PublikationenPublications
Papers
Laura V. Glaser, Simone Rieger, Sybille Thumann, Cornelia Kuklik-Roos, Dietmar E Martin, Kerstin C. Maier, Marie L. Harth-Hertle, Björn Grüning, Rolf Backofen, Stefan Krebs, Helmut Blum, EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells, PLoS Pathogens, accepted.
, , Bettina Kempkes, Papers
Alexandra Schubö, Collecting SARS-CoV-2 Encoded miRNAs via Text Mining, Bioinformatics and Biomedical Engineering, Springer International Publishing, pp. 429–441, 2022.
, Markus Joppich, , Papers
Amelie S. Lotz-Havla, Mathias Woidy, Philipp Guder, iBRET Screen of the ABCD1 Peroxisomal Network and Mutation-Induced Network Perturbations., Journal of proteome research, vol. 20, pp. 4366–4380, 2021.
, Julian M. Klingbeil, Ana-Maria Bulau, Anja Schultze, Ilona Dahmen, Heidi Noll-Puchta, Stephan Kemp, Ralf Erdmann, , Ania C. Muntau, Sören W. Gersting, Xiuye Wang, Liang Liu, Adam W. Whisnant, Thomas Hennig, Lara Djakovic, Nabila Haque, Cindy Bach, Rozanne M. Sandri-Goldin, Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation., PLoS genetics, vol. 17, pp. e1009263, 2021.
, , Lars Dölken, Yongsheng Shi, Shalaka Wahane, Xianxiao Zhou, Xiang Zhou, Lei Guo, Diversified transcriptional responses of myeloid and glial cells in spinal cord injury shaped by HDAC3 activity., Science advances, vol. 7, 2021.
, , Aarthi Ramakrishnan, Li Shen, , Bin Zhang, Roland H. Friedel, Hongyan Zou, Yong Huang, Rut Tejero, Vivian K. Lee, Concetta Brusco, Theodore Hannah, Taylor B. Bertucci, Chrystian Junqueira Alves, Igor Katsyv, Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics, Communications Biology, Springer Science and Business Media LLC, vol. 4, no. 1, 2021.
, Ramsey Foty, Bin Zhang, , Guohao Dai, Hongyan Zou, Roland H. Friedel, 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.
, Adam W. Whisnant, Lara Djakovic, Andrzej J. Rutkowski, , , 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, , Lars Dölken, Daniel F. R. Boehmer, Simone Formisano, Carina C. de Oliveira Mann, Stephan A. Mueller, OAS1/RNase L executes RIG-I ligand–dependent tumor cell apoptosis, Science Immunology, Science Immunology, vol. 6, no. 61, 2021.
, Philipp Metzger, Meino Rohlfs, Christine Hörth, Lorenz Kocheise, Stefan F. Lichtenthaler, Karl-Peter Hopfner, Stefan Endres, Simon Rothenfusser, , Peter Duewell, Max Schnurr, Lars M. Koenig, Theses
Leonie Pohl, Integrative and Differential Analysis of Gene Expression and Alternative Splicing, Bachelor Thesis, LFE Bioinformatik, LMU München, 2021.
Alexandra Schubö, Analysis of miRNA-Mediated Virus-Host Interactions in SARS-CoV-2 Infections, Bachelor Thesis, LFE Bioinformatik, LMU München, 2021.
Franziska Koller, Analysis of the role of cis-elements for changes in RNA polymerase II pausing, Bachelor Thesis, LFE Bioinformatik, LMU München, 2021.
Papers
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, Integrative functional genomics decodes herpes simplex virus 1., Nature communications, vol. 11, pp. 2038, 2020.
, Markus Landthaler, Friedrich Grässer, Paul J. Lehner, , , Lars Dölken, Xiang Zhou, Shalaka Wahane, 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.
, , , Kleopatra Avrampou, Venetia Zachariou, Lei Guo, Bin Zhang, Xijing He, Roland H. Friedel, Hongyan Zou, Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution, GigaScience, vol. 9, no. 6, 2020.
, , Amrei L Menzel, , Joppich M, Olenchuk M, Mayer JM, Emslander Q, Jimenez-Soto LF, Zimmer R, SEQU-INTO: Early detection of impurities, contamination and off-targets (ICOs) in long read/MinION sequencing., Comput Struct Biotechnol J., vol. 18, pp. 1342-1351, 2020.
Xiuye Wang, Thomas Hennig, Adam W. Whisnant, Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27, Nature Communications, vol. 11, 2020.
, Bhupesh K. Prusty, , Elmira Forouzmand, William K. Hu, Luke Erber, Yue Chen, Rozanne M. Sandri-Goldin, Lars Dölken, Yongsheng Shi, Theses
Assessment of Differential Alternative Splicing Methods, Master Thesis, LFE Bioinformatik, LMU München, 2020.
, Robustness of Gene Set Enrichment or Dependence on Differential Expression Processing, Master Thesis, LFE Bioinformatik, LMU München, 2020.
, Papers
Rut Tejero, Yong Huang, Igor Katsyv, Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment, EBioMedicine, vol. 42, pp. 252-269, 2019.
, Jung-Yi Lin, Jessica Tome-Garcia, Nicolas Daviaud, Yuanshuo Wang, Bin Zhang, Nadejda M Tsankova, , Hongyan Zou, Roland H Friedel, Andrii Bugai, Alexandre J C Quaresma, P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress, Molecular cell, vol. 74, no. 2, pp. 254-267, 2019.
, Tina Lenasi, Robert Düster, Christopher R Sibley, Koh Fujinaga, Petra Kukanja, Thomas Hennig, Melanie Blasius, Matthias Geyer, Jernej Ule, Lars Dölken, Matjaž Barborič, Christina Funk, Verena Raschbichler, Diana Lieber, Jens Wetschky, Eileen K Arnold, Jacqueline Leimser, Michael Biggel, 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.
, Zsolt Ruzsics, Susanne M Bailer, Michaela Rohrmoser, MIR sequences recruit zinc finger protein ZNF768 to expressed genes, Nucleic Acids Research, vol. 47, no. 2, pp. 700-715, 2019.
, 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, , Dirk Eick, Comparison of six breast cancer classifiers using qPCR, Bioinformatics, 2019.
, Martina Vetter, Melanie Gündert, , Christine Fathke, Susanne E Ulbrich, Christoph Thomssen, , Eva J Kantelhardt, YESdb: integrative analysis of environmental stress in yeast, Database, vol. 2019, 2019.
, , , Moritz Mühlhofer, The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins, Cell Reports, vol. 29, no. 13, pp. 4593-4607, 2019.
, Christopher G Stratil, , Elena Kunold, Nina C. Bach, Stephan A. Sieber, Martin Haslbeck, , Johannes Buchner, 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, Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3, Journal of Experimental Medicine, Rockefeller University Press, 2019.
, Stefanie M. Hauck, Michael Sattler, Arie Geerlof, Veit Hornung, Vigo Heissmeyer, Christian Schulz, Mathias Heikenwalder, Elke Glasmacher, Constantin Ammar, Multi-Reference Spectral Library Yields Almost Complete Coverage of Heterogeneous LC-MS/MS Data Sets, Journal of Proteome Research, vol. 18, no. 4, pp. 1553-1566, 2019.
, , Andreas Schmidt, Axel Imhof, , Philipp Metzger, Sabrina V. Kirchleitner, 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.
, Lars M. Koenig, Christine Hörth, Carlotta A. Rambuscheck, Daniel Böhmer, Julia Ahlfeld, Sebastian Kobold, , Stefan Endres, Max Schnurr, Peter Duewell, Anil Paul Chirackal Manavalan, Kveta Pilarova, CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes, EMBO reports, pp. e47592, 2019.
, Koen Bartholomeeusen, Michal Rajecky, Jan Oppelt, Prashant Khirsariya, Kamil Paruch, Lumir Krejci, , Dalibor Blazek, Papers
Watchdog - a workflow management system for the distributed analysis of large-scale experimental data, BMC Bioinformatics, vol. 19, no. 97, 2018.
, , Thomas Hennig, Marco Michalski, Andrzej J. Rutkowski, Lara Djakovic, Adam W. Whisnant, 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.
, Bhaskar Anand Jha, Marisa A. P. Baptista, Anne L’Hernault, , Lars Dölken, , Kathrin Davari, Johannes Lichti, 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.
, Elke Glasmacher, Theses
Methods for Interactive analysis of Differential Alternative Splicing (MIDAS), Bachelor Thesis, LFE Bioinformatik, LMU München, 2018.
, Analysis of Predicted Mass Spectra and Peptide Identification, Bachelor Thesis, LFE Bioinformatik, LMU München, 2018.
, Methods for explaining biological systems and high-throughput data., PhD Thesis, LMU München, 2018.
, Papers
Emanuel Wyler, Jennifer Menegatti, Vedran Franke, Christine Kocks, Anastasiya Boltengagen, Thomas Hennig, Kathrin Theil, Andrzej Rutkowski, Carmelo Ferrai, Laura Baer, Lisa Kermas, Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection, Genome Biology, vol. 18, no. 1, pp. 209, 2017.
, Nikolaus Rajewsky, Altuna Akalin, Lars Dölken, Friedrich Grässer, Markus Landthaler, Maximilian Hastreiter, Tim Jeske, Jonathan Hoser, KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis, Bioinformatics, vol. 33, no. 10, pp. 1565-1567, 2017.
, Kaarin Ahomaa, , Sebastian J. Kopetzky, Jan-Dominik Quell, H.-Werner Mewes, , Prediction of Poly(A) Sites by Poly(A) Read Mapping, PLOS ONE, vol. 12, no. 1, pp. 1-32, 2017.
, , RelExplain—integrating data and networks to explain biological processes, Bioinformatics, vol. 33, no. 12, pp. 1837-1844, 2017.
, , , RelExplain—integrating data and networks to explain biological processes, Bioinformatics, vol. 33, no. 12, pp. 1837-1844, 2017.
, , , Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, Henriette Uhlenhaut, Matthias Heinig, 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.
