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, , , Bettina Kempkes, EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells, PLoS Pathogens, accepted.
Papers
, Adam W. Whisnant, Thomas Hennig, Lara Djakovic, Lars Dölken, , HSV-1 infection induces a downstream shift of the +1 nucleosome, Journal of Virology, vol. 99, no. 4, pp. e0208624, 2025.
Theses
Wenjia Zhong, Analysis of Plant microRNAs with Text Mining, Bachelor Thesis, LFE Bioinformatik, LMU München, 2025.
Papers
Moritz Mühlhofer, Felix Offensperger, Sarah Reschke, Georg Wallmann, , , Maximilian Riedl, Helmut Blum, Martin Haslbeck, , Johannes Buchner, Deletion of the transcription factors Hsf1, Msn2 and Msn4 in yeast uncovers transcriptional reprogramming in response to proteotoxic stress, FEBS Letters, vol. 598, no. 6, pp. 635-657, 2024.
Denise Ohnezeit, Jiabin Huang, Ute Westerkamp, Veronika Brinschwitz, Claudia Schmidt, Thomas Günther, Manja Czech-Sioli, Samira Weißelberg, Tabea Schlemeyer, Jacqueline Nakel, Julia Mai, Sabrina Schreiner, Carola Schneider, , Hella Schwanke, Melanie M. Brinkmann, Adam Grundhoff, Nicole Fischer, Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling, PLoS pathogens, vol. 20, no. 8, pp. e1012426, 2024.
Theses
Leonie Pohl, Beyond One Reference Genome: Pangenomic Variant Calling for Personalized Medicine, Master Thesis, LFE Bioinformatik, LMU München, 2024.
Aaron Roth, Efficient Read Mapping to a Pangenomic Reference Region with Splice-Graphs, Bachelor Thesis, LFE Bioinformatik, LMU München, 2024.
Papers
, Computational Integration of HSV-1 Multi-omics Data., Methods in molecular biology, vol. 2610, pp. 31–48, 2023.
, , RegCFinder: targeted discovery of genomic subregions with differential read density, Bioinformatics Advances, vol. 3, no. 1, pp. vbad085, 2023.
, Thomas Hennig, Pilar Graßl, Lara Djakovic, Adam W. Whisnant, Christopher S. Jürges, Franziska Koller, , , Lars Dölken, , HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes, Journal of Virology, vol. 97, no. 5, pp. e00381-23, 2023.
Zhijia Wang, Monika Macakova, Andrii Bugai, Sergey G. Kuznetsov, Antti Hassinen, Tina Lenasi, Swapnil Potdar, , Matjaz Barboric, P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway., Nucleic acids research, vol. 51, pp. 1687–1706, 2023.
Manivel Lodha, Ihsan Muchsin, Christopher Jürges, Vanda Juranic Lisnic, Anne L'Hernault, Andrzej J. Rutkowski, Bhupesh K. Prusty, Arnhild Grothey, Andrea Milic, Thomas Hennig, Stipan Jonjic, , , Lars Dölken, Decoding murine cytomegalovirus., PLoS pathogens, vol. 19, pp. e1010992, 2023.
Hella Schwanke, Vladimir Goncalves Magalhaes, Stefan Schmelz, Emanuel Wyler, Thomas Hennig, Thomas Günther, Adam Grundhoff, Lars Dölken, Markus Landthaler, Marco van Ham, Lothar Jänsch, Konrad Büssow, Joop van den Heuvel, Wulf Blankenfeldt, , , Melanie M. Brinkmann, The Cytomegalovirus M35 Protein Directly Binds to the Interferon-beta Enhancer and Modulates Transcription of Ifnb1 and Other IRF3-Driven Genes., Journal of virology, vol. 97, pp. e0040023, 2023.
Lara Djakovic, Thomas Hennig, Katharina Reinisch, Andrea Milic, Adam W. Whisnant, Katharina Wolf, , Tobias Haas, Arnhild Grothey, Christopher S. Jürges, , Elmar Wolf, , , Lars Dölken, The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes., Nature communications, vol. 14, pp. 4591, 2023.
Zhijia Wang, Samu V. Himanen, Heidi M. Haikala, , Anniina Vihervaara, Matjaz Barboric, Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release., Nucleic acids research, vol. 51, pp. 10970–10991, 2023.
Theses
David Wagemann, Conserved Binding Sites for Splicing and Alternative Splicing, Bachelor Thesis, LFE Bioinformatik, LMU München, 2023.
Xiheng He, Annotation and Assessment of AlphaFold2 Structures for Protein Isoforms, Bachelor Thesis, LFE Bioinformatik, LMU München, 2023.
Lukas Jaeger, Bioinformatic Methods of Individual and Pangenome Variations, Bachelor Thesis, LFE Bioinformatik, LMU München, 2023.
Papers
, Lara Djakovic, , Thomas Hennig, Adam W. Whisnant, Simone Backes, Lars Dölken, , HSV-1 and influenza infection induce linear and circular splicing of the long NEAT1 isoform., PloS one, vol. 17, pp. e0276467, 2022.
Milan Hluchý, Pavla Gajdušková, Igor Ruiz de los Mozos, Michal Rájecký, , Benedict-Tilman Berger, Zuzana Slabá, David Potěšil, , Jernej Ule, Zbyněk Zdráhal, Stefan Knapp, Kamil Paruch, , Dalibor Blazek, CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1, Nature, vol. 609, no. 7928, pp. 829-834, 2022.
Alexandra Schubö, , Markus Joppich, , Collecting SARS-CoV-2 Encoded miRNAs via Text Mining, Bioinformatics and Biomedical Engineering, Springer International Publishing, pp. 429–441, 2022.
Theses
Samuel Klein, Cross Species protein Isoform Alignment (CSI-A), Master Thesis, LFE Bioinformatik, LMU München, 2022.
Papers
Daniel F. R. Boehmer, Simone Formisano, Carina C. de Oliveira Mann, Stephan A. Mueller, , 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, OAS1/RNase L executes RIG-I ligand–dependent tumor cell apoptosis, Science Immunology, Science Immunology, vol. 6, no. 61, 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, 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.
Yong Huang, Rut Tejero, Vivian K. Lee, Concetta Brusco, Theodore Hannah, Taylor B. Bertucci, Chrystian Junqueira Alves, Igor Katsyv, , Ramsey Foty, Bin Zhang, , Guohao Dai, Hongyan Zou, Roland H. Friedel, Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics, Communications Biology, Springer Science and Business Media LLC, vol. 4, no. 1, 2021.
Shalaka Wahane, Xianxiao Zhou, Xiang Zhou, Lei Guo, , , Aarthi Ramakrishnan, Li Shen, , Bin Zhang, Roland H. Friedel, Hongyan Zou, Diversified transcriptional responses of myeloid and glial cells in spinal cord injury shaped by HDAC3 activity., Science advances, vol. 7, 2021.
