Christoph Dieterich

Christoph Dieterich

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Christoph Dieterich

Publications by authors named "Christoph Dieterich"

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A secreted microRNA disrupts autophagy in distinct tissues of Caenorhabditis elegans upon ageing.

Nat Commun 2019 Oct 23;10(1):4827. Epub 2019 Oct 23.

State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Rd, 200031, Shanghai, China.

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http://www.nature.com/articles/s41467-019-12821-2
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http://dx.doi.org/10.1038/s41467-019-12821-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811558PMC
October 2019

Deep Learning Approaches Outperform Conventional Strategies in De-Identification of German Medical Reports.

Stud Health Technol Inform 2019 Sep;267:101-109

Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg.

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http://dx.doi.org/10.3233/SHTI190813DOI Listing
September 2019

MedEx - Data Analytics for Medical Domain Experts in Real-Time.

Stud Health Technol Inform 2019 Sep;267:142-149

Klaus Tschira Institute for Integrative Computational Cardiology.

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http://dx.doi.org/10.3233/SHTI190818DOI Listing
September 2019

Monitoring Cell-Type-Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress.

Circ Res 2019 Aug 9;125(4):431-448. Epub 2019 Jul 9.

From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).

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http://dx.doi.org/10.1161/CIRCRESAHA.119.314817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690133PMC
August 2019

On the optimal design of metabolic RNA labeling experiments.

PLoS Comput Biol 2019 Aug 7;15(8):e1007252. Epub 2019 Aug 7.

Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1007252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699717PMC
August 2019

circtools-a one-stop software solution for circular RNA research.

Bioinformatics 2019 Jul;35(13):2326-2328

Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg.

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http://dx.doi.org/10.1093/bioinformatics/bty948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6596886PMC
July 2019

The E3 ubiquitin ligase UBR5 interacts with the H/ACA ribonucleoprotein complex and regulates ribosomal RNA biogenesis in embryonic stem cells.

FEBS Lett 2019 Jul 31. Epub 2019 Jul 31.

Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany.

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http://dx.doi.org/10.1002/1873-3468.13559DOI Listing
July 2019

Identification of Methylated Transcripts Using the TRIBE Approach.

Methods Mol Biol 2019 ;1870:89-106

Laboratory of RNA Epigenetics, Institute of Molecular Biology (IMB), Mainz, Germany.

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http://link.springer.com/10.1007/978-1-4939-8808-2_7
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http://dx.doi.org/10.1007/978-1-4939-8808-2_7DOI Listing
May 2019

Computational approaches for circular RNA analysis.

Wiley Interdiscip Rev RNA 2019 05 20;10(3):e1528. Epub 2019 Feb 20.

Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany.

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http://dx.doi.org/10.1002/wrna.1528DOI Listing
May 2019

Deregulated Splicing Is a Major Mechanism of RNA-Induced Toxicity in Huntington's Disease.

J Mol Biol 2019 Apr 31;431(9):1869-1877. Epub 2019 Jan 31.

German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, North Rhine-Westphalia, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.01.034DOI Listing
April 2019

The RNA-Protein Interactome of Differentiated Kidney Tubular Epithelial Cells.

J Am Soc Nephrol 2019 04 13;30(4):564-576. Epub 2019 Mar 13.

Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany;

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http://dx.doi.org/10.1681/ASN.2018090914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442340PMC
April 2019

Deep Computational Circular RNA Analytics from RNA-seq Data.

Methods Mol Biol 2018 ;1724:9-25

Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany.

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http://link.springer.com/10.1007/978-1-4939-7562-4_2
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http://dx.doi.org/10.1007/978-1-4939-7562-4_2DOI Listing
January 2019

Identification and regulation of the long non-coding RNA Heat2 in heart failure.

J Mol Cell Cardiol 2019 01 13;126:13-22. Epub 2018 Nov 13.

Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Theodor Stern Kai 7, Frankfurt, Germany; German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany; Kerckhoff Heart and Thorax Center, Department of Cardiology, Bad Nauheim, Germany.

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https://linkinghub.elsevier.com/retrieve/pii/S00222828183038
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http://dx.doi.org/10.1016/j.yjmcc.2018.11.004DOI Listing
January 2019

RNA Modification Level Estimation with pulseR.

Genes (Basel) 2018 Dec 10;9(12). Epub 2018 Dec 10.

Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany.