, Elke Glasmacher, Matthias Barann, Manananggal - A Novel Viewer For Alternative Splicing Events, BMC Bioinformatics, vol. 18, pp. 120, 2017.
, , Tim-Michael Decker, Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1, Scientific Reports, 2017.
, Stefan Krebs, Nilay Shah, Helmut Blum, , Dirk Eick, Theses
Stefan Weber, Enhanced Suffix Arrays: Analysis of Efficient Implementations in Java, Master Thesis, LFE Bioinformatik, LMU München, 2017.
Expression data analysis and regulatory network inference by means of correlation patterns, PhD Thesis, LMU München, 2017.
, Papers
Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data, PLoS ONE, vol. 11, no. 10, 2016.
, , , Vinicius Henrique Silva, Luciana Correia Almeida Regitano, Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle, PLOS ONE, vol. 11, no. 6, pp. e0157711, 2016.
, Fábio Pértille, Poliana Fernanda Giachetto, Ricardo Augusto Brassaloti, Natália Silva Morosini, , Luiz Lehmann Coutinho, Patricia Schöppner, Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins, Journal of Molecular Biology, vol. 428, no. 8, pp. 1544-57, 2016.
, T Braun, M Daake, B Richter, Oliver F Lange, Martin Zacharias, , Martin Haslbeck, Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis, BMC Bioinformatics, vol. 17, pp. 45, 2016.
, , , Jian-Nan Zhang, Uwe Michel, Christof Lenz, Calpain-mediated cleavage of collapsin response mediator protein-2 drives acute axonal degeneration, Scientific Reports, vol. 6, pp. 37050, 2016.
, Sarah Köster, Zara d’Hedouville, Lars Tönges, Henning Urlaub, Mathias Bähr, Paul Lingor, Jan C. Koch, Cross-Species Conservation of Context-Specific Networks, BMC Systems Biology, vol. 10, no. 76, 2016.
, , Theses
Alexander Grün, Differential Splicing in TCGA Data, Master Thesis, LFE Bioinformatik, LMU, 2016.
Markus Gruber, Differential Analysis of Different Gene Products, Master Thesis, LFE Bioinformatik, LMU, 2016.
Marco Lombardi, Implementation and Evaluation of Algorithms for Approximate Tandem Repeats, Master Thesis, LFE Bioinformatik, LMU München, 2016.
Computing Hybridization Networks Using Agreement Forests, PhD Thesis, Ludwig-Maximilians-Universität München, 2016.
, Florian Hölzlwimmer, Network-based Analysis of Expression Time Series, Bachelor Thesis, LFE Bioinformatik, LMU, 2016.
Daniel Schmitz, Algorithmische Erzeugung von NGS-Panels sowie Berechnung von Allelfrequenzen in der molekulargenetischen Diagnostik, Bachelor Thesis, LFE Bioinformatik, LMU München, 2016.
, , Cross-Species Network and Transcript Transfer, PhD Thesis, Ludwig-Maximilians-Universität München, 2016.
, Papers
Addressing false discoveries in network inference, Bioinformatics, vol. 31, no. 17, pp. 2836-43, 2015.
, Stefan Altmann, , , , Computing all hybridization networks for multiple binary phylogenetic input trees, BMC Bioinformatics, vol. 16, no. 236, pp. 439-441, 2015.
, Andreas Osterman, Thorsten Stellberger, Anna Gebhardt, Marisa Kurz, The Hepatitis E virus intraviral interactome, Scientific reports, vol. 5, pp. 13872, 2015.
, Peter Uetz, Hans Nitschko, Armin Baiker, Maria G. Vizoso-Pinto, Yasuhiro Murakawa, Michael Hinz, Janina Mothes, Anja Schuetz, Michael Uhl, Emanuel Wyler, Tomoharu Yasuda, Guido Mastrobuoni, RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway., Nature communications, vol. 6, pp. 7367, 2015.
, Lars Dölken, Stefan Kempa, Marc Schmidt-Supprian, Nils Blüthgen, Rolf Backofen, Udo Heinemann, Jana Wolf, Claus Scheidereit, Markus Landthaler, Count ratio model reveals bias affecting NGS fold changes, Nucleic Acids Research, pp. pii: gkv696., 2015.
, , Sabine Hünten, Markus Kaller, Friedel Drepper, Silke Oeljeklaus, p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses., Molecular & cellular proteomics : MCP, 2015.
, , Anne Dueck, Norbert Eichner, , Gunter Meister, , Bettina Warscheid, Heiko Hermeking, Alternative splicing in next generation sequencing data of Saccharomyces Cerevisiae, PLoS ONE, 2015.
, , Martin Haslbeck, , ContextMap 2: fast and accurate context-based RNA-seq mapping., BMC bioinformatics, vol. 16, pp. 122, 2015.
, Evelyn Kirner, , , , Andrzej J. Rutkowski, Wide-spread disruption of host transcription termination in HSV-1 infection, Nature Communications, vol. 6, no. 7126, 2015.
, Anne L’Hernault, , Markus Schilhabel, Colin Crump, Philip Rosenstiel, Stacey Efstathiou, , , Lars Dölken, Theses
Anna-Kathrin Kopetzki, On Closest String Problems for Different Distances and Norms, Bachelor Thesis, LFE Bioinformatik / LMU München, 2015.
Katharina Schmid, Efficient Construction of de Bruijn Graphs Using Suffix Arrays, Bachelor Thesis, LFE Bioinformatik / LMU München, 2015.
Julia Sophia Gerke, Integrated analysis of gene expression data and clinical data, Master Thesis, LFE Bioinformatik / LMU München, 2015.
Vinicius H. Silva, Metabolic pathways and meat tenderness: from CNVs to gene expression in Nelore cattle breed, Master Thesis, Escola Superior de Agricultura Luiz de Queiroz (ESALQ) / Universidade de São Paulo (USP), 2015.
Papers
Tatyana Goldberg, Maximilian Hecht, Tobias Hamp, Timothy Karl, Guy Yachdav, Nadeem Ahmed, Uwe Altermann, Philipp Angerer, Sonja Ansorge, Kinga Balasz, Michael Bernhofer, Alexander Betz, Laura Cizmadija, Kieu Trinh Do, Julia Gerke, Robert Greil, Vadim Joerdens, Maximilian Hastreiter, Katharina Hembach, Max Herzog, Maria Kalemanov, LocTree3 prediction of localization., Nucleic acids research, vol. 42, pp. W350-5, 2014.
, Alice Meier, Hassan Nasir, Ulrich Neumaier, Verena Prade, Jonas Reeb, Aleksandr Sorokoumov, Ilira Troshani, Susann Vorberg, Sonja Waldraff, Jonas Zierer, Henrik Nielsen, Burkhard Rost, , Jürgen Haas, Diana Lieber, Georg Malterer, Lukasz Jaskiewicz, Mihaela Zavolan, Lars Dölken, , Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression, Nature Biotechnology, no. Nov 2, 2014.
, N Zach, R Norel, Johann Hawe, D Schoenfeld, G Stolovitsky, M L Leitner, et al, 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.
, To be, or not to be: konservierte eukaryotische Regulationsnetzwerke?, BIOspektrum, vol. 20, no. 5, pp. 514-516, 2014.
, , Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests, arXiv:1408.3044, 2014.
, Refining ensembles of predicted gene regulatory networks based on characteristic interaction sets, PLoS One, vol. 9, no. 2, pp. e84596, 2014.
, Jonas Zierer, , Theses
Matthias Danner, Implementierung und Evaluierung einer fehlertoleranten Textsuche basierend auf Suffix-Arrays, Bachelor Thesis, LFE Bioinformatik / LMU München, 2014.
Elisabeth Frank, Evaluation of transcript reconstruction methods for newly transcribed RNA measurements, Bachelor Thesis, LMU München, 2014.
Yvonne Awaloff, Reconstruction of microbial transcripts from RNA-seq experiments, Bachelor Thesis, LMU München, 2014.
Julia Söllner, Evaluation of RNA-seq mapping methods for newly transcribed RNA measurements, Bachelor Thesis, LMU München, 2014.
Laura Schiller, Efficient computation of hybridization networks, Master Thesis, LFE Bioinformatik / LMU München, 2014.
Evelyn Kirner, Detektion von zirkulären RNAs in Sequenzierdaten, Bachelor Thesis, LMU München, 2014.
Algorithmic Methods for Systems Biology of Herpes-viral microRNAs, PhD Thesis, LMU München, 2014.
, Bioinformatics methods for the biological interpretation of high-throughput experiments, Habilitation, Ludwig-Maximilians-Universität München, 2014.
, Papers
Mining RNA-Seq Data for Infections and Contaminations, PloS one, vol. 8, pp. e73071, 2013.
, , , , A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae, Nucleic Acids Research, vol. 41, no. 18, pp. 8452-8463, 2013.
, , Simon Dirmeier, , , Lenac Roviš T, Bailer SM, Pothineni VR, Ouwendijk WJ, Šimić H, Babić M, Miklić K, Malić S, Verweij MC, Baiker A, Comprehensive analysis of varicella-zoster virus proteins using a new monoclonal antibody collection, J Virol. 2013, vol. 87, no. 12, pp. 6943-54, 2013.
, von Brunn A, , Früh K, Verjans GM, Jonjić S, Jürgen Haas, Herbert B. Schiller, Michaela-Rosemarie Hermann, Julien Polleux, Timothée Vignaud, Sara Zanivan, 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.
, Zhiqi Sun, Aurelia Raducanu, Kay-E Gottschalk, Manuel Théry, Matthias Mann, Reinhard Fässler, Mayuko Kurome, Factors Influencing the Efficiency of Generating Genetically Engineered Pigs by Nuclear Transfer: Multi-Factorial Analysis of a Large Data Set, BMC Biotechnology, vol. 13, no. 43, 2013.
