PUBLICATIONS

2020 - 2022

2020 (12)

  • M. H. Bailey, W. U. Meyerson, L. J. Dursi, L. B. Wang, G. Dong, W. W. Liang, A. Weerasinghe, H. Binder, et al. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020. 11: 4748.
  • Sarah J Berkemer, Lisa-Katharina Maier, Fabian Amman, Stephan H Bernhart, Julia Wörtz, Pascal Märkle, Friedhelm Pfeiffer, Peter F Stadler, Anita Marchfelder. Identification of RNA 3´ ends and termination sites in Haloferax volcanii. RNA biology. 2020. 1-14.
  • Campbell PJ, Getz G, Korbel JO, Stuart JM, Jennings JL, Stein LD, Perry MD, Nahal-Bose HK, Ouellette BFF, Li CH, H. Binder, S. Bernhardt, P. Stadler. Pan-cancer analysis of whole genomes. Nature. 2020. 578: 82-93.
  • L. Erber, P. Franz, H. Betat, S. Prohaska, M. Morl. Divergent Evolution of Eukaryotic CC- and A-Adding Enzymes. Int J Mol Sci. 2020. 21:
  • B. Fischer, A. M. Sedlmeier, S. Hartwig, C. L. Schlett, W. Ahrens, F. Bamberg, H. Baurecht, H. Becher, K. Berger, H. Binder, B. Bohn, P. R. Carr, S. Castell, C. W. Franzke, J. Fricke, S. Gastell, K. H. Greiser, K. Gunther, L. Jaeschke, R. Kaaks, Y. Kemmling, L. Krist, O. Kuss, N. Legath, W. Lieb, J. Linseisen, M. Loffler, K. B. Michels, R. Mikolajczyk, T. Niedermaier, K. Norman, N. Obi, A. Peters, T. Pischon, T. Schikowski, S. Schipf, B. Schmidt, M. B. Schulze, A. Stang, J. Stojicic, D. Tiller, H. Volzke, S. Waniek, M. F. Leitzmann. [Anthropometric measures in the German National Cohort-more than weight and height]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2020. 63: 290-300.
  • A. Frenzel, H. Binder, N. Walter, K. Wirkner, M. Loeffler, H. Loeffler-Wirth. The aging human body shape. NPJ Aging Mech Dis. 2020. 6: 5.
  • C. H. Li, S. D. Prokopec, R. X. Sun, F. Yousif, H. Binder, et al. Sex differences in oncogenic mutational processes. Nat Commun. 2020. 11: 4330.
  • H. Loeffler-Wirth, J. Reikowski, S. Hakobyan, J. Wagner, H. Binder. oposSOM-Browser: an interactive tool to explore omics data landscapes in health science. 2020.
  • H. Loeffler-Wirth, M. Schmidt, H. Binder. Covid-19 Transmission Trajectories-Monitoring the Pandemic in the Worldwide Context. Viruses. 2020. 12:
  • M. Nikoghosyan, M. Schmidt, K. Margaryan, H. Loeffler-Wirth, A. Arakelyan, H. Binder. SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks. MDPI Journals Genes. 2020. 11: 21.
  • Paurnima Patil, Agata Cieslak, Stephan H Bernhart, Umut H Toprak, Rabea Wagener, Cristina López, Laura Wiehle, Susanne Bens, Janine Altmüller, Marek Franitza. Reconstruction of rearranged T‐cell receptor loci by whole genome and transcriptome sequencing gives insights into the initial steps of T‐cell prolymphocytic leukemia. Genes, Chromosomes and Cancer. 2020. 59: 261-267.
  • M. Schmidt, H. Loeffler-Wirth, H. Binder. Developmental scRNAseq Trajectories in Gene- and Cell-State Space-The Flatworm Example. Genes (Basel). 2020. 11:

2017 - 2019

2019 (11)

  • A. Arakelyan, L. Nersisyan, M. Nikoghosyan, S. Hakobyan, A. Simonyan, L. Hopp, H. Loeffler-Wirth, H. Binder. Transcriptome-Guided Drug Repositioning. Pharmaceutics. 2019. 11:
  • N.C. Bilz, E. Willscher, H. Binder, J. Bohnke, M.L. Stanifer, D. Hubner, S. Boulant, U.G. Liebert, C. Claus. Teratogenic Rubella Virus Alters the Endodermal Differentiation Capacity of Human Induced Pluripotent Stem Cells. Cells. 2019. 8:
  • H. Binder, E. Willscher, H. Loeffler-Wirth, L. Hopp, D. T. W. Jones, S. M. Pfister, M. Kreuz, D. Gramatzki, E. Fortenbacher, B. Hentschel, M. Loeffler, et al. DNA methylation, transcriptome and genetic copy number signatures of diffuse cerebral WHO grade II/III gliomas resolve cancer heterogeneity and development. Acta Neuropathol Commun. 2019. 7: 019-0704.
  • Alexander Donath, Frank Jühling, Marwa Al-Arab, Stephan H Bernhart, Franziska Reinhardt, Peter F Stadler, Martin Middendorf, Matthias Bernt. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic acids research. 2019. 47: 10543-10552.
  • M. Herberg, S. Siebert, M. Quaas, T. Thalheim, K. Rother, M. Hussong, J. Altmuller, C. Kerner, J. Galle, M. R. Schweiger, G. Aust. Loss of Msh2 and a single-radiation hit induce common, genome-wide, and persistent epigenetic changes in the intestine. Clin Epigenetics. 2019. 11: 019-0639.
  • H. Loeffler-Wirth, M. Kreuz, L. Hopp, A. Arakelyan, A. Haake, S. B. Cogliatti, A. C. Feller, M. L. Hansmann, D. Lenze, P. Moller, H. K. Muller - Hermelink, E. Fortenbacher, E. Willscher, G. Ott, A. Rosenwald, C. Pott, C. Schwaenen, H. Trautmann, S. Wessendorf, H. Stein, M. Szczepanowski, L. Trumper, M. Hummel, W. Klapper, R. Siebert, M. Loeffler, H. Binder. A modular transcriptome map of mature B cell lymphomas. Genome Med. 2019. 11: 019-0637.
  • C. Lopez, K. Kleinheinz, S. M. Aukema, M. Rohde, S. H. Bernhart, D. Hubschmann, R. Wagener, U. H. Toprak, F. Raimondi, M. Kreuz, H. Binder, G. Doose, L. Hopp, P. F. Stadler, M. Loeffler, et al. Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. Nat Commun. 2019. 10: 019-08578.
  • L. Nersisyan, L. Hopp, H. Loeffler-Wirth, J. Galle, M. Loeffler, A. Arakelyan, H. Binder. Telomere Length Maintenance and Its Transcriptional Regulation in Lynch Syndrome and Sporadic Colorectal Carcinoma. Front Oncol. 2019. 9:
  • Nikoghosyan M, S Hakobyan, A Hovhannisyan, H. Loeffler-Wirth, H. Binder, A. Arakelyan. Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians – A Machine Learning Approach. Frontiers in Genetics. 2019. 10:
  • S. Thones, S. Rother, T. Wippold, J. Blaszkiewicz, K. Balamurugan, S. Moeller, G. Ruiz-Gomez, M. Schnabelrauch, D. Scharnweber, A. Saalbach, J. Rademann, M. T. Pisabarro, V. Hintze, U. Anderegg. Hyaluronan/collagen hydrogels containing sulfated hyaluronan improve wound healing by sustained release of heparin-binding EGF-like growth factor. Acta Biomater. 2019. 86: 135-147.
  • Sigrid Uxa, Stephan H Bernhart, Christina FS Mages, Martin Fischer, Robin Kohler, Steve Hoffmann, Peter F Stadler, Kurt Engeland, Gerd A Müller. DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation. Nucleic acids research. 2019. 47: 9087-9103.

2018 (17)

  • Gero Doose, Stephan H Bernhart, Rabea Wagener, Steve Hoffmann. DIEGO: detection of differential alternative splicing using Aitchison’s geometry. Bioinformatics. 2018. 34: 1066-1068.
  • Y. A. Miroshnikova, H. Q. Le, D. Schneider, T. Thalheim, M. Rubsam, N. Bremicker, J. Polleux, N. Kamprad, M. Tarantola, I. Wang, M. Balland, C. M. Niessen, J. Galle, S. A. Wickstrom. Adhesion forces and cortical tension couple cell proliferation and differentiation to drive epidermal stratification. Nat Cell Biol. 2018. 20: 69-80.
  • A Ustaszewski, J Paczkowska, J Janiszewska, S Hartmann, J Bein, S Bernhart, R Siebert, ML Hansmann, M Giefing. PO-379 Novel tumour specific miRNA expressed in classical hodgkin lymphoma cell lines. 2018.
  • T. Thalheim, M. Quaas, M. Herberg, U. D. Braumann, C. Kerner, M. Loeffler, G. Aust, J. Galle. Linking stem cell function and growth pattern of intestinal organoids. Dev Biol. 2018. 433: 254-261.
  • T. Thalheim, L. Hopp, H. Binder, G. Aust, J. Galle. On the Cooperation between Epigenetics and Transcription Factor Networks in the Specification of Tissue Stem Cells. Epigenomes. 2018. 2: 20.
  • T. Thalheim, M. Herberg, J. Galle. Linking DNA Damage and Age-Related Promoter DNA Hyper-Methylation in the Intestine. In: Genes 2018.
  • Aniela Skrzypczyk, Stephanie Kehr, Ilona Krystel, Stephan H Bernhart, Shibashish Giri, Augustinus Bader, Peter F Stadler. Noncoding RNA transcripts during differentiation of induced pluripotent stem cells into hepatocytes. Stem cells international. 2018. 2018:
  • Hilmar Quentmeier, Claudia Pommerenke, Stephan H Bernhart, Wilhelm G Dirks, Vivien Hauer, Steve Hoffmann, Stefan Nagel, Reiner Siebert, Cord C Uphoff, Margarete Zaborski. RBFOX2 and alternative splicing in B-cell lymphoma. Blood cancer journal. 2018. 8: 1-4.
  • H. Loeffler-Wirth, M. Vogel, T. Kirsten, F. Glock, T. Poulain, A. Korner, M. Loeffler, W. Kiess, H. Binder. Longitudinal anthropometry of children and adolescents using 3D-body scanning. PLoS One. 2018. 13: e0203628.
  • S. N. Grobner, B. C. Worst, et al. The landscape of genomic alterations across childhood cancers. Nature. 2018. 555: 321-327.
  • H. Loeffler-Wirth, H. Binder, E. Willscher, T. Gerber, M. Kunz. Pseudotime Dynamics in Melanoma Single-Cell Transcriptomes Reveals Different Mechanisms of Tumor Progression. Biology. 2018. 7: 23.
  • M. D. Laubichler, S. J. Prohaska, P. F. Stadler. Toward a mechanistic explanation of phenotypic evolution: The need for a theory of theory integration. J Exp Zool B Mol Dev Evol. 2018. 330: 5-14.
  • M. Kunz, H. Loffler-Wirth, M. Dannemann, E. Willscher, G. Doose, J. Kelso, T. Kottek, B. Nickel, L. Hopp, J. Landsberg, S. Hoffmann, T. Tuting, P. Zigrino, C. Mauch, J. Utikal, M. Ziemer, H. J. Schulze, M. Holzel, A. Roesch, S. Kneitz, S. Meierjohann, A. Bosserhoff, H. Binder, M. Schartl. RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas. Oncogene. 2018. 37: 6136-6151.
  • L. Hopp, H. Loeffler-Wirth, L. Nersisyan, A. Arakelyan, H. Binder. Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome. Front Immunol. 2018. 9: 1620.
  • L. Hopp, H. Loffler-Wirth, J. Galle, H. Binder. Combined SOM-portrayal of gene expression and DNA methylation landscapes disentangles modes of epigenetic regulation in glioblastoma. Epigenomics. 2018. 10: 745-764.
  • S. N. Grobner, B. C. Worst, J. Weischenfeldt, I. Buchhalter, K. Kleinheinz, V. A. Rudneva, P. D. Johann, G. P. Balasubramanian, M. Segura-Wang, S. Brabetz, S. Bender, B. Hutter, D. Sturm, E. Pfaff, D. Hubschmann, G. Zipprich, M. Heinold, J. Eils, C. Lawerenz, S. Erkek, S. Lambo, S. Waszak, C. Blattmann, A. Borkhardt, M. Kuhlen, A. Eggert, S. Fulda, M. Gessler, J. Wegert, R. Kappler, D. Baumhoer, S. Burdach, R. Kirschner-Schwabe, U. Kontny, A. E. Kulozik, D. Lohmann, S. Hettmer, C. Eckert, S. Bielack, M. Nathrath, C. Niemeyer, G. H. Richter, J. Schulte, R. Siebert, F. Westermann, J. J. Molenaar, G. Vassal, H. Witt, B. Burkhardt, C. P. Kratz, O. Witt, C. M. van Tilburg, C. M. Kramm, G. Fleischhack, U. Dirksen, S. Rutkowski, M. Fruhwald, K. von Hoff, S. Wolf, T. Klingebiel, E. Koscielniak, P. Landgraf, J. Koster, A. C. Resnick, J. Zhang, Y. Liu, X. Zhou, A. J. Waanders, D. A. Zwijnenburg, P. Raman, B. Brors, U. D. Weber, P. A. Northcott, K. W. Pajtler, M. Kool, R. M. Piro, J. O. Korbel, M. Schlesner, R. Eils, D. T. W. Jones, P. Lichter, L. Chavez, M. Zapatka, S. M. Pfister. Author Correction: The landscape of genomic alterations across childhood cancers. Nature. 2018. 559: E10.
  • Melanie von Brandenstein, Stephan H Bernhart, Andreas Pansky, Claudia Richter, Tobias Kohl, Martina Deckert, Axel Heidenreich, Peter F Stadler, Manuel Montesinos-Rongen, Jochen WU Fries. Beyond the 3′ UTR binding–microRNA-induced protein truncation via DNA binding. Oncotarget. 2018. 9: 32855.

2017 (19)

