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| 1 | Normalization Using Weighted Negative Second Order Exponential Error Functions(NeONORM) Provides Robustness Against Asym-metries in Comparative Transcriptome Profiles and Avoids False Calls显示文摘Studies on high-throughput global gene expression using microarray technology have generated ever larger amounts of systematic transcriptome data. A major challenge in exploiting these heterogeneous datasets is how to normalize the expres- sion profiles by inter-assay methods. Different non-linear and linear normalization methods have been developed, which essentially rely on the hypothesis that the true or perceived logarithmic fold-change distributions between two different assays are symmetric in nature. However, asymmetric gene expression changes are fre- quently observed, leading to suboptimal normalization results and in consequence potentially to thousands of false calls. Therefore, we have specifically investigated asymmetric comparative transcriptome profiles and developed the normalization using weighted negative second order exponential error functions (NeONORM) for robust and global inter-assay normalization. NeONORM efficiently damps true gene regulatory events in order to minimize their misleading impact on the nor- malization process. We evaluated NeONORM’s applicability using artificial and true experimental datasets, both of which demonstrated that NeONORM could be systematically applied to inter-assay and inter-condition comparisons. | Sebastian Noth Guillaume Brysbaert Arndt Benecke | 2006 | Genomics, Proteomics & Bioinformatics2006，4，2： | 4 |
| 2 | High-Sensitivity Transcriptome Data Structure and Implications for Analysis and Biologic Interpretation显示文摘Novel microarray technologies such as the AB1700 platform from Applied Biosys-tems promise significant increases in the signal dynamic range and a higher sensi-tivity for weakly expressed transcripts. We have compared a representative set ofAB1700 data with a similarly representative Affymetrix HG-U133A dataset. TheAB1700 design extends the signal dynamic detection range at the lower bound byone order of magnitude. The lognormal signal distribution profiles of these high-sensitivity data need to be represented by two independent distributions. Theadditional second distribution covers those transcripts that would have gone unde-tected using the Affymetrix technology. The signal-dependent variance distribu-tion in the AB1700 data is a non-trivial function of signal intensity, describableusing a composite function. The drastically different structure of these high-sensitivity transcriptome profiles requires adaptation or even redevelopment ofthe standard microarray analysis methods. Based on the statistical properties, wehave derived a signal variance distribution model for AB1700 data that is neces-sary for such development. Interestingly, the dual lognormal distribution observedin the AB1700 data reflects two fundamentally different biologic mechanisms oftranscription initiation. | Sebastian Noth Guillaume Brysbaert Franois-Xavier Pellay Arndt Benecke | 2006 | Genomics, Proteomics & Bioinformatics2006，4，4： | 3 |
| 3 | Quality Assessment of Transcriptome Data Using Intrinsic Statistical Properties显示文摘In view of potential application to biomedical diagnosis,tight transcriptome data quality control is compulsory.Usually,quality control is achieved using labeling and hybridization controls added at different stages throughout the processing of the biologic RNA samples.These control measures,however,only reflect the performance of the individual technical manipulations during the entire process and have no bearing as to the continued integrity of the RNA sample itself.Here we demonstrate that intrinsic statistical properties of the resulting transcriptome data signal and signal-variance distributions and their invariance can be identified independently of the animal species studied and the labeling protocol used.From these invariant properties we have developed a data model,the parameters of which can be estimated from individual experiments and used to compute relative quality measures based on similarity with large reference datasets.These quality measures add supplementary,non-redundant information to standard quality control estimates based on spike-in and hybridization controls,and are exploitable in data analysis.A software application for analyzing datasets as well as a reference dataset for AB1700 arrays are provided.They should allow AB1700 users to easily integrate this method into their analysis pipeline,and might instigate similar developments for other transcriptome platforms. | Guillaume Brysbaert Franois-Xavier Pellay Sebastian Noth Arndt Benecke | 2010 | Genomics, Proteomics & Bioinformatics2010，8，1： | 2 |
