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Journal article

Pekayvaz, Kami ORCID logoORCID: https://orcid.org/0000-0003-4040-650X; Losert, Corinna ORCID logoORCID: https://orcid.org/0000-0002-5997-4702; Knottenberg, Viktoria; Gold, Christoph; Blokland, Irene V. van; Oelen, Roy ORCID logoORCID: https://orcid.org/0000-0002-5026-6531; Groot, Hilde E.; Benjamins, Jan Walter ORCID logoORCID: https://orcid.org/0000-0002-5701-0539; Brambs, Sophia; Kaiser, Rainer ORCID logoORCID: https://orcid.org/0000-0003-1750-3395; Gottschlich, Adrian ORCID logoORCID: https://orcid.org/0000-0002-2898-4182; Hoffmann, Gordon Victor; Eivers, Luke; Martinez-Navarro, Alejandro ORCID logoORCID: https://orcid.org/0000-0003-3893-1719; Bruns, Nils; Stiller, Susanne; Akgöl, Sezer ORCID logoORCID: https://orcid.org/0000-0002-3154-3214; Yue, Keyang; Polewka, Vivien; Escaig, Raphael; Joppich, Markus ORCID logoORCID: https://orcid.org/0000-0002-6665-8951; Janjic, Aleksandar; Popp, Oliver; Kobold, Sebastian ORCID logoORCID: https://orcid.org/0000-0002-5612-4673; Petzold, Tobias ORCID logoORCID: https://orcid.org/0000-0001-7805-5632; Zimmer, Ralf; Enard, Wolfgang; Saar, Kathrin ORCID logoORCID: https://orcid.org/0000-0002-4483-1557; Mertins, Philipp ORCID logoORCID: https://orcid.org/0000-0002-2245-528X; Huebner, Norbert ORCID logoORCID: https://orcid.org/0000-0002-1218-6223; Harst, Pim van der ORCID logoORCID: https://orcid.org/0000-0002-2713-686X; Franke, Lude H.; Wijst, Monique G. P. van der ORCID logoORCID: https://orcid.org/0000-0003-1520-3970; Massberg, Steffen ORCID logoORCID: https://orcid.org/0000-0001-7387-3986; Heinig, Matthias ORCID logoORCID: https://orcid.org/0000-0002-5612-1720; Nicolai, Leo ORCID logoORCID: https://orcid.org/0000-0003-0776-5885 and Stark, Konstantin ORCID logoORCID: https://orcid.org/0000-0002-5369-8399 (2024): Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes. In: Nature Medicine [Forthcoming] [PDF, 16MB]

