2023
Papers
Caroline C. Friedel,
Computational Integration of HSV-1 Multi-omics Data., Methods in molecular biology, vol. 2610, pp. 31–48, 2023.
Elena Weiß,
Caroline C. Friedel,
RegCFinder: targeted discovery of genomic subregions with differential read density, Bioinformatics Advances, vol. 3, no. 1, pp. vbad085, 2023.
Elena Weiß, Thomas Hennig, Pilar Graßl, Lara Djakovic, Adam W. Whisnant, Christopher S. Jürges, Franziska Koller,
Michael Kluge,
Florian Erhard, Lars Dölken,
Caroline C. Friedel,
HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes, Journal of Virology, vol. 0, no. 0, pp. e00381-23, 2023.
Zhijia Wang, Monika Macakova, Andrii Bugai, Sergey G. Kuznetsov, Antti Hassinen, Tina Lenasi, Swapnil Potdar,
Caroline C. Friedel, Matjaz Barboric,
P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway., Nucleic acids research, vol. 51, pp. 1687–1706, 2023.
Manivel Lodha, Ihsan Muchsin, Christopher Jürges, Vanda Juranic Lisnic, Anne L'Hernault, Andrzej J. Rutkowski, Bhupesh K. Prusty, Arnhild Grothey, Andrea Milic, Thomas Hennig, Stipan Jonjic,
Caroline C. Friedel,
Florian Erhard, Lars Dölken,
Decoding murine cytomegalovirus., PLoS pathogens, vol. 19, pp. e1010992, 2023.
Hella Schwanke, Vladimir Goncalves Magalhaes, Stefan Schmelz, Emanuel Wyler, Thomas Hennig, Thomas Günther, Adam Grundhoff, Lars Dölken, Markus Landthaler, Marco van Ham, Lothar Jänsch, Konrad Büssow, Joop van den Heuvel, Wulf Blankenfeldt,
Caroline C. Friedel,
Florian Erhard, Melanie M. Brinkmann,
The Cytomegalovirus M35 Protein Directly Binds to the Interferon-beta Enhancer and Modulates Transcription of Ifnb1 and Other IRF3-Driven Genes., Journal of virology, vol. 97, pp. e0040023, 2023.
Lara Djakovic, Thomas Hennig, Katharina Reinisch, Andrea Mili?, Adam W. Whisnant, Katharina Wolf,
Elena Weiß, Tobias Haas, Arnhild Grothey, Christopher S. Jürges,
Michael Kluge, Elmar Wolf,
Florian Erhard,
Caroline C. Friedel, Lars Dölken,
The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes., Nature communications, vol. 14, pp. 4591, 2023.
Zhijia Wang, Samu V. Himanen, Heidi M. Haikala,
Caroline C. Friedel, Anniina Vihervaara, Matjaz Barboric,
Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release., Nucleic acids research, vol. 51, pp. 10970–10991, 2023.
2022
Papers
Marie-Sophie Friedl, Lara Djakovic,
Michael Kluge, Thomas Hennig, Adam W. Whisnant, Simone Backes, Lars Dölken,
Caroline C. Friedel,
HSV-1 and influenza infection induce linear and circular splicing of the long NEAT1 isoform., PloS one, vol. 17, pp. e0276467, 2022.
Milan Hluchý, Pavla Gajdušková, Igor Ruiz de los Mozos, Michal Rájecký,
Michael Kluge, Benedict-Tilman Berger, Zuzana Slabá, David Potěšil,
Elena Weiß, Jernej Ule, Zbyněk Zdráhal, Stefan Knapp, Kamil Paruch,
Caroline C. Friedel, Dalibor Blazek,
CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1, Nature, vol. 609, no. 7928, pp. 829-834, 2022.
2021
Papers
Daniel F. R. Boehmer, Simone Formisano, Carina C. de Oliveira Mann, Stephan A. Mueller,
Michael Kluge, Philipp Metzger, Meino Rohlfs, Christine Hörth, Lorenz Kocheise, Stefan F. Lichtenthaler, Karl-Peter Hopfner, Stefan Endres, Simon Rothenfusser,
Caroline C. Friedel, Peter Duewell, Max Schnurr, Lars M. Koenig,
OAS1/RNase L executes RIG-I ligand–dependent tumor cell apoptosis, Science Immunology, Science Immunology, vol. 6, no. 61, 2021.