Xiuye Wang, Liang Liu, Adam W. Whisnant, Thomas Hennig, Lara Djakovic, Nabila Haque, Cindy Bach, Rozanne M. Sandri-Goldin, , , Lars Dölken, Yongsheng Shi, Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation., PLoS genetics, vol. 17, pp. e1009263, 2021.
Amelie S. Lotz-Havla, Mathias Woidy, Philipp Guder, , Julian M. Klingbeil, Ana-Maria Bulau, Anja Schultze, Ilona Dahmen, Heidi Noll-Puchta, Stephan Kemp, Ralf Erdmann, , Ania C. Muntau, Sören W. Gersting, iBRET Screen of the ABCD1 Peroxisomal Network and Mutation-Induced Network Perturbations., Journal of proteome research, vol. 20, pp. 4366–4380, 2021.
Theses
Franziska Koller, Analysis of the role of cis-elements for changes in RNA polymerase II pausing, Bachelor Thesis, LFE Bioinformatik, LMU München, 2021.
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.
Papers
Xiuye Wang, Thomas Hennig, Adam W. Whisnant, , Bhupesh K. Prusty, , Elmira Forouzmand, William K. Hu, Luke Erber, Yue Chen, Rozanne M. Sandri-Goldin, Lars Dölken, Yongsheng Shi, Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27, Nature Communications, vol. 11, 2020.
, , Amrei L Menzel, , Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution, GigaScience, vol. 9, no. 6, 2020.
Joppich M and Olenchuk M and Mayer JM and Emslander Q and Jimenez-Soto LF and 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.
Xiang and Wahane Shalaka and Friedl Marie-Sophie and Kluge Michael and Friedel Caroline C. and Avrampou Kleopatra and Zachariou Venetia and Guo Lei and Zhang Bin and He Xijing and Friedel Roland H. and Zou Hongyan Zhou, 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.
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, , Markus Landthaler, Friedrich Grässer, Paul J. Lehner, , , Lars Dölken, Integrative functional genomics decodes herpes simplex virus 1., Nature communications, vol. 11, pp. 2038, 2020.
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
Anil Paul Chirackal Manavalan, Kveta Pilarova, , Koen Bartholomeeusen, Michal Rajecky, Jan Oppelt, Prashant Khirsariya, Kamil Paruch, Lumir Krejci, , Dalibor Blazek, CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes, EMBO reports, pp. e47592, 2019.
Philipp Metzger, Sabrina V. Kirchleitner, , Lars M. Koenig, Christine Hörth, Carlotta A. Rambuscheck, Daniel Böhmer, Julia Ahlfeld, Sebastian Kobold, , Stefan Endres, Max Schnurr, Peter Duewell, 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.
Constantin Ammar, , , Andreas Schmidt, Axel Imhof, , 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.
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, , Stefanie M. Hauck, Michael Sattler, Arie Geerlof, Veit Hornung, Vigo Heissmeyer, Christian Schulz, Mathias Heikenwalder, Elke Glasmacher, Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3, Journal of Experimental Medicine, Rockefeller University Press, 2019.
Michaela Rohrmoser, , 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, MIR sequences recruit zinc finger protein ZNF768 to expressed genes, Nucleic Acids Research, vol. 47, no. 2, pp. 700-715, 2019.
, Martina Vetter, Melanie Gündert, , Christine Fathke, Susanne E Ulbrich, Christoph Thomssen, , Eva J Kantelhardt, Comparison of six breast cancer classifiers using qPCR, Bioinformatics, 2019.
, , , YESdb: integrative analysis of environmental stress in yeast, Database, vol. 2019, 2019.
Moritz Mühlhofer, , Christopher G Stratil, , Elena Kunold, Nina C. Bach, Stephan A. Sieber, Martin Haslbeck, , Johannes Buchner, The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins, Cell Reports, vol. 29, no. 13, pp. 4593-4607, 2019.
Andrii Bugai, Alexandre J C Quaresma, , Tina Lenasi, Robert Düster, Christopher R Sibley, Koh Fujinaga, Petra Kukanja, Thomas Hennig, Melanie Blasius, Matthias Geyer, Jernej Ule, Lars Dölken, Matjaž Barborič, P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress, Molecular cell, vol. 74, no. 2, pp. 254-267, 2019.
Christina Funk, Verena Raschbichler, Diana Lieber, Jens Wetschky, Eileen K Arnold, Jacqueline Leimser, Michael Biggel, , Zsolt Ruzsics, Susanne M Bailer, 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.
Rut Tejero, Yong Huang, Igor Katsyv, , Jung-Yi Lin, Jessica Tome-Garcia, Nicolas Daviaud, Yuanshuo Wang, Bin Zhang, Nadejda M Tsankova, , Hongyan Zou, Roland H Friedel, Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment, EBioMedicine, vol. 42, pp. 252-269, 2019.
Papers
Kathrin Davari, Johannes Lichti, , Elke Glasmacher, 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.
Thomas Hennig, Marco Michalski, Andrzej J. Rutkowski, Lara Djakovic, Adam W. Whisnant, , Bhaskar Anand Jha, Marisa A. P. Baptista, Anne L’Hernault, , Lars Dölken, , 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.
Michael and Friedel Caroline C. Kluge, Watchdog - a workflow management system for the distributed analysis of large-scale experimental data, BMC Bioinformatics, vol. 19, no. 97, 2018.
Theses
, Methods for explaining biological systems and high-throughput data., PhD Thesis, LMU München, 2018.
, Analysis of Predicted Mass Spectra and Peptide Identification, Bachelor Thesis, LFE Bioinformatik, LMU München, 2018.
, Methods for Interactive analysis of Differential Alternative Splicing (MIDAS), Bachelor Thesis, LFE Bioinformatik, LMU München, 2018.
Papers
Tim-Michael Decker, , Stefan Krebs, Nilay Shah, Helmut Blum, , Dirk Eick, Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1, Scientific Reports, 2017.
Matthias Barann, , , Manananggal - A Novel Viewer For Alternative Splicing Events, BMC Bioinformatics, vol. 18, pp. 120, 2017.
Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, Henriette Uhlenhaut, Matthias Heinig, , Elke Glasmacher, 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.
, , , RelExplain—integrating data and networks to explain biological processes, Bioinformatics, vol. 33, no. 12, pp. 1837-1844, 2017.
, , 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.
Maximilian Hastreiter, Tim Jeske, Jonathan Hoser, , Kaarin Ahomaa, , Sebastian J. Kopetzky, Jan-Dominik Quell, H.-Werner Mewes, , KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis, Bioinformatics, vol. 33, no. 10, pp. 1565-1567, 2017.
Emanuel and Menegatti Jennifer and Franke Vedran and Kocks Christine and Boltengagen Anastasiya and Hennig Thomas and Theil Kathrin and Rutkowski Andrzej and Ferrai Carmelo and Baer Laura and Kermas Lisa and Friedel Caroline and Rajewsky Nikolaus and Akalin Altuna and Dölken Lars and Grässer Friedrich and Landthaler Markus Wyler, Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection, Genome Biology, vol. 18, no. 1, pp. 209, 2017.