Kaiser, Rainer ORCID logoORCID: https://orcid.org/0000-0003-1750-3395; Gold, Christoph ORCID logoORCID: https://orcid.org/0009-0008-8994-1021; Joppich, Markus ORCID logoORCID: https://orcid.org/0000-0002-6665-8951; Loew, Quentin; Akhalkatsi, Anastassia; Mueller, Tonina T. ORCID logoORCID: https://orcid.org/0000-0002-3123-3064; Offensperger, Felix; Droste zu Senden, Augustin; Popp, Oliver ORCID logoORCID: https://orcid.org/0000-0001-6240-4666; Fina, Lea di; Knottenberg, Viktoria; Martinez-Navarro, Alejandro ORCID logoORCID: https://orcid.org/0000-0003-3893-1719; Eivers, Luke ORCID logoORCID: https://orcid.org/0000-0002-6049-0377; Anjum, Afra ORCID logoORCID: https://orcid.org/0000-0002-1976-4102; Escaig, Raphael; Bruns, Nils; Briem, Eva ORCID logoORCID: https://orcid.org/0009-0003-7506-3882; Dewender, Robin ORCID logoORCID: https://orcid.org/0009-0003-1192-3791; Muraly, Abhinaya ORCID logoORCID: https://orcid.org/0000-0003-2114-7696; Akgöl, Sezer ORCID logoORCID: https://orcid.org/0000-0002-3154-3214; Ferraro, Bartolo ORCID logoORCID: https://orcid.org/0000-0003-3340-5605; Hoeflinger, Jonathan K. L. ORCID logoORCID: https://orcid.org/0000-0002-8823-2177; Polewka, Vivien; Khaled, Najib Ben ORCID logoORCID: https://orcid.org/0000-0002-9681-2542; Allgeier, Julian ORCID logoORCID: https://orcid.org/0000-0001-7536-5715; Tiedt, Steffen ORCID logoORCID: https://orcid.org/0000-0002-8817-8457; Dichgans, Martin ORCID logoORCID: https://orcid.org/0000-0002-0654-387X; Engelmann, Bernd; Enard, Wolfgang ORCID logoORCID: https://orcid.org/0000-0002-4056-0550; Mertins, Philipp ORCID logoORCID: https://orcid.org/0000-0002-2245-528X; Hubner, Norbert ORCID logoORCID: https://orcid.org/0000-0002-1218-6223; Weckbach, Ludwig ORCID logoORCID: https://orcid.org/0000-0002-0981-2246; Zimmer, Ralf; Massberg, Steffen ORCID logoORCID: https://orcid.org/0000-0001-7387-3986; Stark, Konstantin ORCID logoORCID: https://orcid.org/0000-0002-5369-8399; Nicolai, Leo ORCID logoORCID: https://orcid.org/0000-0003-0776-5885 and Pekayvaz, Kami ORCID logoORCID: https://orcid.org/0000-0003-4040-650X (2024): Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment. In: Science Advances, Vol. 10, No. 12, eadl1710 [PDF, 22MB]

Pekayvaz, Kami; Gold, Christoph; Hoseinpour, Parandis; Engel, Anouk; Martinez-Navarro, Alejandro; Eivers, Luke; Coletti, Raffaele; Joppich, Markus; Dionisio, Flavio; Kaiser, Rainer; Tomas, Lukas; Janjic, Aleksandar; Knott, Maximilian; Mehari, Fitsumbirhan; Polewka, Vivien; Kirschner, Megan; Boda, Annegret; Nicolai, Leo; Schulz, Heiko; Titova, Anna; Kilani, Badr; Lorenz, Michael; Fingerle-Rowson, Gunter; Bucala, Richard; Enard, Wolfgang; Zimmer, Ralf; Weber, Christian; Libby, Peter; Schulz, Christian; Massberg, Steffen and Stark, Konstantin (2023): Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation. In: Immunity, Vol. 56, No. 10 [PDF, 9MB]

Nitz, Katrin; Lacy, Michael; Bianchini, Mariaelvy; Wichapong, Kanin; Kücükgöze, Irem Avcilar; Bonfiglio, Cecilia A.; Migheli, Roberta; Wu, Yuting; Burger, Carina; Li, Yuanfang; Forne, Ignasi; Ammar, Constantin; Janjic, Aleksandar; Mohanta, Sarajo; Duchene, Johan; Heemskerk, Johan W. M.; Megens, Remco T. A.; Schwedhelm, Edzard; Huveneers, Stephan; Lygate, Craig A.; Santovito, Donato; Zimmer, Ralf; Imhof, Axel; Weber, Christian; Lutgens, Esther and Atzler, Dorothee (2022): The Amino Acid Homoarginine Inhibits Atherogenesis by Modulating T-Cell Function. In: Circulation Research, Vol. 131, No. 8: pp. 701-712

Schink, Severin; Ammar, Constantin; Chang, Yu-Fang; Zimmer, Ralf and Basan, Markus (2022): Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival. In: Molecular Systems Biology, Vol. 18, No. 12, e11160