  • A. Arakelyan, L. Nersisyan, D. Poghosyan, L. Khondkaryan, A. Hakobyan, H. Loffler-Wirth, E. Melanitou, H. Binder. Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles. PLoS One. 2017. 12: e0187572.
  • K. Keysselt, T. Kreutzmann, K. Rother, C. Kerner, K. Krohn, J. Przybilla, P. Buske, H. Loffler-Wirth, M. Loeffler, J. Galle, G. Aust. Different in vivo and in vitro transformation of intestinal stem cells in mismatch repair deficiency. Oncogene. 2017. 36: 2750-2761.
  • T. Thalheim, M. Herberg, M. Loeffler, J. Galle. The Regulatory Capacity of Bivalent Genes-A Theoretical Approach. Int J Mol Sci. 2017. 18:
  • K. Rohde, M. Klos, L. Hopp, X. Liu, M. Keller, M. Stumvoll, A. Dietrich, M. R. Schon, D. Gartner, T. Lohmann, M. Dressler, P. Kovacs, H. Binder, M. Bluher, Y. Bottcher. IRS1 DNA promoter methylation and expression in human adipose tissue are related to fat distribution and metabolic traits. Sci Rep. 2017. 7: 12369.
  • C. L. Richards, C. Alonso, C. Becker, O. Bossdorf, E. Bucher, M. Colome-Tatche, W. Durka, J. Engelhardt, B. Gaspar, A. Gogol-Doring, I. Grosse, T. P. van Gurp, K. Heer, I. Kronholm, C. Lampei, V. Latzel, M. Mirouze, L. Opgenoorth, O. Paun, S. J. Prohaska, S. A. Rensing, P. F. Stadler, E. Trucchi, K. Ullrich, K. J. F. Verhoeven. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecol Lett. 2017. 20: 1576-1590.
  • J. Przybilla, L. Hopp, M. Lubbert, M. Loeffler, J. Galle. Targeting DNA hypermethylation: Computational modeling of DNA demethylation treatment of acute myeloid leukemia. Epigenetics. 2017. 12: 886-896.
  • S. J. Prohaska, S. J. Berkemer, F. Gartner, T. Gatter, N. Retzlaff, C. Honer Zu Siederdissen, P. F. Stadler. Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem. J Math Biol. 2017.
  • Christina FS Mages, Axel Wintsche, Stephan H Bernhart, Gerd A Mueller. The DREAM complex through its subunit Lin37 cooperates with Rb to initiate quiescence. Elife. 2017. 6: e26876.
  • H. Loeffler-Wirth, M. Vogel, T. Kirsten, F. Glock, T. Poulain, A. Korner, M. Loeffler, W. Kiess, H. Binder. Body typing of children and adolescents using 3D-body scanning. PLoS One. 2017. 12: e0186881.
  • M. Keller, L. Hopp, X. Liu, T. Wohland, K. Rohde, R. Cancello, M. Klös, K. Bacos, M. Kern, F. Eichelmann, A. Dietrich, M. R. Schön, D. Gärtner, T. Lohmann, M. Dreßler, M. Stumvoll, P. Kovacs, A. DiBlasio, C. Ling, H. Binder, M. Blüher, Y. Böttcher. Genome-wide DNA promoter methylation and transcriptome analysis in human adipose tissue unravels novel candidate genes for obesity. Molecular Metabolism. 2017. 6: 86-100.
  • H. Binder, L. Hopp, M. R. Schweiger, S. Hoffmann, F. Juhling, M. Kerick, B. Timmermann, S. Siebert, C. Grimm, L. Nersisyan, A. Arakelyan, M. Herberg, P. Buske, H. Loeffler-Wirth, M. Rosolowski, C. Engel, J. Przybilla, M. Peifer, N. Friedrichs, G. Moeslein, M. Odenthal, M. Hussong, S. Peters, S. Holzapfel, J. Nattermann, R. Hueneburg, W. Schmiegel, B. Royer-Pokora, S. Aretz, M. Kloth, M. Kloor, R. Buettner, J. Galle, M. Loeffler. Genomic and transcriptomic heterogeneity of colorectal tumours arising in Lynch syndrome. J Pathol. 2017. 243: 242-254.
  • H. Indrischek, S. J. Prohaska, V. V. Gurevich, E. V. Gurevich, P. F. Stadler. Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes. BMC Evol Biol. 2017. 17: 163.
  • S. Hoehme, A. Friebel, S. Hammad, D. Drasdo, J. G. Hengstler. Creation of Three-Dimensional Liver Tissue Models from Experimental Images for Systems Medicine. Methods Mol Biol. 2017. 1506: 319-362.
  • Z. Hamidouche, K. Rother, J. Przybilla, A. Krinner, D. Clay, L. Hopp, C. Fabian, A. Stolzing, H. Binder, P. Charbord, J. Galle. Bistable Epigenetic States Explain Age-Dependent Decline in Mesenchymal Stem Cell Heterogeneity. Stem Cells. 2017. 35: 694-704.
  • T. Gerber, E. Willscher, H. Loeffler-Wirth, L. Hopp, D. Schadendorf, M. Schartl, U. Anderegg, G. Camp, B. Treutlein, H. Binder, M. Kunz. Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq. Oncotarget. 2017. 8: 846-862.
  • J. G. Camp, K. Sekine, T. Gerber, H. Loeffler-Wirth, H. Binder, M. Gac, S. Kanton, J. Kageyama, G. Damm, D. Seehofer, L. Belicova, M. Bickle, R. Barsacchi, R. Okuda, E. Yoshizawa, M. Kimura, H. Ayabe, H. Taniguchi, T. Takebe, B. Treutlein. Multilineage communication regulates human liver bud development from pluripotency. Nature. 2017. 546: 533-538.
  • H Cakir. Dysregulated signal progagation in a MYC-associated Boolean gene network in B-cell lymphoma. . Biology, Engineering and Medicine. 2017.
  • M. Cakir, H. Wirth, A. Arakelyan, H. Binder. Dysregulated signal progagation in a MYC-associated Booleas gene network in B-cell lymphoma. Biology. 2017. 2: 1-11.
  • S. Thones, L. M. Kutz, S. Oehmichen, J. Becher, K. Heymann, A. Saalbach, W. Knolle, M. Schnabelrauch, S. Reichelt, U. Anderegg. New E-beam-initiated hyaluronan acrylate cryogels support growth and matrix deposition by dermal fibroblasts. Int J Biol Macromol. 2017. 94: 611-620.

2014 - 2016

2016 (43)

  • A. Arakelyan, L. Nersisyan, M. Pentrak, H. Loeffler-Wirth, H. Binder. Cartography of Pathway Signal Perturbations Identifies Distinct Molecular Pathomechanisms in Malignant and Chronic Lung Diseases. Front Genet. 2016. 7: 79.
  • L. Nersisyan, H. Loeffler-Wirth, A. Arakelyan, H. Binder. Gene set- and pathway- centered cancer - A bioinformatics perspective. . International Journal of Knowledge Discovery in Bioinformatics. 2016.
  • H. Loeffler-Wirth, E. Willscher, P. Ahnert, K. Wirkner, C. Engel, M. Loeffler, H. Binder. Novel Anthropometry Based on 3D-Bodyscans Applied to a Large Population Based Cohort. PLoS One. 2016. 11: e0159887.
  • H. Loeffler-Wirth, E. Willscher, P. Ahnert, K. Wirkner, C. Engel, M. Loeffler, H. Binder. Novel Anthropometry Based on 3D-Bodyscans Applied to a Large Population Based Cohort. PLoS One. 2016. 11: e0159887.
  • D. Mangani, M. Weller, E. Seyed Sadr, E. Willscher, K. Seystahl, G. Reifenberger, G. Tabatabai, H. Binder, H. Schneider. Limited role for transforming growth factor-beta pathway activation-mediated escape from VEGF inhibition in murine glioma models. Neuro Oncol. 2016. 18: 1610-1621.
  • D. Mangani, M. Weller, E. Seyed Sadr, E. Willscher, K. Seystahl, G. Reifenberger, G. Tabatabai, H. Binder, H. Schneider. Limited role for transforming growth factor-beta pathway activation-mediated escape from VEGF inhibition in murine glioma models. Neuro Oncol. 2016. 18: 1610-1621.
  • M. Matjusaitis, G. Chin, E. A. Sarnoski, A. Stolzing. Biomarkers to identify and isolate senescent cells. Ageing Res Rev. 2016. 29: 1-12.
  • L. Mueller, D. Gerighausen, M. Farman, D. Zeckzer. Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering. BMC Bioinformatics. 2016. 17: 377.
  • Y. Naaldijk, C. Jager, C. Fabian, C. Leovsky, A. Bluher, L. Rudolph, A. Hinze, A. Stolzing. Effect of systemic transplantation of bone marrow-derived mesenchymal stem cells on neuropathology markers in APP/PS1 Alzheimer mice. Neuropathol Appl Neurobiol. 2016.
  • Y. Naaldijk, A. A. Johnson, A. Friedrich-Stockigt, A. Stolzing. Cryopreservation of dermal fibroblasts and keratinocytes in hydroxyethyl starch-based cryoprotectants. BMC Biotechnol. 2016. 16: 85.
  • Jessica Okosun, Rachel L Wolfson, Jun Wang, Shamzah Araf, Lucy Wilkins, Brian M Castellano, Leire Escudero-Ibarz, Ahad Fahad Al Seraihi, Julia Richter, Stephan H Bernhart. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nature genetics. 2016. 48: 183.
  • D. C. Krakauer, L. Mueller, S. J. Prohaska, P. F. Stadler. Design specifications for cellular regulation. Theory Biosci. 2016. 135: 231-240.
  • J. Okosun, R. L. Wolfson, J. Wang, S. Araf, L. Wilkins, B. M. Castellano, L. Escudero-Ibarz, A. F. Al Seraihi, J. Richter, S. H. Bernhart, A. Efeyan, S. Iqbal, J. Matthews, A. Clear, J. A. Guerra-Assuncao, C. Bodor, H. Quentmeier, C. Mansbridge, P. Johnson, A. Davies, J. C. Strefford, G. Packham, S. Barrans, A. Jack, M. Q. Du, M. Calaminici, T. A. Lister, R. Auer, S. Montoto, J. G. Gribben, R. Siebert, C. Chelala, R. Zoncu, D. M. Sabatini, J. Fitzgibbon. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet. 2016. 48: 183-8.
  • D. Patra Bhattacharya, S. Canzler, S. Kehr, J. Hertel, I. Grosse, P. F. Stadler. Phylogenetic distribution of plant snoRNA families. BMC Genomics. 2016. 17: 969.
  • A. Perdomo-Sabogal, K. Nowick, I. Piccini, R. Sudbrak, H. Lehrach, M. L. Yaspo, H. J. Warnatz, R. Querfurth. Human Lineage-Specific Transcriptional Regulation through GA-Binding Protein Transcription Factor Alpha (GABPa). Mol Biol Evol. 2016. 33: 1231-44.
  • F. Righetti, A. M. Nuss, C. Twittenhoff, S. Beele, K. Urban, S. Will, S. H. Bernhart, P. F. Stadler, P. Dersch, F. Narberhaus. Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A. 2016. 113: 7237-42.
  • Francesco Righetti, Aaron M Nuss, Christian Twittenhoff, Sascha Beele, Kristina Urban, Sebastian Will, Stephan H Bernhart, Peter F Stadler, Petra Dersch, Franz Narberhaus. Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis. Proceedings of the National Academy of Sciences. 2016. 113: 7237-7242.
  • L. Rohani, C. Fabian, H. Holland, Y. Naaldijk, R. Dressel, H. Loeffler-Wirth, H. Binder, A. Arnold, A. Stolzing. Generation of human induced pluripotent stem cells using non-synthetic mRNA. Stem Cell Res. 2016. 16: 662-72.
  • A. Shostak, B. Ruppert, N. Ha, P. Bruns, U. H. Toprak, R. Eils, M. Schlesner, A. Diernfellner, M. Brunner. MYC/MIZ1-dependent gene repression inversely coordinates the circadian clock with cell cycle and proliferation. Nat Commun. 2016. 7: 11807.
  • Anton Shostak, Bianca Ruppert, Nati Ha, Philipp Bruns, Umut H Toprak, Roland Eils, Matthias Schlesner, Axel Diernfellner, Michael Brunner. MYC/MIZ1-dependent gene repression inversely coordinates the circadian clock with cell cycle and proliferation. Nature communications. 2016. 7: 1-11.
  • M. Laube, A. Stolzing, U. H. Thome, C. Fabian. Therapeutic potential of mesenchymal stem cells for pulmonary complications associated with preterm birth. Int J Biochem Cell Biol. 2016. 74: 18-32.
  • Frank Jühling, Helene Kretzmer, Stephan H Bernhart, Christian Otto, Peter F Stadler, Steve Hoffmann. metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome research. 2016. 26: 256-262.
  • S. H. Bernhart, H. Kretzmer, L. M. Holdt, F. Juehling, O. Ammerpohl, A. K. Bergmann, B. H. Northoff, G. Doose, R. Siebert, P. F. Stadler, S. Hoffmann. Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. Sci Rep. 2016. 6: 37393.
  • T. R. Heathman, A. Stolzing, C. Fabian, Q. A. Rafiq, K. Coopman, A. W. Nienow, B. Kara, C. J. Hewitt. Scalability and process transfer of mesenchymal stromal cell production from monolayer to microcarrier culture using human platelet lysate. Cytotherapy. 2016. 18: 523-35.
  • Stephan H Bernhart, Helene Kretzmer, Lesca M Holdt, Frank Jühling, Ole Ammerpohl, Anke K Bergmann, Bernd H Northoff, Gero Doose, Reiner Siebert, Peter F Stadler. Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. Scientific reports. 2016. 6: 37393.
  • S. Berto, A. Perdomo-Sabogal, D. Gerighausen, J. Qin, K. Nowick. A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe. Front Genet. 2016. 7: 31.
  • D. E. Blasi, S. Wichmann, H. Hammarstrom, P. F. Stadler, M. H. Christiansen. Sound-meaning association biases evidenced across thousands of languages. Proc Natl Acad Sci U S A. 2016. 113: 10818-23.
  • S. Canzler, P. F. Stadler, J. Hertel. U6 snRNA intron insertion occurred multiple times during fungi evolution. RNA Biol. 2016. 13: 119-27.
  • G. Domin, S. Findeiss, M. Wachsmuth, S. Will, P. F. Stadler, M. Moerl. Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Res. 2016.
  • T. Gerber, E. Willscher, H. Loeffler-Wirth, L. Hopp, D. Schadendorf, M. Schartl, U. Anderegg, G. Camp, B. Treutlein, H. Binder, M. Kunz. Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq. Oncotarget. 2016.
  • A. Ghallab, G. Celliere, S. G. Henkel, D. Driesch, S. Hoehme, U. Hofmann, S. Zellmer, P. Godoy, A. Sachinidis, M. Blaszkewicz, R. Reif, R. Marchan, L. Kuepfer, D. Haussinger, D. Drasdo, R. Gebhardt, J. G. Hengstler. Model-guided identification of a therapeutic strategy to reduce hyperammonemia in liver diseases. J Hepatol. 2016. 64: 860-71.
  • J. Gu, J. Jost, S. Liu, P. F. Stadler. Spectral classes of regular, random, and empirical graphs. Linear Algebra and its Applications. 2016. 489: 30-49.
  • M. Herberg, I. Glauche, T. Zerjatke, M. Winzi, F. Buchholz, I. Roeder. Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics. J R Soc Interface. 2016. 13:
  • F. Juehling, H. Kretzmer, S. H. Bernhart, C. Otto, P. F. Stadler, S. Hoffmann. metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 2016. 26: 256-62.
  • Kebria Hezaveh, Andreas Kloetgen, Stephan H Bernhart, Kunal Das Mahapatra, Dido Lenze, Julia Richter, Andrea Haake, Anke K Bergmann, Benedikt Brors, Birgit Burkhardt. Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis. Haematologica. 2016. 101: 1380-1389.
  • K. Hezaveh, A. Kloetgen, S. H. Bernhart, K. D. Mahapatra, D. Lenze, J. Richter, A. Haake, A. K. Bergmann, B. Brors, B. Burkhardt, A. Claviez, H. G. Drexler, R. Eils, S. Haas, S. Hoffmann, D. Karsch, W. Klapper, K. Kleinheinz, J. Korbel, H. Kretzmer, M. Kreuz, R. Kuppers, C. Lawerenz, E. Leich, M. Loeffler, L. Mantovani-Loeffler, C. Lopez, A. C. McHardy, P. Moller, M. Rohde, P. Rosenstiel, A. Rosenwald, M. Schilhabel, M. Schlesner, I. Scholz, P. F. Stadler, S. Stilgenbauer, S. Sungalee, M. Szczepanowski, L. Trumper, M. A. Weniger, R. Siebert, A. Borkhardt, M. Hummel, J. I. Hoell. Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis. Haematologica. 2016. 101: 1380-1389.
  • M. Hoelzer, V. Krahling, F. Amman, E. Barth, S. H. Bernhart, V. A. Carmelo, M. Collatz, G. Doose, F. Eggenhofer, J. Ewald, J. Fallmann, L. M. Feldhahn, M. Fricke, J. Gebauer, A. J. Gruber, F. Hufsky, H. Indrischek, S. Kanton, J. Linde, N. Mostajo, R. Ochsenreiter, K. Riege, L. Rivarola-Duarte, A. H. Sahyoun, S. J. Saunders, S. E. Seemann, A. Tanzer, B. Vogel, S. Wehner, M. T. Wolfinger, R. Backofen, J. Gorodkin, I. Grosse, I. Hofacker, S. Hoffmann, C. Kaleta, P. F. Stadler, S. Becker, M. Marz. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Sci Rep. 2016. 6: 34589.
  • Martin Hölzer, Verena Krähling, Fabian Amman, Emanuel Barth, Stephan H Bernhart, Victor AO Carmelo, Maximilian Collatz, Gero Doose, Florian Eggenhofer, Jan Ewald. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Scientific reports. 2016. 6: 34589.
  • H. Indrischek, N. Wieseke, P. F. Stadler, S. J. Prohaska. The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. Algorithms Mol Biol. 2016. 11: 1.
  • N. Jagiella, B. Mueller, M. Mueller, I. E. Vignon-Clementel, D. Drasdo. Inferring Growth Control Mechanisms in Growing Multi-cellular Spheroids of NSCLC Cells from Spatial-Temporal Image Data. PLoS Comput Biol. 2016. 12: e1004412.
  • A. A. Johnson, Y. Naaldijk, C. Hohaus, H. J. Meisel, I. Krystel, A. Stolzing. Protective effects of alpha phenyl-tert-butyl nitrone and ascorbic acid in human adipose derived mesenchymal stem cells from differently aged donors. Aging (Albany NY). 2016.
  • H. Jorjani, S. Kehr, D. J. Jedlinski, R. Gumienny, J. Hertel, P. F. Stadler, M. Zavolan, A. R. Gruber. An updated human snoRNAome. Nucleic Acids Res. 2016. 44: 5068-82.
  • T. Thalheim, P. Buske, J. Przybilla, K. Rother, M. Loeffler, J. Galle. Stem cell competition in the gut: insights from multi-scale computational modelling. J R Soc Interface. 2016. 13:

2015 (32)