, Barbara Keßler, Valeri Zakhartchenko, Nikolai Klymiuk, Annegret Wünsch, Anne Richter, Andrea Bähr, Katrin Krähe, Katinka Burkhardt, Krzysztof Flisikowski, Tatiana Flisikowska, Claudia Merkl, Martina Landmann, Marina Durkovic, Alexander Tschukes, Simone Kraner, Dirk Schindelhauer, , Alexander Kind, Hiroshi Nagashima, Angelika Schnieke, , Eckhard Wolf, Sorg D, Danowski K, Korenkova V, Rusnakova V, Microfluidic high-throughput RT-qPCR measurements of the immune response of primary bovine mammary epithelial cells cultured from milk to mastitis pathogens, Animal, vol. 7, no. 5, pp. 799-805, 2013.
, , Meyer HH, Kliem H, RIP-chip enrichment analysis, Bioinformatics, vol. 29, no. 1, September 2012, Basel, Switzerland, pp. 77–83, 2013.
, Lars Dölken, , Kaspar Burger, Bastian Mühl, Markus Kellner, Michaela Rohrmoser, Anita Gruber-Eber, 4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response, RNA biology, vol. 10, 2013.
, , Lars Dölken, Dirk Eick, K Danowski, JJ Gross, K Gellrich, T Petri, HA Van Dorland, RM Bruckmaier, HD Reichenbach, Metabolic status and oestrous cycle in dairy cows, International Journal of Livestock Production, vol. 4, no. 9, pp. 135–147, 2013.
, HHD Meyer, FJ Schwarz, H Kliem, PARma: identification of microRNA target sites in AGO-PAR-CLIP data., Genome biology, vol. 14, pp. R79, 2013.
, Lars Dölken, Lukasz Jaskiewicz, , Schrynemackers M, On protocols and measures for the validation of supervised methods for the inference of biological networks, Front Genet., vol. 4, pp. 262, 2013.
, Geurts P, Robert Maier, A Turing test for artificial expression data, Bioinformatics, vol. 29, no. 20, pp. 2603-2609, 2013.
, , Computational analysis of virus-host interactomes, Methods in molecular biology, vol. 1064, pp. 115-30, 2013.
, Harth-Hertle ML, Scholz BA, Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9, PLoS Pathogens, vol. 9, no. 9, pp. e1003638, 2013.
, Glaser LV, Dölken L, , Bettina Kempkes, Roland H. Friedel, Clonal expansion of transposon insertions identifies candidate cancer genes in a PiggyBac mutagenesis screen, PLoS ONE, vol. 8, no. 8, pp. e72338, 2013.
, , Roland Rad, Philippe Soriano, Mirko Trilling, Nicolas Bellora, Andrzej J. Rutkowski, Miranda de Graaf, Paul Dickinson, Kevin Robertson, Olivia Prazeres da Costa, Peter Ghazal, 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.
, M. Mar Alba, Lars Dölken, Samantha J. Griffiths, Manfred Koegl, Chris Boutell, Helen L. Zenner, Colin Crump, 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.
, , Gerald Barry, Kimberley Martin, Marie H. Craigon, Rui Chen, Lakshmi N. Kaza, Even Fossum, John K. Fazakerley, Stacey Efstathiou, , Peter Ghazal, Jürgen Haas, Bernd Rädle, Andrzej Rutkoswki, Zsolt Ruzsics, 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.
, Ulrich H Koszinowski, Lars Dölken, Complementing the Eukaryotic Protein Interactome, PLOS One, vol. 8, no. 6, pp. e66635, 2013.
, , Ronny Kramer, A commonly used rumen-protected conjugated linoleic acid supplement marginally affects fatty acid distribution of body tissues and gene expression of mammary gland in heifers during early lactation, Lipids in Health and Disease, vol. 12, no. 96, 2013.
, , Dirk von Soosten, Sven Dänicke, Eva-Maria Weber, , Juergen Rehage, Gerhard Jahreis, Theses
Judith Boldt, Entwicklung eines Validierungs-Programms von Real-Time PCRs in der GVO-Analytik, Bachelor Thesis, LMU München, 2013.
Lars von den Driesch, Evolutionary conservation of PAR-CLIP microRNA target sites, Bachelor Thesis, LFE Bioinformatik / LMU München, 2013.
Alexander Grün, Interactive Modeling of Complex Hypothesis Using Ontologies, Bachelor Thesis, LFE Bioinformatik / LMU München, 2013.
, Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic, PhD Thesis, LMU München, 2013.
, Papers
Celine Scornavacca, Simone Linz, A First Step Toward Computing All Hybridization Networks For Two Rooted Binary Phylogenetic Trees, Journal of Computational Biology, vol. 19, no. 11, pp. 1227-1242, 2012.
, Rigorous assessment of gene set enrichment tests, Bioinformatics, vol. bts164v1-bts164, pp. 7, 2012.
, , , , Inferring Gene Regulatory Networks by ANOVA, Bioinformatics, vol. 28, no. 10, pp. 1376-1382, 2012.
, , , , , Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution., Genome research, vol. 22, pp. 2031-42, 2012.
, , Kaspar Burger, Zsolt Ruzsics, Stefan Krebs, Stefanie Kaufmann, Georg Malterer, Anne L’Hernault, Markus Schilhabel, Stefan Schreiber, Philip Rosenstiel, , Dirk Eick, , Lars Dölken, Detecting outlier peptides in quantitative high-throughput mass spectrometry data, Journal of Proteomics, vol. 75, no. 11, pp. 3230-9, 2012.
, , Milan Spasic, Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm, PLoS Genet, vol. 8, no. 1, pp. e1002433, 2012.
, Johanna Schott, Jochen Kreth, Kathrin Leppek, Sarah Hofmann, Sevim Ozgur, Georg Stoecklin, Daniel Marbach, James C Costello, Wisdom of crowds for robust gene network inference., Nature methods, vol. 9, pp. 796-804, 2012.
, Nicole M Vega, Robert J Prill, Diogo M Camacho, Kyle R Allison, Manolis Kellis, James J Collins, Gustavo Stolovitzky, Lisa Marcinowski, Michael Lidschreiber, Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection, PLoS Pathog, vol. 8, no. 9, pp. e1002908, 2012.
, Martina Rieder, Jens B. Bosse, Bernd Rädle, , Ildiko Györy, Miranda de Graaf, Olivia Prazeres da Costa, Philip Rosenstiel, , , Zsolt Ruzsics, Lars Dölken, Marcinowski L, Tanguy M, Krmpotic A, Rädle B, Lisnić VJ, Tuddenham L, Chane-Woon-Ming B, Ruzsics Z, Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo, PLoS Pathogens, vol. 8, no. 2, pp. e1002510, 2012.
, Benkartek C, Babic M, , Trgovcich J, Koszinowski UH, Jonjic S, Pfeffer S, Lars Dölken, Robert Lindner, A comprehensive evaluation of alignment algorithms in the context of RNA-Seq, PLoS ONE, vol. 7, no. 12, pp. e52403, 2012.
, ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes, Proceedings of the German Conference on Bioinformatics (GCB), vol. 26, pp. 69-81, 2012.
, Matthias Böck, , Tobias Stögbauer, Experiment and Mathematical Modeling of Gene Expression Dynamics in a Cell-Free System, Integrative Biology, vol. 4 (5), pp. 494 - 501, 2012.
, , Joachim O. Rädler, A context-based approach to identify the most likely mapping for RNA-seq experiments, BMC Bioinformatics, vol. 13(Suppl 6), pp. S9, 2012.
, , , , Detection and correction of probe-level artefacts on microarrays, BMC Bioinformatics, vol. 13, pp. 114, 2012.
, , , , Space Efficient Modifications to Structator - a Fast Index-Based Search Tool for RNA Sequence-Structure Patterns, Proceedings of the 11th International Symposium on Experimental Algorithms (SEA 2012) (Ralf Klasing, ed.), Springer Verlag, vol. 7276, Bordeaux, France, June 7-9, 2012, pp. 27-38, 2012.
, , Theses
Lucia Puchbauer, Analysis of High-Throughput Data in Oncology, Master Thesis, LFE Bioinformatik / LMU München, 2012.
Johann Hawe, Prediction of disease progression in patients with Amyotrophic Lateral Sclerosis, Bachelor Thesis, Bioinformatics, LMU München, 2012.
Activity of microRNAs and transcription factors in Gene Regulatory Networks, PhD Thesis, LMU München, 2012.
, RELEXplain - Relation Networks Explaining Biological Processes, Master Thesis, LFE Bioinformatik / LMU München, 2012.
, Papers
Contextual analysis of RNAi-based functional screens using interaction networks, Bioinformatics, vol. 27, pp. 2707-2713, 2011.
, , MIRTFnet: analysis of miRNA regulated transcription factors, PLoS One, pp. 6(8):e22519, 2011.
, , , Dintner Sebastian, Anna Staroń, Co-evolution of ABC-transporters and two-component regulatory systems as resistance modules against antimicrobial peptides in Firmicutes bacteria, Journal of Bacteriology, vol. 193, no. 15, pp. 3851–3862, 2011.
, , Thorsten Mascher, Susanne Gebhard, From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems, Bioinformatics, vol. 27, no. 13, pp. i366-i373, 2011.
, , , Nicola Mulder, , Zhen Wang, Guohui Ding, Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes, Molecular Biology and Evolution, vol. 28, no. 3, pp. 1131-40, 2011.
, Hong Li, Lei Liu, Rong Zeng, Yoshio Tateno, Yixue Li, Susanne Pfefferle, Julia Schöpf, Manfred Kögl, The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors, PLoS Pathog, vol. 7, no. 10, pp. e1002331, 2011.
, 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, , Imke Steffen, Friedemann Weber, Volker Thiel, Georg Herrler, Heinz-Jürgen Thiel, Christel Schwegmann-Weßels, Stefan Pöhlmann, Jürgen Haas, Christian Drosten, Albrecht von Brunn, Herbert B. Schiller, 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.
, Cyril Boulegue, Reinhard Fässler, Experiment Specific Expression Patterns, RECOMB 2011, Research in Computational Molecular Biology (Vineet Bafna, S. Cenk Sahinalp, eds.), Springer, vol. 15, pp. 339-354, 2011.