Pekayvaz, Kami ORCID logoORCID: https://orcid.org/0000-0003-4040-650X; Leunig, Alexander ORCID logoORCID: https://orcid.org/0000-0002-9179-9203; Kaiser, Rainer ORCID logoORCID: https://orcid.org/0000-0003-1750-3395; Joppich, Markus ORCID logoORCID: https://orcid.org/0000-0002-6665-8951; Brambs, Sophia; Janjic, Aleksandar ORCID logoORCID: https://orcid.org/0000-0001-7180-5381; Popp, Oliver; Nixdorf, Daniel ORCID logoORCID: https://orcid.org/0000-0003-1612-9952; Fumagalli, Valeria; Schmidt, Nora ORCID logoORCID: https://orcid.org/0000-0002-3232-3491; Polewka, Vivien; Anjum, Afra ORCID logoORCID: https://orcid.org/0000-0002-1976-4102; Knottenberg, Viktoria; Eivers, Luke; Wange, Lucas E. ORCID logoORCID: https://orcid.org/0000-0002-3275-9156; Gold, Christoph; Kirchner, Marieluise ORCID logoORCID: https://orcid.org/0000-0002-7049-534X; Muenchhoff, Maximilian ORCID logoORCID: https://orcid.org/0000-0001-7016-0470; Hellmuth, Johannes C. ORCID logoORCID: https://orcid.org/0000-0001-8409-3037; Scherer, Clemens ORCID logoORCID: https://orcid.org/0000-0003-2816-6793; Rubio-Acero, Raquel; Eser, Tabea; Deák, Flora; Puchinger, Kerstin; Kuhl, Niklas; Linder, Andreas; Saar, Kathrin ORCID logoORCID: https://orcid.org/0000-0002-4483-1557; Tomas, Lukas ORCID logoORCID: https://orcid.org/0000-0001-9371-8721; Schulz, Christian ORCID logoORCID: https://orcid.org/0000-0002-8149-0747; Wieser, Andreas; Enard, Wolfgang ORCID logoORCID: https://orcid.org/0000-0002-4056-0550; Kroidl, Inge; Geldmacher, Christof; Bergwelt-Baildon, Michael von ORCID logoORCID: https://orcid.org/0000-0002-1952-052X; Keppler, Oliver T.; Munschauer, Mathias ORCID logoORCID: https://orcid.org/0000-0001-6143-4548; Iannacone, Matteo ORCID logoORCID: https://orcid.org/0000-0002-9370-2671; Zimmer, Ralf; Mertins, Philipp ORCID logoORCID: https://orcid.org/0000-0002-2245-528X; Hubner, Norbert; Hoelscher, Michael; Massberg, Steffen ORCID logoORCID: https://orcid.org/0000-0001-7387-3986; Stark, Konstantin ORCID logoORCID: https://orcid.org/0000-0002-5369-8399 and Nicolai, Leo ORCID logoORCID: https://orcid.org/0000-0003-0776-5885 (2022): Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection. In: Nature Communications, Vol. 13, 1018 [PDF, 7MB]

Geistlinger, Ludwig; Csaba, Gergely; Santarelli, Mara; Ramos, Marcel; Schiffer, Lucas; Turaga, Nitesh; Law, Charity; Davis, Sean; Carey, Vincent; Morgan, Martin; Zimmer, Ralf and Waldron, Levi (2021): Toward a gold standard for benchmarking gene set enrichment analysis. In: Briefings in Bioinformatics, Vol. 22, No. 1: pp. 545-556

