Our team is actively involved in image analysis and machine learning research, particularly in High Content Screening since 2010. 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 our current software solutions.
| 2019 |
| Casanova A, Low SH, Québatte M, Sedzicki J, Tschon T, Ketterer M, Smith K, Emmenlauer M, Ben-Tekaya H, Dehio C. (2019). A role for the VPS retromer in Brucella intracellular replication revealed by genomewide siRNA screening. mSphere 4: e00380-19 |
| Dirmeier, S., Emmenlauer, M., Dehio, C. et al. (2019). PyBDA: a command line tool for automated analysis of big biological data sets. BMC Bioinformatics 20, 564 |
| Michael Bauer, Justin W. Flatt, Daria Seiler, Bettina Cardel, Mario Emmenlauer, Karin Boucke, Maarit Suomalainen, Silvio Hemmi, Urs Greber (2019). The E3 Ubiquitin Ligase Mind Bomb 1 Controls Adenovirus Genome Release at the Nuclear Pore Complex. Cell Reports Volume 29, Issue 12 |
| Liu, Y., Mi, Y., Mueller, T. et al. (2019). Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nat Biotechnol 37, 314–322 |
| 2018 |
| Sumana Srivatsa, Jack Kuipers, Fabian Schmich, Simone Eicher, Mario Emmenlauer, Christoph Dehio, Niko Beerenwinkel (2018). Improved pathway reconstruction from RNA interference screens by exploiting off-target effects. Bioinformatics, Volume 34, Issue 13, 01 July 2018, Pages i519–i527 |
| Neha Daga, Simone Eicher, Abhilash Kannan, Alain Casanova, Shyan H Low, Saskia Kreibich, Daniel Andritschke, Mario Emmenlauer, Jeremy L Jenkins, Wolf-Dietrich Hardt, Urs Greber, Christoph Dehio, Christian von Mering (2018). Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition. Nucleic Acids Research, Volume 46, Issue 18, 12 October 2018, Pages 9309–9320 |
| Yansheng Liu, Yang Mi, Torsten Mueller, Saskia Kreibich, Evan G. Williams, Audrey Van Drogen, Christelle Borel, Pierre-Luc Germain, Max Frank, Isabell Bludau, Martin Mehnert, Michael Seifert, Mario Emmenlauer, Isabel Sorg, Fedor Bezrukov, Frederique Sloan Bena, Hu Zhou, Christoph Dehio, Giuseppe Testa, Julio Saez-Rodriguez, Stylianos E. Antonarakis, Wolf-Dietrich Hardt, Ruedi Aebersold (2018). Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results. bioRxiv |
| Kozak, K., Rinn, B., Leven, O., Emmenlauer, M. (2018). Strategies and Solutions to Maintain and Retain Data from High Content Imaging, Analysis, and Screening Assays. Johnston, P., Trask, O. (eds) High Content Screening. Methods in Molecular Biology, vol 1683. Humana Press, New York, NY. |
| 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. |