Logo Logo

Publications by Zimmer, Ralf

Up a level
Export as [feed] RSS 1.0 [feed] RSS 2.0
Group by: Item Type | Date
Jump to: 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2003
Number of items: 45.

2018

Haas, Jürgen G.; Weber, Julia; Gonzalez, Orland; Zimmer, Ralf; Griffiths, Samantha J. (2018): Antiviral activity of the mineralocorticoid receptor NR3C2 against Herpes simplex virus Type 1 (HSV-1) infection. In: Scientific Reports, Vol. 8, No. 1 [PDF, 1MB]

Wei, Yuanyuan; Corbalan-Campos, Judit; Gurung, Rashmi; Natarelli, Lucia; Zhu, Mengyu; Exner, Nicole; Erhard, Florian; Greulich, Franziska; Geiler, Claudia; Uhlenhaut, N. Henriette; Zimmer, Ralf; Schober, Andreas (2018): Dicer in Macrophages Prevents Atherosclerosis by Promoting Mitochondrial Oxidative Metabolism. In: Circulation, Vol. 138, No. 18: pp. 2007-2020 [PDF, 7kB]

Tavakkolkhah, Pegah; Zimmer, Ralf; Küffner, Robert (2018): Detection of network motifs using three-way ANOVA.
In: PLOS One 13(8), e0201382 [PDF, 2MB]

Geistlinger, Ludwig; Silva, Vinicius Henrique da; Mello Cesar, Aline Silva; Tizioto, Polyana Cristine; Waldron, Levi; Zimmer, Ralf; Correia de Almeida Regitano, Luciana; Coutinho, Luiz Lehmann (2018): Widespread modulation of gene expression by copy number variation in skeletal muscle. In: Scientific Reports, Vol. 8, 1399 [PDF, 2MB]

Erhard, Florian; Halenius, Anne; Zimmermann, Cosima; L'Hernault, Anne; Kowalewski, Daniel J.; Weekes, Michael P.; Stevanovic, Stefan; Zimmer, Ralf; Doelken, Lars (2018): Improved Ribo-seq enables identification of cryptic translation events. In: Nature Methods, Vol. 15, No. 5: pp. 363-366

Natarelli, Lucia; Geissler, Claudia; Csaba, Gergely; Wei, Yuanyuan; Zhu, Mengyu; di Francesco, Andrea; Hartmann, Petra; Zimmer, Ralf; Schober, Andreas (2018): miR-103 promotes endothelial maladaptation by targeting lncWDR59. In: Nature Communications, Vol. 9, 2645 [PDF, 4MB]

2017

Natarelli, Lucia; Hartmann, Petra; Wei, Yuanyuan; Geissler, Claudia; Csaba, Gergely; Zimmer, Ralf; Schober, Andreas (2017): MIR-103 target LNCWDR59 to affect endothelial proliferation balanced by NOTCH1 and WNT signaling co-activation. In: Atherosclerosis, Vol. 263, E5-E5

Berchtold, Evi; Csaba, Gergely; Zimmer, Ralf (2017): RelExplain-integrating data and networks to explain biological processes. In: Bioinformatics, Vol. 33, No. 12: pp. 1837-1844

Glaser, Laura V.; Rieger, Simone; Thumann, Sybille; Beer, Sophie; Kuklik-Roos, Cornelia; Martin, Dietmar E.; Maier, Kerstin C.; Harth-Hertle, Marie L.; Grüning, Björn; Backofen, Rolf; Krebs, Stefan; Blum, Helmut; Zimmer, Ralf; Erhard, Florian; Kempkes, Bettina (2017): EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells.
In: PLOS Pathogens 13(10), e1006664 [PDF, 8MB]

Barann, Matthias; Zimmer, Ralf; Birzele, Fabian (2017): Manananggal - a novel viewer for alternative splicing events. In: BMC Bioinformatics 18:120 [PDF, 3MB]

2016

Berchtold, Evi; Csaba, Gergely; Zimmer, Ralf (2016): Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data.
In: PLOS ONE 11(10), e0164513 [PDF, 2MB]