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http://www.mdpi.com/2073-4425/9/12/619
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http://dx.doi.org/10.3390/genes9120619DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316556PMC
December 2018

De-Identification of German Medical Admission Notes.

Stud Health Technol Inform 2018 ;253:165-169

Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim.

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November 2018

A Vastly Increased Chemical Variety of RNA Modifications Containing a Thioacetal Structure.

Angew Chem Int Ed Engl 2018 06 27;57(26):7893-7897. Epub 2018 Apr 27.

Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany.

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http://dx.doi.org/10.1002/anie.201713188DOI Listing
June 2018

Insights into the ubiquitin-proteasome system of human embryonic stem cells.

Sci Rep 2018 03 6;8(1):4092. Epub 2018 Mar 6.

Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931, Cologne, Germany.

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http://dx.doi.org/10.1038/s41598-018-22384-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5840266PMC
March 2018

Circular RNAs in the cardiovascular system.

Noncoding RNA Res 2018 Mar 25;3(1):1-11. Epub 2018 Feb 25.

Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg.

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https://linkinghub.elsevier.com/retrieve/pii/S24680540173004
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http://dx.doi.org/10.1016/j.ncrna.2018.02.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6084836PMC
March 2018

A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells.

Nat Commun 2017 11 13;8(1):1456. Epub 2017 Nov 13.

Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany.

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http://dx.doi.org/10.1038/s41467-017-01744-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5682285PMC
November 2017

pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments.

Bioinformatics 2017 Oct;33(20):3305-3307

Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg.

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https://academic.oup.com/bioinformatics/article/33/20/3305/3
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http://dx.doi.org/10.1093/bioinformatics/btx368DOI Listing
October 2017

Flexbar 3.0 - SIMD and multicore parallelization.

Bioinformatics 2017 Sep;33(18):2941-2942

Institute of Bioinformatics, Department of Mathematics and Computer Science, FU Berlin, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx330DOI Listing
September 2017

Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses.

BMC Genomics 2017 Sep 5;18(1):686. Epub 2017 Sep 5.

Institute of Biology, Molecular Parasitology, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 14, 10115, Berlin, Germany.

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http://dx.doi.org/10.1186/s12864-017-4095-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5584376PMC
September 2017

Prognostic Relevance of Tumor Purity and Interaction with MGMT Methylation in Glioblastoma.

Mol Cancer Res 2017 05 1;15(5):532-540. Epub 2017 Feb 1.

Department of Experimental Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany.

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http://dx.doi.org/10.1158/1541-7786.MCR-16-0322DOI Listing
May 2017

Bayesian prediction of RNA translation from ribosome profiling.

Nucleic Acids Res 2017 04;45(6):2960-2972

Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkw1350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389577PMC
April 2017

JACUSA: site-specific identification of RNA editing events from replicate sequencing data.

BMC Bioinformatics 2017 Jan 3;18(1). Epub 2017 Jan 3.

Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology at the Department of Internal Medicine III, University Hospital Heidelberg, Im Neuenheimer Feld 669, Heidelberg, 69120, Germany.

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http://dx.doi.org/10.1186/s12859-016-1432-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210316PMC
January 2017

Reducing RBM20 activity improves diastolic dysfunction and cardiac atrophy.

J Mol Med (Berl) 2016 12 26;94(12):1349-1358. Epub 2016 Nov 26.

Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.

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http://dx.doi.org/10.1007/s00109-016-1483-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5143357PMC
December 2016

Somatic increase of CCT8 mimics proteostasis of human pluripotent stem cells and extends C. elegans lifespan.

Nat Commun 2016 11 28;7:13649. Epub 2016 Nov 28.

Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, Cologne 50931, Germany.

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http://dx.doi.org/10.1038/ncomms13649DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133698PMC
November 2016

SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans.

Mol Biosyst 2016 10;12(11):3447-3458

Instituto di Tecnologie Biomediche - Consiglio Nazionale delle Ricerche, via F.lli Cervi 93, 20090, Segrate, Milano, Italy.

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http://dx.doi.org/10.1039/c6mb00453aDOI Listing
October 2016

Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts.

Genomics Proteomics Bioinformatics 2016 08 27;14(4):216-23. Epub 2016 Apr 27.

Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK), Heidelberg/Mannheim, Germany.

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http://dx.doi.org/10.1016/j.gpb.2016.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996846PMC
August 2016

Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment.