  • H. Betat, T. Mede, S. Tretbar, L. Steiner, P. F. Stadler, M. Mörl, S. J. Prohaska. The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer. Nucleic Acids Res. 2015. 43: 6739-46.
  • H. Kretzmer, S. H. Bernhart, W. Wang, A. Haake, M. A. Weniger, A. K. Bergmann, M. J. Betts, E. Carrillo-de-Santa-Pau, G. Doose, J. Gutwein, J. Richter, V. Hovestadt, B. Huang, D. Rico, F. Juhling, J. Kolarova, Q. Lu, C. Otto, R. Wagener, J. Arnolds, B. Burkhardt, A. Claviez, H. G. Drexler, S. Eberth, R. Eils, P. Flicek, S. Haas, M. Hummel, D. Karsch, H. H. Kerstens, W. Klapper, M. Kreuz, C. Lawerenz, D. Lenze, M. Loeffler, C. Lopez, R. A. MacLeod, J. H. Martens, M. Kulis, J. I. Martin-Subero, P. Moller, I. Nagel, S. Picelli, I. Vater, M. Rohde, P. Rosenstiel, M. Rosolowski, R. B. Russell, M. Schilhabel, M. Schlesner, P. F. Stadler, M. Szczepanowski, L. Trumper, H. G. Stunnenberg, R. Kuppers, O. Ammerpohl, P. Lichter, R. Siebert, S. Hoffmann, B. Radlwimmer. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nat Genet. 2015. 47: 1316-25.
  • M. Weller, R. G. Weber, E. Willscher, V. Riehmer, B. Hentschel, M. Kreuz, J. Felsberg, U. Beyer, H. Löffler-Wirth, K. Kaulich, J. P. Steinbach, C. Hartmann, D. Gramatzki, J. Schramm, M. Westphal, G. Schackert, M. Simon, T. Martens, J. Bostrom, C. Hagel, M. Sabel, D. Krex, J. C. Tonn, W. Wick, S. Noell, U. Schlegel, B. Radlwimmer, T. Pietsch, M. Löffler, A. von Deimling, H. Binder, G. Reifenberger. Molecular classification of diffuse cerebral WHO grade II/III gliomas using genome- and transcriptome-wide profiling improves stratification of prognostically distinct patient groups. Acta Neuropathol. 2015. 129: 679-93.
  • A. Watarai, L. Schirmer, S. Thones, U. Freudenberg, C. Werner, J. C. Simon, U. Anderegg. TGFbeta functionalized starPEG-heparin hydrogels modulate human dermal fibroblast growth and differentiation. Acta Biomater. 2015. 25: 65-75.
  • R. Wagener, S. M. Aukema, M. Schlesner, A. Haake, B. Burkhardt, A. Claviez, H. G. Drexler, M. Hummel, M. Kreuz, M. Loeffler, M. Rosolowski, C. Lopez, P. Moller, J. Richter, M. Rohde, M. J. Betts, R. B. Russell, S. H. Bernhart, S. Hoffmann, P. Rosenstiel, M. Schilhabel, M. Szczepanowski, L. Trumper, W. Klapper, R. Siebert. The PCBP1 gene encoding poly(rC) binding protein I is recurrently mutated in Burkitt lymphoma. Genes Chromosomes Cancer. 2015. 54: 555-64.
  • Rabea Wagener, Sietse M Aukema, Matthias Schlesner, Andrea Haake, Birgit Burkhardt, Alexander Claviez, Hans G Drexler, Michael Hummel, Markus Kreuz, Markus Loeffler. The PCBP1 gene encoding poly (rc) binding protein i is recurrently mutated in B urkitt lymphoma. Genes, Chromosomes and Cancer. 2015. 54: 555-564.
  • P. Van Liedekerke, M. M. Palm, N. Jagiella, D. Drasdo. Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results. Computational Particle Mechanics. 2015. 2: 401-444.
  • K. Sygnecka, C. Heine, N. Scherf, M. Fasold, H. Binder, C. Scheller, H. Franke. Nimodipine enhances neurite outgrowth in dopaminergic brain slice co-cultures. Int J Dev Neurosci. 2015. 40: 1-11.
  • M. Schmid, J. Smith, D. W. Burt, B. L. Aken, P. B. Antin, A. L. Archibald, C. Ashwell, P. J. Blackshear, C. Boschiero, C. T. Brown, S. C. Burgess, H. H. Cheng, W. Chow, D. J. Coble, A. Cooksey, R. P. Crooijmans, J. Damas, R. V. Davis, D. J. de Koning, M. E. Delany, T. Derrien, T. T. Desta, I. C. Dunn, M. Dunn, H. Ellegren, L. Eory, I. Erb, M. Farre, M. Fasold, D. Fleming, P. Flicek, K. E. Fowler, L. Fresard, D. P. Froman, V. Garceau, P. P. Gardner, A. A. Gheyas, D. K. Griffin, M. A. Groenen, T. Haaf, O. Hanotte, A. Hart, J. Hasler, S. B. Hedges, J. Hertel, K. Howe, A. Hubbard, D. A. Hume, P. Kaiser, D. Kedra, S. J. Kemp, C. Klopp, K. E. Kniel, R. Kuo, S. Lagarrigue, S. J. Lamont, D. M. Larkin, R. A. Lawal, S. M. Markland, F. McCarthy, H. A. McCormack, M. C. McPherson, A. Motegi, S. A. Muljo, A. Munsterberg, R. Nag, I. Nanda, M. Neuberger, A. Nitsche, C. Notredame, H. Noyes, R. O'Connor, E. A. O'Hare, A. J. Oler, S. C. Ommeh, H. Pais, M. Persia, F. Pitel, L. Preeyanon, P. Prieto Barja, E. M. Pritchett, D. D. Rhoads, C. M. Robinson, M. N. Romanov, M. Rothschild, P. F. Roux, C. J. Schmidt, A. S. Schneider, M. G. Schwartz, S. M. Searle, M. A. Skinner, C. A. Smith, P. F. Stadler, T. E. Steeves, C. Steinlein, L. Sun, M. Takata, I. Ulitsky, Q. Wang, Y. Wang, others. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res. 2015. 145: 78-179.
  • B. Mueller, M. Bovet, Y. Yin, D. Stichel, M. Malz, M. Gonzalez-Vallinas, A. Middleton, V. Ehemann, J. Schmitt, T. Muley, M. Meister, E. Herpel, S. Singer, A. Warth, P. Schirmacher, D. Drasdo, F. Matthaus, K. Breuhahn. Concomitant expression of far upstream element (FUSE) binding protein (FBP) interacting repressor (FIR) and its splice variants induce migration and invasion of non-small cell lung cancer (NSCLC) cells. J Pathol. 2015. 237: 390-401.
  • H. Löffler-Wirth, M. Kalcher, H. Binder. oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor. Bioinformatics. 2015. 31: 3225-7.
  • M. Löffler, C. Engel, P. Ahnert, D. Alfermann, K. Arelin, R. Baber, F. Beutner, H. Binder, E. Brahler, R. Burkhardt, U. Ceglarek, C. Enzenbach, M. Fuchs, H. Gläsmer, F. Girlich, A. Hagendorff, M. Hantzsch, U. Hegerl, S. Henger, T. Hensch, A. Hinz, V. Holzendorf, D. Husser, A. Kersting, A. Kiel, T. Kirsten, J. Kratzsch, K. Krohn, T. Luck, S. Melzer, J. Netto, M. Nuchter, M. Raschpichler, F. G. Rauscher, S. G. Riedel-Heller, C. Sander, M. Scholz, P. Schonknecht, M. L. Schröter, J. C. Simon, R. Speer, J. Staker, R. Stein, Y. Stobel-Richter, M. Stumvoll, A. Tarnok, A. Teren, D. Teupser, F. S. Then, A. Tonjes, R. Treudler, A. Villringer, A. Weissgerber, P. Wiedemann, S. Zachariae, K. Wirkner, J. Thiery. The LIFE-Adult-Study: objectives and design of a population-based cohort study with 10,000 deeply phenotyped adults in Germany. BMC Public Health. 2015. 15: 691.
  • M. Loeffler, C. Engel, P. Ahnert, D. Alfermann, K. Arelin, R. Baber, F. Beutner, H. Binder, E. Brahler, R. Burkhardt, U. Ceglarek, C. Enzenbach, M. Fuchs, H. Glaesmer, F. Girlich, A. Hagendorff, M. Hantzsch, U. Hegerl, S. Henger, T. Hensch, A. Hinz, V. Holzendorf, D. Husser, A. Kersting, A. Kiel, T. Kirsten, J. Kratzsch, K. Krohn, T. Luck, S. Melzer, J. Netto, M. Nuchter, M. Raschpichler, F. G. Rauscher, S. G. Riedel-Heller, C. Sander, M. Scholz, P. Schonknecht, M. L. Schroeter, J. C. Simon, R. Speer, J. Staker, R. Stein, Y. Stobel-Richter, M. Stumvoll, A. Tarnok, A. Teren, D. Teupser, F. S. Then, A. Tonjes, R. Treudler, A. Villringer, A. Weissgerber, P. Wiedemann, S. Zachariae, K. Wirkner, J. Thiery. The LIFE-Adult-Study: objectives and design of a population-based cohort study with 10,000 deeply phenotyped adults in Germany. BMC Public Health. 2015. 15: 691.
  • M. D. Laubichler, P. F. Stadler, S. J. Prohaska, K. Nowick. The relativity of biological function. Theory Biosci. 2015. 134: 143-7.
  • V. Kumar, J. E. Bouameur, J. Bar, R. H. Rice, H. T. Hornig-Do, D. R. Roop, N. Schwarz, S. Brodesser, S. Thiering, R. E. Leube, R. J. Wiesner, P. Vijayaraj, C. B. Brazel, S. Heller, H. Binder, H. Loeffler-Wirth, P. Seibel, T. M. Magin. A keratin scaffold regulates epidermal barrier formation, mitochondrial lipid composition, and activity. J Cell Biol. 2015. 211: 1057-75.
  • Helene Kretzmer, Stephan H Bernhart, Wei Wang, Andrea Haake, Marc A Weniger, Anke K Bergmann, Matthew J Betts, Enrique Carrillo-de-Santa-Pau, Gero Doose, Jana Gutwein. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nature genetics. 2015. 47: 1316.
  • H. Binder, L. Hopp, K. Lembcke, H. Wirth. Personalized disease phenotypes from massive omics data. In: Big Data Analytics in Bioinformatics and Healthcare , IGI Global , Hershey, PA, USA. 2015. 359-378. Ed: Baoying, Wang and Ruowang, Li and William, Perrizo.
  • S. R. Kolora, R. Faria, A. Weigert, S. Schaffer, A. Grimm, K. Henle, A. H. Sahyoun, P. F. Stadler, K. Nowick, C. Bleidorn, M. Schlegel. The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis. Mitochondrial DNA. 2015. 1-3.
  • F. Jühling, H. Kretzmer, S. H. Bernhart, C. Otto, P. F. Stadler, S. Hoffmann. metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 2015.
  • L. Hopp, E. Willscher, H. Löffler-Wirth, H. Binder. Function Shapes Content: DNA-Methylation Marker Genes and their Impact for Molecular Mechanisms of Glioma. Journal of Cancer Research Updates. 2015. 11/2015: 127-148.
  • L. Hopp, L. Nersisyan, H. Löffler-Wirth, A. Arakelyan, H. Binder. Epigenetic Heterogeneity of B-Cell Lymphoma: Chromatin Modifiers. Genes (Basel). 2015. 6: 1076-112.
  • L. Hopp, H. Löffler-Wirth, H. Binder. Epigenetic Heterogeneity of B-Cell Lymphoma: DNA Methylation, Gene Expression and Chromatin States. Genes (Basel). 2015. 6: 812-40.
  • S. Hoffmann, P. F. Stadler, K. Strimmer. A simple data-adaptive probabilistic variant calling model. Algorithms Mol Biol. 2015. 10: 10.
  • M. Herberg, T. Zerjatke, W. de Back, I. Glauche, I. Roeder. Image-based quantification and mathematical modeling of spatial heterogeneity in ESC colonies. Cytometry A. 2015. 87: 481-90.
  • M. Herberg, I. Roeder. Computational modelling of embryonic stem-cell fate control. Development. 2015. 142: 2250-60.
  • A. Ghallab, G. Celliere, S. G. Henkel, D. Driesch, S. Höhme, U. Hofmann, S. Zellmer, P. Godoy, A. Sachinidis, M. Blaszkewicz, R. Reif, R. Marchan, L. Küpfer, D. Haussinger, D. Drasdo, R. Gebhardt, J. G. Hengstler. Model guided identification and therapeutic implications of an ammonia sink mechanism. J Hepatol. 2015.
  • P. P. Gardner, M. Fasold, S. W. Burge, M. Ninova, J. Hertel, S. Kehr, T. E. Steeves, S. Griffiths-Jones, P. F. Stadler. Conservation and losses of non-coding RNAs in avian genomes. PLoS One. 2015. 10: e0121797.
  • A. Friebel, J. Neitsch, T. Johann, S. Hammad, J. G. Hengstler, D. Drasdo, S. Höhme. TiQuant: software for tissue analysis, quantification and surface reconstruction. Bioinformatics. 2015. 31: 3234-6.
  • G. Doose, A. Haake, S. H. Bernhart, C. Lopez, S. Duggimpudi, F. Wojciech, A. K. Bergmann, A. Borkhardt, B. Burkhardt, A. Claviez, L. Dimitrova, S. Haas, J. I. Hoell, M. Hummel, D. Karsch, W. Klapper, K. Kleo, H. Kretzmer, M. Kreuz, R. Kuppers, C. Lawerenz, D. Lenze, M. Loeffler, L. Mantovani-Loffler, P. Moller, G. Ott, J. Richter, M. Rohde, P. Rosenstiel, A. Rosenwald, M. Schilhabel, M. Schneider, I. Scholz, S. Stilgenbauer, H. G. Stunnenberg, M. Szczepanowski, L. Trumper, M. A. Weniger, S. Hoffmann, R. Siebert, I. Iaccarino. MINCR is a MYC-induced lncRNA able to modulate MYC's transcriptional network in Burkitt lymphoma cells. Proc Natl Acad Sci U S A. 2015. 112: E5261-70.
  • L. A. D'Alessandro, S. Höhme, A. Henney, D. Drasdo, U. Klingmüller. Unraveling liver complexity from molecular to organ level: challenges and perspectives. Prog Biophys Mol Biol. 2015. 117: 78-86.
  • H. Binder, H. Wirth. Analysis of Large-Scale OMIC Data Using Self Organizing Maps. In: Encyclopedia of Information Science and Technology, Third Edition, IGI Global , Hershey, PA, USA. 2015. 1642-1653. Ed: Mehdi, Khosrow-Pour.
  • C. Zu Siederdissen, S. J. Prohaska, P. F. Stadler. Algebraic Dynamic Programming over general data structures. BMC Bioinformatics. 2015. 16 Suppl 19: S2.

2014 (53)