, , , Detecting outlier peptides in quantitative high-throughput mass spectrometry data, Detecting outlier peptides in quantitative high-throughput mass spectrometry data, September 2011, Weihenstephan, Germany, 2011.
, , Fast computation of minimum hybridization networks, Bioinformatics, vol. 28, no. 2, pp. 191-197, 2011.
, Celine Scornavacca, Alberto Cenci, Daniel H Huson, Virus-host interactomes and global models of virus-infected cells, Trends in Microbiology, vol. 19, no. 10, pp. 501-8, 2011.
, Jürgen Haas, Space-Efficient Preprocessing Schemes for Range Minimum Queries on Static Arrays, SIAM Journal on Computing, vol. 40, no. 2, pp. 465-492, 2011.
, , Theses
Vadim Jördens, Optimization of Homology-based Structure Models, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
miRNA regulation mechanisms of Herpes viruses, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
, Uwe Altermann, Analysis of Expression Data of Tissue Mixtures, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Philipp Angerer, Model Based Data Viewing and Analysis, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Michael Bernhofer, Analysis of Virus Host Interaction Networks, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Jonas Zierer, Transcript Quantification Biases in Next Generation Sequencing Data, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Andreas Kolberg, Automatische Klassifizierung von Alternativen Splicing-Events in Proteinstrukturen, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Papers
Carola Marzi, Eva Albrecht, Pirro G. Hysi, Vasiliki Lagou, Melanie Waldenberger, Anke Tönjes, Inga Prokopenko, Katharina Heim, Hannah Blackburn, Janina S. Ried, Marcus E. Kleber, Massimo Mangino, Barbara Thorand, Annette Peters, Christopher J. Hammond, Harald Grallert, Bernhard O. Boehm, Peter Kovacs, Genome-wide association study identifies two novel regions at 11p15.5-p13 and 1p31 with major impact on acute-phase serum amyloid A, PLoS Genetics, vol. 6, no. 11, pp. e1001213, 2010.
, Holger Prokisch, Bernhard R. Winkelmann, Tim D. Spector, H.-Erich Wichmann, Michael Stumvoll, Nicole Soranzo, Winfried März, Wolfgang Koenig, Thomas Illig, Christian Gieger, An Automatic Layout Algorithm for BPEL Processes, SoftVis ’10: Proceedings of the 5th ACM Symposium on Software visualization, ACM, New York, NY, USA, 2010.
, Philip Effinger, Markus Held, Michael Kaufmann, Vorescore - fold recognition improved by rescoring of protein structure models, Bioinformatics, vol. 26, no. 18, pp. i482-i488, 2010.
, , Classification of ncRNAs using position and size information in deep sequencing data, Bioinformatics, vol. 26, no. 18, pp. i426-i432, 2010.
, , HALO - A Java framework for precise transcript half-life determination, Bioinformatics, vol. 26, no. 9, pp. 1264-1266, 2010.
, Stefanie Kaufmann, Lars Dölken, , Lars Dölken, Georg Malterer, 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.
, Sheila Kothe, , Guillaume Suffert, Lisa Marcinowski, Natalie Motsch, Stephanie Barth, Michaela Beizinger, Diana Lieber, Susanne M. Bailer, Reinhard Hoffmann, Zsolt Ruzsics, Elisabeth Kremmer, Sebastien Pfeffer, , Ulrich H Koszinowski, Friedrich Grässer, Gunter Meister, Jürgen Haas, Finding Range Minima in the Middle: Approximations and Applications, Mathematics in Computer Science, vol. 3, no. 1, pp. 17-30, 2010.
, , Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing, Proceedings of the International Workshop on Combinatorial Algorithms (IWOCA’08) (Mirka Miller, Koichi Wada, eds.), College Publications, vol. 12, September 13-15, 2008, Nagoya, Japan, pp. 239-252, 2010.
, , Petri Nets with Fuzzy Logic (PNFL): Reverse Engineering and Parametrization, PLoS One, vol. 5, pp. e12807, 2010.
, , , , miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature, BMC Bioinformatics, vol. 11, pp. 135, 2010.
, , , , Wolfgang Fischer, Strain-specific genes of Helicobacter pylori: Genome evolution driven by a novel type IV secretion system and genomic island transfer, Nucleic Acids Research, vol. 38, no. 18, pp. 6089-101, 2010.
, Stefanie Rohrer, Matthias Zeiller, Arno Karnholz, Reinhard Hoffmann, , Rainer Haas, Analysis of High-throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life, Ausgezeichnete Informatikdissertationen 2009, GI-Edition Lecture Notes in Informatics, 2010.
, Fuzzy modeling, Modeling in Systems Biology: The Petri Net Approach (Ina Koch, Wolfgang Reisig, Falk Schreiber, eds.), Springer, 2010.
, , , 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.
, , , Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis, PLoS Computational Biology, vol. 6, no. 6, pp. e1000799, 2010.
, Tanja Oberwinkler, Locedie Mansueto, Friedhelm Pfeifer, Eduardo Mendoza, , Dieter Oesterhelt, Visualization of Complex BPEL Models, Proc. of the 17th International Symposium on Graph Drawing (GD ’09), 2010.
, Philip Effinger, Markus Held, Michael Kaufmann, Stephan Kottler, Theses
Markus Meier, Visualisierung von Repeats im Genom, Bachelor Thesis, LFE Bioinformatik, LMU München, 2010.
Quality Check and Differential Expression Using Newly Synthesized RNA, Bachelor Thesis, LFE Bioinformatik, LMU München, 2010.
, Florian Goebels, Network Oriented Transfer of Experimental Data Between Organisms, Diploma Thesis, LFE Bioinformatik, LMU München, 2010.
Bernd Streppel, Representation of Structure Variations of Protein Families by Partial Order Graphs, Bachelor Thesis, LFE Bioinformatik, LMU München, 2010.
Gene Graph Enrichment Analysis (GGEA): Mapping of Gene Expression Data onto Networks of Biochemical Processes, Diploma Thesis, LFE Bioinformatik, LMU München, 2010.
, Sebastian Ullherr, Prediction of Transcript Half-Lives, Bachelor Thesis, LFE Bioinformatik, LMU München, 2010.
Papers
Metabolic tagging and purification of nascent RNA: Implications for transcriptomics, Molecular BioSystems, vol. 5, no. 11, pp. 1271-8, 2009.
, Lars Dölken, Conserved principles of mammalian transcriptional regulation revealed by RNA half-life, Nucleic Acids Research, vol. 37, no. 17, pp. e115, 2009.
, Lars Dölken, Zsolt Ruzsics, Ulrich Koszinowski, , Even Fossum, Evolutionarily conserved herpesviral protein interaction networks., PLoS Pathog, vol. 5, no. 9, pp. e1000570, 2009.
, 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, , Hélène Boulet, Manfred Koegl, Susanne M. Bailer, Ulrich Koszinowski, Trey Ideker, Peter Uetz, , Jürgen Haas, Simon W. Ginzinger, Marko Skocibusic, CheckShift Improved: Fast Chemical Shift Reference Correction with High Accuracy, Journal of Biomolecular NMR, vol. 44, no. 4, pp. 207-211, 2009.
, Identifying the topology of protein complexes from affinity purification assays, Bioinformatics, vol. 25, no. 16, pp. 2140-2146, 2009.
, , Simon W. Ginzinger, Murray Coles, SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database, Journal of Biomolecular NMR, vol. 43, no. 3, pp. 179-185, 2009.
AG Moll, MT Lindenmeyer, M Kretzler, PJ Nelson, Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays, PLoS ONE, vol. 4, no. 3, pp. e4702, 2009.
, CD Cohen, Systematic Comparison of SCOP and CATH: A new Gold Standard for Protein Structure Analysis, BMC Structural Biology, vol. 9, no. 23, 2009.
, , , Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum, PloS Computational Biology, vol. 5, no. 4, pp. e1000332, 2009.
, Susanne Gronau, Friedhelm Pfeiffer, Eduardo Mendoza, , Dieter Oesterhelt, Algorithmische Systembiologie mit Petrinetzen – Von qualitativen zu quantitativen Systemmodellen, Informatik-Spektrum, vol. 32, no. 4, pp. 310-319, 2009.
, , , , , , , , Philippe Audebaud, New Development in Extracting Tail Recursive Programs from Proofs, Pre-Proceedings of the 19th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR’09), Coimbra, Portugal, September 9-11, 2009, 2009.
, Automatic Synthesis of an Efficient Algorithm for the Similarity of Strings Problem, Proceedings of the 4th Workshop on Automated Formal Methods (AFM’09) (H. Saidi, N. Shankar, eds.), Grenoble, France, June 27, 2009, pp. 23-30, 2009.
, O. Gonzalez, S. Gronau, F. Pfeiffer, E. Mendoza, Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum, PloS Computational Biology, vol. 5, no. 4, pp. e1000332, 2009.
, D. Oesterhelt, Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast, Journal of Computational Biology, vol. 16, no. 8, pp. 1-17, 2009.
, Jan Krumsiek, , Nino Shervashidze, SVN Vishwanathan, Efficient Graphlet Kernels for Large Graph Comparison, 12th International Conference on Artificial Intelligence and Statistics (AISTATS), Society for Artificial Intelligence and Statistics, Clearwater Beach, Fl, USA, April, 16-18, 2009, 2009.
, Kurt Mehlhorn, Karsten Borgwardt, Theses
Program Development by Proof Transformation, PhD Thesis, LMU München, 2009.
, Johannes Bräuer, Optimization of 3D Protein Structure Models, Bachelor Thesis, LFE Bioinformatik, LMU München, 2009.
Mark Heron, Network Oriented Analysis of CLA Expression Data, Bachelor Thesis, LFE Bioinformatik, LMU München, 2009.
Yanxiang Zhou, Small RNA Annotation and Analysis in Deep Sequencing Data, Bachelor Thesis, LFE Bioinformatik, LMU München, 2009.
Jeremias Weihmann, Genome-Rearrangements: Sortieren mit erweiterten Transreversals, Diploma Thesis, LFE Bioinformatik / LMU München, 2009.