Nat Cell Biol 2016 08 11;18(8):864-75. Epub 2016 Jul 11.

Paul Gerson Unna Group 'Skin Homeostasis and Ageing', Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.

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http://dx.doi.org/10.1038/ncb3387DOI Listing
August 2016

Specific identification and quantification of circular RNAs from sequencing data.

Bioinformatics 2016 04 9;32(7):1094-6. Epub 2015 Nov 9.

Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9B, 50931 Cologne, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btv656DOI Listing
April 2016

Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals.

Nat Commun 2016 Mar 22;7:10944. Epub 2016 Mar 22.

Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, Cologne 50931, Germany.

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http://dx.doi.org/10.1038/ncomms10944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804169PMC
March 2016

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 2015 20;10(5):e0125745. Epub 2015 May 20.

Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125745PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4439058PMC
February 2016

A protocol for chemical mutagenesis in Strongyloides ratti.

Exp Parasitol 2015 Nov 9;158:2-7. Epub 2015 Mar 9.

Department Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.exppara.2015.03.001DOI Listing
November 2015

Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling.

Methods 2015 Sep 20;85:75-89. Epub 2015 Jun 20.

Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.06.013DOI Listing
September 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 2015 Sep 3;16:668. Epub 2015 Sep 3.

Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, Germany.

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http://dx.doi.org/10.1186/s12864-015-1858-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4558960PMC
September 2015

Integrin-linked kinase regulates the niche of quiescent epidermal stem cells.

Nat Commun 2015 Sep 8;6:8198. Epub 2015 Sep 8.

Paul Gerson Unna Group 'Skin Homeostasis and Ageing', Max Planck Institute for Biology of Ageing, Cologne 50931, Germany.

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http://dx.doi.org/10.1038/ncomms9198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4569844PMC
September 2015

Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus.

BMC Evol Biol 2015 Sep 15;15:185. Epub 2015 Sep 15.

Max-Planck Institute for Biology of Aging, Joseph-Stelzmann-Str. 9b, Köln, 50866, Germany.

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http://dx.doi.org/10.1186/s12862-015-0466-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570658PMC
September 2015

A coding-independent function of an alternative Ube3a transcript during neuronal development.

Nat Neurosci 2015 May 13;18(5):666-73. Epub 2015 Apr 13.

Institute of Physiological Chemistry, Biochemical-Pharmacological Center Marburg, Philipps University Marburg, Marburg, Germany.

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http://dx.doi.org/10.1038/nn.3996DOI Listing
May 2015

CWC22-dependent pre-mRNA splicing and eIF4A3 binding enables global deposition of exon junction complexes.

Nucleic Acids Res 2015 May 13;43(9):4687-700. Epub 2015 Apr 13.

Institute for Genetics, University of Cologne, D-50674 Cologne, Germany

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http://dx.doi.org/10.1093/nar/gkv320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482076PMC
May 2015

A Grhl2-dependent gene network controls trophoblast branching morphogenesis.

Development 2015 Mar;142(6):1125-36

Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, Berlin 13125, Germany Experimental and Clinical Research Center, a collaboration between the Max Delbrück Center and the Medical Faculty of the Charité, Robert-Rössle-Str. 10, Berlin 13125, Germany Department of Nephrology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, Berlin 10117, Germany

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http://dx.doi.org/10.1242/dev.113829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6517833PMC
March 2015

Mitofusin 2 is required to maintain mitochondrial coenzyme Q levels.

J Cell Biol 2015 Feb;208(4):429-42

Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden

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http://dx.doi.org/10.1083/jcb.201411100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332246PMC
February 2015

Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals.

Cell Rep 2015 Jan 31;10(2):170-7. Epub 2014 Dec 31.

Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Robert Roessle Straße 10, 13125 Berlin-Buch, Germany. Electronic address:

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http://www.cell.com/cell-reports/pdf/S2211-1247(14)01048-1.p
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http://linkinghub.elsevier.com/retrieve/pii/S221112471401048
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http://dx.doi.org/10.1016/j.celrep.2014.12.019DOI Listing
January 2015

Disorder and residual helicity alter p53-Mdm2 binding affinity and signaling in cells.

Nat Chem Biol 2014 Dec 2;10(12):1000-2. Epub 2014 Nov 2.

1] Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, USA. [2] Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida, USA.