Pesch, Robert; Zimmer, Ralf (2016): Cross-species Conservation of context-specific networks. In: BMC Systems Biology 10:76 [PDF, 2MB]

da Silva, Vinicius Henrique; De Almeida Regitano, Luciana Correia; Geistlinger, Ludwig; Pértille, Fábio; Giachetto, Poliana Fernanda; Brassaloti, Ricardo Augusto; Morosini, Natália Silva; Zimmer, Ralf; Coutinho, Luiz Lehmann (2016): Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle.
In: PLOS ONE 11(6), e0157711 [PDF, 1MB]

Geistlinger, Ludwig; Csaba, Gergely; Zimmer, Ralf (2016): Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. In: BMC Bioinformatics 17:45 [PDF, 1MB]

Viola, Joana R.; Lemnitzer, Patricia; Jansen, Yvonne; Csaba, Gergely; Winter, Carla; Neideck, Carlos; Silvestre-Roig, Carlos; Dittmar, Gunnar; Döring, Yvonne; Drechsler, Maik; Weber, Christian; Zimmer, Ralf; Cenac, Nicolas; Soehnlein, Oliver (2016): Resolving Lipid Mediators Maresin 1 and Resolvin D2 Prevent Atheroprogression in Mice. In: Circulation Research, Vol. 119, No. 9: pp. 1030-1038

Schöppner, Patricia; Csaba, Gergely; Braun, Tatjana; Daake, Marina; Richter, Bettina; Lange, Oliver F.; Zacharias, Martin; Zimmer, Ralf; Haslbeck, Martin (2016): Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins. In: Journal of Molecular Biology, Vol. 428, No. 8: pp. 1544-1557

2015

Bonfert, Thomas; Kirner, Evelyn; Csaba, Gergely; Zimmer, Ralf; Friedel, Caroline C. (2015): ContextMap 2: fast and accurate context-based RNA-seq mapping. In: BMC Bioinformatics 16:122 [PDF, 1MB]

Erhard, Florian; Zimmer, Ralf (2015): Count ratio model reveals bias affecting NGS fold changes. In: Nucleic Acids Research, Vol. 43, No. 20, e136 [PDF, 1MB]

Schreiber, Konrad; Csaba, Gergely; Haslbeck, Martin; Zimmer, Ralf (2015): Alternative Splicing in Next Generation Sequencing Data of Saccharomyces cerevisiae.
In: PLOS ONE 10(10), e0140487 [PDF, 1MB]

Rutkowski, Andrzej J.; Erhard, Florian; L'Hernault, Anne; Bonfert, Thomas; Schilhabel, Markus; Crump, Colin; Rosenstiel, Philip; Efstathiou, Stacey; Zimmer, Ralf; Friedel, Caroline C.; Dölken, Lars (2015): Widespread disruption of host transcription termination in HSV-1 infection. In: Nature Communications, Vol. 6, 7126 [PDF, 1MB]

2014

Beard, Philippa M.; Griffiths, Samantha J.; Gonzalez, Orland; Haga, Ismar R.; Jowers, Tali Pechenick; Reynolds, Danielle K.; Wildenhain, Jan; Tekotte, Hille; Auer, Manfred; Tyers, Mike; Ghazal, Peter; Zimmer, Ralf; Haas, Jürgen (2014): A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference.
In: PLOS ONE 9(6), e98431 [PDF, 1MB]

2013

Kramer, Ronny; Wolf, Simone; Petri, Tobias; Soosten, Dirk von; Dänicke, Sven; Weber, Eva-Maria; Zimmer, Ralf; Rehage, Juergen; Jahreis, Gerhard (2013): A commonly used rumen-protected conjugated linoleic acid supplement marginally affects fatty acid distribution of body tissues and gene expression of mammary gland in heifers during early lactation. In: Lipids in Health and Disease 12:96 [PDF, 445kB]

