Kliniken & Institute … Kliniken Zentrum für Innere… Internal Medicine III:… Research Klaus-Tschira-Institut… Publications

Publications

Boileau E.; Doroudgar S.; Riechert E.; Jürgensen L.; CaoHo T.; Katus H.; Völkers M; Dieterich C.; A multi-network comparative analysis of transcriptome and translatome in cardiac remodeling; fgene.2020.583124

Müller T, Boileau E, Talyan S, Kehr D, Varadi K, Busch M, Most P, Krijgsveld J, Dieterich C. Updated and enhanced pig cardiac transcriptome based on long-read RNA sequencing and proteomics. J Mol Cell Cardiol. 2020 Oct 10;150:23-31

Camacho Londoño JE.; Kuryshev V.; Zorn M.; Saar K.; Tian Q.; Hübner N.; Nawroth P.; Dietrich A.; Birnbaumer L.; Lipp P.; Dieterich C.; Freichel M.; ` Transcriptional signatures regulated by TRPC1/C4-mediated Background Ca 2+ entry after pressure-overload induced cardiac remodelling´; Prog Biophysics & Molecular Biology Journal 29, 0079

Kapoor U.; Licht K.; Amman F.; Jakobi T.; Martin D.; Dieterich C.; Jantsch M.; ` ADAR-deficiency perturbs the global splicing landscape in mouse tissues´; Genome Res, 29, 256933

Weichmann F.; Hett R.; Schepers A.; Ito-Kureha T.; Flatley A.; Slama K.; Hastert F.; Angstmann N.; Cardoso CM.; König J.; Huettelmaier S.; Dieterich C.; Canzar S.; Helm M.; Heissmeyer V.; Feederle R.; Meister G.; ` Validation strategies for antibodies targeting modified ribonucleotides´; RNA 7, 076026

Jakobi T.; Siede D.; Eschenbach J.; Heumüller AW.; Busch M.; Nietsch R.; Meder B.; Most P.; Dimmeler S.; Backs J.; Katus HA.; Dieterich C.; `Deep Characterization of Circular RNAs from Human Cardiovascular Cell Models and Cardiac Tissue´; Cells 9, 1616

Gerbracht JV.; Boehm V.; Britto-Borges T.; Kallabis S, Wiederstein JL.; Ciriello S.; Aschemeier DU.; Krüger M.; Frese CK.; Altmüller J.; Dieterich C.; Gehring NH.; `CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex´; Nucleic Acids Res. 4, 564

Weigelt CM.; Sehgal R.; Tain LS.; Cheng J.; Eßer J.; Pahl A.; Dieterich C.; Grönke S.; Partridge L.; `An Insulin – Sensitive Circular RNA that Regulates Lifespan in Drosophila.´; Mol Cell Journal 79, 268

Pradas-Juni, M.; Hansmeier, N. R.; Link, J. C.; Schmidt, E.; Larsen, B. D.; Klemm, P.; Meola, N.; Topel, H.; Loureiro, R.; Dhaouadi, I.; Kiefer, C. A.; Schwarzer, R.; Khani, S.; Oliverio, M.; Awazawa, M.; Frommolt, P.; Heeren, J.; Scheja, L.; Heine, M.; Dieterich, C.; Büning, H.; Yang, L.; Cao, H.; Jesus, D. F. D.; Kulkarni, R. N.; Zevnik, B.; Tröder, S. E.; Knippschild, U.; Edwards, P. A.; Lee, R. G.; Yamamoto, M.; Ulitsky, I.; Fernandez-Rebollo, E.; Vallim, T. Q. d. A. & Kornfeld, J.-W. (2020), 'A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism.', Nature communications 11, 644.

Saez, I.; Gerbracht, J. V.; Koyuncu, S.; Lee, H. J.; Horn, M.; Kroef, V.; Denzel, M. S.; Dieterich, C.; Gehring, N. H. & Vilchez, D. (2020), 'The E3 ubiquitin ligase UBR5 interacts with the H/ACA ribonucleoprotein complex and regulates ribosomal RNA biogenesis in embryonic stem cells.', FEBS letters 594, 175--188.

Ahuja, G.; Bartsch, D.; Yao, W.; Geissen, S.; Frank, S.; Aguirre, A.; Russ, N.; Messling, J.-E.; Dodzian, J.; Lagerborg, K. A.; Vargas, N. E.; Muck, J. S.; Brodesser, S.; Baldus, S.; Sachinidis, A.; Hescheler, J.; Dieterich, C.; Trifunovic, A.; Papantonis, A.; Petrascheck, M.; Klinke, A.; Jain, M.; Valenzano, D. R. & Kurian, L. (2019), 'Loss of genomic integrity induced by lysosphingolipid imbalance drives ageing in the heart.', EMBO reports 20.