Theses
, Expression data analysis and regulatory network inference by means of correlation patterns, PhD Thesis, LMU München, 2017.
Stefan Weber, Enhanced Suffix Arrays: Analysis of Efficient Implementations in Java, Master Thesis, LFE Bioinformatik, LMU München, 2017.
Papers
, , Cross-Species Conservation of Context-Specific Networks, BMC Systems Biology, vol. 10, no. 76, 2016.
Jian-Nan Zhang, Uwe Michel, Christof Lenz, , Sarah Köster, Zara d’Hedouville, Lars Tönges, Henning Urlaub, Mathias Bähr, Paul Lingor, Jan C. Koch, Calpain-mediated cleavage of collapsin response mediator protein-2 drives acute axonal degeneration, Scientific Reports, vol. 6, pp. 37050, 2016.
, , , Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis, BMC Bioinformatics, vol. 17, pp. 45, 2016.
Patricia Schöppner, , T Braun, M Daake, B Richter, Oliver F Lange, Martin Zacharias, , Martin Haslbeck, 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.
Vinicius Henrique Silva, Luciana Correia Almeida Regitano, , Fábio Pértille, Poliana Fernanda Giachetto, Ricardo Augusto Brassaloti, Natália Silva Morosini, , Luiz Lehmann Coutinho, Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle, PLOS ONE, vol. 11, no. 6, pp. e0157711, 2016.
, , , Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data, PLoS ONE, vol. 11, no. 10, 2016.
Theses
, Cross-Species Network and Transcript Transfer, PhD Thesis, Ludwig-Maximilians-Universität München, 2016.
Daniel Schmitz, Algorithmische Erzeugung von NGS-Panels sowie Berechnung von Allelfrequenzen in der molekulargenetischen Diagnostik, Bachelor Thesis, LFE Bioinformatik, LMU München, 2016.
Florian Hölzlwimmer, Network-based Analysis of Expression Time Series, Bachelor Thesis, LFE Bioinformatik, LMU, 2016.
, Computing Hybridization Networks Using Agreement Forests, PhD Thesis, Ludwig-Maximilians-Universität München, 2016.
Marco Lombardi, Implementation and Evaluation of Algorithms for Approximate Tandem Repeats, Master Thesis, LFE Bioinformatik, LMU München, 2016.
Markus Gruber, Differential Analysis of Different Gene Products, Master Thesis, LFE Bioinformatik, LMU, 2016.
Alexander Grün, Differential Splicing in TCGA Data, Master Thesis, LFE Bioinformatik, LMU, 2016.
Papers
Andrzej J. Rutkowski, , Anne L’Hernault, , Markus Schilhabel, Colin Crump, Philip Rosenstiel, Stacey Efstathiou, , , Lars Dölken, Wide-spread disruption of host transcription termination in HSV-1 infection, Nature Communications, vol. 6, no. 7126, 2015.
, Evelyn Kirner, , , , ContextMap 2: fast and accurate context-based RNA-seq mapping., BMC bioinformatics, vol. 16, pp. 122, 2015.
Andreas Osterman, Thorsten Stellberger, Anna Gebhardt, Marisa Kurz, , Peter Uetz, Hans Nitschko, Armin Baiker, Maria G. Vizoso-Pinto, The Hepatitis E virus intraviral interactome, Scientific reports, vol. 5, pp. 13872, 2015.
Yasuhiro Murakawa, Michael Hinz, Janina Mothes, Anja Schuetz, Michael Uhl, Emanuel Wyler, Tomoharu Yasuda, Guido Mastrobuoni, , Lars Dölken, Stefan Kempa, Marc Schmidt-Supprian, Nils Blüthgen, Rolf Backofen, Udo Heinemann, Jana Wolf, Claus Scheidereit, Markus Landthaler, RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway., Nature communications, vol. 6, pp. 7367, 2015.
, , Count ratio model reveals bias affecting NGS fold changes, Nucleic Acids Research, pp. pii: gkv696., 2015.
Sabine Hünten, Markus Kaller, Friedel Drepper, Silke Oeljeklaus, , , Anne Dueck, Norbert Eichner, , Gunter Meister, , Bettina Warscheid, Heiko Hermeking, p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses., Molecular & cellular proteomics : MCP, 2015.
, , Martin Haslbeck, , Alternative splicing in next generation sequencing data of Saccharomyces Cerevisiae, PLoS ONE, 2015.
, Computing all hybridization networks for multiple binary phylogenetic input trees, BMC Bioinformatics, vol. 16, no. 236, pp. 439-441, 2015.
, Stefan Altmann, , , , Addressing false discoveries in network inference, Bioinformatics, vol. 31, no. 17, pp. 2836-43, 2015.
Theses
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.
Julia Sophia Gerke, Integrated analysis of gene expression data and clinical data, Master Thesis, LFE Bioinformatik / LMU München, 2015.
Katharina Schmid, Efficient Construction of de Bruijn Graphs Using Suffix Arrays, Bachelor Thesis, LFE Bioinformatik / LMU München, 2015.
Anna-Kathrin Kopetzki, On Closest String Problems for Different Distances and Norms, Bachelor Thesis, LFE Bioinformatik / LMU München, 2015.
Papers
, Jonas Zierer, , Refining ensembles of predicted gene regulatory networks based on characteristic interaction sets, PLoS One, vol. 9, no. 2, pp. e84596, 2014.
, Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests, arXiv:1408.3044, 2014.
, , To be, or not to be: konservierte eukaryotische Regulationsnetzwerke?, BIOspektrum, vol. 20, no. 5, pp. 514-516, 2014.
, 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.
, N Zach, R Norel, Johann Hawe, D Schoenfeld, G Stolovitsky, M L Leitner, et al, Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression, Nature Biotechnology, no. Nov 2, 2014.
, Jürgen Haas, Diana Lieber, Georg Malterer, Lukasz Jaskiewicz, Mihaela Zavolan, Lars Dölken, , Widespread context-dependency of microRNA-mediated regulation., Genome research, 2014.
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, , Alice Meier, Hassan Nasir, Ulrich Neumaier, Verena Prade, Jonas Reeb, Aleksandr Sorokoumov, Ilira Troshani, Susann Vorberg, Sonja Waldraff, Jonas Zierer, Henrik Nielsen, Burkhard Rost, LocTree3 prediction of localization., Nucleic acids research, vol. 42, pp. W350-5, 2014.
Theses
, Bioinformatics methods for the biological interpretation of high-throughput experiments, Habilitation, Ludwig-Maximilians-Universität München, 2014.
, Algorithmic Methods for Systems Biology of Herpes-viral microRNAs, PhD Thesis, LMU München, 2014.
Evelyn Kirner, Detektion von zirkulären RNAs in Sequenzierdaten, Bachelor Thesis, LMU München, 2014.
Laura Schiller, Efficient computation of hybridization networks, Master Thesis, LFE Bioinformatik / 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.
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.