Kurome, Mayuko; Geistlinger, Ludwig; Kessler, Barbara; Zakhartchenko, Valeri; Klymiuk, Nikolai; Wuensch, Annegret; Richter, Anne; Baehr, Andrea; Kraehe, Katrin; Burkhardt, Katinka; Flisikowski, Krzysztof; Flisikowska, Tatiana; Merkl, Claudia; Landmann, Martina; Durkovic, Marina; Tschukes, Alexander; Kraner, Simone; Schindelhauer, Dirk; Petri, Tobias; Kind, Alexander; Nagashima, Hiroshi; Schnieke, Angelika; Zimmer, Ralf; Wolf, Eckhard (2013): Factors influencing the efficiency of generating genetically engineered pigs by nuclear transfer: multi-factorial analysis of a large data set. In: BMC Biotechnology 13:43 [PDF, 617kB]

Erhard, Florian; Doelken, Lars; Jaskiewicz, Lukasz; Zimmer, Ralf (2013): PARma: identification of microRNA target sites in AGO-PAR-CLIP data. In: Genome Biology 14:R79 [PDF, 3MB]

2012

Marcinowski, Lisa; Lidschreiber, Michael; Windhager, Lukas; Rieder, Martina; Bosse, Jens B.; Rädle, Bernd; Bonfert, Thomas; Györy, Ildiko; de Graaf, Miranda; Prazeres da Costa, Olivia; Rosenstiel, Philip; Friedel, Caroline C.; Zimmer, Ralf; Ruzsics, Zsolt; Dölken, Lars (September 2012): Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection.
In: PLOS Pathogens 8(9), e1002908 [PDF, 1MB]

Marcinowski, Lisa; Tanguy, Mélanie; Krmpotic, Astrid; Rädle, Bernd; Lisnić, Vanda J.; Tuddenham, Lee; Chane-Woon-Ming, Béatrice; Ruzsics, Zsolt; Erhard, Florian; Benkartek, Corinna; Babic, Marina; Zimmer, Ralf; Trgovcich, Joanne; Koszinowski, Ulrich H.; Jonjic, Stipan; Pfeffer, Sébastien; Dölken, Lars (February 2012): Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo.
In: PLOS Pathogens 8(2), e1002510 [PDF, 1MB]

Petri, Tobias; Berchtold, Evi; Zimmer, Ralf; Friedel, Caroline C. (2012): Detection and correction of probe-level artefacts on microarrays. In: BMC Bioinformatics 13:114 [PDF, 1MB]

Bonfert, Thomas; Csaba, Gergely; Zimmer, Ralf; Friedel, Caroline C. (2012): A context-based approach to identify the most likely mapping for RNA-seq experiments. In: BMC Bioinformatics 13:S9 [PDF, 1MB]

2011

Pfefferle, Susanne; Schöpf, Julia; Kögl, Manfred; Friedel, Caroline C.; Müller, Marcel A.; Carbajo-Lozoya, Javier; Stellberger, Thorsten; Dall'Armi, Ekatarina von; Herzog, Petra; Kallies, Stefan; Niemeyer, Daniela; Ditt, Vanessa; Kuri, Thomas; Züst, Roland; Pumpor, Ksenia; Hilgenfeld, Rolf; Schwarz, Frank; Zimmer, Ralf; Steffen, Imke; Weber, Friedemann; Thiel, Volker; Herrler, Georg; Thiel, Heinz-Jürgen; Schwegmann-Wessels, Christel; Pöhlmann, Stefan; Haas, Juergen G.; Drosten, Christian; Brunn, Albrecht von (October 2011): The SARS-coronavirus-host interactome. Identification of cyclophilins as target for pan-coronavirus inhibitors.
In: PLOS Pathogens 7(10), e1002331 [PDF, 1MB]

Naeem, Haroon; Küffner, Robert; Zimmer, Ralf (2011): MIRTFnet: analysis of miRNA regulated transcription factors.
In: PLOS ONE 6(8), e22519 [PDF, 628kB]

2010

Küffner, Robert; Petri, Tobias; Windhager, Lukas; Zimmer, Ralf (20. September 2010): Petri Nets with Fuzzy Logic (PNFL): Reverse Engineering and Parametrization.
In: PLOS ONE 5(9), e12807 [PDF, 1MB]

