, M. & Costa, I. G. (2014), ‘Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications.’, Bioinformatics (Oxford, England) 30, 3143-51.

Freischmidt, A.; Muller, K.; Zondler, L.; Weydt, P.; Volk, A. E.; Bozic, A. L.; Walter, M.; Bonin, M.; Mayer, B.; von Arnim, C. A. F.; Otto, M.; Dieterich, C.; Holzmann, K.; Andersen, P. M.; Ludolph, A. C.; Danzer, K. M. & Weishaupt, J. H. (2014), ‘Serum microRNAs in patients with genetic amyotrophic lateral sclerosis and pre-manifest mutation carriers.’, Brain : a journal of neurology 137, 2938-50.

Cinkornpumin, J. K.; Wisidagama, D. R.; Rapoport, V.; Go, J. L.; Dieterich, C.; Wang, X.; Sommer, R. J. & Hong, R. L. (2014), ‘A host beetle pheromone regulates development and behavior in the nematode Pristionchus pacificus.’, eLife 3.

Sinha, A.; Langnick, C.; Sommer, R. J. & Dieterich, C. (2014), ‘Genome-wide analysis of trans-splicing in the nematode Pristionchus pacificus unravels conserved gene functions for germline and dauer development in divergent operons.’, RNA (New York, N.Y.) 20, 1386-97.

Heitlinger, E.; Spork, S.; Lucius, R. & Dieterich, C. (2014), ‘The genome of Eimeria falciformis–reduction and specialization in a single host apicomplexan parasite.’, BMC genomics 15, 696.

Albritton, S. E.; Kranz, A.-L.; Rao, P.; Kramer, M.; Dieterich, C. & Ercan, S. (2014), ‘Sex-biased gene expression and evolution of the x chromosome in nematodes.’, Genetics 197, 865-83.

Gregersen, L. H.; Schueler, M.; Munschauer, M.; Mastrobuoni, G.; Chen, W.; Kempa, S.; Dieterich, C. & Landthaler, M. (2014), ‘MOV10 Is a 5′ to 3′ RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3′ UTRs.’, Molecular cell 54, 573-85.

Rodelsperger, C.; Neher, R. A.; Weller, A. M.; Eberhardt, G.; Witte, H.; Mayer, W. E.; Dieterich, C. & Sommer, R. J. (2014), ‘Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data.’, Genetics 196, 1153-65.

Munschauer, M.; Schueler, M.; Dieterich, C. & Landthaler, M. (2014), ‘High-resolution profiling of protein occupancy on polyadenylated RNA transcripts.’, Methods (San Diego, Calif.) 65, 302-9.

Schueler, M.; Munschauer, M.; Gregersen, L. H.; Finzel, A.; Loewer, A.; Chen, W.; Landthaler, M. & Dieterich, C. (2014), ‘Differential protein occupancy profiling of the mRNA transcriptome.‘, Genome biology 15, R15.

Schafer, N.; Yu, Z.; Wagener, A.; Millrose, M. K.; Reissmann, M.; Bortfeldt, R.; Dieterich, C.; Adamski, J.; Wang-Sattler, R.; Illig, T. & Brockmann, G. A. (2014), ‘Changes in metabolite profiles caused by genetically determined obesity in mice.‘, Metabolomics : Official journal of the Metabolomic Society 10, 461-472.

Piechotta, M. & Dieterich, C. (2013), ‘ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores.’, Bioinformatics (Oxford, England) 29, 1809-10.

Li, N.; You, X.; Chen, T.; Mackowiak, S. D.; Friedlander, M. R.; Weigt, M.; Du, H.; Gogol-Doring, A.; Chang, Z.; Dieterich, C.; Hu, Y. & Chen, W. (2013), ‘Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.‘, Nucleic acids research 41, 3619-34.

Ahmed, R.; Chang, Z.; Younis, A. E.; Langnick, C.; Li, N.; Chen, W.; Brattig, N. & Dieterich, C. (2013), ‘Conserved miRNAs are candidate post-transcriptional regulators of developmental arrest in free-living and parasitic nematodes.‘, Genome biology and evolution 5, 1246-60.

Dieterich, C. & Stadler, P. F. (2013), ‘Computational biology of RNA interactions.’, Wiley interdisciplinary reviews. RNA 4, 107-20.