Caroline C. Friedel, Adam W. Whisnant, Lara Djakovic, Andrzej J. Rutkowski,
Marie-Sophie Friedl,
Michael Kluge, James C. Williamson, Somesh Sai, Ramon Oliveira Vidal, Sascha Sauer, Thomas Hennig, Arnhild Grothey, Andrea Milić, Bhupesh K. Prusty, Paul J. Lehner, Nicholas J. Matheson,
Florian Erhard, Lars Dölken,
Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level, Journal of Virology, American Society for Microbiology Journals, vol. 95, no. 3, 2021.
Yong Huang, Rut Tejero, Vivian K. Lee, Concetta Brusco, Theodore Hannah, Taylor B. Bertucci, Chrystian Junqueira Alves, Igor Katsyv,
Michael Kluge, Ramsey Foty, Bin Zhang,
Caroline C. Friedel, Guohao Dai, Hongyan Zou, Roland H. Friedel,
Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics, Communications Biology, Springer Science and Business Media LLC, vol. 4, no. 1, 2021.
Shalaka Wahane, Xianxiao Zhou, Xiang Zhou, Lei Guo,
Marie-Sophie Friedl,
Michael Kluge, Aarthi Ramakrishnan, Li Shen,
Caroline C. Friedel, Bin Zhang, Roland H. Friedel, Hongyan Zou,
Diversified transcriptional responses of myeloid and glial cells in spinal cord injury shaped by HDAC3 activity., Science advances, vol. 7, 2021.
Xiuye Wang, Liang Liu, Adam W. Whisnant, Thomas Hennig, Lara Djakovic, Nabila Haque, Cindy Bach, Rozanne M. Sandri-Goldin,
Florian Erhard,
Caroline C. Friedel, Lars Dölken, Yongsheng Shi,
Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation., PLoS genetics, vol. 17, pp. e1009263, 2021.
Amelie S. Lotz-Havla, Mathias Woidy, Philipp Guder,
Caroline C. Friedel, Julian M. Klingbeil, Ana-Maria Bulau, Anja Schultze, Ilona Dahmen, Heidi Noll-Puchta, Stephan Kemp, Ralf Erdmann,
Ralf Zimmer, Ania C. Muntau, Sören W. Gersting,
iBRET Screen of the ABCD1 Peroxisomal Network and Mutation-Induced Network Perturbations., Journal of proteome research, vol. 20, pp. 4366–4380, 2021.
2020
Papers
Xiuye Wang, Thomas Hennig, Adam W. Whisnant,
Florian Erhard, Bhupesh K. Prusty,
Caroline C. Friedel, Elmira Forouzmand, William K. Hu, Luke Erber, Yue Chen, Rozanne M. Sandri-Goldin, Lars Dölken, Yongsheng Shi,
Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27, Nature Communications, vol. 11, 2020.
Michael Kluge,
Marie-Sophie Friedl, Amrei L Menzel,
Caroline C. Friedel,
Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution, GigaScience, vol. 9, no. 6, 2020.
Xiang and Wahane Shalaka and Friedl Marie-Sophie and Kluge Michael and Friedel Caroline C. and Avrampou Kleopatra and Zachariou Venetia and Guo Lei and Zhang Bin and He Xijing and Friedel Roland H. and Zou Hongyan Zhou,
Microglia and macrophages promote corralling, wound compaction and recovery after spinal cord injury via Plexin-B2, Nature Neuroscience, vol. 23, no. 3, pp. 337-350, 2020.
Adam W. Whisnant, Christopher S. Jürges, Thomas Hennig, Emanuel Wyler, Bhupesh Prusty, Andrzej J. Rutkowski, Anne L'hernault, Lara Djakovic, Margarete Göbel, Kristina Döring, Jennifer Menegatti, Robin Antrobus, Nicholas J. Matheson, Florian W. H. Künzig, Guido Mastrobuoni, Chris Bielow, Stefan Kempa, Chunguang Liang, Thomas Dandekar,
Ralf Zimmer, Markus Landthaler, Friedrich Grässer, Paul J. Lehner,
Caroline C. Friedel,
Florian Erhard, Lars Dölken,
Integrative functional genomics decodes herpes simplex virus 1., Nature communications, vol. 11, pp. 2038, 2020.