  • M. Ahmad, K. Frei, E. Willscher, A. Stefanski, K. Kaulich, P. Roth, K. Stuhler, G. Reifenberger, H. Binder, M. Weller. How Stemlike Are Sphere Cultures From Long-term Cancer Cell Lines? Lessons From Mouse Glioma Models. J Neuropathol Exp Neurol. 2014. 73: 1062-77.
  • C. Otto, P. F. Stadler, S. Hoffmann. Lacking alignments? The next generation sequencing mapper segemehl revisited. Bioinformatics. 2014.
  • A. Leal-Egana, U.-D. Braumann, A. Diaz-Cuenca, A. Bader. Textural Analysis of Dynamic Modifications at the Cell-Hydrogel Interface. In: Biotechnology Volume 10: Nanobiotechnology , Studium Press LLC , Houston. 2014. 10: 439-472. Ed: Kumar, Ashok.
  • M. Lechner, M. Hernandez-Rosales, D. Dörr, N. Wieseke, A. Thevenin, J. Stoye, R. K. Hartmann, S. J. Prohaska, P. F. Stadler. Orthology detection combining clustering and synteny for very large datasets. PLoS One. 2014. 9: e105015.
  • M. Löffler, M. Kreuz, A. Haake, D. Hasenclever, H. Trautmann, C. Arnold, K. Winter, K. Koch, W. Klapper, R. Scholtysik, M. Rosolowski, S. Hoffmann, O. Ammerpohl, M. Szczepanowski, D. Herrmann, R. Kuppers, C. Pott, R. Siebert. Genomic and epigenomic co-evolution in follicular lymphomas. Leukemia. 2014.
  • Martin Machyna, Stephanie Kehr, Korinna Straube, Dennis Kappei, Frank Buchholz, Falk Butter, Jernej Ule, Jana Hertel, Peter F Stadler, Karla M Neugebauer. The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies. Molecular Cell. 2014. 56: 389-399.
  • G. A. Müller, A. Wintsche, K. Stangner, S. J. Prohaska, P. F. Stadler, K. Engeland. The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. Nucleic Acids Res. 2014. 42: 10331-50.
  • G. A. Müller, A. Wintsche, K. Stangner, S. J. Prohaska, P. F. Stadler, K. Engeland. The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. Nucleic Acids Res. 2014. 42: 10331-50.
  • S. A. Munro, S. P. Lund, P. S. Pine, H. Binder, D. A. Clevert, A. Conesa, J. Dopazo, M. Fasold, S. Hochreiter, H. Hong, N. Jafari, D. P. Kreil, P. P. Labaj, S. Li, Y. Liao, S. M. Lin, J. Meehan, C. E. Mason, J. Santoyo-Lopez, R. A. Setterquist, L. Shi, W. Shi, G. K. Smyth, N. Stralis-Pavese, Z. Su, W. Tong, C. Wang, J. Wang, J. Xu, Z. Ye, Y. Yang, Y. Yu, M. Salit. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nat Commun. 2014. 5: 5125.
  • L. Nersisyan, H. Loeffler-Wirth, A. Arakelyan, H. Binder. Gene Set- and Pathway- Centered Knowledge Discovery Assigns Transcriptional Activation Patterns in Brain, Blood, and Colon Cancer: A Bioinformatics Perspective. International Journal of Knowledge Discovery in Bioinformatics (IJKDB). 2014. 4: 46-69.
  • L. Nersisyan, H. Wurth, A. Gevorgyan, H. Binder, A. Arakelyan. Methylation associated pathway activity deregulation in lung adenocarcinoma. European Respiratory Journal. 2014. 44:
  • A. Nitsche, G. Doose, H. Tafer, M. Robinson, N. R. Saha, M. Gerdol, A. Canapa, S. Hoffmann, C. T. Amemiya, P. F. Stadler. Atypical RNAs in the coelacanth transcriptome. J Exp Zool B Mol Dev Evol. 2014. 322: 342-51.
  • A.A. Parikesit, L. Steiner, P.F. Stadler, S.J. Prohaska. Pitfalls of Ascertainment Biases in Genome Annotations —Computing Comparable Protein Domain Distributions in Eukarya. Malaysian Journal of Fundamental and Applied Sciences. 2014. 10, No. 2: 13-033.
  • Konstantin Klemm, Jing Qin, PeterF Stadler. Geometry and Coarse-Grained Representations of Landscapes. In: Recent Advances in the Theory and Application of Fitness Landscapes, Springer Berlin Heidelberg 2014. 6: 153-176. Ed: Richter, Hendrik and Engelbrecht, Andries.
  • A. Perdomo-Sabogal, S. Kanton, M. B. Walter, K. Nowick. The role of gene regulatory factors in the evolutionary history of humans. Curr Opin Genet Dev. 2014. 29: 60-7.
  • J. Przybilla, T. Rohlf, M. Löffler, J. Galle. Understanding epigenetic changes in aging stem cells--a computational model approach. Aging Cell. 2014. 13: 320-8.
  • G. Reifenberger, R. G. Weber, V. Riehmer, K. Kaulich, E. Willscher, H. Wirth, J. Gietzelt, B. Hentschel, M. Westphal, M. Simon, G. Schackert, J. Schramm, J. Matschke, M. C. Sabel, D. Gramatzki, J. Felsberg, C. Hartmann, J. P. Steinbach, U. Schlegel, W. Wick, B. Radlwimmer, T. Pietsch, J. C. Tonn, A. von Deimling, H. Binder, M. Weller, M. Loeffler. Molecular characterization of long-term survivors of glioblastoma using genome- and transcriptome-wide profiling. Int J Cancer. 2014.
  • L. Rivarola-Duarte, C. Otto, F. Jühling, S. Schreiber, D. Bedulina, L. Jakob, A. Gurkov, D. Axenov-Gribanov, A. H. Sahyoun, M. Lucassen, J. Hackermüller, S. Hoffmann, F. Sartoris, H. O. Portner, M. Timofeyev, T. Luckenbach, P. F. Stadler. A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus. J Exp Zool B Mol Dev Evol. 2014. 322: 177-89.
  • A. H. Sahyoun, M. Bernt, P. F. Stadler, K. Tout. GC skew and mitochondrial origins of replication. Mitochondrion. 2014. 17C: 56-66.
  • P. Scheibe, A. Lazareva, U. D. Braumann, A. Reichenbach, P. Wiedemann, M. Francke, F. G. Rauscher. Parametric model for the 3D reconstruction of individual fovea shape from OCT data. Exp Eye Res. 2014. 119: 19-26.
  • F. Schliess, S. Höhme, S. G. Henkel, A. Ghallab, D. Driesch, J. Bottger, R. Guthke, M. Pfaff, J. G. Hengstler, R. Gebhardt, D. Haussinger, D. Drasdo, S. Zellmer. Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration. Hepatology. 2014.
  • H. Schneider, S. Bartschat, G. Doose, L. Maciel, E. Pizani, M. Bassani, F. A. Torres, S. Will, T. Raiol, M. Brigido, M. E. Walter, P. F. Stadler. Advances in bioinformatics and computational biology : 9th Brazilian Symposium on Bioinformatics, BSB 2014, Belo Horizonte, Brazil, October 28-30, 2014 : proceedings. 2014.
  • S. Wende, E. G. Platzer, F. Jühling, J. Putz, C. Florentz, P. F. Stadler, M. Morl. Biological evidence for the world's smallest tRNAs. Biochimie. 2014. 100: 151-8.
  • H. Wirth, M. V. Cakir, L. Hopp, H. Binder. Analysis of MicroRNA Expression Using Machine Learning. Methods Mol Biol. 2014. 1107: 257-78.
  • H. Wirth, M.V. Çakir, L. Hopp, H. Binder. Analysis of MicroRNA Expression Using Machine Learning. In: miRNomics: MicroRNA Biology and Computational Analysis, Humana Press 2014. 1107: 257-278. Ed: Yousef, Malik and Allmer, Jens.
  • Konstantin Klemm, PeterF Stadler. Rugged and Elementary Landscapes. In: Theory and Principled Methods for the Design of Metaheuristics, Springer Berlin Heidelberg 2014. 41-61. Ed: Borenstein, Yossi and Moraglio, Alberto.
  • S. Kehr, S. Bartschat, H. Tafer, P. F. Stadler, J. Hertel. Matching of Soulmates: coevolution of snoRNAs and their targets. Mol Biol Evol. 2014. 31: 455-67.
  • J. C. Alfonso, N. Jagiella, L. Nunez, M. A. Herrero, D. Drasdo. Estimating dose painting effects in radiotherapy: a mathematical model. PLoS One. 2014. 9: e89380.
  • M. V. Cakir, H. Wirth, L. Hopp, H. Binder. MicroRNA Expression Landscapes in Stem Cells, Tissues, and Cancer. Methods Mol Biol. 2014. 1107: 279-302.
  • F. Amman, M. T. Wolfinger, R. Lorenz, I. L. Hofacker, P. F. Stadler, S. Findeiss. TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinformatics. 2014. 15: 89.
  • A. M. Andres, K. Nowick. Editorial overview: genetics of human evolution: the genetics of human origins. Curr Opin Genet Dev. 2014. 29: v-vii.
  • A. Arakelyan, L. Nersisyan, H. Wirth, H. Binder. Mining common pathway deregulation profiles in lung diseases. European Respiratory Journal. 2014. 44:
  • R. Backofen, F. Amman, F. Costa, S. Findeiss, A. S. Richter, P. F. Stadler. Bioinformatics of prokaryotic RNAs. RNA Biol. 2014. 11:
  • S. Bartschat, S. Kehr, H. Tafer, P. F. Stadler, J. Hertel. snoStrip: a snoRNA annotation pipeline. Bioinformatics. 2014. 30: 115-6.
  • G. Besnard, F. Juhling, E. Chapuis, L. Zedane, E. Lhuillier, T. Mateille, S. Bellafiore. Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing. C R Biol. 2014. 337: 295-301.
  • H. Binder, H. Wirth, A. Arakelyan, K. Lembcke, E. Tiys, V. Ivanisenko, N. Kolchanov, A. Kononikhin, I. Popov, E. Nikolaev, L. Pastushkova, I. Larina. Time-course human urine proteomics in space-flight simulation experiments. BMC Genomics. 2014. 15: S2.
  • SEQC/MAQC-III Consortium (H Binder). A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol. 2014. 32: 903-14.
  • P. Buske, J. Przybilla, M. Löffler, J. Galle. The intestinal stem cell niche: a computational tissue approach. Biochem Soc Trans. 2014. 42: 671-7.
  • M. V. Cakir, H. Binder, H. Wirth. Profiling of Genetic Switches using Boolean Implications in Expression Data. J Integr Bioinform. 2014. 11: 246.
  • Mehmet Volkan Çakir, Henry Wirth, Lydia Hopp, Hans Binder. MicroRNA Expression Landscapes in Stem Cells, Tissues, and Cancer. In: miRNomics: MicroRNA Biology and Computational Analysis, Humana Press 2014. 1107: 279-302. Ed: Yousef, Malik and Allmer, Jens.
  • Christian Höner zu Siederdissen, SonjaJ Prohaska, PeterF Stadler. Dynamic Programming for Set Data Types. In: Advances in Bioinformatics and Computational Biology, Springer International Publishing 2014. 8826: 57-64. Ed: Campos, Sérgio.
  • P. Charbord, C. Pouget, H. Binder, F. Dumont, G. Stik, P. Levy, F. Allain, C. Marchal, J. Richter, B. Uzan, F. Pflumio, F. Letourneur, H. Wirth, E. Dzierzak, D. Traver, T. Jaffredo, C. Durand. A systems biology approach for defining the molecular framework of the hematopoietic stem cell niche. Cell Stem Cell. 2014. 15: 376-91.
  • J. C. Dohm, A. E. Minoche, D. Holtgrawe, S. Capella-Gutierrez, F. Zakrzewski, H. Tafer, O. Rupp, T. R. Sorensen, R. Stracke, R. Reinhardt, A. Goesmann, T. Kraft, B. Schulz, P. F. Stadler, T. Schmidt, T. Gabaldon, H. Lehrach, B. Weisshaar, H. Himmelbauer. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature. 2014. 505: 546-9.
  • D. Drasdo, J. Bode, U. Dahmen, O. Dirsch, S. Dooley, R. Gebhardt, A. Ghallab, P. Godoy, D. Haussinger, S. Hammad, S. Höhme, H. G. Holzhutter, U. Klingmüller, L. Kuepfer, J. Timmer, M. Zerial, J. G. Hengstler. The virtual liver: state of the art and future perspectives. Arch Toxicol. 2014. 88: 2071-5.
  • D. Drasdo, S. Höhme, J. G. Hengstler. How predictive QUANTITATIVE MODELING OF TISSUE ORGANIZATION can inform liver disease pathogenesis. J Hepatol. 2014.
  • Mario Fasold, Hans Binder. Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data. Microarrays. 2014. 3: 322-339.
  • Mario Fasold, Hans Binder. Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data. Microarrays. 2014. 3: 322.
  • S. Hammad, S. Höhme, A. Friebel, I. von Recklinghausen, A. Othman, B. Begher-Tibbe, R. Reif, P. Godoy, T. Johann, A. Vartak, K. Golka, P. O. Bucur, E. Vibert, R. Marchan, B. Christ, S. Dooley, C. Meyer, I. Ilkavets, U. Dahmen, O. Dirsch, J. Bottger, R. Gebhardt, D. Drasdo, J. G. Hengstler. Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three-dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis. Arch Toxicol. 2014. 88: 1161-83.
  • M. Herberg, T. Kalkan, I. Glauche, A. Smith, I. Roeder. A model-based analysis of culture-dependent phenotypes of mESCs. PLoS One. 2014. 9: e92496.
  • Jana Hertel, David Langenberger, PeterF Stadler. Computational Prediction of MicroRNA Genes. In: RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods, Humana Press 2014. 1097: 437-456. Ed: Gorodkin, Jan and Ruzzo, Walter L.
  • S. Hoffmann, C. Otto, G. Doose, A. Tanzer, D. Langenberger, S. Christ, M. Kunz, L. Holdt, D. Teupser, J. Hackermueller, P. F. Stadler. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection. Genome Biol. 2014. 15: R34.
  • M. R. Höhe, G. M. Church, H. Lehrach, T. Kroslak, S. Palczewski, K. Nowick, S. Schulz, E. K. Suk, T. Huebsch. Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes. Nat Commun. 2014. 5: 5569.
  • O. Wolkenhauer, C. Auffray, O. Brass, J. Clairambault, A. Deutsch, D. Drasdo, F. Gervasio, L. Preziosi, P. Maini, A. Marciniak-Czochra, C. Kossow, L. Kuepfer, K. Rateitschak, I. Ramis-Conde, B. Ribba, A. Schuppert, R. Smallwood, G. Stamatakos, F. Winter, H. Byrne. Enabling multiscale modeling in systems medicine. Genome Med. 2014. 6: 21.

2011 - 2013

2013 (28)

  • F. Amman, S. H. Bernhart, G. Doose, I. L. Hofacker, J. Qin, P. F. Stadler, S. Will. The Trouble with Long-Range Base Pairs in RNA Folding. In: Advances in Bioinformatics and Computational Biology: 8th Brazilian Symposium on Bioinformatics, BSB 2013, Recife, Brazil, November 3-7, 2013, Proceedings, Springer International Publishing , Cham. 2013. 1-11. Ed: Setubal, João C. and Almeida, Nalvo F.
  • J. Lehmann, P. F. Stadler, V. Krauss. Near intron pairs and the metazoan tree. Mol Phylogenet Evol. 2013. 66: 811-23.
  • S. Will, M. F. Siebauer, S. Heyne, J. Engelhardt, P. F. Stadler, Reiche, R. Backofen. LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. Algorithms Mol Biol. 2013. 8: 14.
  • M. Weber, N. Scherf, T. Kahl, U. D. Braumann, P. Scheibe, J. P. Kuska, R. Bayer, A. Buttner, H. Franke. Quantitative analysis of astrogliosis in drug-dependent humans. Brain Res. 2013. 1500: 72-87.
  • M. Wachsmuth, S. Findeiss, N. Weissheimer, P. F. Stadler, M. Morl. De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res. 2013. 41: 2541-51.
  • M. Tang, N. Vauchelet, I. Cheddadi, I. Vignon-Clementel, D. Drasdo, B. Perthame. Composite waves for a cell population system modeling tumor growth and invasion. Chinese Annals of Mathematics, Series B. 2013. 34: 295-318.
  • P. Scheibe, A. Lazareva, U. D. Braumann, A. Reichenbach, P. Wiedemann, M. Francke, F. G. Rauscher. Parametric model for the 3D reconstruction of individual fovea shape from OCT data. Exp Eye Res. 2013. 119C: 19-26.
  • H. Sánchez-Cruz, H. Sossa-Azuela, U-D. Braumann, E. Bribiesca. The Euler-Poincaré Formula Through Contact Surfaces of Voxelized Objects. Journal of Applied Research and Technology. 2013. 11: 65-78.
  • A. Oberbach, N. Jehmlich, N. Schlichting, M. Heinrich, S. Lehmann, H. Wirth, H. Till, J. U. Stolzenburg, U. Volker, V. Adams, J. Neuhaus. Molecular fingerprint of high fat diet induced urinary bladder metabolic dysfunction in a rat model. PLoS One. 2013. 8: e66636.
  • K. Nowick, M. Carneiro, R. Faria. A prominent role of KRAB-ZNF transcription factors in mammalian speciation?. Trends Genet. 2013. 29: 130-9.
  • S. A. Müller, S. Findeiss, S. R. Pernitzsch, D. K. Wissenbach, P. F. Stadler, I. L. Hofacker, M. von Bergen, S. Kalkhof. Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. J Proteomics. 2013. 86: 27-42.
  • Ronny Lorenz, Stephan H Bernhart, Jing Qin, Christian Höner zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L Hofacker, Peter F Stadler. 2D meets 4G: G-quadruplexes in RNA secondary structure prediction. IEEE/ACM transactions on computational biology and bioinformatics. 2013. 10: 832-844.
  • R. Lorenz, S. H. Bernhart, J. Qin, C. Höner zu Siederdissen, A. Tanzer, F. Amman, I. L. Hofacker, P. F. Stadler. 2D meets 4G: G-quadruplexes in RNA secondary structure prediction. IEEE/ACM Trans Comput Biol Bioinform. 2013. 10: 832-44.
  • D. Langenberger, M. V. Cakir, S. Hoffmann, P. F. Stadler. Dicer-Processed Small RNAs: Rules and Exceptions. J Exp Zool B Mol Dev Evol. 2013. 320: 35-46.
  • Fabian Amman, Stephan H Bernhart, Gero Doose, Ivo L Hofacker, Jing Qin, Peter F Stadler, Sebastian Will. The trouble with long-range base pairs in RNA folding. In: Brazilian Symposium on Bioinformatics, Springer, Cham 2013. 1-11.
  • S. Kehr, S. Bartschat, H. Tafer, P. F. Stadler, J. Hertel. Matching of Soulmates: Coevolution of snoRNAs and Their Targets. Mol Biol Evol. 2013.
  • L. Hopp, H. Wirth, M. Fasold, H. Binder. Portraying the expression landscapes of cancer subtypes: a glioblastoma multiforme and prostate cancer case study. Systems Biomedicine. 2013. 1:
  • L. M. Holdt, S. Hoffmann, K. Sass, D. Langenberger, M. Scholz, K. Krohn, K. Finstermeier, A. Stahringer, W. Wilfert, F. Beutner, S. Gielen, G. Schuler, G. Gabel, H. Bergert, I. Bechmann, P. F. Stadler, J. Thiery, D. Teupser. Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet. 2013. 9: e1003588.
  • M. Hellmuth, M. Hernandez-Rosales, K. T. Huber, V. Moulton, P. F. Stadler, N. Wieseke. Orthology relations, symbolic ultrametrics, and cographs. J Math Biol. 2013. 66: 399-420.
  • A. Harrison, H. Binder, A. Buhot, C. J. Burden, E. Carlon, C. Gibas, L. J. Gamble, A. Halperin, J. Hooyberghs, D. P. Kreil, R. Levicky, P. A. Noble, A. Ott, B. M. Pettitt, D. Tautz, A. E. Pozhitkov. Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Res. 2013. 41: 2779-96.
  • S. Giri, U. D. Braumann, P. Giri, A. Acikgoz, P. Scheibe, K. Nieber, A. Bader. Nanostructured self-assembling peptides as a defined extracellular matrix for long-term functional maintenance of primary hepatocytes in a bioartificial liver modular device. Int J Nanomedicine. 2013. 8: 1525-39.
  • M. Fasold, H. Binder. AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data. Bioinformatics. 2013. 29: 129-31.
  • G. Doose, M. Alexis, R. Kirsch, S. Findeiss, D. Langenberger, R. Machne, M. Morl, S. Hoffmann, P. F. Stadler. Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data. RNA Biol. 2013. 10: 1204-10.
  • H. Binder, L. Steiner, J. Przybilla, T. Rohlf, S. Prohaska, J. Galle. Transcriptional regulation by histone modifications: towards a theory of chromatin re-organization during stem cell differentiation. Phys Biol. 2013. 10: 026006.
  • M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz, G. Fritzsch, J. Putz, M. Middendorf, P. F. Stadler. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013. 69: 313-9.
  • G. Aust, C. Kerner, S. Gonsior, D. Sittig, H. Schneider, P. Buske, M. Scholz, N. Dietrich, S. Oldenburg, O. N. Karpus, J. Galle, S. Amasheh, J. Hamann. Mice overexpressing CD97 in intestinal epithelial cells provide a unique model for mammalian postnatal intestinal cylindrical growth. Mol Biol Cell. 2013. 24: 2256-68.
  • C. Arnold, P. F. Stadler, S. J. Prohaska. Chromatin computation: epigenetic inheritance as a pattern reconstruction problem. J Theor Biol. 2013. 336: 61-74.
  • H. Wirth. Analyse molekularbiologischer Daten mittels Self-organizing Maps. In: Ausgezeichnete Informatikdissertationen Teil: 2012, Hölldobler, S. Gesellschaft für Informatik e.V., Bonn , Bonn. 2013. Lecture Notes in Informatics D-13: 291-300. Ed: GI-Edition.