Papers
Ronny Kramer, , , Dirk von Soosten, Sven Dänicke, Eva-Maria Weber, , Juergen Rehage, Gerhard Jahreis, 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.
, , Complementing the Eukaryotic Protein Interactome, PLOS One, vol. 8, no. 6, pp. e66635, 2013.
Bernd Rädle, Andrzej Rutkoswki, Zsolt Ruzsics, , Ulrich H Koszinowski, Lars Dölken, 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.
Samantha J. Griffiths, Manfred Koegl, Chris Boutell, Helen L. Zenner, Colin Crump, , , Gerald Barry, Kimberley Martin, Marie H. Craigon, Rui Chen, Lakshmi N. Kaza, Even Fossum, John K. Fazakerley, Stacey Efstathiou, , Peter Ghazal, Jürgen Haas, 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.
Mirko Trilling, Nicolas Bellora, Andrzej J. Rutkowski, Miranda de Graaf, Paul Dickinson, Kevin Robertson, Olivia Prazeres da Costa, Peter Ghazal, , M. Mar Alba, Lars Dölken, 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.
Roland H. Friedel, , , Roland Rad, Philippe Soriano, Clonal expansion of transposon insertions identifies candidate cancer genes in a PiggyBac mutagenesis screen, PLoS ONE, vol. 8, no. 8, pp. e72338, 2013.
Harth-Hertle ML, Scholz BA, , Glaser LV, Dölken L, , Bettina Kempkes, 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.
Kaspar Burger, Bastian Mühl, Markus Kellner, Michaela Rohrmoser, Anita Gruber-Eber, , , Lars Dölken, Dirk Eick, 4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response, RNA biology, vol. 10, 2013.
, Computational analysis of virus-host interactomes, Methods in molecular biology, vol. 1064, pp. 115-30, 2013.
K Danowski, JJ Gross, K Gellrich, T Petri, HA Van Dorland, RM Bruckmaier, HD Reichenbach, , HHD Meyer, FJ Schwarz, H Kliem, Metabolic status and oestrous cycle in dairy cows, International Journal of Livestock Production, vol. 4, no. 9, pp. 135–147, 2013.
Robert Maier, , , A Turing test for artificial expression data, Bioinformatics, vol. 29, no. 20, pp. 2603-2609, 2013.
Schrynemackers M, , Geurts P, On protocols and measures for the validation of supervised methods for the inference of biological networks, Front Genet., vol. 4, pp. 262, 2013.
, Lars Dölken, Lukasz Jaskiewicz, , PARma: identification of microRNA target sites in AGO-PAR-CLIP data., Genome biology, vol. 14, pp. R79, 2013.
, Lars Dölken, , RIP-chip enrichment analysis, Bioinformatics, vol. 29, no. 1, September 2012, Basel, Switzerland, pp. 77–83, 2013.
Mayuko Kurome, , 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, 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.
Sorg D, Danowski K, Korenkova V, Rusnakova V, , , Meyer HH, Kliem H, 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.
Herbert B. Schiller, Michaela-Rosemarie Hermann, Julien Polleux, Timothée Vignaud, Sara Zanivan, , Zhiqi Sun, Aurelia Raducanu, Kay-E Gottschalk, Manuel Théry, Matthias Mann, Reinhard Fässler, 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.
Lenac Roviš T, Bailer SM, Pothineni VR, Ouwendijk WJ, Šimić H, Babić M, Miklić K, Malić S, Verweij MC, Baiker A, , von Brunn A, , Früh K, Verjans GM, Jonjić S, Jürgen Haas, Comprehensive analysis of varicella-zoster virus proteins using a new monoclonal antibody collection, J Virol. 2013, vol. 87, no. 12, pp. 6943-54, 2013.
, , Simon Dirmeier, , , A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae, Nucleic Acids Research, vol. 41, no. 18, pp. 8452-8463, 2013.
, , , , Mining RNA-Seq Data for Infections and Contaminations, PloS one, vol. 8, pp. e73071, 2013.
Theses
, Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic, PhD Thesis, LMU München, 2013.
Alexander Grün, Interactive Modeling of Complex Hypothesis Using Ontologies, Bachelor Thesis, LFE Bioinformatik / LMU München, 2013.
Lars von den Driesch, Evolutionary conservation of PAR-CLIP microRNA target sites, Bachelor Thesis, LFE Bioinformatik / LMU München, 2013.
Judith Boldt, Entwicklung eines Validierungs-Programms von Real-Time PCRs in der GVO-Analytik, Bachelor Thesis, LMU München, 2013.
Papers
, , 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.
, , , , Detection and correction of probe-level artefacts on microarrays, BMC Bioinformatics, vol. 13, pp. 114, 2012.
, , , , A context-based approach to identify the most likely mapping for RNA-seq experiments, BMC Bioinformatics, vol. 13(Suppl 6), pp. S9, 2012.
Tobias Stögbauer, , , Joachim O. Rädler, Experiment and Mathematical Modeling of Gene Expression Dynamics in a Cell-Free System, Integrative Biology, vol. 4 (5), pp. 494 - 501, 2012.
, Matthias Böck, , ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes, Proceedings of the German Conference on Bioinformatics (GCB), vol. 26, pp. 69-81, 2012.
Robert Lindner, , A comprehensive evaluation of alignment algorithms in the context of RNA-Seq, PLoS ONE, vol. 7, no. 12, pp. e52403, 2012.
Marcinowski L, Tanguy M, Krmpotic A, Rädle B, Lisnić VJ, Tuddenham L, Chane-Woon-Ming B, Ruzsics Z, , Benkartek C, Babic M, , Trgovcich J, Koszinowski UH, Jonjic S, Pfeffer S, Lars Dölken, 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.
Lisa Marcinowski, Michael Lidschreiber, , Martina Rieder, Jens B. Bosse, Bernd Rädle, , Ildiko Györy, Miranda de Graaf, Olivia Prazeres da Costa, Philip Rosenstiel, , , Zsolt Ruzsics, Lars Dölken, Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection, PLoS Pathog, vol. 8, no. 9, pp. e1002908, 2012.
Milan Spasic, , Johanna Schott, Jochen Kreth, Kathrin Leppek, Sarah Hofmann, Sevim Ozgur, Georg Stoecklin, Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm, PLoS Genet, vol. 8, no. 1, pp. e1002433, 2012.
, , Kaspar Burger, Zsolt Ruzsics, Stefan Krebs, Stefanie Kaufmann, Georg Malterer, Anne L’Hernault, Markus Schilhabel, Stefan Schreiber, Philip Rosenstiel, , Dirk Eick, , Lars Dölken, Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution., Genome research, vol. 22, pp. 2031-42, 2012.
, , Detecting outlier peptides in quantitative high-throughput mass spectrometry data, Journal of Proteomics, vol. 75, no. 11, pp. 3230-9, 2012.
Daniel Marbach, James C Costello, , Nicole M Vega, Robert J Prill, Diogo M Camacho, Kyle R Allison, Manolis Kellis, James J Collins, Gustavo Stolovitzky, Wisdom of crowds for robust gene network inference., Nature methods, vol. 9, pp. 796-804, 2012.