Stefan Heinisch, Integration of Textmining Priors into Structural Inference of Bayesian Networks, Bachelor Thesis, LFE Bioinformatik / LMU München, 2009.
Maximilian Miller, miRNA-Target-Networks, Bachelor Thesis, LFE Bioinformatik / LMU München, 2009.
Nikolas Gross, Prediction of Protein Secondary Structure, Bachelor Thesis, LFE Bioinformatik / LMU München, 2009.
Analysis of High-Throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life, PhD Thesis, LMU München, 2009.
, Alternative Splicing and Protein Structure Evolution, PhD Thesis, LMU München, 2009.
, Reconstruction, Modeling and Analysis of Haloarcheal Metabolic Networks, PhD Thesis, LMU München, 2009.
, Papers
Christian Gieger, Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum, PLoS Genetics, vol. 4, no. 11, pp. e1000282, 2008.
, Elisabeth Altmaier, Martin Hrabé-de-Angelis, Florian Kronenberg, Thomas Meitinger, Hans-Werner Mewes, H.-Erich Wichmann, Klaus M. Weinberger, Jerzy Adamski, Thomas Illig, Karsten Suhre, Lars Dölken, Zsolt Ruzsics, Bernd Rädle, High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay, RNA, vol. 14, no. 9, pp. 1959–1972, 2008.
, , Jörg Mages, Reinhard Hoffmann, Paul Dickinson, Thorsten Forster, Peter Ghazal, Ulrich H Koszinowski, Jan Krumsiek, ProCope–protein complex prediction and evaluation, Bioinformatics, vol. 24, no. 18, pp. 2115–2116, 2008.
, , Protein structure alignment considering phenotypic plasticity, Bioinformatics, vol. 24, pp. 98–104, 2008.
, , , Alternative splicing and protein structure evolution, Nucleic Acids Res., vol. 36, pp. 550–558, 2008.
, , , AutoPSI: a database for automatic structural classification of protein sequences and structures, Nucleic Acids Res., vol. 36, pp. 398–401, 2008.
, Jan Erik Gewehr, , ProSAS: a database for analyzing alternative splicing in the context of protein structures, Nucleic Acids Res., vol. 36, pp. D63–68, 2008.
, , Franziska Meier, Florian Oefinger, Christian Potthast, , Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Overview of BioCreative II gene normalization., Genome Biology, vol. 9, no. Supplement 2, pp. S3, 2008.
, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L, Michaela Falb, Kerstin Müller, Lisa Königsmaier, Tanja Oberwinkler, Patrick Horn, Susanne von Gronau, Metabolism of halophilic archaea, Extremophiles, vol. 12, no. 2, pp. 177-196, 2008.
, Friedhelm Pfeiffer, Erich Bornberg-Bauer, Dieter Oesterhelt, Normalization and gene p-value estimation: issues in microarray data processing, Bioinform Biol Insights, vol. 2, pp. 291-305, 2008.
, , T. Aigner, , Program Development by Proof Transformation: Recent Evolutions, 15th International Conferences on Logic for Programming, Artificial Intelligence and Reasoning (LPAR’08), Doha, Qatar, November 22-27, 2008, 2008.
, Extraction of Efficient Programs from Proofs: The Case of Structural Induction over Natural Numbers, Local Proceedings of the Fourth Conference on Computability in Europe: Logic and Theory of Algorithms (CiE’08) (A. Beckmann, C. Dimitracopoulos, B. Löwe, eds.), Athens, Greece, June 15-20, 2008, pp. 64-76, 2008.
, 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.
, , Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes, Bioinformatics, vol. 24, no. 10, pp. 1257-63, 2008.
, , Reconstruction, modeling & analysis of Halobacterium salinarum R-1metabolism, Mol Biosyst, vol. 4, no. 2, pp. 148-59, 2008.
, S. Gronau, M. Falb, F. Pfeiffer, E. Mendoza, , D. Oesterhelt, Normalization strategies for mRNA expression data in cartilage research, Osteoarthritis Cartilage, vol. 16, pp. 947-955, 2008.
, Jochen Haag, Pia M. Gebhard, , Thomas Aigner, Jörn Marialke, Simon Tietze, Similarity based docking, J. Chem. Inf. Model., vol. 48, no. 1, pp. 186–196, 2008.
, Automatic Determination of Reaction Mappings and Reaction Center Information. 2. Validation on a Biochemical Reaction Database, J. Chem. Inf. Model., vol. 48, no. 6, pp. 1190–1198, 2008.
, Oliver Sacher, Robert Körner, Johann Gasteiger, Robert Körner, Determination of Reaction Mappings and Reaction Center Information: The Imaginary Transition State Energy approach, J. Chem. Inf. Model., vol. 48, no. 6, pp. 1181–1189, 2008.
, Microarray analyses of transdifferentiated mesenchymal stem cells, Journal of Cellular Biochemistry, vol. 103, no. 2, pp. 413-433, 2008.
, Tatjana Schilling, , Ludger Klein-Hitpass, Franz Jakob, Norbert Schütze, Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic, German Conference on Bioinformatics, Gesellschaft für Informatik, vol. P-136, September 9-12, 2008, Dresden, Germany, pp. 106-115, 2008.
, , Graph-based sequence annotation using a data integration approach, Journal of Integrative Bioinformatics, vol. 5, no. 2, 2008.
, Artem Lysenko, Matthew Hindle, Keywan Hassani-Pak, Ralf Thiele, Christopher J. Rawlings, Jacob Köhler, Jan Taubert, Analysis of a Modification of Gusfield’s Recursive Algorithm for Reconstructing Ultrametric Trees, Information Processing Letters, vol. 108, no. 4, pp. 222-225, 2008.
, 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.
, Jan Krumsiek, , Practical Entropy-Bounded Schemes for O(1)-Range Minimum Queries, Proceedings of the 2008 Data Compression Conference (DCC’08) (J.A. Storer, M.W. Marcellin, eds.), IEEE Computer Society, Snowbird, Utah, U.S.A., March 25-27, 2008, pp. 272-281, 2008.
, , Horst Martin Stühler, Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing, Local Proceedings of the 19th International Workshop on Combinatorial Algorithms (IWOCA’08) (Mirka Miller, Koichi Wada, eds.), Nagoya, Japan, September 13-15, 2008, pp. 239-252, 2008.
, , FERN - a Java framework for stochastic simulation and evaluation of reaction networks, BMC Bioinformatics, vol. 9, no. 1, pp. 356, 2008.
, , , Theses
Sebastian Pölsterl, Comparison of Alternative Splicing in Higher Organisms, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Thomas Mair, Analysis of Alternative Splicing of Proteins, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Annabelle Teresa Klarl, Konstruktion und Anwendung von Affixarrays, Bachelor Thesis, LFE Bioinformatik, LMU München, 2008.
Simon Berger, Protonation State and Enzyme Substrate Interaction, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Stefan Brandmaier, Strukturelle Analyse von alternativem Splicing, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Petri Net Based System for Spatio-Temporal Simulation of Gene Regulation, Diploma Thesis, LFE Bioinformatik/LMU München, 2008.
, Theresa Niederberger, Regelbasierte Extraktion von Proteinwechselwirkungen, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Marko Skocibusic, Improving CheckShift, Diploma Thesis, LFE Bioinformatik, LMU München, 2008.
Simon W. Ginzinger, Bioinformatics Methods for NMR Chemical Shift Data, PhD Thesis, LMU München, 2008.
Papers
Simon W. Ginzinger, Fabian Gerick, Murray Coles, CheckShift: Automatic Correction of Inconsistent Chemical Shift Referencing, Journal of Biomolecular NMR, vol. 39, no. 3, pp. 223-227, 2007.
, Jan Erik Gewehr, Volker Hintermair, AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings, Bioinformatics, vol. 23, no. 10, pp. 1203-1210, 2007.
, Vorolign - Fast Structural Alignment using Voronoi Contacts, Bioinformatics, vol. 23, no. 2, pp. e205-e211, 2007.
, Jan Erik Gewehr, , , Alexander Zien, Pia M. Gebhard, Phenotyping of chondrocytes in vivo and in vitro using cDNA array technology, Clin Orthop Relat Res, vol. 460, pp. 226-33, 2007.
, Thomas Aigner, Jan Erik Gewehr, Martin Szugat, BioWeka–extending the Weka framework for bioinformatics, Bioinformatics, vol. 23, no. 5, pp. 651-653, 2007.
, Z. Fan, S. Soder, S. Oehler, Activation of interleukin-1 signaling cascades in normal and osteoarthritic articular cartilage, Am J Pathol, vol. 171, no. 3, pp. 938-946, 2007.
, Thomas Aigner, Thomas Aigner, Jochen Haag, Functional genomics, evo-devo and systems biology: a chance to overcome complexity?, Curr Opin Rheumatol, vol. 19, no. 5, pp. 463-470, 2007.
, Predicting activated conformations of substrates in enzyme binding sites, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), 2007.
, Jörn Marialke, Robert Körner, Simon Tietze, Simon Tietze, Jörn Marialke, Robert Körner, Graph-Based Molecular Alignment (GMA), Journal of Chemical Information and Modelling, vol. 47, no. 2, pp. 591-601, 2007.
, Simon Tietze, GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein-Ligand Complexes, Journal of Chemical Information and Modelling, vol. 47, no. 4, pp. 1657–1672, 2007.
, Andreas Steffen, Carolin Thiele, Simon Tietze, Christian Strassnig, Andreas Kämper, Thomas Lengauer, Gerhard Wenz, Improved Cyclodextrin-Based Receptors for Camptothecin by Inverse Virtual Screening, Chemistry 2007, vol. 13, no. 24, pp. 6801-6809, 2007.
, Markus Böhl, Simon Tietze, Andrea Sokoll, Sineej Madathil, Frank Pfennig, Flavonoids Affect Actin Functions in Cytoplasm and Nucleus, Biophysical Journal, vol. 93, no. 8, pp. 2767-2780, 2007.
