Binder – Omics bioinformatics for health and systems biology

SHORT INTRODUCTION

We are interested in molecular determinants and mechanisms that govern human’s health under a systems perspective. We focus on genomic regulation by pursuing a holistic view on different ‘omics’ realms (genome, epigenome, transcriptome, and also proteome and metabolome) and different levels of organization (molecular, cellular, tissue etc.) and relations (e.g. pathways, interaction nets).

From a methodical perspective we pursue a data-driven approach by developing and applying algorithms and methods that aim at extracting relevant biological information from large sets of high-throughput data, e.g. collected in large-scale patient-cohorts, and at developing and validating conceptual or even mathematical models e.g. about cancer progression, human development and ageing. The molecular portrayal method developed by us uses algorithms of artificial intelligence to disentangle large and complex data. The method is complemented by a comprehensive pipeline of downstream analysis tasks such as class discovery, marker selection, functional knowledge mining and it includes visualization tools down to the single sample level.

Presently we mainly investigate a series of cancer entities such as brain, colon, skin and blood malignancies; infectious diseases and also genomic and transcriptomic features of healthy populations as reference. We analyze large scale molecular data (especially DNA, RNA and Meth Seq) generated in patient cohorts, epidemiological collectives, single cell experiments and also ‘traditional’ cell-line experiments.

We are open for interesting problems and data which fit into these topics. Because the group is nearly exclusively financed via third party funds we prefer joint projects.

PUBLICATIONS

2020 (9)

  • 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.
  • 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.
  • 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.
  • M. Schmidt, H. Loeffler-Wirth, H. Binder. Developmental scRNAseq Trajectories in Gene- and Cell-State Space-The Flatworm Example. Genes (Basel). 2020. 11:

2019 (7)

  • 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.
  • 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:

2018 (6)

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

2017 (9)

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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. 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.
  • 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.

2016 (8)

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

2015 (11)

  • 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.
  • 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.
  • 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.
  • 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, 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.
  • 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.
  • 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. 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.
  • 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.
  • 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. 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.

2014 (16)

  • 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.
  • A. Arakelyan, L. Nersisyan, H. Wirth, H. Binder. Mining common pathway deregulation profiles in lung diseases. European Respiratory Journal. 2014. 44:
  • 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.
  • M. V. Cakir, H. Binder, H. Wirth. Profiling of Genetic Switches using Boolean Implications in Expression Data. J Integr Bioinform. 2014. 11: 246.
  • 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.
  • 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.
  • 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.
  • 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. 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:
  • 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.
  • 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.

2013 (4)

  • 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. Fasold, H. Binder. AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data. Bioinformatics. 2013. 29: 129-31.
  • 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.
  • 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:

2012 (7)

  • 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.
  • 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.
  • M. Fasold, H. Binder. Estimating RNA-quality using GeneChip microarrays. BMC Genomics. 2012. 13: 186.
  • 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.
  • 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.
  • 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.

2011 (7)

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

2010 (6)

  • 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.
  • C. J. Burden, H. Binder. Physico-chemical modelling of target depletion during hybridization on oligonulceotide microarrays. Phys Biol. 2010. 7: 016004.
  • C. J Burden, H. Binder. Reply to 'Linking probe thermodynamics to microarray quantification'. Physical Biology. 2010. 7: 048002.
  • 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.

2009 (5)

  • 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.
  • 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.
  • 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.

2008 (2)

  • Hans Binder, Knut Krohn, Stephan Preibisch. "Hook" calibration of GeneChip-microarrays: chip characteristics and expression measures. Algorithms for Molecular Biology. 2008. 3:11:
  • Hans Binder, Stephan Preibisch. "Hook"-calibration of GeneChip-microarrays: theory and algorithm. Algorithms Mol Biol. 2008. 3: 12.

2007 (1)

  • H. Binder. Water near lipid membranes as seen by infrared spectroscopy. Eur Biophys J. 2007. 36: 265-79.

2006 (5)

  • 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.
  • 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.

2005 (3)

  • 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.

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 (6)

  • H. Binder. The moleculare architecture of lipid membranes - New insights from Hydration-tuning infrared linear dichroism spectroscopy. Appl. Spectroscopy Rev. 2003. 38: 15-69.
  • H Binder, G. Lindblom. Charge-dependent translocation of the Trojan peptide penetratin across lipid membranes. Biophysical Journal. 2003. 85: 982-995.
  • 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.
  • 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.
  • 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.
  • 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.

MISCELLANEOUS