2019
Papers
Anil Paul Chirackal Manavalan, Kveta Pilarova,
Michael Kluge, Koen Bartholomeeusen, Michal Rajecky, Jan Oppelt, Prashant Khirsariya, Kamil Paruch, Lumir Krejci,
Caroline C. Friedel, Dalibor Blazek,
CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes, EMBO reports, pp. e47592, 2019.
Philipp Metzger, Sabrina V. Kirchleitner,
Michael Kluge, Lars M. Koenig, Christine Hörth, Carlotta A. Rambuscheck, Daniel Böhmer, Julia Ahlfeld, Sebastian Kobold,
Caroline C. Friedel, Stefan Endres, Max Schnurr, Peter Duewell,
Immunostimulatory RNA leads to functional reprogramming of myeloid-derived suppressor cells in pancreatic cancer, Journal for ImmunoTherapy of Cancer, vol. 7, no. 1, pp. 288, 2019.
Matthias von Gamm, Annalisa Schaub, Alisha N. Jones, Christine Wolf, Gesine Behrens, Johannes Lichti, Katharina Essig, Anna Macht, Joachim Pircher, Andreas Ehrlich, Kathrin Davari, Dhruv Chauhan, Benjamin Busch, Wolfgang Wurst, Regina Feederle, Annette Feuchtinger, Matthias H. Tschöp,
Caroline C. Friedel, Stefanie M. Hauck, Michael Sattler, Arie Geerlof, Veit Hornung, Vigo Heissmeyer, Christian Schulz, Mathias Heikenwalder, Elke Glasmacher,
Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3, Journal of Experimental Medicine, Rockefeller University Press, 2019.
Michaela Rohrmoser,
Michael Kluge, Yousra Yahia, Anita Gruber-Eber, Muhammad Ahmad Maqbool, Ignasi Forné, Stefan Krebs, Helmut Blum, Ann Katrin Greifenberg, Matthias Geyer, Nicolas Descostes, Axel Imhof, Jean-Christophe Andrau,
Caroline C. Friedel, Dirk Eick,
MIR sequences recruit zinc finger protein ZNF768 to expressed genes, Nucleic Acids Research, vol. 47, no. 2, pp. 700-715, 2019.
Andrii Bugai, Alexandre J C Quaresma,
Caroline C. Friedel, Tina Lenasi, Robert Düster, Christopher R Sibley, Koh Fujinaga, Petra Kukanja, Thomas Hennig, Melanie Blasius, Matthias Geyer, Jernej Ule, Lars Dölken, Matjaž Barborič,
P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress, Molecular cell, vol. 74, no. 2, pp. 254-267, 2019.
Christina Funk, Verena Raschbichler, Diana Lieber, Jens Wetschky, Eileen K Arnold, Jacqueline Leimser, Michael Biggel,
Caroline C. Friedel, Zsolt Ruzsics, Susanne M Bailer,
Comprehensive analysis of nuclear export of herpes simplex virus type 1 tegument proteins and their Epstein-Barr virus orthologs, Traffic (Copenhagen, Denmark), vol. 20, pp. 152–167, 2019.
Rut Tejero, Yong Huang, Igor Katsyv,
Michael Kluge, Jung-Yi Lin, Jessica Tome-Garcia, Nicolas Daviaud, Yuanshuo Wang, Bin Zhang, Nadejda M Tsankova,
Caroline C. Friedel, Hongyan Zou, Roland H Friedel,
Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment, EBioMedicine, vol. 42, pp. 252-269, 2019.
2018
Papers
Kathrin Davari, Johannes Lichti,
Caroline C. Friedel, Elke Glasmacher,
Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation, J Vis Exp., vol. 133, no. e56752, 2018.
Thomas Hennig, Marco Michalski, Andrzej J. Rutkowski, Lara Djakovic, Adam W. Whisnant,
Marie-Sophie Friedl, Bhaskar Anand Jha, Marisa A. P. Baptista, Anne L’Hernault,
Florian Erhard, Lars Dölken,
Caroline C. Friedel,
HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes, PLOS Pathogens, Public Library of Science, vol. 14, no. 3, pp. 1-27, 2018.