, , , , , Inferring Gene Regulatory Networks by ANOVA, Bioinformatics, vol. 28, no. 10, pp. 1376-1382, 2012.
, , , , Rigorous assessment of gene set enrichment tests, Bioinformatics, vol. bts164v1-bts164, pp. 7, 2012.
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.
Theses
, RELEXplain - Relation Networks Explaining Biological Processes, Master Thesis, LFE Bioinformatik / LMU München, 2012.
, Activity of microRNAs and transcription factors in Gene Regulatory Networks, PhD Thesis, LMU München, 2012.
Johann Hawe, Prediction of disease progression in patients with Amyotrophic Lateral Sclerosis, Bachelor Thesis, Bioinformatics, LMU München, 2012.
Lucia Puchbauer, Analysis of High-Throughput Data in Oncology, Master Thesis, LFE Bioinformatik / LMU München, 2012.
Papers
, , Space-Efficient Preprocessing Schemes for Range Minimum Queries on Static Arrays, SIAM Journal on Computing, vol. 40, no. 2, pp. 465-492, 2011.
, Jürgen Haas, Virus-host interactomes and global models of virus-infected cells, Trends in Microbiology, vol. 19, no. 10, pp. 501-8, 2011.
, Celine Scornavacca, Alberto Cenci, Daniel H Huson, Fast computation of minimum hybridization networks, Bioinformatics, vol. 28, no. 2, pp. 191-197, 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.
, , , Experiment Specific Expression Patterns, RECOMB 2011, Research in Computational Molecular Biology (Vineet Bafna, S. Cenk Sahinalp, eds.), Springer, vol. 15, pp. 339-354, 2011.
Herbert B. Schiller, , Cyril Boulegue, Reinhard Fässler, 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.
Susanne Pfefferle, Julia Schöpf, Manfred Kögl, , 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, The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors, PLoS Pathog, vol. 7, no. 10, pp. e1002331, 2011.
Zhen Wang, Guohui Ding, , Hong Li, Lei Liu, Rong Zeng, Yoshio Tateno, Yixue Li, Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes, Molecular Biology and Evolution, vol. 28, no. 3, pp. 1131-40, 2011.
, , , Nicola Mulder, , From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems, Bioinformatics, vol. 27, no. 13, pp. i366-i373, 2011.
Dintner Sebastian, Anna Staroń, , , Thorsten Mascher, Susanne Gebhard, 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.
, , , MIRTFnet: analysis of miRNA regulated transcription factors, PLoS One, pp. 6(8):e22519, 2011.
, , Contextual analysis of RNAi-based functional screens using interaction networks, Bioinformatics, vol. 27, pp. 2707-2713, 2011.
Theses
Andreas Kolberg, Automatische Klassifizierung von Alternativen Splicing-Events in Proteinstrukturen, 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.
, 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.
Vadim Jördens, Optimization of Homology-based Structure Models, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Papers
, Philip Effinger, Markus Held, Michael Kaufmann, Stephan Kottler, Visualization of Complex BPEL Models, Proc. of the 17th International Symposium on Graph Drawing (GD ’09), 2010.
, Tanja Oberwinkler, Locedie Mansueto, Friedhelm Pfeifer, Eduardo Mendoza, , Dieter Oesterhelt, Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis, PLoS Computational Biology, vol. 6, no. 6, pp. e1000799, 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.
, , , Fuzzy modeling, Modeling in Systems Biology: The Petri Net Approach (Ina Koch, Wolfgang Reisig, Falk Schreiber, eds.), Springer, 2010.
, Analysis of High-throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life, Ausgezeichnete Informatikdissertationen 2009, GI-Edition Lecture Notes in Informatics, 2010.
Wolfgang Fischer, , Stefanie Rohrer, Matthias Zeiller, Arno Karnholz, Reinhard Hoffmann, , Rainer Haas, 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.
, , , , miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature, BMC Bioinformatics, vol. 11, pp. 135, 2010.
, , , , Petri Nets with Fuzzy Logic (PNFL): Reverse Engineering and Parametrization, PLoS One, vol. 5, pp. e12807, 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.
, , Finding Range Minima in the Middle: Approximations and Applications, Mathematics in Computer Science, vol. 3, no. 1, pp. 17-30, 2010.
Lars Dölken, Georg Malterer, , 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, 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.
, Stefanie Kaufmann, Lars Dölken, , HALO - A Java framework for precise transcript half-life determination, Bioinformatics, vol. 26, no. 9, pp. 1264-1266, 2010.
, , Classification of ncRNAs using position and size information in deep sequencing data, Bioinformatics, vol. 26, no. 18, pp. i426-i432, 2010.
, , Vorescore - fold recognition improved by rescoring of protein structure models, Bioinformatics, vol. 26, no. 18, pp. i482-i488, 2010.
, Philip Effinger, Markus Held, Michael Kaufmann, An Automatic Layout Algorithm for BPEL Processes, SoftVis ’10: Proceedings of the 5th ACM Symposium on Software visualization, ACM, New York, NY, USA, 2010.
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, , Holger Prokisch, Bernhard R. Winkelmann, Tim D. Spector, H.-Erich Wichmann, Michael Stumvoll, Nicole Soranzo, Winfried März, Wolfgang Koenig, Thomas Illig, Christian Gieger, 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.
Theses
Sebastian Ullherr, Prediction of Transcript Half-Lives, 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.
Markus Meier, Visualisierung von Repeats im Genom, Bachelor Thesis, LFE Bioinformatik, LMU München, 2010.
Papers
Nino Shervashidze, SVN Vishwanathan, , Kurt Mehlhorn, Karsten Borgwardt, 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.
, Jan Krumsiek, , Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast, Journal of Computational Biology, vol. 16, no. 8, pp. 1-17, 2009.
O. Gonzalez, S. Gronau, F. Pfeiffer, E. Mendoza, , D. Oesterhelt, Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum, PloS Computational Biology, vol. 5, no. 4, pp. e1000332, 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.
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.
, , , , , , , , Algorithmische Systembiologie mit Petrinetzen – Von qualitativen zu quantitativen Systemmodellen, Informatik-Spektrum, vol. 32, no. 4, pp. 310-319, 2009.
, Susanne Gronau, Friedhelm Pfeiffer, Eduardo Mendoza, , Dieter Oesterhelt, Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum, PloS Computational Biology, vol. 5, no. 4, pp. e1000332, 2009.
, , , Systematic Comparison of SCOP and CATH: A new Gold Standard for Protein Structure Analysis, BMC Structural Biology, vol. 9, no. 23, 2009.
AG Moll, MT Lindenmeyer, M Kretzler, PJ Nelson, , CD Cohen, Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays, PLoS ONE, vol. 4, no. 3, pp. e4702, 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.
, , Identifying the topology of protein complexes from affinity purification assays, Bioinformatics, vol. 25, no. 16, pp. 2140-2146, 2009.
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.
