Publications

BioDataAnalysis founder Mario Emmenlauer has been actively involved in High Content Screening research and analysis since 2010 through his engagement in the consortia InfectX and TargetInfectX. As a result of this work, there are a number of publications that make use of image analysis research and methods that lead to the development of BioDataAnalysis CellAnalyzer.

2017
Riba, Andrea; Emmenlauer, Mario; Chen, Amy; Sigoillot, Frederic; Cong, Feng; Dehio, Christoph; Jenkins, Jeremy; Zavolan, Mihaela (2017). Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results. Cell systems, 4(2), 182-193.e4.
Milivojevic, Milica; Dangeard, Anne-Sophie; Kasper, Christoph Alexander; Tschon, Therese; Emmenlauer, Mario; Pique, Claudine; Schnupf, Pamela; Guignot, Julie; Arrieumerlou, Cecile (2017). ALPK1 controls TIFA/TRAF6-dependent innate immunity against heptose-1,7-bisphosphate of gram-negative bacteria.. PLoS Pathog, 13(2):e1006224.
2016
Andritschke, Daniel; Dilling, Sabrina; Emmenlauer, Mario; Welz, Tobias; Schmich, Fabian; Misselwitz, Benjamin; Rämö, Pauli; Rottner, Klemens; Kerkhoff, Eugen; Wada, Teiji; Penninger, Josef M; Beerenwinkel, Niko; Horvath, Peter; Dehio, Christoph; Hardt, Wolf-Dietrich (2016). A Genome-Wide siRNA Screen Implicates Spire1/2 in SipA-Driven Salmonella Typhimurium Host Cell Invasion. PloS one, 11(9), e0161965.
Casanova, Alain; Low, Shyan H; Emmenlauer, Mario; Conde-Alvarez, Raquel; Salcedo, Suzana P; Gorvel, Jean-Pierre; Dehio, Christoph (2016). Microscopy-based Assays for High-throughput Screening of Host Factors Involved in Brucella Infection of Hela Cells. Journal of visualized experiments : JoVE, (114), e54263.
2015
Kreibich, Saskia; Emmenlauer, Mario; Fredlund, Jennifer; Rämö, Pauli; Münz, Christian; Dehio, Christoph; Enninga, Jost; Hardt, Wolf-Dietrich (2015). Autophagy Proteins Promote Repair of Endosomal Membranes Damaged by the Salmonella Type Three Secretion System 1. Cell host & microbe, 18(5), 527-37.
Schmich, Fabian; Szczurek, Ewa; Kreibich, Saskia; Dilling, Sabrina; Andritschke, Daniel; Casanova, Alain; Low, Shyan Huey; Eicher, Simone; Muntwiler, Simone; Emmenlauer, Mario; Rämo, Pauli; Conde-Alvarez, Raquel; von Mering, Christian; Hardt, Wolf-Dietrich; Dehio, Christoph; Beerenwinkel, Niko (2015). Erratum to: gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens. Genome biology, 16, 233.
Schmich, Fabian; Szczurek, Ewa; Kreibich, Saskia; Dilling, Sabrina; Andritschke, Daniel; Casanova, Alain; Low, Shyan Huey; Eicher, Simone; Muntwiler, Simone; Emmenlauer, Mario; Rämö, Pauli; Conde-Alvarez, Raquel; von Mering, Christian; Hardt, Wolf-Dietrich; Dehio, Christoph; Beerenwinkel, Niko (2015). gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens. Genome biology, 16, 220.
Siebourg-Polster, Juliane; Mudrak, Daria; Emmenlauer, Mario; Rämö, Pauli; Dehio, Christoph; Greber, Urs; Fröhlich, Holger; Beerenwinkel, Niko (2015). NEMix: single-cell nested effects models for probabilistic pathway stimulation. PLoS computational biology, 11(4), e1004078.
Kühbacher, Andreas; Emmenlauer, Mario; Rämo, Pauli; Kafai, Natasha; Dehio, Christoph; Cossart, Pascale; Pizarro-Cerdá, Javier (2015). Genome-Wide siRNA Screen Identifies Complementary Signaling Pathways Involved in Listeria Infection and Reveals Different Actin Nucleation Mechanisms during Listeria Cell Invasion and Actin Comet Tail Formation. mBio, 6(3), e00598-15.
2014
Franceschini, Andrea; Meier, Roger; Casanova, Alain; Kreibich, Saskia; Daga, Neha; Andritschke, Daniel; Dilling, Sabrina; Rämö, Pauli; Emmenlauer, Mario; Kaufmann, Andreas; Conde-Álvarez, Raquel; Low, Shyan Huey; Pelkmans, Lucas; Helenius, Ari; Hardt, Wolf-Dietrich; Dehio, Christoph; von Mering, Christian (2014). Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proceedings of the National Academy of Sciences of the United States of America, 111(12), 4548-53.
Rämö, P; Drewek, A; Arrieumerlou, C; Beerenwinkel, N; Ben-Tekaya, H; Bühlmann, P; Cardel, B; Casanova, A; Conde-Alvarez, R; Cossart, P; Csúcs, G; Eicher, S; Emmenlauer, M; Greber, U; Hardt, W-D; Helenius, A; Kasper, C; Kaufmann. A; Kreibich, S; Kühbacher, A; Kunszt, P.; Low, SH; Mercer, J; Mudrak, D; Muntwiler, S; Pelkmans, L; Pizarro-Cerdá, J; Podvinec, M; Pujadas, E; Rinn, B; Rouilly, V; Schmich, F; Siebourg, J; Snijder, B; Stebler, M; Studer, G; Szczurek, E; Truttmann, M; von Mering, C; Vonderheit, A; Yakimovich, A; Dehio, C (2014). Simultaneous analysis of large-scale RNAi screens for pathogen entry. BMC Genomics, 15, 1162.
2013
Farhan, Muhammad; Ruusuvuori, Pekka; Emmenlauer, Mario; Rämö, Pauli; Dehio, Christoph; Yli-Harja, Olli (2013). Multi-scale Gaussian representation and outline-learning based cell image segmentation. BMC Bioinformatics, 14 Suppl 10, S6.