Dodt, M.; Roehr, J. T.; Ahmed, R. & Dieterich, C. (2012), ‘FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms.’, Biology 1, 895-905.

Sinha, A.; Sommer, R. J. & Dieterich, C. (2012), ‘Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans.’, BMC genomics 13, 254.

Baltz, A. G.; Munschauer, M.; Schwanhausser, B.; Vasile, A.; Murakawa, Y.; Schueler, M.; Youngs, N.; Penfold-Brown, D.; Drew, K.; Milek, M.; Wyler, E.; Bonneau, R.; Selbach, M.; Dieterich, C. & Landthaler, M. (2012), ‘The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts.’, Molecular cell 46, 674-90.

Anders, G.; Mackowiak, S. D.; Jens, M.; Maaskola, J.; Kuntzagk, A.; Rajewsky, N.; Landthaler, M. & Dieterich, C. (2012), ‘doRiNA: a database of RNA interactions in post-transcriptional regulation.’, Nucleic acids research 40, D180-6.

Adamidi, C.; Wang, Y.; Gruen, D.; Mastrobuoni, G.; You, X.; Tolle, D.; Dodt, M.; Mackowiak, S. D.; Gogol-Doering, A.; Oenal, P.; Rybak, A.; Ross, E.; Sanchez Alvarado, A.; Kempa, S.; Dieterich, C.; Rajewsky, N. & Chen, W. (2011), ‘De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.’, Genome research 21, 1193-200.

Ogawa, A.; Bento, G.; Bartelmes, G.; Dieterich, C. & Sommer, R. J. (2011), ‘Pristionchus pacificus daf-16 is essential for dauer formation but dispensable for mouth form dimorphism.’, Development (Cambridge, England) 138, 1281-4.

Mayer, W. E.; Schuster, L. N.; Bartelmes, G.; Dieterich, C. & Sommer, R. J. (2011), ‘Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover.‘, BMC evolutionary biology 11, 13.

Borchert, N.; Dieterich, C.; Krug, K.; Schutz, W.; Jung, S.; Nordheim, A.; Sommer, R. J. & Macek, B. (2010), ‘Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models.’, Genome research 20, 837-46.

Frohler, S. & Dieterich, C. (2010), ‘ACCUSA–accurate SNP calling on draft genomes.’, Bioinformatics (Oxford, England) 26, 1364-5.

Rodelsperger, C. & Dieterich, C. (2010), ‘CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes.’, PloS one 5, e8861.

Frohler, S. & Dieterich, C. (2009), ‘3PD: Rapid design of optimal primers for chromosome conformation capture assays.’, BMC genomics 10, 635.

Schweikert, G.; Zien, A.; Zeller, G.; Behr, J.; Dieterich, C.; Ong, C. S.; Philips, P.; De Bona, F.; Hartmann, L.; Bohlen, A.; Kruger, N.; Sonnenburg, S. & Ratsch, G. (2009), ‘mGene: accurate SVM-based gene finding with an application to nematode genomes.‘, Genome research 19, 2133-43.

Dieterich, C. & Sommer, R. J. (2009), ‘How to become a parasite – lessons from the genomes of nematodes.‘, Trends in genetics : TIG 25, 203-9.

Rodelsperger, C. & Dieterich, C. (2008), ‘Syntenator: multiple gene order alignments with a gene-specific scoring function.’, Algorithms for molecular biology : AMB 3, 14.

Dieterich, C.; Clifton, S. W.; Schuster, L. N.; Chinwalla, A.; Delehaunty, K.; Dinkelacker, I.; Fulton, L.; Fulton, R.; Godfrey, J.; Minx, P.; Mitreva, M.; Roeseler, W.; Tian, H.; Witte, H.; Yang, S.-P.; Wilson, R. K. & Sommer, R. J. (2008), ‘The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism.’, Nature genetics 40, 1193-8.

Rae, R.; Riebesell, M.; Dinkelacker, I.; Wang, Q.; Herrmann, M.; Weller, A. M.; Dieterich, C. & Sommer, R. J. (2008), ‘Isolation of naturally associated bacteria of necromenic Pristionchus nematodes and fitness consequences.‘, The Journal of experimental biology 211, 1927-36.