, Lars Dölken, Zsolt Ruzsics, Ulrich Koszinowski, , Conserved principles of mammalian transcriptional regulation revealed by RNA half-life, Nucleic Acids Research, vol. 37, no. 17, pp. e115, 2009.
Even Fossum, , 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, Evolutionarily conserved herpesviral protein interaction networks., PLoS Pathog, vol. 5, no. 9, pp. e1000570, 2009.
, Lars Dölken, Metabolic tagging and purification of nascent RNA: Implications for transcriptomics, Molecular BioSystems, vol. 5, no. 11, pp. 1271-8, 2009.
Theses
, Alternative Splicing and Protein Structure Evolution, PhD Thesis, LMU München, 2009.
, Reconstruction, Modeling and Analysis of Haloarcheal Metabolic Networks, PhD Thesis, LMU München, 2009.
, Analysis of High-Throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life, PhD Thesis, 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.
Jeremias Weihmann, Genome-Rearrangements: Sortieren mit erweiterten Transreversals, Diploma Thesis, LFE Bioinformatik / LMU München, 2009.
Yanxiang Zhou, Small RNA Annotation and Analysis in Deep Sequencing Data, Bachelor Thesis, LFE Bioinformatik, LMU München, 2009.
Mark Heron, Network Oriented Analysis of CLA Expression Data, Bachelor Thesis, LFE Bioinformatik, LMU München, 2009.
Johannes Bräuer, Optimization of 3D Protein Structure Models, Bachelor Thesis, LFE Bioinformatik, LMU München, 2009.
, Program Development by Proof Transformation, PhD Thesis, LMU München, 2009.
Papers
, , , FERN - a Java framework for stochastic simulation and evaluation of reaction networks, BMC Bioinformatics, vol. 9, no. 1, pp. 356, 2008.
, , 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.
, , Horst Martin Stühler, 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.
, Jan Krumsiek, , 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.
, Analysis of a Modification of Gusfield’s Recursive Algorithm for Reconstructing Ultrametric Trees, Information Processing Letters, vol. 108, no. 4, pp. 222-225, 2008.
, Artem Lysenko, Matthew Hindle, Keywan Hassani-Pak, Ralf Thiele, Christopher J. Rawlings, Jacob Köhler, Jan Taubert, Graph-based sequence annotation using a data integration approach, Journal of Integrative Bioinformatics, vol. 5, no. 2, 2008.
, , 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.
, Tatjana Schilling, , Ludger Klein-Hitpass, Franz Jakob, Norbert Schütze, Microarray analyses of transdifferentiated mesenchymal stem cells, Journal of Cellular Biochemistry, vol. 103, no. 2, pp. 413-433, 2008.
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.
, Oliver Sacher, Robert Körner, Johann Gasteiger, 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.
Jörn Marialke, Simon Tietze, , Similarity based docking, J. Chem. Inf. Model., vol. 48, no. 1, pp. 186–196, 2008.
, Jochen Haag, Pia M. Gebhard, , Thomas Aigner, Normalization strategies for mRNA expression data in cartilage research, Osteoarthritis Cartilage, vol. 16, pp. 947-955, 2008.
, S. Gronau, M. Falb, F. Pfeiffer, E. Mendoza, , D. Oesterhelt, Reconstruction, modeling & analysis of Halobacterium salinarum R-1metabolism, Mol Biosyst, vol. 4, no. 2, pp. 148-59, 2008.
, , Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes, Bioinformatics, vol. 24, no. 10, pp. 1257-63, 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.
, 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.
, 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.
, , T. Aigner, , Normalization and gene p-value estimation: issues in microarray data processing, Bioinform Biol Insights, vol. 2, pp. 291-305, 2008.
Michaela Falb, Kerstin Müller, Lisa Königsmaier, Tanja Oberwinkler, Patrick Horn, Susanne von Gronau, , Friedhelm Pfeiffer, Erich Bornberg-Bauer, Dieter Oesterhelt, Metabolism of halophilic archaea, Extremophiles, vol. 12, no. 2, pp. 177-196, 2008.
Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, , Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L, Overview of BioCreative II gene normalization., Genome Biology, vol. 9, no. Supplement 2, pp. S3, 2008.
, Jan Erik Gewehr, , AutoPSI: a database for automatic structural classification of protein sequences and structures, Nucleic Acids Res., vol. 36, pp. 398–401, 2008.
, , Franziska Meier, Florian Oefinger, Christian Potthast, , ProSAS: a database for analyzing alternative splicing in the context of protein structures, Nucleic Acids Res., vol. 36, pp. D63–68, 2008.
, , , Alternative splicing and protein structure evolution, Nucleic Acids Res., vol. 36, pp. 550–558, 2008.
, , , Protein structure alignment considering phenotypic plasticity, Bioinformatics, vol. 24, pp. 98–104, 2008.
Lars Dölken, Zsolt Ruzsics, Bernd Rädle, , , Jörg Mages, Reinhard Hoffmann, Paul Dickinson, Thorsten Forster, Peter Ghazal, Ulrich H Koszinowski, High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay, RNA, vol. 14, no. 9, pp. 1959–1972, 2008.
Jan Krumsiek, , , ProCope–protein complex prediction and evaluation, Bioinformatics, vol. 24, no. 18, pp. 2115–2116, 2008.
Christian Gieger, , 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, Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum, PLoS Genetics, vol. 4, no. 11, pp. e1000282, 2008.
Theses
Simon W. Ginzinger, Bioinformatics Methods for NMR Chemical Shift Data, PhD Thesis, LMU München, 2008.
Marko Skocibusic, Improving CheckShift, Diploma Thesis, LFE 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.
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.
Thomas Mair, Analysis of Alternative Splicing of Proteins, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Sebastian Pölsterl, Comparison of Alternative Splicing in Higher Organisms, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Papers
Amihood Amir, , Moshe Lewenstein, 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.
K.M. Borgwardt, , SVN Vishwanathan, H.P. Kriegel, An efficient sampling scheme for comparison of large graphs, Mining and Learning with Graphs, Electronic Proceedings, no. 1, 2007.
Albrecht von Brunn, Carola Teepe, Jeremy C. Simpson, Rainer Pepperkok, , , Rhonda Roberts, Jürgen Haas, Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome, PLoS ONE, vol. 2, no. 5, pp. e459, 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.
, , 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.
, , Influence of degree correlations on network structure and stability in protein-protein interaction networks, BMC Bioinformatics, vol. 8, pp. 297, 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.
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.
, , , RelEx - Relation extraction using dependency parse trees, Bioinformatics, vol. 23, no. 3, pp. 365-371, 2007.
, , Human Gene Normalization by an Integrated Approach including Abbreviation Resolution and Disambiguation, Second BioCreative Challenge Evaluation Workshop, 2007.
Andreas Steffen, , On the ease of predicting the thermodynamic properties of beta-cyclodextrin inclusion complexes, Chem Cent J., vol. 1, no. 29, 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, 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.