2012 (37)

  • A. Arnold, Y.M. Naaldijk, C. Fabian, H. Wirth, H. Binder, G. Nikkhah, L. Armstrong, A. Stolzing. Reprogramming of Human Huntington Fibroblasts Using mRNA. ISRN Cell Biology. 2012. 2012: 12.
  • T. Rohlf, L. Steiner, J. Przybilla, S. Prohaska, H. Binder, J. Galle. Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin. Epigenomics. 2012. 4: 205-19.
  • C. Otto, K. Reiche, J. Hackermüller. Detection of differentially expressed segments in tiling array data. Bioinformatics. 2012. 28: 1471-9.
  • C. Otto, P. F. Stadler, S. Hoffmann. Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics. 2012. 28: 1698-704.
  • J. Przybilla, J. Galle, T. Rohlf. Is adult stem cell aging driven by conflicting modes of chromatin remodeling?. Bioessays. 2012. 34: 841-8.
  • I. Ramis-Conde, D. Drasdo. From genotypes to phenotypes: classification of the tumour profiles for different variants of the cadherin adhesion pathway. Phys Biol. 2012. 9: 036008.
  • Julia Richter, Matthias Schlesner, Steve Hoffmann, Markus Kreuz, Ellen Leich, Birgit Burkhardt, Maciej Rosolowski, Ole Ammerpohl, Rabea Wagener, Stephan H Bernhart. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nature genetics. 2012. 44: 1316.
  • J. Richter, M. Schlesner, S. Hoffmann, M. Kreuz, E. Leich, B. Burkhardt, M. Rosolowski, O. Ammerpohl, R. Wagener, S. H. Bernhart, D. Lenze, M. Szczepanowski, M. Paulsen, S. Lipinski, R. B. Russell, S. Adam-Klages, G. Apic, A. Claviez, D. Hasenclever, V. Hovestadt, N. Hornig, J. O. Korbel, D. Kube, D. Langenberger, C. Lawerenz, J. Lisfeld, K. Meyer, S. Picelli, J. Pischimarov, B. Radlwimmer, T. Rausch, M. Rohde, M. Schilhabel, R. Scholtysik, R. Spang, H. Trautmann, T. Zenz, A. Borkhardt, H. G. Drexler, P. Moller, R. A. Macleod, C. Pott, S. Schreiber, L. Trumper, M. Loeffler, P. F. Stadler, P. Lichter, R. Eils, R. Kuppers, M. Hummel, W. Klapper, P. Rosenstiel, A. Rosenwald, B. Brors, R. Siebert. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet. 2012. 44: 1316-1320.
  • Patrick Scheibe, Philipp Wüstling, Christian Voigt, Thomas Hierl, Ulf-Dietrich Braumann. Inkrementelle lokal-adaptive Binarisierung zur Unterdrückung von Artefakten in der Knochenfeinsegmentierung. In: Bildverarbeitung für die Medizin 2012 SE - 34, Springer Berlin Heidelberg DA - 2012/01/01 2012. 189-194 LA - German. Ed: Tolxdorff, Thomas and Deserno, Thomas Martin and Handels, Heinz and Meinzer, Hans-Peter DO - 10.1007/978-3-642-28502-8_34.
  • R. Lorenz, I. L. Hofacker, S. H. Bernhart. Folding RNA/DNA hybrid duplexes. Bioinformatics. 2012. 28: 2530-1.
  • N. Scherf, M. Herberg, K. Thierbach, T. Zerjatke, T. Kalkan, P. Humphreys, A. Smith, I. Glauche, I. Roeder. Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions. Bioinformatics. 2012. 28: i556-i561.
  • Nico Scherf, Christian Ludborzs, Konstantin Thierbach, Jens-Peer Kuska, Ulf-Dietrich Braumann, Patrick Scheibe, Tilo Pompe, Ingmar Glauche, Ingo Röder. FluidTracks. In: Bildverarbeitung für die Medizin 2012 SE - 12, Springer Berlin Heidelberg DA - 2012/01/01 2012. 57-62 LA - German. Ed: Tolxdorff, Thomas and Deserno, Thomas Martin and Handels, Heinz and Meinzer, Hans-Peter DO - 10.1007/978-3-642-28502-8_12.
  • C. Schmidtke, S. Findeiss, C. M. Sharma, J. Kuhfuss, S. Hoffmann, J. Vogel, P. F. Stadler, U. Bonas. Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res. 2012. 40: 2020-31.
  • P. Smialowski, G. Doose, P. Torkler, S. Kaufmann, D. Frishman. PROSO II--a new method for protein solubility prediction. FEBS J. 2012. 279: 2192-200.
  • L. Steiner, L. Hopp, H. Wirth, J. Galle, H. Binder, S. J. Prohaska, T. Rohlf. A global genome segmentation method for exploration of epigenetic patterns. PLoS One. 2012. 7: e46811.
  • H. Wirth, M. von Bergen, H. Binder. Mining SOM expression portraits: feature selection and integrating concepts of molecular function. BioData Min. 2012. 5: 18.
  • Ronny Lorenz, Ivo L Hofacker, Stephan H Bernhart. Folding RNA/DNA hybrid duplexes. Bioinformatics. 2012. 28: 2530-2531.
  • Ronny Lorenz, Stephan H Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman, Ivo L Hofacker, Peter F Stadler. RNA folding algorithms with G-quadruplexes. In: Brazilian Symposium on Bioinformatics, Springer, Berlin, Heidelberg 2012. 49-60.
  • P. Buske, J. Przybilla, M. Loeffler, N. Sachs, T. Sato, H. Clevers, J. Galle. On the biomechanics of stem cell niche formation in the gut--modelling growing organoids. FEBS J. 2012. 279: 3475-87.
  • J. Hertel, S. Bartschat, A. Wintsche, C. Otto, P. F. Stadler. Evolution of the let-7 microRNA family. RNA Biol. 2012. 9: 231-41.
  • G. Doose, D. Metzler. Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots. Bioinformatics. 2012. 28: 2242-8.
  • D. Drasdo, S. Höhme. Modeling the impact of granular embedding media, and pulling versus pushing cells on growing cell clones. New Journal of Physics. 2012. 14: 055025.
  • J. Einenkel, U. D. Braumann, W. Steller, H. Binder, L. C. Horn. Suitability of infrared microspectroscopic imaging for histopathology of the uterine cervix. Histopathology. 2012. 60: 1084-98.
  • J. Engelhardt, P. F. Stadler. Hidden treasures in unspliced EST data. Theory Biosci. 2012. 131: 49-57.
  • M. Fasold, H. Binder. Estimating RNA-quality using GeneChip microarrays. BMC Genomics. 2012. 13: 186.
  • B. Frerich, K. Winter, K. Scheller, U. D. Braumann. Comparison of different fabrication techniques for human adipose tissue engineering in severe combined immunodeficient mice. Artif Organs. 2012. 36: 227-37.
  • Conrad Helm, Stephan H Bernhart, Christian Höner zu Siederdissen, Birgit Nickel, Christoph Bleidorn. Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida. Molecular phylogenetics and evolution. 2012. 64: 198-203.
  • H. G. Holzhutter, D. Drasdo, T. Preusser, J. Lippert, A. M. Henney. The virtual liver: a multidisciplinary, multilevel challenge for systems biology. Wiley Interdiscip Rev Syst Biol Med. 2012. 4: 221-35.
  • M. Löffler, L. Greulich, P. Scheibe, P. Kahl, Z. Shaikhibrahim, U. D. Braumann, J. P. Kuska, N. Wernert. Classifying prostate cancer malignancy by quantitative histomorphometry. J Urol. 2012. 187: 1867-75.
  • F. Jühling, J. Putz, M. Bernt, A. Donath, M. Middendorf, C. Florentz, P. F. Stadler. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res. 2012. 40: 2833-45.
  • F. Jühling, J. Putz, C. Florentz, P. F. Stadler. Armless mitochondrial tRNAs in Enoplea (Nematoda). RNA Biol. 2012. 9: 1161-6.
  • Stephanie Keller-Schmidt, Konstantin Klemm. A Model of macroevolution as a branching Process based on Innovations doi:10.1142/S0219525912500439. Advances in Complex Systems. 2012. 15: 1250043.
  • K. Klemm, A. Mehta, P. F. Stadler. Landscape encodings enhance optimization. PLoS One. 2012. 7: e34780.
  • C. E. Kupper, R. R. Rosencrantz, B. Henssen, H. Pelantova, S. Thones, A. Drozdova, V. Kren, L. Elling. Chemo-enzymatic modification of poly-N-acetyllactosamine (LacNAc) oligomers and N,N-diacetyllactosamine (LacDiNAc) based on galactose oxidase treatment. Beilstein J Org Chem. 2012. 8: 712-25.
  • D. Langenberger, S. Pundhir, C. T. Ekstrom, P. F. Stadler, S. Hoffmann, J. Gorodkin. deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinformatics. 2012. 28: 17-24.
  • H. Wirth, M. von Bergen, J. Murugaiyan, U. Rosler, T. Stokowy, H. Binder. MALDI-typing of infectious algae of the genus Prototheca using SOM portraits. J Microbiol Methods. 2012. 88: 83-97.
  • K. Nowick, M. Carneiro, R. Faria. A prominent role of KRAB-ZNF transcription factors in mammalian speciation?. 2012.

2011 (44)

  • A. Bateman, S. Agrawal, E. Birney, E. A. Bruford, J. M. Bujnicki, G. Cochrane, J. R. Cole, M. E. Dinger, A. J. Enright, P. P. Gardner, D. Gautheret, S. Griffiths-Jones, J. Harrow, J. Herrero, I. H. Holmes, H. D. Huang, K. A. Kelly, P. Kersey, A. Kozomara, T. M. Lowe, M. Marz, S. Moxon, K. D. Pruitt, T. Samuelsson, P. F. Stadler, A. J. Vilella, J. H. Vogel, K. P. Williams, M. W. Wright, C. Zwieb. RNAcentral: A vision for an international database of RNA sequences. Rna. 2011. 17: 1941-6.
  • J. D. Raincrow, K. Dewar, C. Stocsits, S. J. Prohaska, C. T. Amemiya, P. F. Stadler, C. H. Chiu. Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny. J Exp Zool B Mol Dev Evol. 2011. 316: 451-64.
  • P. Menzel, P. F. Stadler, J. Gorodkin. maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. Bioinformatics. 2011. 27: 317-25.
  • N. Morbt, J. Tomm, R. Feltens, I. Mogel, S. Kalkhof, K. Murugesan, H. Wirth, C. Vogt, H. Binder, I. Lehmann, M. von Bergen. Chlorinated benzenes cause concomitantly oxidative stress and induction of apoptotic markers in lung epithelial cells (A549) at nonacute toxic concentrations. J Proteome Res. 2011. 10: 363-78.
  • K. Nowick, C. Fields, T. Gernat, D. Caetano-Anolles, N. Kholina, L. Stubbs. Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species. PLoS One. 2011. 6: e21553.
  • A. Oberbach, M. Blüher, H. Wirth, H. Till, P. Kovacs, Y. Kullnick, N. Schlichting, J. M. Tomm, U. Rolle-Kampczyk, J. Murugaiyan, H. Binder, A. Dietrich, M. von Bergen. Combined proteomic and metabolomic profiling of serum reveals association of the complement system with obesity and identifies novel markers of body fat mass changes. J Proteome Res. 2011. 10: 4769-88.
  • C. Otto, S. Hoffmann, J. Gorodkin, P. F. Stadler. Fast local fragment chaining using sum-of-pair gap costs. Algorithms Mol Biol. 2011. 6: 4.
  • A. A. Parikesit, P. F. Stadler, S. J. Prohaska. Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions. Genes. 2011. 2: 912-924.
  • M. Perseke, J. Hetmank, M. Bernt, P. F. Stadler, M. Schlegel, D. Bernhard. The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria. BMC Evol Biol. 2011. 11: 134.
  • S. J. Prohaska, P. F. Stadler. The use and abuse of -omes. Methods Mol Biol. 2011. 719: 173-96.
  • D. Rose, M. Hiller, K. Schutt, J. Hackermüller, R. Backofen, P. F. Stadler. Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinformatics. 2011. 27: 1894-900.
  • M. Marz, A. R. Gruber, C. Höner Zu Siederdissen, F. Amman, S. Badelt, S. Bartschat, S. H. Bernhart, W. Beyer, S. Kehr, R. Lorenz, A. Tanzer, D. Yusuf, H. Tafer, I. L. Hofacker, P. F. Stadler. Animal snoRNAs and scaRNAs with exceptional structures. RNA Biol. 2011. 8: 938-46.
  • D. Rose, P. F. Stadler. Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOT. Frontiers in Genetics. 2011. 2: 69.
  • L. Steiner, P.F. Stadler, M. Cysouw. A Pipeline for Computational Historical Linguistics. Language Dynamics and Change. 2011. 1: 89-127.
  • E. K. Suk, G. K. McEwen, J. Duitama, K. Nowick, S. Schulz, S. Palczewski, S. Schreiber, D. T. Holloway, S. McLaughlin, H. Peckham, C. Lee, T. Hübsch, M. R. Höhe. A comprehensively molecular haplotype-resolved genome of a European individual. Genome Res. 2011. 21: 1672-85.
  • H. Tafer, F. Amman, F. Eggenhofer, P. F. Stadler, I. L. Hofacker. Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics. 2011. 27: 1934-40.
  • A. Tramontano, A. Donath, S. H. Bernhart, K. Reiche, G. Bohmdorfer, P. F. Stadler, A. Bachmair. Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer. Virology. 2011. 412: 75-82.
  • S. Washietl, S. Findeiss, S. A. Müller, S. Kalkhof, M. von Bergen, I. L. Hofacker, P. F. Stadler, N. Goldman. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. Rna. 2011. 17: 578-94.
  • H. Wirth, M. Löffler, M. von Bergen, H. Binder. Expression cartography of human tissues using self organizing maps. BMC Bioinformatics. 2011. 12: 306.
  • H. Wirth, M. von Bergen, J. Murugaiyan, U. Rosler, T. Stokowy, H. Binder. MALDI-typing of infectious algae of the genus Prototheca using SOM portraits. J Microbiol Methods. 2011. 88: 83-97.
  • M. Marz, P. F. Stadler. RNA interactions. Adv Exp Med Biol. 2011. 722: 20-38.
  • I. Lozada-Chavez, P. F. Stadler, S. J. Prohaska. "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity. Orig Life Evol Biosph. 2011. 41: 587-607.
  • Stephan H Bernhart, Ullrike Mückstein, Ivo L Hofacker. RNA Accessibility in cubic time. Algorithms for Molecular Biology. 2011. 6: 3.
  • F. Ghanbarnejad, K. Klemm. Stability of Boolean and continuous dynamics. Phys Rev Lett. 2011. 107: 188701.
  • H. Binder, M. Fasold, L. Hopp, M.V. Cakir, L. Nikkhah G. Armstrong, A. Stolzing. Portraying high-dimensional -omics data with individual resolution. In: CAMDA 2011.
  • H. Binder, M. Fasold, L. Hopp, V. Cakir, M. von Bergen, H. Wirth. Genomic and molecular Phenotypic Portraits - Exploring The "Omes" With Individual Resolution. In: 6th International Symposium on Health Informatics and Bioinformatics (HIBIT) 2011. 115-122. Ed: Explore, IEEE.
  • D. Buck, S. Cepok, S. Hoffmann, V. Grummel, A. Jochim, A. Berthele, H. P. Hartung, R. Wassmuth, B. Hemmer. Influence of the HLA-DRB1 genotype on antibody development to interferon beta in multiple sclerosis. Arch Neurol. 2011. 68: 480-7.
  • D. Drasdo, S. Höhme, J. G. Hengstler. A quantitative mathematical modeling approach to liver regeneration. In: Liver Regeneration, de Gruyter , Berlin/Boston. 2011. 159-174. Ed: Haeussinger, D.
  • F. Eggenhofer, H. Tafer, P. F. Stadler, I. L. Hofacker. RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res. 2011. 39: W149-54.
  • M. Fasold, D. Langenberger, H. Binder, P. F. Stadler, S. Hoffmann. DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 2011. 39: W112-7.
  • S. Findeiss, J. Engelhardt, S. J. Prohaska, P. F. Stadler. Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids. Biochimie. 2011. 93: 2019-23.
  • S. Findeiss, D. Langenberger, P. F. Stadler, S. Hoffmann. Traces of post-transcriptional RNA modifications in deep sequencing data. Biol Chem. 2011. 392: 305-13.
  • J. G. Hengstler, M. Gehrmann, S. Höhme, D. Drasdo, J. Stewart, M. Schmidt. Systems biology, bioinformatics and medicine approaches to cancer progression outcomes. In: Cancer Systems Biology, Bioinformatics and Medicine, Springer , Dordrecht Heidelberg London New York. 2011. 297-308. Ed: Cesario, A. and Marcus, F.
  • Ronny Lorenz, Stephan H Bernhart, Christian Höner Zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker. ViennaRNA Package 2.0. Algorithms for molecular biology. 2011. 6: 26.
  • M. Hoffmann, J. P. Kuska, M. Zscharnack, M. Löffler, J. Galle. Spatial organization of mesenchymal stem cells in vitro--results from a new individual cell-based model with podia. PLoS One. 2011. 6: e21960.
  • S. Hoffmann. Computational analysis of high throughput sequencing data. Methods Mol Biol. 2011. 719: 199-217.
  • S. Kehr, S. Bartschat, P. F. Stadler, H. Tafer. PLEXY: efficient target prediction for box C/D snoRNAs. Bioinformatics. 2011. 27: 279-80.
  • T. Kirsten, A. Gross, M. Hartung, E. Rahm. GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution. J Biomed Semantics. 2011. 2: 6.
  • David Langenberger, Sebastian Bartschat, Jana Hertel, Steve Hoffmann, Hakim Tafer, Peter Stadler. MicroRNA or Not MicroRNA? Advances in Bioinformatics and Computational Biology. 2011. 6832: 1-9. Ed: Norberto de Souza, Osmar and Telles, Guilherme and Palakal, Mathew.
  • D. Langenberger, S. Pundhir, C. T. Ekstrom, P. F. Stadler, S. Hoffmann, J. Gorodkin. deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinformatics. 2011. 28: 17-24.
  • A. Leal-Egana, U. D. Braumann, A. Diaz-Cuenca, M. Nowicki, A. Bader. Determination of pore size distribution at the cell-hydrogel interface. J Nanobiotechnology. 2011. 9: 24.
  • M. Lechner, S. Findeiss, L. Steiner, M. Marz, P. F. Stadler, S. J. Prohaska. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics. 2011. 12: 124.
  • R. Lorenz, S. H. Bernhart, C. Höner Zu Siederdissen, H. Tafer, C. Flamm, P. F. Stadler, I. L. Hofacker. ViennaRNA Package 2.0. Algorithms Mol Biol. 2011. 6: 26.
  • C. H. zu Siederdissen, S. H. Bernhart, P. F. Stadler, I. L. Hofacker. A folding algorithm for extended RNA secondary structures. Bioinformatics. 2011. 27: i129-36.