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http://edoc.mdc-berlin.de/14422/1/14422oa.pdf
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http://www.nature.com/doifinder/10.1038/nchembio.1668
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http://dx.doi.org/10.1038/nchembio.1668DOI Listing
December 2014

Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications.

Bioinformatics 2014 Nov 1;30(22):3143-51. Epub 2014 Aug 1.

IZKF Computational Biology Research Group, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Computational RNA Biology Lab and Bioinformatics Core, Max Planck Institute for Biology of Ageing, 50931 Cologne, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074, Helmholtz Institute for Biomedical Engineering, 52074, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, 52062 Aachen, Germany and Center of Informatics, Federal University of Pernambuco, 50740560 Recife-PE, Brazil IZKF Computational Biology Research Group, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Computational RNA Biology Lab and Bioinformatics Core, Max Planck Institute for Biology of Ageing, 50931 Cologne, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074, Helmholtz Institute for Biomedical Engineering, 52074, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, 52062 Aachen, Germany and Center of Informatics, Federal University of Pernambuco, 50740560 Recife-PE, Brazil IZKF Computational Biology Research Group, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Computational RNA Biology Lab and Bioinformatics Core, Max Planck Institute for Biology of Ageing, 50931 Cologne, Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074, Helmholtz Institute for Biomedical Engineering, 52074, Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, 52062 Aachen, Germany and Center of Informatics, Federal University of Pernambuco, 50740560 Recife-PE, Brazil.

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http://dx.doi.org/10.1093/bioinformatics/btu519DOI Listing
November 2014

The genome of Eimeria falciformis--reduction and specialization in a single host apicomplexan parasite.

BMC Genomics 2014 Aug 20;15:696. Epub 2014 Aug 20.

Computational RNA Biology and Ageing, Max Plank Institute for Biology of Ageing, Joseph-Stelzmann Straße 9b, 50913 Cologne, Germany.

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http://dx.doi.org/10.1186/1471-2164-15-696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287421PMC
August 2014

MOV10 Is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3' UTRs.

Mol Cell 2014 May 10;54(4):573-85. Epub 2014 Apr 10.

Max-Delbrück-Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.03.017DOI Listing
May 2014

High-resolution profiling of protein occupancy on polyadenylated RNA transcripts.

Methods 2014 Feb 1;65(3):302-9. Epub 2013 Oct 1.

Max-Delbrück-Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert-Rössle Str. 10, 13125 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2013.09.017DOI Listing
February 2014

Changes in metabolite profiles caused by genetically determined obesity in mice.

Metabolomics 2014 19;10(3):461-472. Epub 2013 Oct 19.

Breeding Biology and Molecular Genetics, Department for Crop and Animal Sciences, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany.

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http://dx.doi.org/10.1007/s11306-013-0590-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984667PMC
October 2013

ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores.

Bioinformatics 2013 Jul 16;29(14):1809-10. Epub 2013 May 16.

Bioinformatics in Quantitative Biology, The Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin-Buch, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btt268DOI Listing
July 2013

Computational biology of RNA interactions.

Wiley Interdiscip Rev RNA 2013 Jan-Feb;4(1):107-20. Epub 2012 Nov 8.

Berlin Institute for Medical Systems Biology, Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Straße 10, Berlin, Germany.

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http://dx.doi.org/10.1002/wrna.1147DOI Listing
June 2013

Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.

Nucleic Acids Res 2013 Apr 8;41(6):3619-34. Epub 2013 Feb 8.

Laboratory for Novel sequencing technology, Functional and Medical Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkt072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616697PMC
April 2013

FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms.

Biology (Basel) 2012 Dec 14;1(3):895-905. Epub 2012 Dec 14.

Bioinformatics in Quantitative Biology, Berlin Institute for Medical Systems Biology at the Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.

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http://dx.doi.org/10.3390/biology1030895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009805PMC
December 2012

Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans.

BMC Genomics 2012 Jun 19;13:254. Epub 2012 Jun 19.

Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Tübingen, Germany.

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http://dx.doi.org/10.1186/1471-2164-13-254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443458PMC
June 2012

doRiNA: a database of RNA interactions in post-transcriptional regulation.

Nucleic Acids Res 2012 Jan 15;40(Database issue):D180-6. Epub 2011 Nov 15.

Bioinformatics in Quantitative Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkr1007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245013PMC
January 2012

Pristionchus pacificus daf-16 is essential for dauer formation but dispensable for mouth form dimorphism.