, Karim Fahmy, Herwig O. Gutzeit, Andreas Steffen, Maximilian Karasz, Carolin Thiele, Thomas Lengauer, Andreas Kämper, Gerhard Wenz, Combined Similarity and QSPR Virtual Screening for Guest Molecules of β-Cyclodextrin, New Journal of Chemistry, vol. 31, pp. 1941 - 1949, 2007.
, Stefan Zahler, Simon Tietze, Frank Totzke, Michael Kubbutat, Laurent Meijer, Angelika M. Vollmar, Inverse in silico screening of 5/6/67 substituted Halogenoindirubins reveals PDK1 as target, Chem. Biol., vol. 14, no. 11, pp. 1207-1214, 2007.
, Andreas Steffen, On the ease of predicting the thermodynamic properties of beta-cyclodextrin inclusion complexes, Chem Cent J., vol. 1, no. 29, 2007.
, Human Gene Normalization by an Integrated Approach including Abbreviation Resolution and Disambiguation, Second BioCreative Challenge Evaluation Workshop, 2007.
, , RelEx - Relation extraction using dependency parse trees, Bioinformatics, vol. 23, no. 3, pp. 365-371, 2007.
, , , Simon W. Ginzinger, SimShiftDB: Chemical-Shift-Based Homology Modeling, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria., 2007.
, Simon W. Ginzinger, Thomas Gräupl, SimShiftDB: Chemical-Shift-Based Homology Modeling, Proceedings of the First International Conference on Bioinformatics Research and Development (BIRD’07) (Sepp Hochreiter, Roland Wagner, eds.), Springer, vol. 4414, Berlin, Germany, March 12-14, pp. 357-370, 2007.
, Influence of degree correlations on network structure and stability in protein-protein interaction networks, BMC Bioinformatics, vol. 8, pp. 297, 2007.
, , A New Succinct Representation of RMQ-Information and Improvements in the Enhanced Suffix Array, Proceedings of the International Symposium on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies (ESCAPE’07) (Bo Chen, Mike Paterson, Guochuan Zhang, eds.), Springer-Verlag, vol. 4614, Hangzhou, China, April 7-9, 2007, pp. 459-470, 2007.
, , Paolo Ferragina, Suffix Arrays on Words, Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM’07) (Bin Ma, Kaizhong Zhang, eds.), Springer-Verlag, vol. 4580, London, Ontario, July 9-11, 2007, pp. 328-339, 2007.
, Albrecht von Brunn, Carola Teepe, Jeremy C. Simpson, Rainer Pepperkok, Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome, PLoS ONE, vol. 2, no. 5, pp. e459, 2007.
, , Rhonda Roberts, Jürgen Haas, K.M. Borgwardt, An efficient sampling scheme for comparison of large graphs, Mining and Learning with Graphs, Electronic Proceedings, no. 1, 2007.
, SVN Vishwanathan, H.P. Kriegel, Amihood Amir, Two-Dimensional Range Minimum Queries, Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM’07), (Bin Ma, Kaizhong Zhang, eds.), Springer-Verlag, vol. 4580, London, Ontario, July 9-11, 2007, pp. 286-294, 2007.
, Moshe Lewenstein, Theses
Phenotypic Plasticity as a Measure for Protein Structural Similarity, Master Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
, Sebastian Dümcke, Optimization of Sequence-Structure Alignments using the Vorolign-Scoring Function, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Horst Martin Stühler, Practical Performance of Preprocessing Schemes for Range Minimum Queries, Diploma Thesis, LFE Bioinformatik, LMU München, 2007.
Data Structures for Efficient String Algorithms, PhD Thesis, LMU München, 2007.
, Jan Erik Gewehr, New Methods for the Prediction and Classification of Protein Domains, PhD Thesis, Ludwig-Maximilians-Universität München, 2007.
Volker Hintermair, Comparative Analysis of Bos Taurus and Homo Sapiens DNA Microarrays, Master Thesis, LMU München, 2007.
Text Mining and Gene Expression Analysis - Towards Combined Interpretation of High Throughput Data, PhD Thesis, LMU München, 2007.
, Andreas Grimm, 3D tomographic and single-particle reconstruction using level set methods, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Anton Moll, Splice-isoform analysis using data from standard human gene DNA chips, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Vergleichende Genomanalyse eines neu sequenzierten H.pylori Stamms, Master Thesis, LFE Bioinformatik, LMU München, 2007.
, Matthias Siebert, Voronoi contact patterns for protein function prediction, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Florian Oefinger, A Database for Alternative Splicing in the Context of Protein Structures,, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Alexander Pöschl, Browsing the protein space, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Robert Körner, Analyse biochemischer Reaktionen an Hand von imaginären Übergangszuständen, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Frank Wallrapp, Empirical Scoring Functions for Protein Structure Analysis, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Alex Jarasch, Similarity-Based Analysis of Medium- and High Throughput Screening Data, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Alois Huber, OBMASS: Entwicklung eines linearen Algorithmus zur Berechnung des Bounded Maximum Average Scoring Subsequence Problems, Diploma Thesis, LFE Bioinformatik, LMU München, 2007.
Novel Graph Kernels for Biological Network Comparison, Diploma Thesis, Database and Information Systems/LMU München, 2007.
, Papers
Inferring topology from clustering coefficients in protein-protein interaction networks, BMC Bioinformatics, vol. 7, pp. 519, 2006.
, , Toward the complete interactome, Nat Biotechnol, vol. 24, no. 6, pp. 614-615, 2006.
, , Jan Erik Gewehr, SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles, Bioinformatics, vol. 22, no. 2, pp. 181-187, 2006.
, Parameter estimation using Simulated Annealing for S-system models of biochemical networks, Bioinformatics, vol. 23, no. 4, pp. 480-486, 2006.
, Christoph Küper, Kirsten Jung, Prospero Naval, Eduardo Mendoza, Peter Uetz, Herpesviral protein networks and their interaction with the human proteome, Science, vol. 311, no. 5758, pp. 239-42, 2006.
, Christine Zeretzke, C. Atzler, Armin Baiker, B. Berger, Seesandra V. Rajagopala, M. Roupelieva, Dietlinde Rose, Even Fossum, Jürgen Haas, Martin Szugat, Wikimanie, Entwicklermagazin, vol. 2006, no. 1, pp. 96-99, 2006.
Martin Szugat, Web Servicing the Office, XML and Web Services Magazin, vol. 2006, no. 1, pp. 150-152, 2006.
Joachim Saas, Jochen Haag, D. Rueger, S. Chubinskaya, IL-1beta, but not BMP-7 leads to a dramatic change in the gene expression pattern of human adult articular chondrocytes–portraying the gene expression pattern in two donors, Cytokine, vol. 36, no. 1-2, pp. 90-99, 2006.
, , Eckart Bartnik, Thomas Aigner, H. Redestig, Unsupervised Decision Trees Based on Gene Ontology Terms for the Interpretation of Gene Expression Data, Advances in Data Analysis. Proc. 30th Annual Conference of the German Classification Society (GfKl) (R. Decker, H.-J. Lenz, eds.), Springer-Verlag, Heidelberg-Berlin, 2007, pp. 385-594, 2006.
, , J. Selbig, Dong-Yup Lee, Colored Petri Net Modeling and Simulation of Signal Transduction Pathways, Metabolic Engineering, vol. 8, no. 2, pp. 112-122, 2006.
, Sang-Yup Lee, Thomas Aigner, Large-Scale Gene Expression Profiling of Osteoarthritic Cartilage Degeneration, Arthritis&Rheumatism, vol. 54, no. 11, pp. 3533-3544, 2006.
, Joachim Saas, Pia M. Gebhard, Jochen Haag, Tilo Weiss, Alexander Zien, Franz Obermayer, , Eckart Bartnik, Andreas Kämper, Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies, Journal of Chemical Information and Modelling, vol. 46, no. 2, pp. 903–911, 2006.
, Matthias Rarey, Christel M. Marian, Thomas Lengauer, Gene and protein nomenclature in public databases, BMC Bioinformatics, vol. 7, pp. 372, 2006.
Characterization of Protein Interactions, German Conference on Bioinformatics (GCB) (Daniel Huson, Oliver Kohlbacher, Andrei Lupas, Kay Nieselt, Andreas Zell, eds.), Gesellschaft für Informatik, vol. P-83, Tübingen, Germany, September 19-22, 2006, pp. 64-73, 2006.
, T. Duchrow, , , Thomas Aigner, Pia M Gebhard, cDNA arrays in degenerative arthritis research, Future Rheumatology, vol. 11, pp. 101-109, 2006.
, Hongwei Zhang, K Wayne Marshall, Simon W. Ginzinger, SimShift: Identifying structural similarities from NMR chemical shifts, Bioinformatics, vol. 22, no. 4, pp. 460-465, 2006.
, Optimal String Mining Under Frequency Constraints, Proceedings of the 10th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD’06) (J. Fürnkranz, T. Scheffer, M. Spiliopoulou, eds.), Springer-Verlag, vol. 4213, Berlin, Germany, September 18-22, 2006, pp. 139-150, 2006.
, , Stefan Kramer, Theoretical and Practical Improvements on the RMQ-Problem with Applications to LCA and LCE, Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM’06) (Moshe Lewenstein, Gabriel Valiente, eds.), Springer-Verlag, vol. 4009, Barcelona, Spain, July 5-7, 2006, pp. 36-48, 2006.
, , Chad A. Davis, Fabian Gerick, Volker Hintermair, Reliable gene signatures for microarray classification: assessment of stability and performance, Bioinformatics, vol. 22, no. 19, pp. 2356-2363, 2006.
, , , , Books
Martin Szugat, Jan Erik Gewehr, Cordula Lochmann, Social Software, entwickler.press, 2006.
Theses
Analysis of Protein Sequence-Structure Alignments, Bachelor Thesis, LMU München, 2006.
, Jonathan Hoser, Ein Scheduling System für netzwerkorientierte Bioinformatik Arbeitsabläufe, Bachelor Thesis, LMU München, 2006.
Maximilian Karasz, A Fragment-Based Approach to Virtual Screening, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2006.
Jörn Marialke, Similarity Based Methods for the Prediction of Protein Ligand Complexes, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2006.