Markus Böhl, Simon Tietze, Andrea Sokoll, Sineej Madathil, Frank Pfennig, , Karim Fahmy, Herwig O. Gutzeit, Flavonoids Affect Actin Functions in Cytoplasm and Nucleus, Biophysical Journal, vol. 93, no. 8, pp. 2767-2780, 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.
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.
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.
, Jörn Marialke, Robert Körner, Simon Tietze, 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.
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.
Z. Fan, S. Soder, S. Oehler, , Thomas Aigner, Activation of interleukin-1 signaling cascades in normal and osteoarthritic articular cartilage, Am J Pathol, vol. 171, no. 3, pp. 938-946, 2007.
Jan Erik Gewehr, Martin Szugat, , BioWeka–extending the Weka framework for bioinformatics, Bioinformatics, vol. 23, no. 5, pp. 651-653, 2007.
Alexander Zien, Pia M. Gebhard, , Thomas Aigner, Phenotyping of chondrocytes in vivo and in vitro using cDNA array technology, Clin Orthop Relat Res, vol. 460, pp. 226-33, 2007.
, Jan Erik Gewehr, , , Vorolign - Fast Structural Alignment using Voronoi Contacts, Bioinformatics, vol. 23, no. 2, pp. e205-e211, 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.
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.
Theses
, Novel Graph Kernels for Biological Network Comparison, Diploma Thesis, Database and Information Systems/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.
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.
Robert Körner, Analyse biochemischer Reaktionen an Hand von imaginären Übergangszuständen, 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.
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.
, Vergleichende Genomanalyse eines neu sequenzierten H.pylori Stamms, Master Thesis, LFE 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.
Andreas Grimm, 3D tomographic and single-particle reconstruction using level set methods, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU 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.
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.
Sebastian Dümcke, Optimization of Sequence-Structure Alignments using the Vorolign-Scoring Function, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
, Phenotypic Plasticity as a Measure for Protein Structural Similarity, Master Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Papers
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.
, , 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.
, , Stefan Kramer, 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.
Simon W. Ginzinger, , SimShift: Identifying structural similarities from NMR chemical shifts, Bioinformatics, vol. 22, no. 4, pp. 460-465, 2006.
Thomas Aigner, Pia M Gebhard, , Hongwei Zhang, K Wayne Marshall, cDNA arrays in degenerative arthritis research, Future Rheumatology, vol. 11, pp. 101-109, 2006.
, T. Duchrow, , , 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.
Gene and protein nomenclature in public databases, BMC Bioinformatics, vol. 7, pp. 372, 2006.
Andreas Kämper, , Matthias Rarey, Christel M. Marian, Thomas Lengauer, 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.
Thomas Aigner, , Joachim Saas, Pia M. Gebhard, Jochen Haag, Tilo Weiss, Alexander Zien, Franz Obermayer, , Eckart Bartnik, Large-Scale Gene Expression Profiling of Osteoarthritic Cartilage Degeneration, Arthritis&Rheumatism, vol. 54, no. 11, pp. 3533-3544, 2006.
Dong-Yup Lee, , Sang-Yup Lee, Colored Petri Net Modeling and Simulation of Signal Transduction Pathways, Metabolic Engineering, vol. 8, no. 2, pp. 112-122, 2006.
H. Redestig, , , J. Selbig, 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.
Joachim Saas, Jochen Haag, D. Rueger, S. Chubinskaya, , , Eckart Bartnik, Thomas Aigner, 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.
Martin Szugat, Web Servicing the Office, XML and Web Services Magazin, vol. 2006, no. 1, pp. 150-152, 2006.
Martin Szugat, Wikimanie, Entwicklermagazin, vol. 2006, no. 1, pp. 96-99, 2006.
Peter Uetz, , Christine Zeretzke, C. Atzler, Armin Baiker, B. Berger, Seesandra V. Rajagopala, M. Roupelieva, Dietlinde Rose, Even Fossum, Jürgen Haas, Herpesviral protein networks and their interaction with the human proteome, Science, vol. 311, no. 5758, pp. 239-42, 2006.
, Christoph Küper, Kirsten Jung, Prospero Naval, Eduardo Mendoza, Parameter estimation using Simulated Annealing for S-system models of biochemical networks, Bioinformatics, vol. 23, no. 4, pp. 480-486, 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.
, , Toward the complete interactome, Nat Biotechnol, vol. 24, no. 6, pp. 614-615, 2006.
, , Inferring topology from clustering coefficients in protein-protein interaction networks, BMC Bioinformatics, vol. 7, pp. 519, 2006.
Books
Martin Szugat, Jan Erik Gewehr, Cordula Lochmann, Social Software, entwickler.press, 2006.
Theses
Daniel Güttler, LiMB - Ein interaktiver Browser zur Analyse biomedizinischer Texte mit Hilfe von Textmining, Diploma Thesis, 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.
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.
, Contextual Analysis of Gene Expression Data, PhD Thesis, 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.
Jörn Marialke, Similarity Based Methods for the Prediction of Protein Ligand Complexes, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2006.
, 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.
Papers
, Simon W. Ginzinger, 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.
, , Stefan Kramer, 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.
Simon W. Ginzinger, , SimShift: Identifying Structural Similarities from NMR Chemical Shifts, European Conference on Computational Biology (ECCB05), 2005.
, Katharina H.V. Jahn, Selina Sommer, Stephen Rudd, Hans W. Mewes, Igor V. Tetko, Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage, Bioinfomatics, vol. 21, no. 8, pp. 1383-1388, 2005.
, , , 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.
A Facius, C Englbrecht, , A Groscurth, S Benjamin, S Wanka, HW Mewes, PRIME: a graphical interface for integrating genomic/proteomic databases, Proteomics, vol. 5, no. 1, pp. 76-80, 2005.
Martin Szugat, Daniel Güttler, , , Web Servicing the Biological Office, Bioinformatics, vol. 21, no. (Suppl. 2), pp. 268-269, 2005.
, Robert Körner, Jörn Marialke, Embedded subgraph isomorphism and its applications in cheminformatics and metabolomics, 1st German Conference in Chemoinformatics, 2005.
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.
Thomas Aigner, Joachim Saas, Alexander Zien, , Pia M. Gebhard, Thomas Knorr, 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.
M. Gebauer, Joachim Saas, , Jochen Haag, S. Soder, M. Pieper, Eckart Bartnik, J. Beninga, , Thomas Aigner, 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.
, , Identifying active transcription factors and kinases from expression data, Bioinformatics, vol. 21, no. Suppl 2, pp. 115-122, 2005.
, , Thomas Aigner, , 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.
, Jan Erik Gewehr, 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.
, Daniel Güttler, , , A simple approach for protein name identification: prospects and limits, BMC Bioinformatics, vol. 6, no. (Suppl.1), pp. S15, 2005.
, , Heinz-Theodor Mevissen, , Juliane Fluck, ProMiner: rule-based protein and gene entity recognition, BMC Bioinformatics, vol. 6, no. (Suppl.1), pp. S14, 2005.