Development 2011 Apr 24;138(7):1281-4. Epub 2011 Feb 24.

Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany.

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http://dx.doi.org/10.1242/dev.058909DOI Listing
April 2011

Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover.

BMC Evol Biol 2011 Jan 13;11:13. Epub 2011 Jan 13.

Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Spemannstrasse 37, 72076 Tübingen, Germany.

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http://dx.doi.org/10.1186/1471-2148-11-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032686PMC
January 2011

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models.

Genome Res 2010 Jun 17;20(6):837-46. Epub 2010 Mar 17.

Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.

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http://dx.doi.org/10.1101/gr.103119.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877580PMC
June 2010

ACCUSA--accurate SNP calling on draft genomes.

Bioinformatics 2010 May 1;26(10):1364-5. Epub 2010 Apr 1.

Bioinformatics in Quantitative Biology, The Berlin Institute for Medical Systems Biology at Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin-Buch, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btq138DOI Listing
May 2010

CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes.

PLoS One 2010 Jan 28;5(1):e8861. Epub 2010 Jan 28.

Institute for Medical Genetics, Charité-Universitätsmedizin, Berlin, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812507PMC
January 2010

3PD: Rapid design of optimal primers for chromosome conformation capture assays.

BMC Genomics 2009 Dec 29;10:635. Epub 2009 Dec 29.

Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin-Buch, Germany.

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http://dx.doi.org/10.1186/1471-2164-10-635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811132PMC
December 2009

How to become a parasite - lessons from the genomes of nematodes.

Trends Genet 2009 May 8;25(5):203-9. Epub 2009 Apr 8.

Max-Planck Institute for Developmental Biology, Spemannstrasse 37, D-72076 Tübingen, Germany.

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http://dx.doi.org/10.1016/j.tig.2009.03.006DOI Listing
May 2009

Syntenator: multiple gene order alignments with a gene-specific scoring function.

Algorithms Mol Biol 2008 Nov 6;3:14. Epub 2008 Nov 6.

Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, Tübingen, Germany.

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http://almob.biomedcentral.com/articles/10.1186/1748-7188-3-
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http://dx.doi.org/10.1186/1748-7188-3-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2590594PMC
November 2008

Isolation of naturally associated bacteria of necromenic Pristionchus nematodes and fitness consequences.

J Exp Biol 2008 Jun;211(Pt 12):1927-36

Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Spemannstrasse 37, D-72076 Tübingen, Germany.

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http://jeb.biologists.org/cgi/doi/10.1242/jeb.014944
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June 2008

A Caenorhabditis motif compendium for studying transcriptional gene regulation.

BMC Genomics 2008 Jan 23;9:30. Epub 2008 Jan 23.

Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35 - 37, Tübingen, Germany.

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http://dx.doi.org/10.1186/1471-2164-9-30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248174PMC
January 2008

Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus.

Nucleic Acids Res 2007 Jan 24;35(Database issue):D498-502. Epub 2006 Oct 24.

Department of Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Spemannstrasse 35-37, 72076 Tübingen, Germany.

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http://dx.doi.org/10.1093/nar/gkl804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781148PMC
January 2007

Comparative promoter analysis in vertebrate genomes with the CORG workbench.

Methods Mol Biol 2006 ;338:105-18

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

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http://dx.doi.org/10.1385/1-59745-097-9:105DOI Listing
September 2006

Pristionchus pacificus genomics: from genetics to genome sequence.

WormBook 2006 Aug 14:1-14. Epub 2006 Aug 14.

Department of Evolutionary Biology, Max Planck Institute for Developmental Biology; Tuebingen, D-72076 Germany.

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http://dx.doi.org/10.1895/wormbook.1.116.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4781114PMC
August 2006

SITEBLAST--rapid and sensitive local alignment of genomic sequences employing motif anchors.

Bioinformatics 2005 May 14;21(9):2093-4. Epub 2004 Dec 14.

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

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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May 2005

Comparative promoter region analysis powered by CORG.

BMC Genomics 2005 Feb 21;6:24. Epub 2005 Feb 21.

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

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http://dx.doi.org/10.1186/1471-2164-6-24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555765PMC
February 2005

The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF.

Mol Cell 2004 Dec;16(6):867-80

Abt. Molekularbiologie, Institut für Zellbiologie, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany.

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December 2004