Simon Tietze, Prediction of Specificity in Protein-Ligand Interactions Using Structure Based Virtual Screening, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2006.
Contextual Analysis of Gene Expression Data, PhD Thesis, LMU München, 2006.
, Fabian Gerick, Identification and Correction of Errors in NMR-Chemical Shift Data, Master Thesis, LFE Bioinformatik, LMU München, 2006.
Chad A. Davis, Feature Selection Methods in Bioinformatics, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2006.
Julia Sellmeier, Analysis of Available Bioinformatic Tools for Exploration of Microarray Data using Gene Ontology and Design of a Bioinformatic Tool with a Graphical User Interface for Interactive Exploration of Gene Networks Predicted from Microarray Data, Diploma Thesis, LFE Bioinformatik, LMU München, 2006.
Sebastian Bauer, Vergleich und Visualisierung von Algorithmen zur Konstruktion von Suffix-Arrays anhand sehr langer Texte, Bachelor Thesis, LFE Bioinformatik, LMU München, 2006.
Daniel Güttler, LiMB - Ein interaktiver Browser zur Analyse biomedizinischer Texte mit Hilfe von Textmining, Diploma Thesis, LMU München, 2006.
Papers
QUASAR–scoring and ranking of sequence-structure alignments, Bioinformatics, vol. 21, no. 24, pp. 4425–4426, 2005.
, Jan Erik Gewehr, , Fast Frequent String Mining Using Suffix Arrays, TUM-I0512, Institut für Informatik der Technischen Universität München, no. TUM-I0512, 2005.
, , Stefan Kramer, A simple approach for protein name identification: prospects and limits, BMC Bioinformatics, vol. 6, no. (Suppl.1), pp. S15, 2005.
, Daniel Güttler, , , ProMiner: rule-based protein and gene entity recognition, BMC Bioinformatics, vol. 6, no. (Suppl.1), pp. S14, 2005.
, , Heinz-Theodor Mevissen, , Juliane Fluck, Inference of Developmental Transcription Factor Activities in Drosophila Melanogaster (Extended abstract of oral presentation), Proceedings of the Moscow Conference on Computational Molecular Biology (MCCMB), 2005.
, Jan Erik Gewehr, Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments, German Conference on Bioinformatics (GCB) 2005 (A. Torda, S. Kurtz, Matthias Rarey, eds.), GI, vol. P-71, pp. 77-91, 2005.
, , Thomas Aigner, , Identifying active transcription factors and kinases from expression data, Bioinformatics, vol. 21, no. Suppl 2, pp. 115-122, 2005.
, , M. Gebauer, Joachim Saas, Comparison of the chondrosarcoma cell line SW1353 with primary human adult articular chondrocytes with regard to their gene expression profile and reactivity to IL-1beta, Osteoarthritis Cartilage, vol. 13, no. 8, pp. 697-708, 2005.
, Jochen Haag, S. Soder, M. Pieper, Eckart Bartnik, J. Beninga, , Thomas Aigner, Thomas Aigner, Joachim Saas, Alexander Zien, Analysis of Differential Gene Expression in Healthy and Osteoarthritic Cartilage and Isolated Chondrocytes by Microarray Analysis, Methods in Molecular Medicine, vol. 100, pp. 109-128, 2005.
, Pia M. Gebhard, Thomas Knorr, Thomas Aigner, L. McKenna, Alexander Zien, Z. Fan, Pia M. Gebhard, Gene expression profiling of serum- and interleukin-1beta-stimulated primary human adult articular chondrocytes–a molecular analysis based on chondrocytes isolated from one donor, Cytokine, vol. 31, no. 3, pp. 227-240, 2005.
, Embedded subgraph isomorphism and its applications in cheminformatics and metabolomics, 1st German Conference in Chemoinformatics, 2005.
, Robert Körner, Jörn Marialke, Martin Szugat, Daniel Güttler, Web Servicing the Biological Office, Bioinformatics, vol. 21, no. (Suppl. 2), pp. 268-269, 2005.
, , A Facius, C Englbrecht, PRIME: a graphical interface for integrating genomic/proteomic databases, Proteomics, vol. 5, no. 1, pp. 76-80, 2005.
, A Groscurth, S Benjamin, S Wanka, HW Mewes, Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts, Bioinformatics, vol. 21, no. Suppl 2, pp. 259-267, 2005.
, , , Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage, Bioinfomatics, vol. 21, no. 8, pp. 1383-1388, 2005.
, Katharina H.V. Jahn, Selina Sommer, Stephen Rudd, Hans W. Mewes, Igor V. Tetko, Simon W. Ginzinger, SimShift: Identifying Structural Similarities from NMR Chemical Shifts, European Conference on Computational Biology (ECCB05), 2005.
, Fast Frequent String Mining Using Suffix Arrays, Proceedings of the 5th IEEE International Conference on Data Mining (ICDM’05), IEEE Computer Society, Houston, TX, USA, November 27-30, 2005, pp. 609-612, 2005.
, , Stefan Kramer, A 2-Approximation Algorithm for Sorting by Prefix Reversals, Proceedings of the 13th Annual European Symposium on Algorithms (ESA’05) (Gerth Stølting Brodal, Stefano Leonardi, eds.), Springer-Verlag, vol. 3669, Mallorca, Spain, October 3-6, 2005, pp. 415-425,, 2005.
, Simon W. Ginzinger, Theses
Stephan Vogt, Topic Maps, Bachelor Thesis, LMU München, 2005.
Alexander Kohn, Quantitative Analyse von Protein-Massenspektren, Diploma Thesis, LFE Bioinformatik, LMU München, 2005.
Martin Szugat, BioWeka: Extending the Weka framework for Bioinformatics, Bachelor Thesis, LMU München, 2005.
Inference of Regulatory Networks Using Physical Models, Bachelor Thesis, LFE Bioinformatik, LMU München, 2005.
, Fabian Gerick, Ein programmierbarer Web Service zur Charakterisierung biologischer Objekte, Bachelor Thesis, LMU München, 2005.
Niklas Von Öhsen, Profile-Profile alignment for remote homology and domain detection of proteins, PhD Thesis, Ludwig-Maximilians-Universität München, 2005.
, Papers
ToPNet - an application for interactive analysis of expression data and biological networks, Bioinformatics, vol. 20, no. 9, pp. 1470-1471, 2004.
, , , Niklas Von Öhsen, Ingolf Sommer, Arby: automatic protein structure prediction using profile-profile alignment and confidence measures, Bioinformatics, vol. 20, no. 14, pp. 2228-35, 2004.
, Niklas Von Öhsen, Dopro: Automatic Protein Domain Structure Prediction using a Stochastic Model for Analyzing Homology Search Results, CAFASP 2004, pp. extended abstract, 2004.
, , Peter Uetz, Seesandra V. Rajagopala, From ORFeomes to protein interaction maps in viruses, Genome Res, vol. 14, no. 10B, pp. 2029-2033, 2004.
, Jürgen Haas, New methods for joint analysis of biological networks and expression data, Bioinformatics, vol. 20, no. 10, pp. 1517-1521, 2004.
, , , Dong-Yup Lee, Knowledge representation model for systems-level analysis of signal transduction networks, Genome Inform Ser Workshop Genome Inform, vol. 15, no. 2, pp. 234-243, 2004.
, Sang-Yup Lee, Jan T. Kim, Jan Erik Gewehr, Thomas Martinetz, Binding Matrix: A Novel Approach for Binding Site Recognition, Journal of Bioinformatics and Computational Biology, vol. 2, no. 2, pp. 289-307, 2004.
Jan Erik Gewehr, Niklas Von Öhsen, Combining Secondary Structure Element Alignment and Profile Alignment for Fold Recognition, German Conference on Bioinformatics, GCB 2004 (Robert Giegerich, Jens Stoye, eds.), Gesellschaft für Informatik, vol. P-53, Bielefeld, Germany, October 4-6, 2004, pp. 141-148, 2004.
, T. Crass, I. Antes, R. Basekow, P. Bork, C. Buning, M. Christensen, H. Claussen, C. Ebeling, P. Ernst, K. Heidtke, A. Herrmann, S. O’Keeffe, O. Kiesslich, S. Kolibal, J. O. Korbel, T. Lengauer, I. Liebich, M. van der Linden, H. Luz, K. Meissner, C. von Mering, H. T. Mevissen, HW Mewes, H. Michael, M. Mokrejs, T. Muller, H. Pospisil, M. Rarey, J. G. Reich, R. Schneider, D. Schomburg, S. Schulze-Kremer, K. Schwarzer, I. Sommer, S. Springstubbe, S. Suhai, G. Thoppae, M. Vingron, J. Warfsmann, T. Werner, D. Wetzler, E. Wingender, The Helmholtz Network for Bioinformatics: an integrative web portal forbioinformatics resources, Bioinformatics, vol. 20, no. 2, pp. 268-70, 2004.
, Thomas Aigner, E. Bartnik, F. Sohler, Functional genomics of osteoarthritis: on the way to evaluate disease hypotheses, Clin Orthop Relat Res, no. 427 Suppl, pp. 138-143, 2004.
, Probabilistic methods for predicting protein functions in protein-protein interaction networks, German Conference on Bioinformatics, GCB 2004 (Robert Giegerich, Jens Stoye, eds.), Gesellschaft für Informatik, vol. P-53, Bielefeld, Germany, October 4-6, 2004, pp. 159-168, 2004.
, , , ProMiner: Organism-specific protein name detection using approximate string matching, BioCreative Challenge Evaluation Workshop, 2004.
, , Heinz-Theodor Mevissen, , Juliane Fluck, Exact versus approximate string matching for protein name identification, BioCreative Challenge Evaluation Workshop, 2004.
, Daniel Güttler, , , Theses
Volker Hintermair, Characterisation and Visualisation of Protein Families based on Multicriterial Clustering, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2004.
Andreas Spitzmüller, JRDP - Ein Java Framework für Rekursive Dynamische Programmierung, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2004.
Thomas Obkircher, Eine erweiterbare Bioinformatik Umgebung zur kriterienbasierten Protein Identifizierung, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2004.
