Kliniken & Institute … Kliniken Zentrum für Innere… Innere Medizin III:… Forschung Klaus-Tschira-Institut… Publications

Publications

Worpenberg L, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Dassi E, Aiello G, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Notarangelo M, Ohler U, Dieterich C, Quattrone A, Soldano A, Roignant JY. Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. EMBO J. 2021 Jan 11:e104975. doi: 10.15252/embj.2020104975. Epub ahead of print. PMID: 33428246.

Joglekar A, Prjibelski A, Mahfouz A, Collier P, Lin S, Schlusche AK, Marrocco J, Williams SR, Haase B, Hayes A, Chew JG, Weisenfeld NI, Wong MY, Stein AN, Hardwick SA, Hunt T, Wang Q, Dieterich C, Bent Z, Fedrigo O, Sloan SA, Risso D, Jarvis ED, Flicek P, Luo W, Pitt GS, Frankish A, Smit AB, Ross ME, Tilgner HU. A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. Nat Commun. 2021 Jan 19;12(1):463. doi: 10.1038/s41467-020-20343-5. PMID: 33469025.

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.

RichterPechanski, 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