Research Topics
| Hans BinderSummaryAffiliation: University of Leipzig Country: Germany Publications
| Collaborators
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Detail Information
Publications
G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibrationMario Fasold
Interdisciplinary Centre for Bioinformatics, University Leipzig, Germany
BMC Bioinformatics 11:207. 2010..Probes with runs of at least three guanines (G) in their sequence show abnormal high intensities which reflect rather probe effects than target concentrations. This G-bias requires correction prior to downstream expression analysis...- Mismatch and G-stack modulated probe signals on SNP microarraysHans Binder
Interdisciplinary Centre for Bioinformatics, Universitat Leipzig, Leipzig, Germany
PLoS ONE 4:e7862. 2009..We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates... - Nonspecific hybridization scaling of microarray expression estimates: a physicochemical approach for chip-to-chip normalizationHans Binder
Interdisciplinary Centre for Bioinformatics of Leipzig University, D 4107 Leipzig, Haertelstrasse 16 18, Germany
J Phys Chem B 113:2874-95. 2009..The results emphasize the importance of physicochemical approaches for improving heuristic normalization algorithms to proceed toward quantitative microarray data analysis... - Water near lipid membranes as seen by infrared spectroscopyHans Binder
Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany
Eur Biophys J 36:265-79. 2007..The IR order parameter shows that the water dipoles rearrange from a more parallel towards a more perpendicular orientation with respect to the membrane normal with progressive hydration... - Gene expression density profiles characterize modes of genomic regulation: theory and experimentHans Binder
Interdisciplinary Centre for Bioinformatics of Leipzig University, D 4107 Leipzig, Haertelstr 16 18, Germany
J Biotechnol 149:98-114. 2010..We demonstrate that the study of the global expression pattern provides valuable information about transcriptional regulation which complements conventional searches for differentially expressed single genes... - Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarraysHans Binder
Interdisciplinary Centre for Bioinformatics, University of Leipzig, Haertelstrasse 16 18, D 04107 Leipzig, Germany
Langmuir 21:9287-302. 2005..The presented results imply the refinement of existing algorithms of probe level analysis to correct microarray data for nonspecific background intensities and saturation on the basis of the probe sequence... - Washing scaling of GeneChip microarray expressionHans Binder
Interdisciplinary Centre for Bioinformatics Universität Leipzig, D 4107 Leipzig, Haertelstr 16 18, Germany
BMC Bioinformatics 11:291. 2010..Both the quality of the experimental washing protocol and adequate consideration of washing in intensity calibration ultimately affect the quality of the expression estimates extracted from the microarray intensities... - Specific and nonspecific hybridization of oligonucleotide probes on microarraysHans Binder
Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany
Biophys J 89:337-52. 2005..SC pairings on the average only weakly contribute to duplex stability. The intensity of complementary MM introduces a systematic source of variation which decreases the precision of expression measures based on the MM intensities... - Calibration of microarray gene-expression dataHans Binder
Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany
Methods Mol Biol 576:375-407. 2010..The hook method, in addition, provides a set of chip summary characteristics that evaluate the performance of a given hybridization. The algorithm of the method is briefly described and its performance is exemplified... - Expression cartography of human tissues using self organizing mapsHenry Wirth
Interdisciplinary Centre for Bioinformatics of Leipzig University, D 4107 Leipzig, Hartelstr 16 18, Germany
BMC Bioinformatics 12:306. 2011..The paper aims at bridging the gap between the potency of SOM-machine learning to reduce dimension of high-dimensional data on one hand and practical applications with special emphasis on gene expression analysis on the other hand... - The effect of metal cations on the phase behavior and hydration characteristics of phospholipid membranesHans Binder
Department of Medicine, Institute of Medical Physics and Biophysics, University of Leipzig, Liebigstr 27, Leipzig, Germany
Chem Phys Lipids 115:39-61. 2002..The results are discussed in terms of the lyotropic Hofmeister series and of fusogenic activity of the ionic species... - A molecular view on the interaction of the trojan peptide penetratin with the polar interface of lipid bilayersHans Binder
Department of Biophysical Chemistry, Umea University, Umea, Sweden
Biophys J 87:332-43. 2004.... - Charge-dependent translocation of the Trojan peptide penetratin across lipid membranesHans Binder
Department of Biophysical Chemistry, Umea University, SE 90187 Umea, Sweden
Biophys J 85:982-95. 2003..At a threshold value these effects induce internalization of penetratin presumably via inversely curved transient structures... - Membrane insertion of a lipidated ras peptide studied by FTIR, solid-state NMR, and neutron diffraction spectroscopyDaniel Huster
Junior Research Group Solid State NMR Studies of Membrane Associated Proteins, University of Leipzig, Liebigstrasse 27, D 04103 Leipzig, Germany
J Am Chem Soc 125:4070-9. 2003.... - MALDI-typing of infectious algae of the genus Prototheca using SOM portraitsHenry Wirth
Interdisciplinary Centre for Bioinformatics of Leipzig University, D 4107, Hartelstr 16 18, Leipzig, Germany
J Microbiol Methods 88:83-97. 2012..We apply self-organizing maps (SOM) to portray the MS-spectral data with individual resolution and to improve the typing of Prototheca algae by using meta-spectra representing prototypes of groups of similar-behaving single spectra... - Combined proteomic and metabolomic profiling of serum reveals association of the complement system with obesity and identifies novel markers of body fat mass changesAndreas Oberbach
IFB Adiposity Diseases, Leipzig University Medical Centre, Leipzig, Germany
J Proteome Res 10:4769-88. 2011.... - DARIO: a ncRNA detection and analysis tool for next-generation sequencing experimentsMario Fasold
Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Department of Computer Science, University Leipzig, Germany
Nucleic Acids Res 39:W112-7. 2011..It provides a wide range of analysis features, including quality control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates. The DARIO web site can be accessed at http://dario.bioinf.uni-leipzig.de/... - Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatinThimo Rohlf
Interdisciplinary Centre for Bioinformatics, University Leipzig, D 04107 Leipzig, Hartelstr 16 18, Germany
Epigenomics 4:205-19. 2012..Theoretical predictions that await experimental validation are highlighted and potential extensions of these models towards multiscale models of self-organizing chromatin are discussed... - Chlorinated benzenes cause concomitantly oxidative stress and induction of apoptotic markers in lung epithelial cells (A549) at nonacute toxic concentrationsNora Mörbt
Department of Proteomics, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
J Proteome Res 10:363-78. 2011..Compared to previous results, where cells were exposed to styrene, for the chlorinated aromatic substances besides oxidative stress, apoptosis was found as the predominant cellular response mechanism... - Identification of harmless and pathogenic algae of the genus Prototheca by MALDI-MSMartin von Bergen
Department of Proteomics, UFZ Helmholtz Centre for Environmental Research, Leipzig, Germany
Proteomics Clin Appl 3:774-84. 2009..As a result, pathogenic and nonpathogenic species from the genus Prototheca can be identified, with possible consequences for clinical diagnostics by MALDI-typing... - Delimitation of squamous cell cervical carcinoma using infrared microspectroscopic imagingWolfram Steller
Institute for Analytical Chemistry, Dresden University of Technology, 01062, Dresden, Germany
Anal Bioanal Chem 384:145-54. 2006....