Doroudgar, S.; Hofmann, C.; Boileau, E.; Malone, B.; Riechert, E.; Gorska, A. A.; Jakobi, T.; Sandmann, C.; Jürgensen, L.; Kmietczyk, V.; Malovrh, E.; Burghaus, J.; Rettel, M.; Stein, F.; Younesi, F.; Friedrich, U. A.; Mauz, V.; Backs, J.; Kramer, G.; Katus, H. A.; Dieterich*, C. & Völkers, M. (2019), 'Monitoring Cell-Type-Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress.', Circulation research 125, 431--448. (* shared last author)

Hosseinzadeh, A.; Stylianou, M.; Lopes, J. P.; Müller, D. C.; Häggman, A.; Holmberg, S.; Grumaz, C.; Johansson, A.; Sohn, K.; Dieterich, C. & Urban, C. F. (2019), 'Stable Redox-Cycling Nitroxide Tempol Has Antifungal and Immune-Modulatory Properties.', Frontiers in microbiology 10, 1843.

Ignarski, M.; Rill, C.; Kaiser, R. W. J.; Kaldirim, M.; Neuhaus, R.; Esmaillie, R.; Li, X.; Klein, C.; Bohl, K.; Petersen, M.; Frese, C. K.; Höhne, M.; Atanassov, I.; Rinschen, M. M.; Höpker, K.; Schermer, B.; Benzing, T.; Dieterich, C.; Fabretti, F. & Müller, R.-U. (2019), 'The RNA-Protein Interactome of Differentiated Kidney Tubular Epithelial Cells.', Journal of the American Society of Nephrology : JASN 30, 564--576.

Jakobi, T. & Dieterich, C. (2019), 'Computational approaches for circular RNA analysis.', Wiley interdisciplinary reviews. RNA 10, e1528.

Jebessa, Z. H.; Shanmukha Kumar, D.; Dewenter, M.; Lehmann, L. H.; Xu, C.; Schreiter, F.; Siede, D.; Gong, X.-M.; Worst, B. C.; Federico, G.; Sauer, S. W.; Fischer, T.; Wechselberger, L.; Müller, O. J.; Sossalla, S.; Dieterich, C.; Most, P.; Gröne, H.-J.; Moro, C.; Oberer, M.; Haemmerle, G.; Katus, H. A.; Tyedmers, J. & Backs, J. (2019), 'The lipid droplet-associated protein ABHD5 protects the heart through proteolysis of HDAC4.', Nature metabolism 1, 1157--1167.

Kaiser, R. W. J.; Ignarski, M.; Van Nostrand, E. L.; Frese, C. K.; Jain, M.; Cukoski, S.; Heinen, H.; Schaechter, M.; Seufert, L.; Bunte, K.; Frommolt, P.; Keller, P.; Helm, M.; Bohl, K.; Höhne, M.; Schermer, B.; Benzing, T.; Höpker, K.; Dieterich, C.; Yeo, G. W.; Müller, R.-U. & Fabretti, F. (2019), 'A protein-RNA interaction atlas of the ribosome biogenesis factor AATF.', Scientific reports 9, 11071.

Kindermann, A.; Stepanova, E.; Hund, H.; Geis, N.; Malone, B. & Dieterich, C. (2019), 'MedEx - Data Analytics for Medical Domain Experts in Real-Time.', Studies in health technology and informatics 267, 142--149.

Kmietczyk, V.; Riechert, E.; Kalinski, L.; Boileau, E.; Malovrh, E.; Malone, B.; Gorska, A.; Hofmann, C.; Varma, E.; Jürgensen, L.; Kamuf-Schenk, V.; Altmüller, J.; Tappu, R.; Busch, M.; Most, P.; Katus, H. A.; Dieterich, C. & Völkers, M. (2019), 'm6A-mRNA methylation regulates cardiac gene expression and cellular growth.', Life science alliance 2.

Richter-Pechanski, P.; Amr, A.; Katus, H. A. & Dieterich, C. (2019), 'Deep Learning Approaches Outperform Conventional Strategies in De-Identification of German Medical Reports.', Studies in health technology and informatics 267, 101--109.