2008 - 2010

2010 (35)

  • C. T. Amemiya, T. P. Powers, S. J. Prohaska, J. Grimwood, J. Schmutz, M. Dickson, T. Miyake, M. A. Schoenborn, R. M. Myers, F. H. Ruddle, P. F. Stadler. Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proc Natl Acad Sci U S A. 2010. 107: 3622-7.
  • A. A. Parikesit, P. F. Stadler, S. J. Prohaska. Quantitative Comparison of Genomic-Wide Protein Domain Distributions. In: German Conference on Bioinformatics, Gesellschaft für Informatik 2010. P-173: 93-102. Ed: Schomburg, D. and Grote, A.
  • S. Jänicke, C. Heine, M. Hellmuth, P. F. Stadler, G. Scheuermann. Visualization of graph products. IEEE Trans Vis Comput Graph. 2010. 16: 1082-9.
  • S. Kehr, S. Bartschat, P. F. Stadler, H. Tafer. PLEXY: efficient target prediction for box C/D snoRNAs. Bioinformatics. 2010. 27: 279-280.
  • A. Krinner, M. Hoffmann, M. Löffler, D. Drasdo, J. Galle. Individual fates of mesenchymal stem cells in vitro. BMC Syst Biol. 2010. 4: 73.
  • J. Lehmann, C. Eisenhardt, P. F. Stadler, V. Krauss. Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication. BMC Evol Biol. 2010. 10: 156.
  • O. Minet, P. Scheibe, U. J. Zabarylo. Diagnosis of rheumatoid arthritis using light: correction of motion artefacts and color visualization of multispectral images. J Biophotonics. 2010. 3: 130-137.
  • S. A. Müller, T. Kohajda, S. Findeiss, P. F. Stadler, S. Washietl, M. Kellis, M. von Bergen, S. Kalkhof. Optimization of parameters for coverage of low molecular weight proteins. Anal Bioanal Chem. 2010. 398: 2867-81.
  • S. J. Prohaska, P. F. Stadler, D. C. Krakauer. Innovation in gene regulation: the case of chromatin computation. J Theor Biol. 2010. 265: 27-44.
  • S. Höhme, D. Drasdo. Biomechanical and Nutrient Controls in the Growth of Mammalian Cell Populations. Mathematical Population Studies: An International Journal of Mathematical Demography. 2010. 17: 166-187.
  • M. Riester, P. F. Stadler, K. Klemm. Reconstruction of pedigrees in clonal plant populations. Theor Popul Biol. 2010. 78: 109-17.
  • M. Riester, C. Stephan-Otto Attolini, R. J. Downey, S. Singer, F. Michor. A differentiation-based phylogeny of cancer subtypes. PLoS Comput Biol. 2010. 6: e1000777.
  • P. Scheibe, U. D. Braumann, J. P. Kuska, M. Löffler, J. C. Simon, U. Paasch, T. Wetzig. Image-processing chain for a three-dimensional reconstruction of basal cell carcinomas. Exp Dermatol. 2010. 19: 689-91.
  • C. M. Sharma, S. Hoffmann, F. Darfeuille, J. Reignier, S. Findeiss, A. Sittka, S. Chabas, K. Reiche, J. Hackermüller, R. Reinhardt, P. F. Stadler, J. Vogel. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010. 464: 250-5.
  • M. Sturm, M. Hackenberg, D. Langenberger, D. Frishman. TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics. 2010. 11: 292.
  • H. Tafer, S. Kehr, J. Hertel, I. L. Hofacker, P. F. Stadler. RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics. 2010. 26: 610-6.
  • S. Höhme, D. Drasdo. A cell-based simulation software for multi-cellular systems. Bioinformatics. 2010. 26: 2641-2.
  • S. Höhme, M. Brulport, A. Bauer, E. Bedawy, W. Schormann, M. Hermes, V. Puppe, R. Gebhardt, S. Zellmer, M. Schwarz, E. Bockamp, T. Timmel, J. G. Hengstler, D. Drasdo. Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration. Proc Natl Acad Sci U S A. 2010. 107: 10371-6.
  • C. Arnold, P. F. Stadler. Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees. Algorithms Mol Biol. 2010. 5: 25.
  • C. J Burden, H. Binder. Reply to 'Linking probe thermodynamics to microarray quantification'. Physical Biology. 2010. 7: 048002.
  • C. Bermudez-Santana, C. S. Attolini, T. Kirsten, J. Engelhardt, S. J. Prohaska, S. Steigele, P. F. Stadler. Genomic organization of eukaryotic tRNAs. BMC Genomics. 2010. 11: 270.
  • H. Binder, K. Krohn, C. J. Burden. Washing scaling of GeneChip microarray expression. BMC Bioinformatics. 2010. 11: 291.
  • H. Binder, S. Preibisch, H. Berger, C. J. Burden. Calibration of microarray gene-expression data Physico-chemical modelling of target depletion during hybridization on oligonulceotide microarrays. Methods Mol Biol. 2010. 576: 375-407.
  • H. Binder, H. Wirth, J. Galle. Gene expression density profiles characterize modes of genomic regulation: theory and experiment. J Biotechnol. 2010. 149: 98-114.
  • A. Bräuning, Y. Singh, B. Rignall, A. Buchmann, S. Hammad, A. Othman, I. von Recklinghausen, P. Godoy, S. Höhme, D. Drasdo, J. G. Hengstler, M. Schwarz. Phenotype and growth behavior of residual beta-catenin-positive hepatocytes in livers of beta-catenin-deficient mice. Histochem Cell Biol. 2010. 134: 469-81.
  • C. J. Burden, H. Binder. Physico-chemical modelling of target depletion during hybridization on oligonulceotide microarrays. Phys Biol. 2010. 7: 016004.
  • R. A. Dalloul, J. A. Long, A. V. Zimin, L. Aslam, K. Beal, L. Ann Blomberg, P. Bouffard, D. W. Burt, O. Crasta, R. P. Crooijmans, K. Cooper, R. A. Coulombe, S. De, M. E. Delany, J. B. Dodgson, J. J. Dong, C. Evans, K. M. Frederickson, P. Flicek, L. Florea, O. Folkerts, M. A. Groenen, T. T. Harkins, J. Herrero, S. Hoffmann, H. J. Megens, A. Jiang, P. de Jong, P. Kaiser, H. Kim, K. W. Kim, S. Kim, D. Langenberger, M. K. Lee, T. Lee, S. Mane, G. Marcais, M. Marz, A. P. McElroy, T. Modise, M. Nefedov, C. Notredame, I. R. Paton, W. S. Payne, G. Pertea, D. Prickett, D. Puiu, D. Qioa, E. Raineri, M. Ruffier, S. L. Salzberg, M. C. Schatz, C. Scheuring, C. J. Schmidt, S. Schroeder, S. M. Searle, E. J. Smith, J. Smith, T. S. Sonstegard, P. F. Stadler, H. Tafer, Z. J. Tu, C. P. Van Tassell, A. J. Vilella, K. P. Williams, J. A. Yorke, L. Zhang, H. B. Zhang, X. Zhang, Y. Zhang, K. M. Reed. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 2010. 8:
  • M. Höckel, T. Kahn, J. Einenkel, N. Manthey, U. D. Braumann, G. Hildebrandt, C. Leo, B. Hentschel, P. Vaupel, L. C. Horn. Local spread of cervical cancer revisited: a clinical and pathological pattern analysis. Gynecol Oncol. 2010. 117: 401-8.
  • A. Donath, S. Findeiss, J. Hertel, M. Marz, W. Otto, C. Schulz, P. F. Stadler, S. Wirth. Non-coding RNAs. 2010. 251-293.
  • M. Fasold, P. F. Stadler, H. Binder. G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. BMC Bioinformatics. 2010. 11: 207.
  • S. Findeiss, C. Schmidtke, P. F. Stadler, U. Bonas. A novel family of plasmid-transferred anti-sense ncRNAs. RNA Biol. 2010. 7: 120-4.
  • J. Galle, A. Bader, P. Hepp, W. Grill, B. Fuchs, J. A. Kas, A. Krinner, B. Marquass, K. Müller, J. Schiller, R. M. Schulz, M. von Buttlar, E. von der Burg, M. Zscharnack, M. Löffler. Mesenchymal stem cells in cartilage repair: state of the art and methods to monitor cell growth, differentiation and cartilage regeneration. Curr Med Chem. 2010. 17: 2274-91.
  • I. Glauche, M. Herberg, I. Roeder. Nanog variability and pluripotency regulation of embryonic stem cells--insights from a mathematical model analysis. PLoS One. 2010. 5: e11238.
  • Michael Hartung, Frank Löbe, Heinrich Herre, Erhard Rahm. Management of evolving semantic grid metadata within a collaborative platform. Information Sciences Special Issue on Intelligent Distributed Information Systems. 2010. 180: 1837-1849.
  • O. Wolkenhauer, C. Auffray, S. Baltrusch, N. Bluthgen, H. Byrne, M. Cascante, A. Ciliberto, T. Dale, D. Drasdo, D. Fell, J. E Ferrell, Jr., D. Gallahan, R. Gatenby, U. Gunther, B. D. Harms, H. Herzel, C. Junghanss, M. Kunz, I. van Leeuwen, P. Lenormand, F. Levi, M. Linnebacher, J. Lowengrub, P. K. Maini, A. Malik, K. Rateitschak, O. Sansom, R. Schafer, K. Schurrle, C. Sers, S. Schnell, D. Shibata, J. Tyson, J. Vera, M. White, B. Zhivotovsky, R. Jaster. Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res. 2010. 70: 12-3.

2009 (34)