Michael and Friedel Caroline C. Kluge,
Watchdog - a workflow management system for the distributed analysis of large-scale experimental data, BMC Bioinformatics, vol. 19, no. 97, 2018.
2017
Papers
Tim-Michael Decker,
Michael Kluge, Stefan Krebs, Nilay Shah, Helmut Blum,
Caroline C. Friedel, Dirk Eick,
Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1, Scientific Reports, 2017.
Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, Henriette Uhlenhaut, Matthias Heinig,
Caroline C. Friedel, Elke Glasmacher,
Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing and Translation Events during T Cell Responses, Cell Reports, vol. 19, no. 3, pp. 643–654, 2017.
Thomas Bonfert,
Caroline C. Friedel,
Prediction of Poly(A) Sites by Poly(A) Read Mapping, PLOS ONE, vol. 12, no. 1, pp. 1-32, 2017.
Emanuel and Menegatti Jennifer and Franke Vedran and Kocks Christine and Boltengagen Anastasiya and Hennig Thomas and Theil Kathrin and Rutkowski Andrzej and Ferrai Carmelo and Baer Laura and Kermas Lisa and Friedel Caroline and Rajewsky Nikolaus and Akalin Altuna and Dölken Lars and Grässer Friedrich and Landthaler Markus Wyler,
Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection, Genome Biology, vol. 18, no. 1, pp. 209, 2017.
2016
Papers
Jian-Nan Zhang, Uwe Michel, Christof Lenz,
Caroline C. Friedel, Sarah Köster, Zara d’Hedouville, Lars Tönges, Henning Urlaub, Mathias Bähr, Paul Lingor, Jan C. Koch,
Calpain-mediated cleavage of collapsin response mediator protein-2 drives acute axonal degeneration, Scientific Reports, vol. 6, pp. 37050, 2016.
2015
Papers
Andrzej J. Rutkowski,
Florian Erhard, Anne L’Hernault,
Thomas Bonfert, Markus Schilhabel, Colin Crump, Philip Rosenstiel, Stacey Efstathiou,
Ralf Zimmer,
Caroline C. Friedel, Lars Dölken,
Wide-spread disruption of host transcription termination in HSV-1 infection, Nature Communications, vol. 6, no. 7126, 2015.
Thomas Bonfert, Evelyn Kirner,
Gergely Csaba,
Ralf Zimmer,
Caroline C. Friedel,
ContextMap 2: fast and accurate context-based RNA-seq mapping., BMC bioinformatics, vol. 16, pp. 122, 2015.
Andreas Osterman, Thorsten Stellberger, Anna Gebhardt, Marisa Kurz,
Caroline C. Friedel, Peter Uetz, Hans Nitschko, Armin Baiker, Maria G. Vizoso-Pinto,
The Hepatitis E virus intraviral interactome, Scientific reports, vol. 5, pp. 13872, 2015.
Yasuhiro Murakawa, Michael Hinz, Janina Mothes, Anja Schuetz, Michael Uhl, Emanuel Wyler, Tomoharu Yasuda, Guido Mastrobuoni,
Caroline C. Friedel, Lars Dölken, Stefan Kempa, Marc Schmidt-Supprian, Nils Blüthgen, Rolf Backofen, Udo Heinemann, Jana Wolf, Claus Scheidereit, Markus Landthaler,
RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway., Nature communications, vol. 6, pp. 7367, 2015.
Sabine Hünten, Markus Kaller, Friedel Drepper, Silke Oeljeklaus,
Thomas Bonfert,
Florian Erhard, Anne Dueck, Norbert Eichner,
Caroline C. Friedel, Gunter Meister,
Ralf Zimmer, Bettina Warscheid, Heiko Hermeking,
p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses., Molecular & cellular proteomics : MCP, 2015.
2014
Papers
Caroline C. Friedel,
Treatment of Noise and Artifacts in Affymetrix Arrays, Microarray Image and Data Analysis: Theory and Practice (Luis Rueda, ed.), CRC Press, pp. 251-276, 2014.
Theses
Caroline C. Friedel,
Bioinformatics methods for the biological interpretation of high-throughput experiments, Habilitation, Ludwig-Maximilians-Universität München, 2014.