Dorothee Liebich, Packungsprobleme bei Proteinen, PhD Thesis, Friedrich-Wilhelms-Universität Bonn, 2004.
New Analysis Methods for Gene Expression Data via Construction and Incorporation of Biological Networks, PhD Thesis, Ludwig-Maximilians-Universität München, 2004.
, Patents
Method for Evaluation of Gene Expression and DNA Chip Data using Metabolic/Regulatory Pathways and Statistical Significance Measures with Applications to Drug Target Finding, GMD Forschungszentrum Informationstechnik GmbH, no. PCT Patent application, European patent office 12.11.1999, 2004.
, , Alexander Zien, Fluorescent Energy for Elucidating the 3D Structure of Biological Macromolecules (FETMA), no. PCT Patent application, European patent office 10.08.2001, 2004.
, D. Hoffmann, Papers
Niklas Von Öhsen, Ingolf Sommer, Profile-profile alignment: a powerful tool for protein structure prediction, Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003) (Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein, eds.), Lihue, Hawaii, USA, January 3-7, 2003, pp. 252-63, 2003.
, Thomas Martinetz, Jan Erik Gewehr, Jan T. Kim, Statistical Learning for Detecting Protein-DNA Binding Sites, Proc. of the International Joint Conference on Neural Networks (IJCNN) (D. C. Wunsch II, M. Hasselmo, K. Venayagamoorthy, eds.), IEEE Press, pp. 2940-2945, 2003.
Jan T. Kim, Jan Erik Gewehr, Thomas Martinetz, Binding Matrix: A Novel Approach for Binding Site Recognition, Bioinformatics 2003, Bioinformatics, pp. Poster, 2003.
Jan Erik Gewehr, Jan T. Kim, Thomas Martinetz, On the Correspondence between Scoring Matrices and Binding Site Sequence Distributions, ISMB 2003, Brisbane, pp. Poster, 2003.
Thomas Aigner, The promise and limitations of DNA microarray analysis: comment on the editorial by Firestein and Pisetsky, Arthritis Rheum, vol. 48, no. 3, pp. 860; author reply 862, 2003.
, Alexander Zien, Juliane Fluck, Microarrays: How Many Do You Need?, Journal of Computational Biology, vol. 10, no. 3-4, pp. 653-667, 2003.
, Thomas Lengauer, New methods for joint analysis of biological networks and expression data, Proceedings of the German Conference on Bioinformatics, GCB 2003 (W. Mewes, D. Frishman, V. Heun, S. Kramer, eds.), belleville Verlag, München, Neuherberg and Garching, Germany, October 12-14, 2003, pp. 141-146, 2003.
, , , Thomas Aigner, Alexander Zien, Gene expression in chondrocytes assessed with use of microarrays, Joint Surg Am, vol. 85-A, no. Suppl 2, pp. 117-123, 2003.
, , J. Bone, D. Hofmann, Crystal structure prediction with data mining, J. Mol. Struct., vol. 647, no. 1, pp. 17-39, 2003.
, Playing biology’s name game: identifying protein names in scientific text, Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003) (Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein, eds.), Lihue, Hawaii, USA, January 3-7, 2003, pp. 403-414, 2003.
, Juliane Fluck, Heinz-Theodor Mevissen, , Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices, Computational Molecular Biology (S. Istrail, P. Pevzner, R. Shamir, eds.), North Holland, vol. 12, 2003.
, Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices, Discrete Applied Mathematics, vol. 127, no. 1, pp. 163-177, 2003.
, Books
Grundlegende Algorithmen - Einführung in den Entwurf und die Analyse effizienter Algorithmen, Vieweg Verlag, 2003.
, Werner Mewes, Dmitrij Frishman, Proceedings of the German Conference on Bioinformatics, GCB 2003 (Neuherberg and Garching, Germany, October 12-14, 2003), belleville Verlag München, 2003.
, Stefan Kramer, Theses
William Travis Holton, Evaluation of mapping consistency between public gene and protein databases, Bachelor Thesis, Ludwig-Maximilians-Universität München, 2003.
Automatische Generierung und Verbesserung von Synonymlisten und Entwicklung eines geeigneten Benchmarksystems, Bachelor Thesis, LMU München, 2003.
, Cornelia Donner, Erkennung von Gennamen in wissenschaftlichen Texten - automatische Generierung von Synonymlisten und Präprozessierung der Texte, Bachelor Thesis, LMU München, 2003.
Alexander Zien, Computational Methods for Gene Expression Data Analysis, PhD Thesis, Friedrich-Wilhelms-Universität Bonn, 2003.
Jan Erik Gewehr, The Binding Matrix - A Statistical Learning Approach to Protein-DNA Binding Site Prediction, Diploma Thesis, University of Lübeck, 2003.
Papers
Alexander Zien, Juliane Fluck, Thomas Lengauer, Microarrays: How many do you need?, Proceedings of the Sixth Annual International Conference on Computational Biology, RECOMB 2002 (E Myers, et al, eds.), ACM Press, New York, Washington, DC, USA, April 18-21, 2002, pp. 321-330, 2002.
, Ingolf Sommer, Alexander Zien, Niklas Von Öhsen, Confidence measures for protein fold recognition, Bioinformatics, vol. 18, no. 6, pp. 802-812, 2002.
, Thomas Lengauer, Thomas Martinetz, Jan Erik Gewehr, Jan T. Kim, A Statistical Learning Approach to Predicting Protein-DNA-Binding Sites, European Conference on Computational Biology (ECCB) 2002, pp. Poster, 2002.
ProML - the protein markup language for specification of protein sequences, structures and families, In Silico Biol, vol. 2, no. 3, pp. 313-24, 2002.
, , Thomas Lengauer, J. Freudenberg, A hypergraph-based method for unification of existing protein structure-and sequence-families, In Silico Biol, vol. 2, no. 3, pp. 339-349, 2002.
, , Thomas Lengauer, Prediction of gene functions from biological interactions, RECOMB 2002 (M. Vingron, ed.), vol. Poster, 2002.
, D. Güttler, , , Biological context and the analysis of gene expression data, ECCB 2002 (H.-P. Lenhof, ed.), vol. Poster, 2002.
, D. Güttler, , , Mario Albrecht, Improving fold recognition of protein threading by experimental distance constraints, In Silico Biol, vol. 2, no. 3, pp. 325-337, 2002.
, , Thomas Lengauer, Thomas Aigner, E. Bartnik, Alexander Zien, Functional genomics of osteoarthritis, Pharmacogenomics, vol. 3, no. 5, pp. 635-50, 2002.
, Co-clustering of biological networks and gene expression data, Bioinformatics, vol. 18, no. 90001, pp. S145-S154, 2002.
, Alexander Zien, , Thomas Lengauer, Philippe Ferrara, Evaluation of a fast implicit solvent model for molecular dynamics simulations, Proteins: Structure, Function, and Bioinformatics, vol. 46, no. 1, pp. 24-33, 2002.
, Amedeo Caflisch, Papers
Protein Structure Prediction, Bioinformatics - From Genomes to Drugs (Thomas Lengauer, ed.), Wiley-VCH, pp. 237-313, 2001.
, Thomas Lengauer, Niklas Von Öhsen, Improving profile-profile alignments via log average scoring, Proceedings of the First International Workshop on Algorithms in Bioinformatics (WABI 2001) (O. Gascuel, B.M.E. Moret, eds.), Springer-Verlag, vol. 2149, Århus, Denmark, August 28-31, 2001, pp. 11-26, 2001.
, Ingolf Sommer, Niklas Von Öhsen, Alexander Zien, Confidence Measures for fold recognition, German Conference on Bioinformatics (E. Wingender, ed.), pp. 26-33, 2001.
, Thomas Lengauer, D. Hoffmann, V. Schnaible, S. Wefing, Mario Albrecht, Fast solution of Protein-3D-structures, Coupling of Biological and Electronic Systems, Proceedings of the 2nd caesarium (Karl-Heinz Hoffmann, ed.), Springer-Verlag, pp. 59-78, 2001.
, ProML - The protein markup language for specification of protein sequences, structures and families, German Conference on Bioinformatics (GCB 2001) (E. Wingender, R. Hofestädt, I. Liebich, eds.), Braunschweig, Germany, October 7-10, 2001, pp. 58-67, 2001.
, , Thomas Lengauer, Evaluation of structure prediction models using the ProML specification language, Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), vol. Poster, 2001.
, , Thomas Lengauer, J. Freudenberg, A new method for unification of existing protein structure- and sequence-families, German Conference on Bioinformatics (GCB 2001) (E. Wingender, R. Hofestädt, I. Liebich, eds.), Braunschweig, Germany, October 7-10, 2001, pp. 78-84, 2001.
, , Thomas Lengauer, Mario Albrecht, Protein structure prediction by threading with experimental constraints, Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), vol. Poster, 2001.
, Mario Albrecht, Improving fold recognition of protein threading by experimental distance constraints, German Conference on Bioinformatics (GCB 2001) (E. Windender, R. Hofestädt, I. Liebich, eds.), Braunschweig, Germany, October 7-10, 2001, pp. 68-77, 2001.
, , Thomas Lengauer, Alexander Zien, Thomas Aigner, Centralization: a new method for the normalization of gene expression data, Bioinformatics, vol. 17, no. Suppl.1, pp. S323-S331, 2001.
, Thomas Lengauer, Using simple learning machines to derive a new potential for molecular modelling, in Rational Approaches to Drug Design, Proc. of 13th Eur. Symp. on QSAR, Prous Science, pp. 125-134, 2001.
, D. Hofmann, Thomas Lengauer, D. Hofmann, Derivation of a scoring function for crystal structure prediction, Acta Crystallogr A., vol. 57, no. Pt4, pp. 442-50, 2001.
, Thomas Lengauer, Patents
Frei programmierbares, universelles Parallel-rechnersystem zur Durchführung von allgemeinen Berechnungen, GMD - Forschungszentrum Informationstechnik GmbH, Sankt Augustin, no. PCT Patent application, European patent office 15.04.1998, 2001.
,