  • M.v. Bergen, A. Eidner, F. Schmidt, J. Murugaiyan, H. Wirth, H. Binder, T. Maier, U. Roesler. Identification of harmless and pathogenic algae of the genus Prototheca by MALDI-MS. PROTEOMICS - CLINICAL APPLICATIONS. 2009. 3: 774-784.
  • S. Hoffmann, C. Otto, S. Kurtz, C. M. Sharma, P. Khaitovich, J. Vogel, P. F. Stadler, J. Hackermüller. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol. 2009. 5: e1000502.
  • P. F. Stadler, S. J. Prohaska, C. V. Forst, D. C. Krakauer. Defining genes: a computational framework. Theory Biosci. 2009. 128: 165-70.
  • P. F. Stadler, J. J. Chen, J. Hackermüller, S. Hoffmann, F. Horn, P. Khaitovich, A. K. Kretzschmar, A. Mosig, S. J. Prohaska, X. Qi, K. Schutt, K. Ullmann. Evolution of vault RNAs. Mol Biol Evol. 2009. 26: 1975-91.
  • H. Schmidt, H. Taubert, H. Lange, K. Kriese, W. D. Schmitt, S. Hoffmann, F. Bartel, S. Hauptmann. Small polydispersed circular DNA contains strains of mobile genetic elements and occurs more frequently in permanent cell lines of malignant tumors than in normal lymphocytes. Oncol Rep. 2009. 22: 393-400.
  • K. Scheibye-Alsing, S. Hoffmann, A. Frankel, P. Jensen, P. F. Stadler, Y. Mang, N. Tommerup, M. J. Gilchrist, A. B. Nygard, S. Cirera, C. B. Jorgensen, M. Fredholm, J. Gorodkin. Sequence assembly. Comput Biol Chem. 2009. 33: 121-36.
  • I. Roeder, M. Herberg, M. Horn. An "age"-structured model of hematopoietic stem cell organization with application to chronic myeloid leukemia. Bull Math Biol. 2009. 71: 602-26.
  • M. Riester, P. F. Stadler, K. Klemm. FRANz: reconstruction of wild multi-generation pedigrees. Bioinformatics. 2009. 25: 2134-9.
  • I. Ramis-Conde, M. A. Chaplain, A. R. Anderson, D. Drasdo. Multi-scale modelling of cancer cell intravasation: the role of cadherins in metastasis. Phys Biol. 2009. 6: 16008.
  • M. Radszuweit, M. Block, J. G. Hengstler, E. Scholl, D. Drasdo. Comparing the growth kinetics of cell populations in two and three dimensions. Phys Rev E Stat Nonlin Soft Matter Phys. 2009. 79: 051907.
  • A. Mosig, T. BIyIkoglu, S.J. Prohaska, P.F. Stadler. Discovering cis-regulatory modules by optimizing barbecues. Discrete Applied Mathematics Networks in Computational Biology. 2009. 157: 2458-2468.
  • J. Läuter, F. Horn, M. Rosolowski, E. Glimm. High-dimensional data analysis: selection of variables, data compression and graphics--application to gene expression. Biom J. 2009. 51: 235-51.
  • D. Langenberger, C. Bermudez-Santana, J. Hertel, S. Hoffmann, P. Khaitovich, P. F. Stadler. Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics. 2009. 25: 2298-301.
  • A. Krinner, M. Zscharnack, A. Bader, D. Drasdo, J. Galle. Impact of oxygen environment on mesenchymal stem cell expansion and chondrogenic differentiation. Cell Prolif. 2009. 42: 471-84.
  • B. Kaczkowski, E. Torarinsson, K. Reiche, J.H. Havgaard, P.F. Stadler, J. Gorodkin. Structural profiles of human miRNA families from pairwise clustering. Bioinformatics. 2009. 25: 291-4.
  • T. A. Jones, W. Otto, M. Marz, S. R. Eddy, P. F. Stadler. A survey of nematode SmY RNAs. RNA Biol. 2009. 6: 5-8.
  • M. Höckel, L. C. Horn, N. Manthey, U. D. Braumann, U. Wolf, G. Teichmann, K. Frauenschlager, N. Dornhofer, J. Einenkel. Resection of the embryologically defined uterovaginal (Mullerian) compartment and pelvic control in patients with cervical cancer: a prospective analysis. Lancet Oncol. 2009. 10: 683-92.
  • H Binder, J Brücker, C. J. Burden. Non-specific hybridization scaling of microarray expression estimates - a physico-chemical approach for chip-to-chip normalization. Journal of Physical Chemistry B. 2009. 113: 2874-2895.
  • J. Einenkel, R. Ott, R. Handzel, U. D. Braumann, L. C. Horn. Characteristics and management of diaphragm involvement in patients with primary advanced-stage ovarian, fallopian tube, or peritoneal cancer. Int J Gynecol Cancer. 2009. 19: 1288-97.
  • H. Binder, M. Fasold, T. Glomb. Mismatch and G-stack modulated probe signals on SNP microarrays. PLoS One. 2009. 4: e7862.
  • Hans Binder, Mario Fasold, Torsten Glomb. Systematic bias of genotyping estimates caused by sequence and saturation effects of SNP-microarray. accompanying paper. 2009. submitted:
  • Hans Binder, Stephan Preibisch, Hilmar Berger. Calibration of microarray gene-expression data. In: Methods in Molecular Biology, Humana Press , New York. 2009. 576: 375-407. Ed: Grützmann, R. and Pilarski, C.
  • R. Booy, H. El Bashir, H. Rashid, D. Shingadia, E. Haworth. Influenza and meningococcal disease: lessons for travellers and government from 2 epidemic diseases. Travel Med Infect Dis. 2009. 7: 253-256.
  • H. Byrne, D. Drasdo. Individual-based and continuum models of growing cell populations: a comparison. J Math Biol. 2009. 58: 657-87.
  • S. Cepok, H. Schreiber, S. Hoffmann, D. Zhou, O. Neuhaus, G. von Geldern, S. Hochgesand, S. Nessler, V. Rothhammer, M. Lang, H. P. Hartung, B. Hemmer. Enhancement of Chemokine Expression by Interferon Beta Therapy in Patients With Multiple Sclerosis. Arch Neurol. 2009.
  • J. Erlecke, I. Hartmann, M. Hoffmann, T. Kroll, H. Starke, A. Heller, A. Gloria, H. G. Sayer, T. Johannes, U. Claussen, T. Liehr, I. F. Loncarevic. Automated detection of residual cells after sex-mismatched stem-cell transplantation - evidence for presence of disease-marker negative residual cells. Mol Cytogenet. 2009. 2: 12.
  • M. Hiller, S. Findeiss, S. Lein, M. Marz, C. Nickel, D. Rose, C. Schulz, R. Backofen, S. J. Prohaska, G. Reuter, P. F. Stadler. Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Res. 2009. 19: 1289-300.
  • J. Galle, M. Hoffmann, G. Aust. From single cells to tissue architecture-a bottom-up approach to modelling the spatio-temporal organisation of complex multi-cellular systems. J Math Biol. 2009. 58: 261-283.
  • J. Galle, L. Preziosi. Multiphase and Individual Cell-Based Models of Tumour Growth. In: Mathematics, Developmental Biology and Tumour Growth, American Mathematical Society 2009. 492: 103-123. Ed: Giraldez, F. and Herrero, M. A.
  • J. Galle, L. Preziosi, A. Tosin. Contact inhibition of growth described using a multiphase model and an individual cell based model. Applied Mathematics Letters. 2009. 22: 1483-1490.
  • M. Hartung, T. Kirsten, A. Gross, E. Rahm. OnEX: Exploring changes in life science ontologies. BMC Bioinformatics. 2009. 10: 250.
  • J. Hertel, d.D. Jong, M. Marz, D. Rose, H. Tafer, A. Tanzer, B. Schierwater, Peter F. Stadler. Non-Coding RNA Annotation of the Genome of Trichoplax adhaerens. Nucleic Acids Res. 2009. 37: 1602-1615.
  • M. Zscharnack, C. Poesel, J. Galle, A. Bader. Low oxygen expansion improves subsequent chondrogenesis of ovine bone-marrow-derived mesenchymal stem cells in collagen type I hydrogel. Cells Tissues Organs. 2009. 190: 81-93.
  • A. Gross, M. Hartung, T. Kirsten, E. Rahm. Estimating the Quality of Ontology-Based Annotations by Considering Evolutionary Changes. 2009. 71-87.

2008 (33)

  • Michelle M. Barthet, Khidir W. Hilu. Evaluating evolutionary constraint on the rapidly evolving gene matK using protein composition. J Mol Evol. 2008. 66: 85-97.
  • Lars-Christian Horn, Bettina Hentschel, Ulf-Dietrich Braumann. Malignancy grading, pattern of invasion, and juxtatumoral stromal response (desmoplastic change) in squamous cell carcinoma of the uterine cervix. Int J Gynecol Pathol. 2008. 27: 606-607.
  • Mingang Xu, John R. McCarrey, Norman B. Hecht. A cytoplasmic variant of the KH-type splicing regulatory protein serves as a decay-promoting factor for phosphoglycerate kinase 2 mRNA in murine male germ cells. Nucleic Acids Res. 2008. 36: 7157-7167.
  • Mingyi Xie, Axel Mosig, Xiaodong Qi, Yang Li, Peter F. Stadler, Julian J.-L. Chen. Size Variation and Structural Conservation of Vertebrate Telomerase RNA. J. Biol. Chem. 2008. 283: 2049-2059.
  • N. Victor, J. Lauter, P. Ihm, K. Dietz. Celebrating fifty years of the Biometrical Journal. Biom J. 2008. 50: 901-10.
  • Elisabeth Sonnleitner, Theresa Sorger-Domenigg, Monika J. Madej, Sven Findeiss, Jörg Hackermüller, Alexander Hüttenhofer, Peter F. Stadler, Udo Bäsi, Isabella Moll. Detection of small non-coding RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatics tools. Microbiology. 2008. 154: 3175-3187.
  • N. Scherf, J. P. Kuska, C. Heine, U-D. Braumann, H. Franke. Segmentation of Axonal Fibres in Tissue Slices. In: Bildverarbeitung für die Medizin 2008 Algorithmen — Systeme — Anwendungen, Springer , Berlin Heidelberg. 2008. 178-182. Ed: Tolxdorff, T. and Braun, J. and Deserno, T. and Horsch, A. and Handels, H. and Meinzer, H.-P.
  • Dominic Rose, Julian Jöris, Jörg Hackermüller, Kristin Reiche, Qiang Li, Peter F. Stadler. Duplicated RNA Genes in Teleost Fish Genomes. J. Bioinf. Comp. Biol. 2008. 6: 1157-1175.
  • Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. Stadler, Jörg Hackermüller. NcDNAlign: Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences. Genomics. 2008. 92: 65-74.
  • Ignacio Ramis-Conde, Dirk Drasdo, Alexander R.A. Anderson, Mark A.J. Chaplain. Modeling the influence of the E-cadherin-beta-catenin pathway in cancer cell invasion: a multiscale approach. Biophys J. 2008. 95: 155-165.
  • Sonja J. Prohaska, Peter F. Stadler. Genes. Th. Biosci. 2008. 127: 215-221.
  • Sonja J. Prohaska, Guido Fritzsch, Peter F. Stadler. Rate Variations, Phylogenetics, and Partial Orders. In: Fifth International Workshop on Computational Systems Biology, WCSB 2008, TU Tampere 2008. 133-136. Ed: Ahdesmäki, Miika and Strimmer, Korbinian and Radde, Nicole and Rahnenführer, Jörg and Klemm, Konstantin and Lähdesmäki, Harri and Yli-Harja, Olli.
  • Marleen Perseke, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter F. Stadler, Martin Schlegel. Evolution of Mitochondrial Gene Orders in Echinoderms. Mol. Phylog. Evol. 2008. 47: 855-864.
  • Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska. SynBlast: Assisting the Analysis of Conserved Synteny Information. BMC Bioinformatics. 2008. 9: 351.
  • Veiko Krauss, Christian Thümmler, Franziska Georgi, Jörg Lehmann, Peter F. Stadler, Carina Eisenhardt. Near intron positions are reliable phylogenetic markers: An application to Holometabolous Insects. Mol. Biol. Evol. 2008. 25: 821-830.
  • Christoph Joechl, Mathieu Rederstorff, Jana Hertel, Peter F. Stadler, Ivo L. Hofacker, Markus Schrettl, Hubertus Haas, Alexander Hüttenhofer. Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein-synthesis. Nucleic Acids Res. 2008. 36: 2677-2689.
  • S. Hoffmann, S. Cepok, V. Grummel, K. Lehmann-Horn, J. Hackermüller, P. F. Stadler, H. P. Hartung, A. Berthele, F. Deisenhammer, R. Wassmuth, B. Hemmer. HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis. Am J Hum Genet. 2008. 83: 219-27.
  • A.K.M.A. Baten, S.K. Halgamuge, B.C.H. Chang. Fast splice site detection using information content and feature reduction. BMC Bioinformatics. 2008. 9 Suppl 12:
  • M. Hoffmann, H. H. Chang, S. Huang, D. E. Ingber, M. Löffler, J. Galle. Noise-driven stem cell and progenitor population dynamics. PLoS One. 2008. 3: e2922.
  • Hui Kian Ho, Michael J. Kuiper, Ramamohanarao Kotagiri. PConPy--a Python module for generating 2D protein maps. Bioinformatics. 2008. 24: 2934-2935.
  • Jana Hertel, Ivo L. Hofacker, Peter F. Stadler. snoReport: Computational identification of snoRNAs with unknown targets. Bioinformatics. 2008. 24: 158-164.
  • A. Heffel, P. F. Stadler, S. J. Prohaska, G. Kauer, J. P. Kuska. Process Flow for Classification and Clustering of Fruit Fly Gene Expression Patterns. In: Proc Int Conf Image Proc 2008. 1: 721-724.
  • Michael Hartung, Toralf Kirsten, Erhard Rahm. Analyzing the Evolution of Life Science Ontologies and Mappings http://dx.doi.org/10.1007/978-3-540-69828-9_4. In: Proceedings of the 5th international workshop on Data Integration in the Life Sciences, Springer-Verlag , Evry, France. 2008. 11-27.
  • Andreas R. Gruber, Dorota Koper-Emde, Manja Marz, Hakim Tafer, Stephan Bernhart, Gregor Obernosterer, Axel Mosig, Ivo L. Hofacker, Peter F. Stadler, Bernd-Joachim Benecke. Invertebrate 7SK snRNAs. J. Mol. Evol. 2008. 107-115: 66.
  • Michael Geis, Christian Flamm, Michael T. Wolfinger, Andrea Tanzer, Ivo L. Hofacker, Martin Middendorf, Christian Mandl, Peter F. Stadler, Caroline Thurner. Folding kinetics of large RNAs. J. Mol. Biol. 2008. 379: 160-173.
  • Guido Fritzsch, Manja U. Böhme, Mike Thorndyke, Hiroaki Nakano, Olle Israelsson, Thomas Stach, Martin Schlegel, Thomas Hankeln, Peter F. Stadler. A PCR Survey of Xenoturbella bocki Hox Genes. J. Exp. Zool: Mol. Dev. Evol. 2008. 310B: 278-284.
  • Andreas W.M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grunewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler. Noisy: identification of problematic columns in multiple sequence alignments. Algorithms Mol Biol. 2008. 3: 7.
  • Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Berhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler, Sebastian Will. Variations on RNA Folding and Alignment: Lessons from Benasque. J. Math. Biol. 2008. 56: 129-144.
  • Hans Binder, Stephan Preibisch. "Hook"-calibration of GeneChip-microarrays: theory and algorithm. Algorithms Mol Biol. 2008. 3: 12.
  • Hans Binder, Knut Krohn, Stephan Preibisch. "Hook" calibration of GeneChip-microarrays: chip characteristics and expression measures. Algorithms for Molecular Biology. 2008. 3:11:
  • Stephan H Bernhart, Ivo L Hofacker, Sebastian Will, Andreas R Gruber, Peter F Stadler. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics. 2008. 9: 474.
  • Stephan Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics. 2008. 9: 474.
  • Karsten Zieger. High throughput molecular diagnostics in bladder cancer - on the brink of clinical utility. Mol Oncol. 2008. 1: 384-394.

2005 - 2007

2007 (16)

  • Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf. CREx: inferring genomic rearrangements based on common intervals. Bioinformatics. 2007. 23: 2957-2958.
  • H. Binder. Water near lipid membranes as seen by infrared spectroscopy. Eur Biophys J. 2007. 36: 265-79.
  • Athanasius F. Bompfünewerer, Rolf Backofen, Christoph Flamm, Claudia Fried, Guido Fritzsch, Joerg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Domininc Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will. RNAs Everywhere: Genome-Wide Annotation of Structured RNAs. J. Exp.Zool.B: Mol. Dev. Evol. 2007. 308B: 1-25.
  • The Athanasius F. Bompfünewerer RNA Consortium, Rolf Backofen, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Will Sebastian. RNAs Everywhere: Genome-Wide Annotation of Structured RNAs. J. Exp. Zool. B: Mol. Dev. Evol. 2007. 308B: 1-25.
  • D. Drasdo. Center-based Single-cell Models: An Approach to Multi-cellular Organization Based on a Conceptual Analogy to Colloidal Particles. In: Single-Cell-Based Models in Biology and Medicine, Birkhaeuser , Basel. 2007. 171-196. Ed: Anderson, Alexander R. A. and Chaplain, Mark A. J. and Rejniak, Katarzyna A.
  • Jens Einenkel, Wolfram Steller, Ulf-Dietrich Braumann, Lars-Christian Horn, Christoph Krafft. Unrealistic expectations for IR microspectroscopic imaging. Nat Biotechnol. 2007. 25: 29-31.
  • Susanne Horn, Katrin Ehlers, Guido Fritzsch, Maria Candelaria Gil-Rodriguez, Christian Wilhelm, Reinhard Schnetter. Synchroma grande spec. nov. (Synchromophyceae class. nov., Heterokontophyta): an amoeboid marine alga with unique plastid complexes. Protist. 2007. 158: 277-293.
  • Dayong Jin, Russell Connally, James Piper. Practical time-gated luminescence flow cytometry. I: concepts. Cytometry A. 2007. 71: 783-796.
  • T Kirsten, A Thor, E. Rahm. Instance-based matching of large life science ontologies. In: Lecture Notes in Computer Science, Springer Berlin/Heidelberg 2007. Volume 4544/2007: 172-187.
  • Dennis Loffler, Katja Brocke-Heidrich, Gabriele Pfeifer, Claudia Stocsits, Jorg Hackermüller, Antje K. Kretzschmar, Renate Burger, Martin Gramatzki, Conny Blumert, Kay Bauer, Helena Cvijic, A. Kerstin Ullmann, Peter F. Stadler, Friedemann Horn. Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer. Blood. 2007. 110: 1330-1333.
  • Madleen Perseke, Thomas Hankeln, Bettina Weich, Guido Fritzsch, Peter F. Stadler, Detlef Bernhard, Martin Schlegel. The Mitochondrial DNA of Xenoturbella bocki: Genomic Architecture and Phylogenetic Analysis. Th. Biosci. 2007. 126: 35-42.
  • Yvonne E. Pittelkow, Susan R. Wilson. H-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data. BMC Bioinformatics. 2007. 8: 486.
  • Y. Qiu, P. Yu. Nursing information systems - applying usability testing to assess the training needs for nursing students. Methods Inf Med. 2007. 46: 416-419.
  • E Rahm, T Kirsten, J. Lange. The GeWare data warehouse platform for the analysis of molecular-biological and clinical data. Journal of integrative Bioinformatics. 2007. 4(1):47:
  • M. Rohrschneider, G. Scheuermann, S. Höhme, D. Drasdo. Shape characterization of extracted and simulated tumor samples using topological and geometric measures. Conf Proc IEEE Eng Med Biol Soc. 2007. 2007: 6272-8.
  • D. Voigt, H. Wirth, W. Dilger. A Computational Model for the Cognitive Immune System Theory Based on Learning Classifier Systems. 2007. 264-275.