2013
Papers
Bernd Rädle, Andrzej Rutkoswki, Zsolt Ruzsics,
Caroline C. Friedel, Ulrich H Koszinowski, Lars Dölken,
Metabolic labeling of newly transcribed RNA for high resolution gene expression profiling of RNA synthesis, processing and decay in cell culture, J. Vis. Exp., vol. 78, pp. e50195, 2013.
Samantha J. Griffiths, Manfred Koegl, Chris Boutell, Helen L. Zenner, Colin Crump,
Orland Gonzalez,
Caroline C. Friedel, Gerald Barry, Kimberley Martin, Marie H. Craigon, Rui Chen, Lakshmi N. Kaza, Even Fossum, John K. Fazakerley, Stacey Efstathiou,
Ralf Zimmer, Peter Ghazal, Jürgen Haas,
A systematic analysis of host factors reveals a Med23-interferon-lambda regulatory axis against Herpes simplex virus Type 1 replication, PLoS Pathogens, vol. 9, no. 8, pp. e1003514, 2013.
Mirko Trilling, Nicolas Bellora, Andrzej J. Rutkowski, Miranda de Graaf, Paul Dickinson, Kevin Robertson, Olivia Prazeres da Costa, Peter Ghazal,
Caroline C. Friedel, M. Mar Alba, Lars Dölken,
Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis, Nucleic Acids Research, 2013.
Roland H. Friedel,
Caroline C. Friedel,
Thomas Bonfert, Roland Rad, Philippe Soriano,
Clonal expansion of transposon insertions identifies candidate cancer genes in a PiggyBac mutagenesis screen, PLoS ONE, vol. 8, no. 8, pp. e72338, 2013.
Kaspar Burger, Bastian Mühl, Markus Kellner, Michaela Rohrmoser, Anita Gruber-Eber,
Lukas Windhager,
Caroline C. Friedel, Lars Dölken, Dirk Eick,
4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response, RNA biology, vol. 10, 2013.
Caroline C. Friedel,
Computational analysis of virus-host interactomes, Methods in molecular biology, vol. 1064, pp. 115-30, 2013.
Herbert B. Schiller, Michaela-Rosemarie Hermann, Julien Polleux, Timothée Vignaud, Sara Zanivan,
Caroline C. Friedel, Zhiqi Sun, Aurelia Raducanu, Kay-E Gottschalk, Manuel Théry, Matthias Mann, Reinhard Fässler,
β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments, Nature cell biology, vol. 15, pp. 625-36, 2013.
Thomas Bonfert,
Gergely Csaba,
Ralf Zimmer,
Caroline C. Friedel,
Mining RNA-Seq Data for Infections and Contaminations, PloS one, vol. 8, pp. e73071, 2013.
2012
Papers
Tobias Petri,
Evi Berchtold,
Ralf Zimmer,
Caroline C. Friedel,
Detection and correction of probe-level artefacts on microarrays, BMC Bioinformatics, vol. 13, pp. 114, 2012.
Thomas Bonfert,
Gergely Csaba,
Ralf Zimmer,
Caroline C. Friedel,
A context-based approach to identify the most likely mapping for RNA-seq experiments, BMC Bioinformatics, vol. 13(Suppl 6), pp. S9, 2012.
Robert Lindner,
Caroline C. Friedel,
A comprehensive evaluation of alignment algorithms in the context of RNA-Seq, PLoS ONE, vol. 7, no. 12, pp. e52403, 2012.
Lisa Marcinowski, Michael Lidschreiber,
Lukas Windhager, Martina Rieder, Jens B. Bosse, Bernd Rädle,
Thomas Bonfert, Ildiko Györy, Miranda de Graaf, Olivia Prazeres da Costa, Philip Rosenstiel,
Caroline C. Friedel,
Ralf Zimmer, Zsolt Ruzsics, Lars Dölken,
Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection, PLoS Pathog, vol. 8, no. 9, pp. e1002908, 2012.
Milan Spasic,
Caroline C. Friedel, Johanna Schott, Jochen Kreth, Kathrin Leppek, Sarah Hofmann, Sevim Ozgur, Georg Stoecklin,
Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm, PLoS Genet, vol. 8, no. 1, pp. e1002433, 2012.