Schilling, J.; Broemer, M.; Atanassov, I.; Duernberger, Y.; Vorberg, I.; Dieterich, C.; Dagane, A.; Dittmar, G.; Wanker, E.; van Roon-Mom, W.; Winter, J. & Kraußs, S. (2019), 'Deregulated Splicing Is a Major Mechanism of RNA-Induced Toxicity in Huntington's Disease.', Journal of molecular biology 431, 1869--1877.

Uvarovskii, A.; Naarmann-de Vries, I. S. & Dieterich, C. (2019), 'On the optimal design of metabolic RNA labeling experiments.', PLoS computational biology 15, e1007252.

Worpenberg, L.; Jakobi, T.; Dieterich*, C. & Roignant, J.-Y. (2019), 'Identification of Methylated Transcripts Using the TRIBE Approach.', Methods in molecular biology (Clifton, N.J.) 1870, 89--106.
(* shared last author)

Yigit, G.; Saida, K.; DeMarzo, D.; Miyake, N.; Fujita, A.; Yang Tan, T.; White, S. M.; Wadley, A.; Toliat, M. R.; Motameny, S.; Franitza, M.; Stutterd, C. A.; Chong, P. F.; Kira, R.; Sengoku, T.; Ogata, K.; Guillen Sacoto, M. J.; Fresen, C.; Beck, B. B.; Nürnberg, P.; Dieterich, C.; Wollnik, B.; Matsumoto, N. & Altmüller, J. (2019), 'The recurrent postzygotic pathogenic variant p.Glu47Lys in RHOA causes a novel recognizable neuroectodermal phenotype.', Human mutation.

Zhou, Y.; Wang, X.; Song, M.; He, Z.; Cui, G.; Peng, G.; Dieterich, C.; Antebi, A.; Jing, N. & Shen, Y. (2019), 'A secreted microRNA disrupts autophagy in distinct tissues of Caenorhabditis elegans upon ageing.', Nature communications 10, 4827.

Blackwood, E. A.; Hofmann, C.; Santo Domingo, M.; Bilal, A. S.; Sarakki, A.; Stauffer, W. T.; Arrieta, A.; Thuerauf, D. J.; Kolkhorst, F. W.; Müller, O. J.; Jakobi, T.; Dieterich, C.; Katus, H. A.; Doroudgar, S. & Glembotski, C. C. (2018), 'ATF6 Regulates Cardiac Hypertrophy by Transcriptional Induction of the mTORC1 Activator, Rheb.', Circulation research.

Boeckel, J.-N.; Perret, M. F.; Glaser, S. F.; Seeger, T.; Heumüller, A. W.; Chen, W.; John, D.; Kokot, K. E.; Katus, H. A.; Haas, J.; Lackner, M. K.; Kayvanpour, E.; Grabe, N.; Dieterich, C.; von Haehling, S.; Ebner, N.; Hünecke, S.; Leuschner, F.; Fichtlscherer, S.; Meder, B.; Zeiher, A. M.; Dimmeler, S. & Keller, T. (2018), 'Identification and regulation of the long non-coding RNA Heat2 in heart failure.', Journal of molecular and cellular cardiology 126, 13--22.

Boehm, V.; Britto-Borges, T.; Steckelberg, A.-L.; Singh, K. K.; Gerbracht, J. V.; Gueney, E.; Blazquez, L.; Altmüller, J.; Dieterich, C.* & Gehring, N. H.* (2018), 'Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity.', Molecular cell 72, 482--495.e7. (* corresponding author)

Boileau, E. & Dieterich, C. (2018), 'RNA Modification Level Estimation with pulseR.', Genes 9.

Dal Magro, C.; Keller, P.; Kotter, A.; Werner, S.; Duarte, V.; Marchand, V.; Ignarski, M.; Freiwald, A.; Müller, R.-U.; Dieterich, C.; Motorin, Y.; Butter, F.; Atta, M. & Helm, M. (2018), 'A Vastly Increased Chemical Variety of RNA Modifications Containing a Thioacetal Structure.', Angewandte Chemie (International ed. in English) 57, 7893--7897.

Gomes, C. P. C.; Salgado-Somoza, A.; Creemers, E. E.; Dieterich, C.; Lustrek, M.; Devaux, Y. & network, C. (2018), 'Circular RNAs in the cardiovascular system.', Non-coding RNA research 3, 1--11.

Haarbrandt, B.; Schreiweis, B.; Rey, S.; Sax, U.; Scheithauer, S.; Rienhoff, O.; Knaup-Gregori, P.; Bavendiek, U.; Dieterich, C.; Brors, B.; Kraus, I.; Thoms, C. M.; Jäger, D.; Ellenrieder, V.; Bergh, B.; Yahyapour, R.; Eils, R.; Consortium, H. & Marschollek, M. (2018), 'HiGHmed - An Open Platform Approach to Enhance Care and Research across Institutional Boundaries.', Methods of information in medicine 57, e66--e81.

