Publications

Bernd Fischer, Thomas Sandmann, Thomas Horn, Maximilian Billmann, Varun Chaudhary, Wolfgang Huber, Michael Boutros. A map of directional genetic interactions in a metazoan cell. eLife, e05464, 2015, doi:10.7554/eLife.05464

Anton Khmelinskii, Ewa Blaszczak, Marina Pantazopoulou, Bernd Fischer, Deike J Omnus, Gaëlle Le Dez, Audrey Brossard, Alexander Gunnarsson, Joseph D Barry, Matthias Meurer, Daniel Kirrmaier, Charles Boone, Wolfgang Huber, Gwenaël Rabut, Per O Ljungdahl, Michael Knop. Protein quality control at the inner nuclear membrane. Nature, 516(7513):410-413, 2014.

Christina Laufer, Bernd Fischer, Wolfgang Huber, and Michael Boutros. Measuring genetic interactions in human cells by RNAi and imaging. Nature Protocols, 9(10):2341–2353, 2014.

Paul Theodor Pyl, Julian Gehring, Bernd Fischer, and Wolfgang Huber. h5vc: Scalable nucleotide tallies with hdf5. Bioinformatics, 30(10):1464–1466, 2014.

S Chul Kwon, Hyerim Yi, Katrin Eichelbaum, Sophia Föhr, Bernd Fischer, Kwon Tae You, Alfredo Castello, Jeroen Krijgsveld, Matthias W Hentze, and V Narry Kim. The RNA-binding protein repertoire of embryonic stem cells. Nature structural & molecular biology, 20(9):1122–1130, 2013.

Christoph Sommer, Michael Held, Bernd Fischer, Wolfgang Huber, and Daniel W Gerlich. Cellh5: a format for data exchange in high-content screening. Bioinformatics, 29(12):1580–1582, 2013.

Alfredo Castello, Bernd Fischer, Matthias W Hentze, and Thomas Preiss. RNA-binding proteins in mendelian disease. Trends in Genetics, 29(5):318–327, 2013.

Satoshi Okawa, Bernd Fischer, and Jeroen Krijgsveld. Properties of isotope patterns and their utility for peptide identification in large-scale proteomic experiments. Rapid Communications in Mass Spectrometry, 27(9):1067–1075, 2013.

Christina Laufer, Bernd Fischer, Maximilian Billmann, Wolfgang Huber, and Michael Boutros. Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping. Nature methods, 10(5):427–431, 2013.

Alfredo Castello, Rastislav Horos, Claudia Strein, Bernd Fischer, Katrin Eichelbaum, Lars M Steinmetz, Jeroen Krijgsveld, and Matthias W ?Hentze. System-wide identification of RNA-binding proteins by interactome capture. Nature protocols, 8(3):491–500, 2013.

Matthew C Chambers, Brendan Maclean, Robert Burke, Dario Amodei, Daniel L Ruderman, Steffen Neumann, Laurent Gatto, Bernd Fischer, Brian Pratt, Jarrett Egertson, et al. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology, 30(10):918– 920, 2012.

Alfredo Castello, Bernd Fischer, Katrin Eichelbaum, Rastislav Horos, Benedikt M Beckmann, Claudia Strein, Norman E Davey, David T Humphreys, Thomas Preiss, Lars M Steinmetz, et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell, 149(6):1393–1406, 2012.

Elin Axelsson, Thomas Sandmann, Thomas Horn, Michael Boutros, Wolfgang Huber, and Bernd Fischer. Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi. BMC bioinformatics, 12(1):342, 2011.

Thomas Horn, Thomas Sandmann, Bernd Fischer, Elin Axelsson, Wolfgang Huber, and Michael Boutros. Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nature methods, 8(4):341–346, 2011.

Verena Kaynig, Bernd Fischer, Elisabeth Müller, and Joachim M Buhmann. Fully automatic stitching and distortion correction of transmission electron microscope images. Journal of structural biology, 171(2):163–173, 2010.

Michael Held, Michael HA Schmitz, Bernd Fischer, Thomas Walter, Beate Neumann, Michael H Olma, Matthias Peter, Jan Ellenberg, and Daniel W Gerlich. Cellcognition: time-resolved phenotype annotation in high-throughput live cell imaging. Nature methods, 7(9):747–754, 2010.

Bernd Fischer, Volker Roth, and Joachim M Buhmann. Adaptive bandwidth selection for biomarker discovery in mass spectrometry. Artificial Intelligence in Medicine, 45(2):207–214, 2009.

Rastislav Sramek, Bernd Fischer, Elias Vicari, and Peter Widmayer. Optimal transitions for targeted protein quantification: Best conditioned submatrix selection. Computing and Combinatorics, pages 287–296, 2009.