Lukas Windhager,
Thomas Bonfert, Kaspar Burger, Zsolt Ruzsics, Stefan Krebs, Stefanie Kaufmann, Georg Malterer, Anne L’Hernault, Markus Schilhabel, Stefan Schreiber, Philip Rosenstiel,
Ralf Zimmer, Dirk Eick,
Caroline C. Friedel, Lars Dölken,
Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution., Genome research, vol. 22, pp. 2031-42, 2012.
2011
Papers
Caroline C. Friedel, Jürgen Haas,
Virus-host interactomes and global models of virus-infected cells, Trends in Microbiology, vol. 19, no. 10, pp. 501-8, 2011.
Herbert B. Schiller,
Caroline C. Friedel, Cyril Boulegue, Reinhard Fässler,
Quantitative proteomics of the integrin adhesome reveals a myosin II-dependent recruitment of LIM domain proteins, EMBO Reports, vol. 12, no. 3, pp. 259-66, 2011.
Susanne Pfefferle, Julia Schöpf, Manfred Kögl,
Caroline C. Friedel, Marcel A. Müller, Javier Carbajo-Lozoya, Thorsten Stellberger, Ekatarina von Dall’Armi, Petra Herzog, Stefan Kallies, Daniela Niemeyer, Vanessa Ditt, Thomas Kuri, Roland Züst, Ksenia Pumpor, Rolf Hilgenfeld, Frank Schwarz,
Ralf Zimmer, Imke Steffen, Friedemann Weber, Volker Thiel, Georg Herrler, Heinz-Jürgen Thiel, Christel Schwegmann-Weßels, Stefan Pöhlmann, Jürgen Haas, Christian Drosten, Albrecht von Brunn,
The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors, PLoS Pathog, vol. 7, no. 10, pp. e1002331, 2011.
2010
Papers
Florian Erhard,
Caroline C. Friedel,
Ralf Zimmer,
FERN - Stochastic Simulation and Evaluation of Reaction Networks, Systems Biology for Signaling Networks (Sangdun Choi, ed.), Springer, vol. 1, Part 4, pp. 751-775, 2010.
Caroline C. Friedel,
Analysis of High-throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life, Ausgezeichnete Informatikdissertationen 2009, GI-Edition Lecture Notes in Informatics, 2010.
Lars Dölken, Georg Malterer,
Florian Erhard, Sheila Kothe,
Caroline C. Friedel, Guillaume Suffert, Lisa Marcinowski, Natalie Motsch, Stephanie Barth, Michaela Beizinger, Diana Lieber, Susanne M. Bailer, Reinhard Hoffmann, Zsolt Ruzsics, Elisabeth Kremmer, Sebastien Pfeffer,
Ralf Zimmer, Ulrich H Koszinowski, Friedrich Grässer, Gunter Meister, Jürgen Haas,
Systemic Analysis of Viral and Cellular miRNA Targets in Cells Latently Infected with Human gamma-Herpesviruses through RISC Immunoprecipitation Assays, Cell Host & Microbe, vol. 7, no. 4, pp. 324-334, 2010.
Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken,
Ralf Zimmer,
HALO - A Java framework for precise transcript half-life determination, Bioinformatics, vol. 26, no. 9, pp. 1264-1266, 2010.
2009
Papers
Caroline C. Friedel, Jan Krumsiek,
Ralf Zimmer,
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast, Journal of Computational Biology, vol. 16, no. 8, pp. 1-17, 2009.
Fabian Birzele,
Gergely Csaba,
Florian Erhard,
Caroline C. Friedel,
R Küffner,
Tobias Petri,
Lukas Windhager,
Ralf Zimmer,
Algorithmische Systembiologie mit Petrinetzen – Von qualitativen zu quantitativen Systemmodellen, Informatik-Spektrum, vol. 32, no. 4, pp. 310-319, 2009.
Caroline C. Friedel,
Ralf Zimmer,
Identifying the topology of protein complexes from affinity purification assays, Bioinformatics, vol. 25, no. 16, pp. 2140-2146, 2009.
Caroline C. Friedel, Lars Dölken, Zsolt Ruzsics, Ulrich Koszinowski,
Ralf Zimmer,
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life, Nucleic Acids Research, vol. 37, no. 17, pp. e115, 2009.