Jakobi, T.; Uvarovskii, A. & Dieterich, C. (2018), 'circtools - a one-stop software solution for circular RNA research.', Bioinformatics (Oxford, England).

Lackinger, M.; Sungur, A. Ö.; Daswani, R.; Soutschek, M.; Bicker, S.; Stemmler, L.; Wüst, T.; Fiore, R.; Dieterich, C.; Schwarting, R. K.; Wöhr, M. & Schratt, G. (2018), 'A placental mammal-specific microRNA cluster acts as a natural brake for sociability in mice.', EMBO reports.

Richter-Pechanski, P.; Riezler, S. & Dieterich, C. (2018), 'De-Identification of German Medical Admission Notes.', Studies in health technology and informatics 253, 165--169.

Saez, I.; Koyuncu, S.; Gutierrez-Garcia, R.; Dieterich, C. & Vilchez, D. (2018), 'Insights into the ubiquitin-proteasome system of human embryonic stem cells.', Scientific reports 8, 4092.

Jakobi, T. & Dieterich, C. (2018), 'Deep Computational Circular RNA Analytics from RNA-seq Data.', Methods in molecular biology (Clifton, N.J.) 1724, 9--25.

Sedaghat-Hamedani, F.; Haas, J.; Zhu, F.; Geier, C.; Kayvanpour, E.; Liss, M.; Lai, A.; Frese, K.; Pribe-Wolferts, R.; Amr, A.; Li, D. T.; Samani, O. S.; Carstensen, A.; Bordalo, D. M.; Müller, M.; Fischer, C.; Shao, J.; Wang, J.; Nie, M.; Yuan, L.; Haßsfeld, 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.; Streckfußs-Bömeke, K.; Liao, Y.; Gotthardt, M.; Katus, H. A. & Meder, B. (2017), 'Clinical genetics and outcome of left ventricular non-compaction cardiomyopathy.', European heart journal 38, 3449--3460.

Ju Lee, H.; Bartsch, D.; Xiao, C.; Guerrero, S.; Ahuja, G.; Schindler, C.; Moresco, J. J.; Yates, J. R.; Gebauer, F.; Bazzi, H.; Dieterich, C.; Kurian, L. & Vilchez, D. (2017), 'A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells.', Nature communications 8, 1456.

Uvarovskii, A. & Dieterich, C. (2017), 'pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments.', Bioinformatics (Oxford, England) 33, 3305--3307.

Siede, D.; Rapti, K.; Gorska, A. A.; Katus, H. A.; Altmüller, J.; Boeckel, J. N.; Meder, B.; Maack, C.; Völkers, M.; Müller, O. J.; 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 109, 48--56.

Tain, L. S.; Sehlke, R.; Jain, C.; Chokkalingam, M.; Nagaraj, N.; Essers, P.; Rassner, M.; Grönke, S.; Froelich, J.; Dieterich, C.; Mann, M.; Alic, N.; Beyer, A. & Partridge, L. (2017), 'A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance.', Molecular systems biology 13, 939.

Euskirchen, P.; Radke, J.; Schmidt, M. S.; Schulze Heuling, E.; Kadikowski, E.; Maricos, M.; Knab, F.; Grittner, U.; Zerbe, N.; Czabanka, M.; Dieterich, C.; Miletic, H.; Mørk, S.; Koch, A.; Endres, M. & Harms, C. (2017), 'Cellular heterogeneity contributes to subtype-specific expression of ZEB1 in human glioblastoma.', PloS one 12, e0185376.

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

Ehret, T.; Spork, S.; Dieterich, C.; Lucius, R. & Heitlinger, E. (2017), 'Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses.', BMC genomics 18, 686.

Meyer, I. S.; Jungmann, A.; Dieterich, C.; Zhang, M.; Lasitschka, F.; Werkmeister, S.; Haas, J.; Müller, O. J.; Boutros, M.; Nahrendorf, M.; Katus, H. A.; Hardt, S. E. & Leuschner, F. (2017), 'The cardiac microenvironment uses non-canonical WNT signaling to activate monocytes after myocardial infarction.', EMBO molecular medicine 9, 1279--1293.

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.

 

Books:

 

Circular RNAs

Methods and Protocols

Editors: Dieterich, Christoph, Papantonis, Argyris (Eds.)

Humana Press, 2018