| 4 | The effects of a visual inspection task 显示文摘 | Kennedy A Brysbaert M intermittent illumination on The Quarterly Journal of 1998 51 (1): 135-151 Murray W S | 1998 | Experimental Psychology A1998，，： | 1 |
| 5 | Word skipping in reading: On the interplay of linguistic and visual factors显示文摘 | Denis Drieghe Marc Brysbaert Timothy Desmet Constantijn De Baecke | 2004 | 2004 (1-2)2004，，1： | 1 |
| 6 | Long oligonu- cleotide mi-croarrays for African green monkey gene expres- sion profile analysis 显示文摘 | Jacquelin B Mayau V Brysbaert G | 2007 | FASEB J2007，21，12： | 1 |
| 7 | Generation of Synthetic Transcriptome Data with Defined Statistical Properties for the Development and Testing of New Analysis Methods显示文摘We have previously developed a combined signal/variance distribution model that accounts for the particular statistical properties of datasets generated on the Ap- plied Biosystems AB1700 transcriptome system. Here we show that this model can be efficiently used to generate synthetic datasets with statistical properties virtu- ally identical to those of the actual data by aid of the JAVA application ace.map creator 1.0 that we have developed. The fundamentally different structure of AB1700 transcriptome profiles requires re-evaluation, adaptation, or even rede- velopment of many of the standard microarray analysis methods in order to avoid misinterpretation of the data on the one hand, and to draw full benefit from their increased specificity and sensitivity on the other hand. Our composite data model and the ace.map creator 1.0 application thereby not only present proof of the cor- rectness of our parameter estimation, but also provide a tool for the generation of synthetic test data that will be useful for further development and testing of analysis methods. | Guillaume Brysbaert Sebastian Noth Arndt Benecke | 2007 | Genomics, Proteomics & Bioinformatics2007，5，1： | 1 |
| 8 | Pigment analysis in Bronze Age Aegean and eastern Mediterranean painted plaster by LIBS显示文摘 | Brysbaert A Melessanaki K Anglos D | 2006 | Journal of Archaeological Science2006，33，： | 1 |
| 9 | Semantic and translation priming from a first language to a secondand back : Making sense of the findings 显示文摘 | SCHOONBAERT S DUYCK W BRYSBAERT M ET AL | 2009 | Memory and Cognition2009，37，5： | 1 |
| 10 | Word Kccognition in Bilinguals:Evidence against the Existence of Separate Lexicons显示文摘 | Brysbaert M | | 0，，38： | 1 |
| 11 | Interhemispheric transfer and the processing of fo- veally presented stimuli 显示文摘 | Brysbaert M | 1994 | Behav Brain Res1994，64，12： | 1 |
| 12 | Arabic Number Reading:On the Nature of the Numerical Scale and the Origin of Phonological Recoding显示文摘 | Brysbaert M | 1995 | Journal of Experimental Psychology:General1995，124，4： | 1 |
| 13 | Colateralization of Bro- ca's area and the visual word form area in left-handers: fMRI evidence显示文摘 | Van der Haegen L Cai Q Brysbaert M | 2012 | Brain Lang2012，122，： | 1 |
| 14 | The importance of magnitude information in numerical processing: Evidence from the SNARC effect 显示文摘 | Fias W Brysbaert M Geypens F d' Ydewalle | 1996 | Mathematical Cogni- tion1996，，2： | 1 |
| 15 | Re-examining word length effects in visual word recognition: New evidence from the English Lexicon Project 显示文摘 | New B Ferrand L Pallier C & Brysbaert M | 2006 | Psychonomic Bulletin and Review2006，，1： | 1 |
| 16 | Pigment analysis in Bronze Age Aegean and Eastern Mediterranean painted plaster by laser-induced breakdown spectroscopy (LIBS) 显示文摘 | BRYSBAERT A MELESSANAK K ANGLOS D | 2006 | J Archaeological Science2006，33，8： | 1 |
| 17 | Split fovea theory and the role of the two cerebral hemispheres in reading:a review of the evidence显示文摘 | Ellis AW Brysbaert M | 2010 | Neuropsychologia2010，48，2： | 1 |
| 18 | WordSkipping in Reading:On the Interplay of Linguisticand Visual Factors显示文摘 | Drieghe D Brysbaert M Desmet T | 2004 | European Journal of CognitivePsychology2004，16，1： | 1 |
| 19 | Word Recognition in Bilinguals: Evidence against the Existence of Separate Lexicons 显示文摘 | Brysbaert M | 1998 | Psychological Belgica1998，38，1998： | 1 |
| 20 | Exposure-based models of human parsing: Evidence for the use of coarse-grained (nonlexical) statistical records显示文摘 | Don C. Mitchell Fernando Cuetos Martin M. B. Corley Marc Brysbaert | 1995 | Journal of Psycholinguistic Research1995，，6： | 1 |
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