Even Fossum,
Caroline C. Friedel, Seesandra V. Rajagopala, Björn Titz, Armin Baiker, Tina Schmidt, Theo Kraus, Thorsten Stellberger, Christiane Rutenberg, Silpa Suthram, Sourav Bandyopadhyay, Dietlind Rose, Albrecht von Brunn, Mareike Uhlmann, Christine Zeretzke,
Yu-An Dong, Hélène Boulet, Manfred Koegl, Susanne M. Bailer, Ulrich Koszinowski, Trey Ideker, Peter Uetz,
Ralf Zimmer, Jürgen Haas,
Evolutionarily conserved herpesviral protein interaction networks., PLoS Pathog, vol. 5, no. 9, pp. e1000570, 2009.
Caroline C. Friedel, Lars Dölken,
Metabolic tagging and purification of nascent RNA: Implications for transcriptomics, Molecular BioSystems, vol. 5, no. 11, pp. 1271-8, 2009.
Theses
Caroline C. Friedel,
Analysis of High-Throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life, PhD Thesis, LMU München, 2009.
2008
Papers
Florian Erhard,
Caroline C. Friedel,
Ralf Zimmer,
FERN - a Java framework for stochastic simulation and evaluation of reaction networks, BMC Bioinformatics, vol. 9, no. 1, pp. 356, 2008.
Caroline C. Friedel, Jan Krumsiek,
Ralf Zimmer,
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast, Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2008 (Sorin Istrail, Pavel Pevzner, Michael Waterman, eds.), Springer, vol. 4955, Singapore, March 30 - April 2, 2008, pp. 3-16, 2008.
Caroline C. Friedel,
Ralf Zimmer,
Identifying the topology of protein complexes from affinity purification assays, Proceedings of the German Conference on Bioinformatics (GCB 2008), GI, vol. P-136, September 9-12, 2008, Dresden, Germany, pp. 30-43, 2008.
Lars Dölken, Zsolt Ruzsics, Bernd Rädle,
Caroline C. Friedel,
Ralf Zimmer, Jörg Mages, Reinhard Hoffmann, Paul Dickinson, Thorsten Forster, Peter Ghazal, Ulrich H Koszinowski,
High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay, RNA, vol. 14, no. 9, pp. 1959–1972, 2008.
Jan Krumsiek,
Caroline C. Friedel,
Ralf Zimmer,
ProCope–protein complex prediction and evaluation, Bioinformatics, vol. 24, no. 18, pp. 2115–2116, 2008.
2007
Papers
Albrecht von Brunn, Carola Teepe, Jeremy C. Simpson, Rainer Pepperkok,
Caroline C. Friedel,
Ralf Zimmer, Rhonda Roberts, Jürgen Haas,
Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome, PLoS ONE, vol. 2, no. 5, pp. e459, 2007.
Caroline C. Friedel,
Ralf Zimmer,
Influence of degree correlations on network structure and stability in protein-protein interaction networks, BMC Bioinformatics, vol. 8, pp. 297, 2007.
2006
Papers
Chad A. Davis, Fabian Gerick, Volker Hintermair,
Caroline C. Friedel,
Katrin Fundel,
R Küffner,
Ralf Zimmer,
Reliable gene signatures for microarray classification: assessment of stability and performance, Bioinformatics, vol. 22, no. 19, pp. 2356-2363, 2006.
Caroline C. Friedel,
Ralf Zimmer,
Toward the complete interactome, Nat Biotechnol, vol. 24, no. 6, pp. 614-615, 2006.
Caroline C. Friedel,
Ralf Zimmer,
Inferring topology from clustering coefficients in protein-protein interaction networks, BMC Bioinformatics, vol. 7, pp. 519, 2006.
2005
Papers
Caroline C. Friedel, Katharina H.V. Jahn, Selina Sommer, Stephen Rudd, Hans W. Mewes, Igor V. Tetko,
Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage, Bioinfomatics, vol. 21, no. 8, pp. 1383-1388, 2005.
Theses
Caroline C. Friedel,
On Abstaining Classifiers, Master Thesis, TU München, 2005.
2003
Theses
Caroline C. Friedel,
Automatische Generierung und Verbesserung von Synonymlisten und Entwicklung eines geeigneten Benchmarksystems, Bachelor Thesis, LMU München, 2003.