2006 (16)

  • Hans Binder. Probing gene expression - sequence specific hybridization on microarrays. In: Bioinformatics of Gene Regulation II, Springer Sciences and Business Media 2006. 451-466. Ed: Kolchanov, N. and Hofestaedt, R.
  • H Binder. Thermodynamics of competitive surface adsorption on DNA microarrays. Journal of Physics-Condensed Matter. 2006. 18: S491 - S523.
  • Hans Binder, Stephan Preibisch. GeneChip microarrays - signal intensities, RNA concentrations and probe sequences. Journal of Physics Condensed Matter. 2006. 18: S537-S566.
  • Heinz P. Binder, Elke Mesenholl-Strehler, Paul Pass, P.Christian Endler. Sense of coherence (SOC) among psychotherapists in Austria, differentiated according to number of individually completed training therapy sessions. ScientificWorldJournal. 2006. 6: 2196-2199.
  • U-D. Braumann, J. P. Kuska, J. Einenkel, L.-C. Horn, M. Löffler, M. Höckel. Tumor Invasion Pattern Analysis of Cervical Carcinoma in 3-D. Medizinische Physik. 2006. 10-15.
  • Jens Einenkel, Jens-Peer Kuska, Lars-Christian Horn, Nicolas Wentzensen, Michael Hockel, Ulf-Dietrich Braumann. Combined three-dimensional microscopic visualisation of tumour-invasion front of cervical carcinoma. Lancet Oncol. 2006. 7: 698.
  • Markus Eszlinger, Knut Krohn, Martin Beck, David Kipling, Sarah Forbes-Robertson, Jurgen Lauter, Anke Toenjes, David Wynford-Thomas, Ralf Paschke. Comparison of differential gene expression of hot and cold thyroid nodules with primary epithelial cell culture models by investigation of co-regulated gene sets. Biochim Biophys Acta. 2006. 1763: 263-271.
  • Markus Eszlinger, Malgorzata Wiench, Barbara Jarzab, Knut Krohn, Martin Beck, Jurgen Lauter, Elzbieta Gubala, Krzysztof Fujarewicz, Andrzej Swierniak, Ralf Paschke. Meta- and reanalysis of gene expression profiles of hot and cold thyroid nodules and papillary thyroid carcinoma for gene groups. J Clin Endocrinol Metab. 2006. 91: 1934-1942.
  • Guido Fritzsch, Martin Schlegel, Peter F. Stadler. Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny. J Theor Biol. 2006. 240: 511-520.
  • J. Galle, G. Aust, G. Schaller, T. Beyer, D. Drasdo. Individual cell-based models of the spatial-temporal organization of multicellular systems--achievements and limitations. Cytometry A. 2006. 69: 704-10.
  • J. Galle, D. Sittig, I. Hanisch, M. Wobus, E. Wandel, M. Loeffler, G. Aust. Individual cell-based models of tumor-environment interactions: Multiple effects of CD97 on tumor invasion. Am J Pathol. 2006. 169: 1802-11.
  • L-C. Horn, U. Fischer, G. Raptis, K. Bilek, B. Hentschel, C.E. Richter, U-D. Braumann, J. Einenkel. Pattern of invasion is of prognostic value in surgically treated cervical cancer patients. Gynecol Oncol. 2006. 103: 906-911.
  • Kristin Missal, Michael A. Cross, Dirk Drasdo. Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment. Bioinformatics. 2006. 22: 731-738.
  • Kristin Missal, Xiaopeng Zhu, Dominic Rose, Wei Deng, Geir Skogerbo, Runsheng Chen, Peter F. Stadler. Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. J Exp Zoolog B Mol Dev Evol. 2006. 306: 379-392.
  • Wolfram Steller, Jens Einenkel, Lars-Christian Horn, Ulf-Dietrich Braumann, Hans Binder, Reiner Salzer, Christoph Krafft. Delimitation of squamous cell cervical carcinoma using infrared microspectroscopic imaging. Anal Bioanal Chem. 2006. 384: 145-154.
  • R. L. Winslow, A. Tanskanen, M. Chen, J. L. Greenstein. Multiscale modeling of calcium signaling in the cardiac dyad. Ann N Y Acad Sci. 2006. 1080: 362-75.

2005 (6)

  • Hans Binder, Stephan Preibisch. Specific and non-specific hybridization of oligonucleotide probes on microarrays. Biophysical Journal. 2005. 89: 337-352.
  • Hans Binder, Stephan Preibisch. Specific and non-specific hybridization of oligonucleotide probes on microarrays. Biophysical Journal. 2005. 89: 337-352.
  • H. Binder, S. Preibisch, T. Kirsten. Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays. Langmuir. 2005. 21: 9287-9302.
  • Athanasius F. Bompfuenewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L. Hofacker, Jörg Lehmann, Kristin Missal, Axel Mosig, Bettina Müller, Sonja J. Prohaska, Bärbel M. R. Stadler, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Christina Witwer. Evolutionary Patterns of Non-Coding RNAs. Th. Biosci. 2005. 123: 301-369.
  • M. Eszlinger, K. Krohn, K. Berger, J. Lauter, S. Kropf, M. Beck, D. Fuhrer, R. Paschke. Gene expression analysis reveals evidence for increased expression of cell cycle-associated genes and Gq-protein-protein kinase C signaling in cold thyroid nodules. J Clin Endocrinol Metab. 2005. 90: 1163-70.
  • J. Läuter, E. Glimm, M Eszlinger. Search for relevant sets of variables in a high-dimensional setup keeping the familywise error rate. Statistica Neerlandica. 2005. 59: 298-312.

2002 - 2004

2004 (2)

  • H Binder, T Kirsten, I.L Hofacker, P Stadler, M. Löffler. Interactions in oligonucleotide hybrid duplexes on microarrays. Journal of Physical Chemistry. 2004. eingereicht.
  • H Binder, T Kirsten, M Löffler, P. Stadler. The sensitivity of microarray oligonucleotide probes - variability and the effect of base composition. Journal of Physical Chemistry. 2004. eingereicht.

2003 (1)

  • Hans Binder, Toralf Kirsten, Markus Loeffler, Peter Stadler. Sequence specific sensitivity of oligonucleotide probes. In: Proceedings of the German Bioinformatics Conference 2003 . 2: 145-147.

2003 (30)

  • D. Barth, D. Bernhard, G. Fritzsch, U. Fritz. The freshwater turtle genus Mauremys (Testudienes, Geoemydidae) - a textbook example of an east-west disjunction or a taxonomic misconcept?. Zoologica Scripta. 2003. in press.
  • I Hellmann, I Ebersberger, S Ptak, S Pääbo, M. Przeworski. A Neutral Explanation for the Correlation of Diversity with Recombination Rates in Humans. American Journal of Human Genetics. 2003. 72: 1527-1535.
  • T Rohlf, S. Bornholdt. Spatio-temporal pattern formation in a system of coupled dynamical networks. 2003.
  • T Rohlf, S. Bornholdt. Gene regulatory networks: A discrete model of dynamics and topological evolution. In: Function and regulation of cellular systems: experiments and models, Birkhäuser Verlag Basel , Basel. 2003. in press. Ed: Deutsch, A. and Howard, J. and Falcke, M. and Zimmermann, W.
  • T. Röhl, S. Bornholdt. Self-organized critical neural networks. Phys. Rev. E. 2003. submitted cond-mat/0109256.
  • H Pfeiffer, H Binder, G Klose, K. Heremans. Hydration Pressure and Phase Transitions of Phospholipids - II. Thermotropic Approach. Biochim. Biophys. Acta. 2003. 1609: 148-152.
  • H Pfeiffer, H Binder, G Klose, K. Heremans. Hydration Pressure and Phase Transitions of Phospholipids - I. Piezotropic Approach. Biochim. Biophys. Acta. 2003. 1609: 144-147.
  • K Klemm, V. M Eguiluz, R Toral, M. San Miguel. Role of dimensionality in Axelrod's model for the dissemination of culture. Physica A. 2003. 327: 1.
  • K Klemm, V. M Eguiluz, R Toral, M. San Miguel. Nonequilibrium transitions in complex networks: a model of social interaction. Phys. Rev. E. 2003. 67: 026120.
  • K Klemm, V. M Eguiluz, R Toral, M. San Miguel. Global culture: A noise-induced transition in finite system. Phys. Rev. E. 2003. 67: 045101(R).
  • C Kamp, C.O Wilke, C Adami, S. Bornholdt. Viral evolution under the pressure of an adaptive immune system - optimal mutation rates for viral escape. Complexity. 2003. 8(2): 28-33.
  • C Kamp, S. Bornholdt. Self-organization to critical percolation on a random directed network. 2003.
  • C Kamp, S. Bornholdt. Critical percolation in self-organized media: A case study on random directed networks. Phys. Rev. Lett. 2003. submitted cond-mat/0210410.
  • D Huster, A Vogel, C Katzka, H Scheidt, H Binder, S Dante, T Gutberlet, T Zschörnig, H Waldmann, K. Arnold. Membrane Insertion of a Lipidated ras peptide Studied by FTIR, Solid-state NMR, and Neutron Diffraction Spectroscopy. J. Am. Chem. Soc. 2003. 125: 4070-4079.
  • E Glimm, J. Läuter. On the Admissibility of Stable Spherical Multivariate Tests. Journal of Multivariate Analysis. 2003. 86: 254-265.
  • H. Binder. The moleculare architecture of lipid membranes - New insights from Hydration-tuning infrared linear dichroism spectroscopy. Appl. Spectroscopy Rev. 2003. 38: 15-69.
  • V. M Eguiluz, E Hernandez-Garcia, O Piro, Klemm. K. Effective dimensions and percolation in hierarchically structured scale-free networks. Phys. Rev. E. 2003. 68: 055102(R).
  • H Ebel, J Davidsen, S. Bornholdt. Dynamics of social networks. Complexity. 2003. 8(2): 24-27.
  • H Ebel, S. Bornholdt. Scale-free topology of email networks. 2003.
  • H Ebel, S. Bornholdt. Evolutionary games and the emergence of complex networks. Phys. Rev. Lett. 2003. submitted cond-mat/0211666.
  • H Ebel, S. Bornholdt. Emergence of complex networks from game theoretic interactions. 2003.
  • D Drasdo, S. Höhme. Individual-based approaches to birth and death in avascular tumors. Mathl. Comput. Modelling. 2003. 37: 1163-1175.
  • D Drasdo, S. Höhme. How do Tumors grow in-vitro?. 2003. submitted.
  • D Drasdo, S Dormann, S Höhme, A. Deutsch. Individual-based models of Avascular Tumor growth. In: Functions and regulation of Cellular Systems: Experiments and Models, Birkhäuser , Basel. 2003. Ed: Deutsch, A. and Falcke, M. and Howard, J. and Zimmermann, W.
  • S Bornholdt, T. Röhl. Self-organized critical neural networks. Phys. Rev. E. 2003. 67: 066118.
  • H Boriss, V. Loeschke. Complexity theory provides metaphors for a better understanding of biological processes - a holistic approach to explaining the stress response. In:"The Significance of Complexity", Ashgate: Hampshire, UK. ISBN: 0-7546-0972-3. 2003.
  • F Böhm, H Westphal, S. Bornholdt. Required but disguised: Environmental signals in limestone-marl alternations. Palaeogeography, Palaeoclimatology, Palaeoecology. 2003. 189: 161-178.
  • H Binder, G. Lindblom. Interaction of the Trojan peptide penetratin with anionic lipid membranes - a caloriometric study. Phys. Chem. Chem. Phys. 2003. 5: 5108-5117.
  • H Binder, G. Lindblom. Charge-dependent translocation of the Trojan peptide penetratin across lipid membranes. Biophysical Journal. 2003. 85: 982-995.
  • T. Rohlf, C. Winkler, S. Bornholdt. Emergent Network Structure, Dynamics and Evolution of an Artificial Genome. 2003.

2002 (28)

  • S. Bornholdt. The dynamics of large biological systems: A statistical physics view of macro-evolution. In: Evolutionary Dynamics - Exploring the Interplay of Selection, Neutrality, Accident, and Function, Oxford University Press 2002. 65-80. Ed: Crutchfield, J. P. and Schuster, P.
  • T Kirsten, H.H Do, E Rahm, K. Krohn. Gene Expression Warehousing. 2002.
  • T Rohlf, S. Bornholdt. Criticality in Random Threshold Networks: Annealed Approximation and Beyond. Physica A. 2002. 310: 245-259.
  • S. E Ptak, M. Przeworski. Evidence for population growth in humans is confounded by fine-scale population structure. Trends in Genetics. 2002. 18: 559-563.
  • S. E Ptak, D. Petrov. How intron splicing affects the insertion and deletion profile in Drosophila melanogaster. Genetics. 2002. 162: 1233-1244.
  • S. E Ptak, M. Lachmann. On the evolution of polygamy: a theoretical examination of the polygamy threshold model. Behavioral Ecology. 2002. in press.
  • J Läuter, S. Kropf. Multivariate Inference in Clinical Trials - Tests with Model Choice, Confidence Regions. Biocybernetics and Biomedical Engineering. 2002. 22: 5-16.
  • J. P Kuska, B. Frerich. Nichtlineare Reaktionsdiffusionssysteme und ihre Anwendung zur Bewertung von dreidimensionalen Gewebskulturen. In: Bildverarbeitung für die Medizin 2002, Springer-Verlag 2002. 287-290. Ed: Saupe, D. and Meiler, M. and Kruggel, F. and Handels, H. and Lehmann, T.
  • S Kropf, J Läuter, M Eszlinger, K Krohn, R. Paschke. Nonparametric Multiple Test Procedures with Data-driven Order of Hypotheses and with Weighted Hypotheses. Journal of Statistical Planning and Inference. 2002. submitted.
  • S Kropf, J. Läuter. Multiple Tests for Different Sets of Variables Using a Data- Driven Ordering of Hypotheses, with an Application to Gene Expression Data. Biometrical Journal. 2002. 44: 789-800.
  • K Klemm, P. Alstrøm. Emergence of memory. Europhysics Letters. 2002. 59: 662.
  • T Kirsten, H.H Do, E Rahm, K. Krohn. Gene Expression Warehousing in Leipzig. 2002.
  • T Kirsten, H.H Do, E Rahm, K. Krohn. Gene Expression Warehousing. 2002.
  • C Kamp, S. Bornholdt. From HIV infection to AIDS: A dynamically induced percolation transition?. Proc. Roy. Soc. Lond. 2002. B 269: 2035-2040.
  • S. Bornholdt. Spin models of speculation. 2002.
  • C Kamp, S. Bornholdt. Evolution of competing quasispecies - Strategies for an optimal immune response. 2002.
  • C Kamp, S. Bornholdt. Dynamical emergence of HIV/AIDS incubation period distribution. 2002.
  • C Kamp, S. Bornholdt. Co-evolution of quasispecies: B-cell mutation rates maximize viral error catastrophes, Phys. Rev. Lett. 88 (2002) 068104. Phys. Rev. Lett. 2002. 88: 068104.
  • T Kaizoji, S Bornholdt, Y. Fujiwara. Dynamics of price and trading volume in a spin model of stock markets with heterogeneous agents. Physica A. 2002. 316: 441-452.
  • E Glimm, M Srivastava, J. Läuter. Multivariate Tests of Normal Mean Vectors with Restricted Alternatives. Communications in Statistics B. 2002. 31: 589-604.
  • H Ebel, L. I Mielsch, S. Bornholdt. Scale-free topology of email networks. Phys. Rev. E. 2002. 66: 035103(R).
  • H Ebel, S. Bornholdt. Co-evolutionary games on networks. Phys. Rev. E. 2002. 66: 056118.
  • D Drasdo, S. Höhme. Towards a quantitative single-cell based model approach to growing multicellular spheroids. In: Deformable Modeling and Soft Tissue Simulation, Elsevier Science 2002. in press. Ed: Keeve, E. and Ayache, N.
  • J Davidsen, H Ebel, S. Bornholdt. Emergence of a small world from local interactions: Modeling acquaintance networks. Phys. Rev. Lett. 2002. 88: 128701.
  • U.D. Braumann, J. Galle. Untersuchungen zur Rekonstruktion netzartiger Tumorinvasionsfronten anhand histologischer Serienschnitte. In: Bildverarbeitung für die Medizin 2002 -Algorithmen, Systeme, Anwendungen, Springer-Verlag 2002. 239-242. Ed: Meiler, M. and Saupe, D. and Kruggel, F. and Handels, H. and Lehmann, Th.
  • S Bornholdt, F. Wagner. Stability of money: Phase transitions in an Ising economy. Physica A. 2002. 316: 453-468.
  • S. Bornholdt, H. G. Schuster. Handbook of Graphs and Networks: From the Genome to the Internet. 2002.
  • T Rohlf, C Winkler, S. Bornholdt. Emerging gene regulation network architecture in an artificial genome. 2002.