, , Stefan Kramer, Fast Frequent String Mining Using Suffix Arrays, TUM-I0512, Institut für Informatik der Technischen Universität München, no. TUM-I0512, 2005.
, Jan Erik Gewehr, , QUASAR–scoring and ranking of sequence-structure alignments, Bioinformatics, vol. 21, no. 24, pp. 4425–4426, 2005.
Theses
Niklas Von Öhsen, Profile-Profile alignment for remote homology and domain detection of proteins, PhD Thesis, Ludwig-Maximilians-Universität München, 2005.
Fabian Gerick, Ein programmierbarer Web Service zur Charakterisierung biologischer Objekte, Bachelor Thesis, LMU München, 2005.
, Inference of Regulatory Networks Using Physical Models, Bachelor Thesis, LFE Bioinformatik, 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.
Stephan Vogt, Topic Maps, Bachelor Thesis, LMU München, 2005.
Papers
, Daniel Güttler, , , Exact versus approximate string matching for protein name identification, BioCreative Challenge Evaluation Workshop, 2004.
, , Heinz-Theodor Mevissen, , Juliane Fluck, ProMiner: Organism-specific protein name detection using approximate string matching, BioCreative Challenge Evaluation Workshop, 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.
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.
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.
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.
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.
Dong-Yup Lee, , Sang-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.
, , , New methods for joint analysis of biological networks and expression data, Bioinformatics, vol. 20, no. 10, pp. 1517-1521, 2004.
Peter Uetz, Seesandra V. Rajagopala, , Jürgen Haas, From ORFeomes to protein interaction maps in viruses, Genome Res, vol. 14, no. 10B, pp. 2029-2033, 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.
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.
, , , ToPNet - an application for interactive analysis of expression data and biological networks, Bioinformatics, vol. 20, no. 9, pp. 1470-1471, 2004.
Theses
, New Analysis Methods for Gene Expression Data via Construction and Incorporation of Biological Networks, PhD Thesis, Ludwig-Maximilians-Universität München, 2004.
Dorothee Liebich, Packungsprobleme bei Proteinen, PhD Thesis, Friedrich-Wilhelms-Universität Bonn, 2004.
Thomas Obkircher, Eine erweiterbare Bioinformatik Umgebung zur kriterienbasierten Protein Identifizierung, 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.
Volker Hintermair, Characterisation and Visualisation of Protein Families based on Multicriterial Clustering, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2004.
Patents
, D. Hoffmann, Fluorescent Energy for Elucidating the 3D Structure of Biological Macromolecules (FETMA), no. PCT Patent application, European patent office 10.08.2001, 2004.
, , Alexander Zien, 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.
Papers
, Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices, Discrete Applied Mathematics, vol. 127, no. 1, pp. 163-177, 2003.
, 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.
, Juliane Fluck, Heinz-Theodor Mevissen, , 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.
D. Hofmann, , Crystal structure prediction with data mining, J. Mol. Struct., vol. 647, no. 1, pp. 17-39, 2003.
Thomas Aigner, Alexander Zien, , , J. Bone, Gene expression in chondrocytes assessed with use of microarrays, Joint Surg Am, vol. 85-A, no. Suppl 2, pp. 117-123, 2003.
, , , 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.
Alexander Zien, Juliane Fluck, , Thomas Lengauer, Microarrays: How Many Do You Need?, Journal of Computational Biology, vol. 10, no. 3-4, pp. 653-667, 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.
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.
Jan T. Kim, Jan Erik Gewehr, Thomas Martinetz, Binding Matrix: A Novel Approach for Binding Site Recognition, Bioinformatics 2003, Bioinformatics, pp. Poster, 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.
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.
Books
Werner Mewes, Dmitrij Frishman, , Stefan Kramer, Proceedings of the German Conference on Bioinformatics, GCB 2003 (Neuherberg and Garching, Germany, October 12-14, 2003), belleville Verlag München, 2003.
, Grundlegende Algorithmen - Einführung in den Entwurf und die Analyse effizienter Algorithmen, Vieweg Verlag, 2003.
Theses
Jan Erik Gewehr, The Binding Matrix - A Statistical Learning Approach to Protein-DNA Binding Site Prediction, Diploma Thesis, University of Lübeck, 2003.
Alexander Zien, Computational Methods for Gene Expression Data Analysis, PhD Thesis, Friedrich-Wilhelms-Universität Bonn, 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.
William Travis Holton, Evaluation of mapping consistency between public gene and protein databases, Bachelor Thesis, Ludwig-Maximilians-Universität München, 2003.
Papers
Philippe Ferrara, , Amedeo Caflisch, Evaluation of a fast implicit solvent model for molecular dynamics simulations, Proteins: Structure, Function, and Bioinformatics, vol. 46, no. 1, pp. 24-33, 2002.
, Alexander Zien, , Thomas Lengauer, Co-clustering of biological networks and gene expression data, Bioinformatics, vol. 18, no. 90001, pp. S145-S154, 2002.
Thomas Aigner, E. Bartnik, Alexander Zien, , Functional genomics of osteoarthritis, Pharmacogenomics, vol. 3, no. 5, pp. 635-50, 2002.
Mario Albrecht, , , Thomas Lengauer, Improving fold recognition of protein threading by experimental distance constraints, In Silico Biol, vol. 2, no. 3, pp. 325-337, 2002.
, D. Güttler, , , Biological context and the analysis of gene expression data, ECCB 2002 (H.-P. Lenhof, ed.), vol. Poster, 2002.
, D. Güttler, , , Prediction of gene functions from biological interactions, RECOMB 2002 (M. Vingron, ed.), vol. Poster, 2002.
J. Freudenberg, , , Thomas Lengauer, 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, 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 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.
Ingolf Sommer, Alexander Zien, Niklas Von Öhsen, , Thomas Lengauer, Confidence measures for protein fold recognition, Bioinformatics, vol. 18, no. 6, pp. 802-812, 2002.
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.
Papers
D. Hofmann, , Thomas Lengauer, Derivation of a scoring function for crystal structure prediction, Acta Crystallogr A., vol. 57, no. Pt4, pp. 442-50, 2001.
, D. Hofmann, 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.
Alexander Zien, Thomas Aigner, , Thomas Lengauer, Centralization: a new method for the normalization of gene expression data, Bioinformatics, vol. 17, no. Suppl.1, pp. S323-S331, 2001.
Mario Albrecht, , , Thomas Lengauer, 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.
Mario Albrecht, , Protein structure prediction by threading with experimental constraints, Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), vol. Poster, 2001.
J. Freudenberg, , , Thomas Lengauer, 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, 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, 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.
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.
Ingolf Sommer, Niklas Von Öhsen, Alexander Zien, , Thomas Lengauer, Confidence Measures for fold recognition, German Conference on Bioinformatics (E. Wingender, ed.), pp. 26-33, 2001.
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.
, Thomas Lengauer, Protein Structure Prediction, Bioinformatics - From Genomes to Drugs (Thomas Lengauer, ed.), Wiley-VCH, pp. 237-313, 2001.
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.