Jimmy K Eng, Bernd Fischer, Jonas Grossmann, and Michael J MacCoss. A fast sequest cross correlation algorithm. Journal of proteome research, 7(10):4598–4602, 2008.

Volker Roth and Bernd Fischer. The group-lasso for generalized linear models: uniqueness of solutions and efficient algorithms. International conference on Machine learning, pages 848–855. ACM, 2008.

Verena Kaynig, Bernd Fischer, and Joachim M Buhmann. Probabilistic image registration and anomaly detection by nonlinear warping. In Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on, pages 1–8. IEEE, 2008.

Bernd Fischer, Volker Roth, and Joachim Buhmann. Time-series alignment by non-negative multiple generalized canonical correlation analysis. BMC bioinformatics, 8(Suppl 10):S4, 2007.

Jonas Grossmann, Bernd Fischer, Katja Baerenfaller, Judith Owiti, Joachim M Buhmann, Wilhelm Gruissem, and Sacha Baginsky. A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments. Proteomics, 7(23):4245–4254, 2007.

Franz F Roos, Riko Jacob, Jonas Grossmann, Bernd Fischer, Joachim M Buhmann, Wilhelm Gruissem, Sacha Baginsky, and Peter Widmayer. Pepsplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra. Bioinformatics, 23(22):3016–3023, 2007.

Christian Sigg, Bernd Fischer, Björn Ommer, Volker Roth, and Joachim Buhmann. Nonnegative CCA for audiovisual source separation. In Machine Learning for Signal Processing, 2007 IEEE Workshop on, pages 253–258. IEEE, 2007.

Verena Kaynig, Bernd Fischer, Roger Wepf, and Joachim M Buhmann. Fully automatic registration of electron microscopy images ?with high and low resolution. Microscopy and Microanalysis, 13(S02):198–199, 2007.

Volker Roth and Bernd Fischer. Improved functional prediction of proteins by learning kernel combinations in multilabel settings. BMC bioinformatics, 8(Suppl 2):S12, 2007.

Volker Roth and Bernd Fischer. The kernelHMM: learning kernel combinations in structured output domains. In Pattern Recognition, pages 436–445. Springer Berlin Heidelberg, 2007.

Bernd Fischer, Volker Roth, and Joachim M Buhmann. Time-series alignment by non-negative multiple generalized canonical. Lecture Notes in Computer Science, 4578:505–511, 2007.

Bernd Fischer, Jonas Grossmann, Volker Roth, Wilhelm Gruissem, Sacha Baginsky, and Joachim M Buhmann. Semi-supervised LC/MS alignment for differential proteomics. Bioinformatics, 22(14):e132–e140, 2006.

Peter Wey, Bernd Fischer, Herbert Bay, and Joachim Buhmann. Dense stereo by triangular meshing and cross validation. Pattern Recognition, pages 708–717, 2006.

Hansruedi Peter, Bernd Fischer, and Joachim Buhmann. Probabilistic de novo peptide sequencing with doubly charged ions. Pattern Recognition, pages 424–433, 2006.

Bernd Fischer, Volker Roth, Franz Roos, Jonas Grossmann, Sacha Baginsky, Peter Widmayer, Wilhelm Gruissem, and Joachim M Buhmann. NovoHMM: a hidden Markov model for de novo peptide sequencing. Analytical chemistry, 77(22):7265–7273, 2005.

Bernd Fischer, Volker Roth, Joachim M Buhmann, Jonas Grossmann, Sacha Baginsky, Wilhelm Gruissem, Franz Roos, and Peter Widmayer. A hidden Markov model for de novo peptide sequencing. Neural Information Processing Systems, 17:457–464, 2005.

Bernd Fischer, Volker Roth, and Joachim M Buhmann. Clustering with the connectivity kernel. Advances in Neural Information Processing Systems, 16:89–96, 2004.

Bernd Fischer and Joachim M Buhmann. Bagging for path-based clustering. Pattern Analysis and Machine Intelligence, IEEE Transactions on, 25(11):1411–1415, 2003.

Bernd Fischer and Joachim M. Buhmann. Path-based clustering for grouping of smooth curves and texture segmentation. Pattern Analysis and Machine Intelligence, IEEE Transactions on, 25(4):513– 518, 2003.

Bernd Fischer and Joachim Buhmann. Data resampling for path based clustering. Pattern Recognition, pages 206–214, 2002.

Bernd Fischer, Thomas Zöller, and Joachim Buhmann. Path based pairwise data clustering with application to texture segmentation. Energy Minimization Methods in Computer Vision and Pattern Recognition, pages 235–250, 2001.

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