Omics bioinformatics for health and systems biology

Short Introduction

We are interested in molecular determinants and mechanisms that govern human’s health under a systemics perspective. We focus on genomic regulation which requires 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 finally 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. The molecular portrayal method developed by us uses algorithms of artificial intelligence to disentangle large and complex data. Importantly it is complemented by a comprehensive pipeline for comprehensive downstream analyses including visualization tools down to the single sample level.

Presently we mainly investigate a series of cancer entities such as brain, colon, skin, blood malignancies, infectious diseases and also genomic and transcriptomic features of healthy populations as reference. Large scale molecular data (especially DNA, RNA and Meth Seq) we analyze 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.


2017 (1)

  • 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.

2016 (6)

  • 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. Rohani, C. Fabian, H. Holland, Y. Naaldijk, R. Dressel, H. Loffler-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.
  • 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.
  • 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. 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. Arakelyan, L. Nersisyan, M. Petrek, 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.

2015 (9)

  • 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.
  • 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.
  • 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.
  • 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 2015. 1642-1653.
  • 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.
  • 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 2015. 359-378.

2014 (14)

  • 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.
  • Mario Fasold, Hans Binder. Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data. Microarrays. 2014. 3: 322.
  • 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.
  • 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.
  • Henry Wirth, Mehmet Volkan Çakir, Lydia Hopp, Hans Binder. Analysis of MicroRNA Expression Using Machine Learning. In: miRNomics: MicroRNA Biology and Computational Analysis , Humana Press 2014. 1107: 257-278.
  • H. Wirth, M. V. Cakir, L. Hopp, H. Binder. Analysis of MicroRNA Expression Using Machine Learning. Methods Mol Biol. 2014. 1107: 257-78.
  • 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.
  • 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.
  • 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.
  • Hans Binder, Henry Wirth, Arsen Arakelyan, Kathrin Lembcke, Evgeny Tiys, Vladimir Ivanisenko, Nikolay Kolchanov, Alexey Kononikhin, Igor Popov, Evgeny Nikolaev, Lyudmila Pastushkova, Irina Larina. Time-course human urine proteomics in space-flight simulation experiments. BMC Genomics. 2014. 15: S2.
  • 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.
  • 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.

2013 (5)

  • 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. Hopp, K. Lembcke, H. Binder, H. Wirth. Portraying the Expression Landscapes of B-CellLymphoma-Intuitive Detection of Outlier Samples and of Molecular Subtypes. Biology. 2013. 2: 1411-1437.
  • 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.
  • M. Fasold, H. Binder. AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data. Bioinformatics. 2013. 29: 129-31.
  • 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.

2012 (6)

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

2011 (6)

  • 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.
  • 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.
  • 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.
  • 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.
  • H. Binder, M. Fasold, L. Hopp, V. Cakir, M. von Bergen, H. Wirth. Molecular Phenotypic Portraits - Exploring The "Omes" With Individual Resolution. In: 6th International Symposium on Health Informatics and Bioinformatics (HIBIT) 2011. 115-122.

2010 (6)

  • 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.
  • C. J. Burden, H. Binder. Physico-chemical modelling of target depletion during hybridization on oligonulceotide microarrays. Phys Biol. 2010. 7: 016004.
  • H. Binder, H. Wirth, J. Galle. Gene expression density profiles characterize modes of genomic regulation: theory and experiment. J Biotechnol. 2010. 149: 98-114.
  • 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, K. Krohn, C. J. Burden. Washing scaling of GeneChip microarray expression. BMC Bioinformatics. 2010. 11: 291.

2009 (5)

  • Hans Binder, Stephan Preibisch, Hilmar Berger. Calibration of microarray gene-expression data. In: Methods in Molecular Biology , Humana Press 2009. 576: 375-407.
  • Hans Binder, Mario Fasold, Torsten Glomb. Systematic bias of genotyping estimates caused by sequence and saturation effects of SNP-microarray. accompanying paper. 2009. submitted:
  • H. Binder, M. Fasold, T. Glomb. Mismatch and G-stack modulated probe signals on SNP microarrays. PLoS One. 2009. 4: e7862.
  • 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.
  • 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.

2008 (2)

  • 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:

2007 (1)

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

2006 (5)

  • 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.
  • 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.
  • Hans Binder, Stephan Preibisch. GeneChip microarrays - signal intensities, RNA concentrations and probe sequences. Journal of Physics Condensed Matter. 2006. 18: S537-S566.
  • H Binder. Thermodynamics of competitive surface adsorption on DNA microarrays. Journal of Physics-Condensed Matter. 2006. 18: S491 - S523.
  • Hans Binder. Probing gene expression - sequence specific hybridization on microarrays. In: Bioinformatics of Gene Regulation II , Springer Sciences and Business Media 2006. 451-466.

2005 (3)

  • 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.
  • 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.

2004 (2)

  • 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.
  • H Binder, T Kirsten, I.L Hofacker, P Stadler, M. Löffler. Interactions in oligonucleotide hybrid duplexes on microarrays. Journal of Physical Chemistry. 2004. eingereicht.

2003 (7)

  • 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.
  • 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 Binder, G. Lindblom. Interaction of the Trojan peptide penetratin with anionic lipid membranes - a caloriometric study. Phys. Chem. Chem. Phys. 2003. 5: 5108-5117.
  • 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.
  • H Binder, G. Lindblom. Charge-dependent translocation of the Trojan peptide penetratin across lipid membranes. Biophysical Journal. 2003. 85: 982-995.
  • H. Binder. The moleculare architecture of lipid membranes - New insights from Hydration-tuning infrared linear dichroism spectroscopy. Appl. Spectroscopy Rev. 2003. 38: 15-69.