Gonzalez, Orland; Oberwinkler, Tanja; Mansueto, Locedie; Pfeiffer, Friedhelm; Mendoza, Eduardo; Zimmer, Ralf; Oesterhelt, Dieter (June 2010): Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis.
In: PLOS Computational Biology 6(6), e1000799 [PDF, 1MB]

Naeem, Haroon; Küffner, Robert; Csaba, Gergely; Zimmer, Ralf (2010): miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature. In: BMC Bioinformatics 11:135 [PDF, 1MB]

2009

Fossum, Even; Friedel, Caroline C.; Rajagopala, Seesandra V.; Titz, Björn; Baiker, Armin; Schmidt, Tina; Kraus, Theo; Stellberger, Thorsten; Rutenberg, Christiane; Suthram, Silpa; Bandyopadhyay, Sourav; Rose, Dietlind; Brunn, Albrecht von; Uhlmann, Mareike; Zeretzke, Christine; Dong, Yu-An; Boulet, Hélène; Koegl, Manfred; Bailer, Susanne M.; Koszinowski, Ulrich H.; Ideker, Trey; Uetz, Peter; Zimmer, Ralf; Haas, Jürgen G. (September 2009): Evolutionarily conserved herpesviral protein interaction networks.
In: PLOS Pathogens 5(9), e1000570 [PDF, 1MB]

Gonzalez, Orland; Gronau, Susanne; Pfeiffer, Friedhelm; Mendoza, Eduardo; Zimmer, Ralf; Oesterhelt, Dieter (3. April 2009): Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum.
In: PLOS Computational Biology 5(4), e1000332 [PDF, 1MB]

Moll, Anton G.; Lindenmeyer, Maja T.; Kretzler, Matthias; Nelson, Peter J.; Zimmer, Ralf; Cohen, Clemens D. (2009): Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays.
In: PLOS ONE 4(3), e4702 [PDF, 316kB]

Csaba, Gergely; Birzele, Fabian; Zimmer, Ralf (2009): Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis. In: BMC Structural Biology 9:23 [PDF, 781kB]

2008

Erhard, Florian; Friedel, Caroline C.; Zimmer, Ralf (2008): FERN - a Java framework for stochastic simulation and evaluation of reaction networks. In: BMC Bioinformatics 9:356 [PDF, 546kB]

2007

Brunn, Albrecht von; Teepe, Carola; Simpson, Jeremy C.; Pepperkok, Rainer; Friedel, Caroline C.; Zimmer, Ralf; Roberts, Rhonda; Baric, Ralph; Haas, Jürgen (23. May 2007): Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome.
In: PLOS ONE 2(5), e459 [PDF, 1MB]

Friedel, Caroline C.; Zimmer, Ralf (2007): Influence of degree correlations on network structure and stability in protein-protein interaction networks. In: BMC Bioinformatics 8:297 [PDF, 316kB]

2006

Friedel, Caroline C.; Zimmer, Ralf (2006): Inferring topology from clustering coefficients in protein-protein interaction networks. In: BMC Bioinformatics 7:519 [PDF, 424kB]

Fundel, Katrin; Zimmer, Ralf (2006): Gene and protein nomenclature in public databases. In: BMC Bioinformatics 7:372 [PDF, 340kB]

2005

Fundel, Katrin; Güttler, Daniel; Zimmer, Ralf; Apostolakis, Joannis (2005): A simple approach for protein name identification: prospects and limits. In: BMC Bioinformatics 6:S15 [PDF, 282kB]

Hanisch, Daniel; Fundel, Katrin; Mevissen, Heinz-Theodor; Zimmer, Ralf; Fluck, Juliane (2005): ProMiner: rule-based protein and gene entity recognition. In: BMC Bioinformatics 6:S14 [PDF, 290kB]

2003

Aigner, T.; Bartnik, E.; Zimmer, Ralf (2003): Cell biology and functional genomics of osteoarthritic chondrocytes. In: Arthritis Research & Therapy 5 [PDF, 1MB]

This list was generated on Fri Feb 26 02:52:58 2021 CET.