Hecht, J.; Stricker, S.; Wiecha, U.; Stiege, A.; Panopoulou, G.; Podsiadlowski, L.; Poustka, A. J.; Dieterich, C.; Ehrich, S.; Suvorova, J.; Mundlos, S. & Seitz, V. (2008), ‘Evolution of a core gene network for skeletogenesis in chordates.‘, PLoS genetics 4, e1000025.

Dieterich, C. & Sommer, R. J. (2008), ‘A Caenorhabditis motif compendium for studying transcriptional gene regulation.’, BMC genomics 9, 30.

Hecht, J.; Seitz, V.; Urban, M.; Wagner, F.; Robinson, P. N.; Stiege, A.; Dieterich, C.; Kornak, U.; Wilkening, U.; Brieske, N.; Zwingman, C.; Kidess, A.; Stricker, S. & Mundlos, S. (2007), ‘Detection of novel skeletogenesis target genes by comprehensive analysis of a Runx2(-/-) mouse model.’, Gene expression patterns : GEP 7, 102-12.

Dieterich, C.; Franz, M. W. & Vingron, M. (2007), ‘Developments in CORG: a gene-centric comparative genomics resource.’, Nucleic acids research 35, D32-5.

Dieterich, C.; Roeseler, W.; Sobetzko, P. & Sommer, R. J. (2007), ‘Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus.’, Nucleic acids research 35, D498-502.

Dieterich, C.; Roeseler, W. & Srinivasan, J. (2006), ‘Pristionchus pacificus genomics: from genetics to genome sequence.‘, WormBook : the online review of C. elegans biology, 1-14.

Dieterich, C. & Vingron, M. (2006), ‘Comparative promoter analysis in vertebrate genomes with the CORG workbench.’, Methods in molecular biology (Clifton, N.J.) 338, 105-18.

Cora, D.; Herrmann, C.; Dieterich, C.; Di Cunto, F.; Provero, P. & Caselle, M. (2005), ‘Ab initio identification of putative human transcription factor binding sites by comparative genomics.’, BMC bioinformatics 6, 110.

Michael, M.; Dieterich, C. & Vingron, M. (2005), ‘SITEBLAST–rapid and sensitive local alignment of genomic sequences employing motif anchors.’, Bioinformatics (Oxford, England) 21, 2093-4.

Dieterich, C.; Grossmann, S.; Tanzer, A.; Ropcke, S.; Arndt, P. F.; Stadler, P. F. & Vingron, M. (2005), ‘Comparative promoter region analysis powered by CORG.‘, BMC genomics 6, 24.

Philippar, U.; Schratt, G.; Dieterich, C.; Muller, J. M.; Galgoczy, P.; Engel, F. B.; Keating, M. T.; Gertler, F.; Schule, R.; Vingron, M. & Nordheim, A. (2004), ‘The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF.‘, Molecular cell 16, 867-80.

Dieterich, C.; Rahmann, S. & Vingron, M. (2004), ‘Functional inference from non-random distributions of conserved predicted transcription factor binding sites.‘, Bioinformatics (Oxford, England) 20 Suppl 1, i109-15.

Dieterich, C.; Herwig, R. & Vingron, M. (2003), ‘Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites.’, Bioinformatics (Oxford, England) 19 Suppl 2, ii50-6.

Dieterich, C.; Wang, H.; Rateitschak, K.; Luz, H. & Vingron, M. (2003), ‘CORG: a database for COmparative Regulatory Genomics.’, Nucleic acids research 31, 55-7.

Dieterich, C.; Schandar, M.; Noll, M.; Johannes, F.-J.; Brunner, H.; Graeve, T. & Rupp, S. (2002), ‘In vitro reconstructed human epithelia reveal contributions of Candida albicans EFG1 and CPH1 to adhesion and invasion.’, Microbiology (Reading, England) 148, 497-506.

Dieterich, C.; Cusack, B.; Wang, H.; Rateitschak, K.; Krause, A. & Vingron, M. (2002), ‘Annotating regulatory DNA based on man-mouse genomic comparison.’, Bioinformatics (Oxford, England) 18 Suppl 2, S84-90.

Total 76 Publications; >2500 citations (Google Scholar); h-index = 24 and e-index = 38 (Google Scholar). 22 last author publications; 16 first author publications