A comprehensive evaluation of alignment algorithms in the context of RNA-seq. by Robert Lindner, Caroline C Friedel

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Mining RNA-seq data for infections and contaminations. by Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C Friedel

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Clonal expansion analysis of transposon insertions by high-throughput sequencing identifies candidate cancer genes in a PiggyBac mutagenesis screen. by Roland H Friedel, Caroline C Friedel, Thomas Bonfert, Ruijin Shi, Roland Rad, Philippe Soriano

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Genome-wide assessment of AU-rich elements by the AREScore algorithm. by Milan Spasic, Caroline C Friedel, Johanna Schott, Jochen Kreth, Kathrin Leppek, Sarah Hofmann, Sevim Ozgur, Georg Stoecklin

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Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses by Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, N. Henriette Uhlenhaut, Matthias Heinig, Caroline C. Friedel, Elke Glasmacher

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HSV-1 and influenza infection induce linear and circular splicing of the long NEAT1 isoform by Marie-Sophie Friedl, Lara Djakovic, Michael Kluge, Thomas Hennig, Adam W. Whisnant, Simone Backes, Lars Dölken, Caroline C. Friedel

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Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. by Albrecht von Brunn, Carola Teepe, Jeremy C Simpson, Rainer Pepperkok, Caroline C Friedel, Ralf Zimmer, Rhonda Roberts, Ralph Baric, Jürgen Haas

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Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation. by 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

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Immunostimulatory RNA leads to functional reprogramming of myeloid-derived suppressor cells in pancreatic cancer by 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

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Correction to: Immunostimulatory RNA leads to functional reprogramming of myeloid-derived suppressor cells in pancreatic cancer by 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

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Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironmentResearch in context by 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

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Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27 by Xiuye Wang, Thomas Hennig, Adam W. Whisnant, Florian Erhard, Bhupesh K. Prusty, Caroline C. Friedel, Elmira Forouzmand, William Hu, Luke Erber, Yue Chen, Rozanne M. Sandri-Goldin, Lars Dölken, Yongsheng Shi

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HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes. by 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

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The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes by Lara Djakovic, Thomas Hennig, Katharina Reinisch, Andrea Milić, 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

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Decoding murine cytomegalovirus. by 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

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Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection. by 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

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Evolutionarily conserved herpesviral protein interaction networks. by 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

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The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors. by 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

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Women in the European Virus Bioinformatics Center by Franziska Hufsky, Ana Abecasis, Patricia Agudelo-Romero, Magda Bletsa, Katherine Brown, Claudia Claus, Stefanie Deinhardt-Emmer, Li Deng, Caroline C. Friedel, María Inés Gismondi, Evangelia Georgia Kostaki, Denise Kühnert, Urmila Kulkarni-Kale, Karin J. Metzner, Irmtraud M. Meyer, Laura Miozzi, Luca Nishimura, Sofia Paraskevopoulou, Alba Pérez-Cataluña, Janina Rahlff, Emma Thomson, Charlotte Tumescheit, Lia van der Hoek, Lore Van Espen, Anne-Mieke Vandamme, Maryam Zaheri, Neta Zuckerman, Manja Marz

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