Kaiser, Rainer ORCID logoORCID: https://orcid.org/0000-0003-1750-3395; Leunig, Alexander ORCID logoORCID: https://orcid.org/0000-0002-9179-9203; Pekayvaz, Kami ORCID logoORCID: https://orcid.org/0000-0003-4040-650X; Popp, Oliver ORCID logoORCID: https://orcid.org/0000-0001-6240-4666; Joppich, Markus ORCID logoORCID: https://orcid.org/0000-0002-6665-8951; Polewka, Vivien; Escaig, Raphael; Anjum, Afra ORCID logoORCID: https://orcid.org/0000-0002-1976-4102; Hoffknecht, Marie-Louise ORCID logoORCID: https://orcid.org/0000-0002-5894-0308; Gold, Christoph; Brambs, Sophia; Engel, Anouk; Stockhausen, Sven; Knottenberg, Viktoria; Titova, Anna; Haji, Mohamed; Scherer, Clemens ORCID logoORCID: https://orcid.org/0000-0003-2816-6793; Muenchhoff, Maximilian; Hellmuth, Johannes C.; Saar, Kathrin; Schubert, Benjamin ORCID logoORCID: https://orcid.org/0000-0003-3412-1102; Hilgendorff, Anne ORCID logoORCID: https://orcid.org/0000-0002-3725-996X; Schulz, Christian; Kääb, Stefan ORCID logoORCID: https://orcid.org/0000-0001-8824-3581; Zimmer, Ralf ORCID logoORCID: https://orcid.org/0000-0003-1439-2327; Hübner, Norbert; Massberg, Steffen ORCID logoORCID: https://orcid.org/0000-0001-7387-3986; Mertins, Philipp; Nicolai, Leo ORCID logoORCID: https://orcid.org/0000-0003-0776-5885 and Stark, Konstantin (2021): Self-sustaining IL-8 loops drive a prothrombotic neutrophil phenotype in severe COVID-19. In: JCI Insight, Vol. 6, No. 18, e150862 [PDF, 1MB]

Kaiser, Rainer; Leunig, Alexander; Pekayvaz, Kami; Popp, Oliver; Joppich, Markus; Polewka, Vivien; Escaig, Raphael; Anjum, Afra; Hoffknecht, Marie-Louise; Gold, Christoph; Brambs, Sophia; Engel, Anouk; Stockhausen, Sven; Knottenberg, Viktoria; Titova, Anna; Haji, Mohamed; Scherer, Clemens; Muenchhoff, Maximilian; Hellmuth, Johannes C.; Saar, Kathrin; Schubert, Benjamin; Hilgendorff, Anne; Schulz, Christian; Kaeaeb, Stefan; Zimmer, Ralf; Huebner, Norbert; Massberg, Steffen; Mertins, Philipp; Nicolai, Leo and Stark, Konstantin (2021): Self-sustaining IL-8 loops drive a prothrombotic neutrophil phenotype in severe COVID-19. In: Jci Insight, Vol. 6, No. 18, e150862

Lotz-Havla, Amelie S.; Woidy, Mathias; Guder, Philipp; Friedel, Caroline C.; Klingbeil, Julian M.; Bulau, Ana-Maria; Schultze, Anja; Dahmen, Ilona; Noll-Puchta, Heidi; Kemp, Stephan; Erdmann, Ralf; Zimmer, Ralf; Muntau, Ania C. and Gersting, Soren W. (2021): iBRET Screen of the ABCD1 Peroxisomal Network and Mutation-Induced Network Perturbations. In: Journal of Proteome Research, Vol. 20, No. 9: pp. 4366-4380

da Silva, Vinicius; Ramos, Marcel; Groenen, Martien; Crooijmans, Richard; Johansson, Anna; Regitano, Luciana; Coutinho, Luiz; Zimmer, Ralf; Waldron, Levi and Geistlinger, Ludwig (2020): CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. In: Bioinformatics, Vol. 36, No. 3: pp. 972-973

Whisnant, Adam W.; Jürges, Christopher S.; Hennig, Thomas; Wyler, Emanuel; Prusty, Bhupesh; Rutkowski, Andrzej J.; L'hernault, Anne; Djakovic, Lara; Goebel, Margarete; Doering, Kristina; Menegatti, Jennifer; Antrobus, Robin; Matheson, Nicholas J.; Künzig, Florian W. H.; Mastrobuoni, Guido; Bielow, Chris; Kempa, Stefan; Liang, Chunguang; Dandekar, Thomas; Zimmer, Ralf; Landthaler, Markus; Graesser, Friedrich; Lehner, Paul J.; Friedel, Caroline C.; Erhard, Florian and Dölken, Lars (2020): Integrative functional genomics decodes herpes simplex virus 1. In: Nature Communications, Vol. 11, No. 1, 2038 [PDF, 2MB]

Nicolai, Leo; Leunig, Alexander; Brambs, Sophia; Kaiser, Rainer; Joppich, Markus; Hoffknecht, Marie-Louise; Gold, Christoph; Engel, Anouk; Polewka, Vivien; Muenchhoff, Maximilian; Hellmuth, Johannes C.; Ruhle, Adrian; Ledderose, Stephan; Weinberger, Tobias; Schulz, Heiko; Scherer, Clemens; Rudelius, Martina; Zoller, Michael; Keppler, Oliver T.; Zwissler, Bernhard; Bergwelt-Baildon, Michael von; Kääb, Stefan; Zimmer, Ralf; Buelow, Roman D.; Stillfried, Saskia von; Boor, Peter; Massberg, Steffen; Pekayvaz, Kami and Stark, Konstantin (2020): Vascular neutrophilic inflammation and immunothrombosis distinguish severe COVID-19 from influenza pneumonia. In: Journal of Thrombosis and Haemostasis, Vol. 19, No. 2: pp. 574-581

Joppich, Markus; Olenchuk, Margaryta; Mayer, Julia M.; Emslander, Quirin; Jimenez-Soto, Luisa F. and Zimmer, Ralf (2020): SEQU-INTO: Early detection of impurities, contamination and off-targets (ICOs) in long read/MinION sequencing. In: Computational and Structural Biotechnology Journal, Vol. 18: pp. 1342-1351

Berchtold, Evi; Csaba, Gergely and Zimmer, Ralf (2019): YESdb: integrative analysis of environmental stress in yeast. In: Database-the Journal of Biological Databases and Curation, baz023

Joppich, Markus; Weber, Christian and Zimmer, Ralf (2019): Using Context-Sensitive Text Mining to Identify miRNAs in Different Stages of Atherosclerosis. In: Thrombosis and Haemostasis, Vol. 119, No. 8: pp. 1247-1264

Muehlhofer, Moritz; Berchtold, Evi; Stratil, Chris G.; Csaba, Gergely; Kunold, Elena; Bach, Nina C.; Sieber, Stephan A.; Haslbeck, Martin; Zimmer, Ralf and Buchner, Johannes (2019): The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins. In: Cell Reports, Vol. 29, No. 13

Joppich, Markus and Zimmer, Ralf (2019): From command-line bioinformatics to bioGUI. In: Peerj, Vol. 7, e8111

Sedlar, Karel; Kolek, Jan; Gruber, Markus; Jureckova, Katerina; Branska, Barbora; Csaba, Gergely; Vasylkivska, Maryna; Zimmer, Ralf; Patakova, Petra and Provaznik, Ivo (2019): A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock. In: Biotechnology for Biofuels, Vol. 12, No. 1, 243

Berchtold, Evi; Vetter, Martina; Guendert, Melanie; Csaba, Gergely; Fathke, Christine; Ulbrich, Susanne E.; Thomssen, Christoph; Zimmer, Ralf and Kantelhardt, Eva J. (2019): Comparison of six breast cancer classifiers using qPCR. In: Bioinformatics, Vol. 35, No. 18: pp. 3412-3420

Ammar, Constantin; Gruber, Markus; Csaba, Gergely and Zimmer, Ralf (2019): MS-EmpiRe Utilizes Peptide-level Noise Distributions for Ultra-sensitive Detection of Differentially Expressed Proteins. In: Molecular & Cellular Proteomics, Vol. 18, No. 9: pp. 1880-1892

Ammar, Constantin; Berchtold, Evi; Csaba, Gergely; Schmidt, Andreas; Imhof, Axel and Zimmer, Ralf (2019): Multi-Reference Spectral Library Yields Almost Complete Coverage of Heterogeneous LC-MS/MS Data Sets. In: Journal of Proteome Research, Vol. 18, No. 4: pp. 1553-1566

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

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

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

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

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

Haas, Jürgen G.; Weber, Julia; Gonzalez, Orland; Zimmer, Ralf and 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]

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

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 and 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]

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

Natarelli, Lucia; Hartmann, Petra; Wei, Yuanyuan; Geissler, Claudia; Csaba, Gergely; Zimmer, Ralf and 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

Schöppner, Patricia; Csaba, Gergely; Braun, Tatjana; Daake, Marina; Richter, Bettina; Lange, Oliver F.; Zacharias, Martin; Zimmer, Ralf and 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

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 and 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

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

da Silva, Vinicius Henrique; De Almeida Regitano, Luciana Correia; Geistlinger, Ludwig; Pértille, Fábio; Giachetto, Poliana Fernanda; Brassaloti, Ricardo Augusto; Morosini, Natália Silva; Zimmer, Ralf and 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]

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

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

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

Erhard, Florian and 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 and 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. and Dölken, Lars (2015): Widespread disruption of host transcription termination in HSV-1 infection. In: Nature Communications, Vol. 6, 7126 [PDF, 1MB]

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 and 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]

Kramer, Ronny; Wolf, Simone; Petri, Tobias; Soosten, Dirk von; Dänicke, Sven; Weber, Eva-Maria; Zimmer, Ralf; Rehage, Juergen and 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 and 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 and Zimmer, Ralf (2013): PARma: identification of microRNA target sites in AGO-PAR-CLIP data. In: Genome Biology 14:R79 [PDF, 3MB]

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 and 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 and 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 and 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 and 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]

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

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

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 and 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 and 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]

Csaba, Gergely; Birzele, Fabian and 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]

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

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

Brunn, Albrecht von; Teepe, Carola; Simpson, Jeremy C.; Pepperkok, Rainer; Friedel, Caroline C.; Zimmer, Ralf; Roberts, Rhonda; Baric, Ralph and 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. and Zimmer, Ralf (2007): Influence of degree correlations on network structure and stability in protein-protein interaction networks. In: BMC Bioinformatics 8:297 [PDF, 316kB]

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

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

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

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

Conference or Workshop Item

Sedlar, Karel ORCID logoORCID: https://orcid.org/0000-0002-8269-4020 and Zimmer, Ralf ORCID logoORCID: https://orcid.org/0000-0003-1439-2327 (2022): Comparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model Bacterium. 9th International Work-Conference, IWBBIO 2022, Maspalomas, Gran Canaria, Spain, June 27–30, 2022. Rojas, Ignacio; Valenzuela, Olga; Rojas, Fernando; Herrera, Luis Javier and Ortuño, Francisco (eds.) : In: Bioinformatics and Biomedical Engineering. 9th International Work-Conference, IWBBIO 2022, Maspalomas, Gran Canaria, Spain, June 27–30, 2022, Proceedings, Part II, Lecture Notes in Computer Science Vol. 13347 Cham, Switzerland: Springer. pp. 45-56

Schubö, Alexandra ORCID logoORCID: https://orcid.org/0000-0002-3970-2240; Hadziahmetovic, Armin ORCID logoORCID: https://orcid.org/0000-0002-3765-5460; Joppich, Markus ORCID logoORCID: https://orcid.org/0000-0002-6665-8951 and Zimmer, Ralf ORCID logoORCID: https://orcid.org/0000-0003-1439-2327 (2022): Collecting SARS-CoV-2 Encoded miRNAs via Text Mining. 9th International Work-Conference, IWBBIO 2022, Maspalomas, Gran Canaria, Spain, June 27–30, 2022. In: Bioinformatics and Biomedical Engineering. 9th International Work-Conference, IWBBIO 2022, Maspalomas, Gran Canaria, Spain, June 27–30, 2022, Proceedings, Part I, Lecture Notes in Computer Science Vol. 13346 Cham: Springer. pp. 429-441

This list was generated on Sun Jun 16 07:17:21 2024 CEST.