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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 | New Porous Sili-con Formation Technology Using Internal Current Gen-eration with Galvanic Elements显示文摘 | Splinter A Stürmann J Benecke W | 2001 | Sensors and Actu-ators2001，92，： | 1 |
| 5 | Long-term treatment of cervical dystonia with Botulinum toxin A:Efficacy,safety,and antibody frequency German Dystonia Study Group显示文摘 | Kessler KR Skutta M Benecke R | 1999 | J Neurol1999，246，： | 1 |
| 6 | The EBD test-a clinical test for the detection of antibodies to botulinum toxin type A显示文摘 | Kessler KR Benecke R | 1997 | Mov Disord1997，12，： | 1 |
| 7 | Photosynthesis and transpiration of Pinus radiata under natural conditions in a forest stand 显示文摘 | Benecke U | 1980 | Oecologia1980，44，： | 1 |
| 8 | Current prespective on temporal bone trauma显示文摘 | Nosan DK Benecke JE Jr Murr AH | 1997 | Otolaryngol Head Neck Sug1997，117，1： | 1 |
| 9 | Treatment with interferon-a2b and ribavirin improves outcome in MERS-CoV-infected rhesus macaques 显示文摘 | Falzarano D de Wit E Rasmussen AL Feldmann F Oku- mura A Scott DP Brining D Bushmaker T Martellaro C Baseler L Benecke AG Katze MG Munster VJ Feldma- nn H | 2013 | Nat Med2013，19，10： | 1 |
| 10 | Transcranial Doppler ultrasonography of carotid-basilar collateral circulation in subclavian steal显示文摘 | Klingelh6fer J Conrad B Benecke R | 1988 | Stroke1988，19，8： | 1 |
| 11 | Substantia nigra echogenicity is normal in non-extrapyramidal cerebral disorders but increased in Parkinson’s disease显示文摘 | Walter U Wittstock M Benecke R | 2002 | J Neural Transm2002，109，： | 1 |
| 12 | Origin and histo- ry of mitochondrial DNA lineages in domestic horses 显示文摘 | CIESLAK M PRUVOST M BENECKE N | 2010 | PLoS ONE2010，5，15： | 1 |
| 13 | A simple, small and low cost permanent magnet design to produce homogeneous magnetic fields 显示文摘 | MANZ B BENECKE M VOLKE F | 2008 | Journal of Magnetic Resonance2008，192，1： | 1 |
| 14 | Aviod purine-rich foods, drink a lot, reduce weight, the most important recipes a gainst hyperuricemia 显示文摘 | Benecke M | 2003 | MMW Fareschr Med2003，145，3132： | 1 |
| 15 | Xeomin in the treatment of cervical dystonia显示文摘 | Benecke R | 2009 | Eur J Neurol2009，16，2： | 1 |
| 16 | Botulinum toxin type B(NeuroBloc)in patients with botulinum toxin type Aantibody-induced therapy failure显示文摘 | Dressler D Benecke R Bigalke H | 2003 | J Neurol2003，250，： | 1 |
| 17 | Shoulder dysfunction in stroke hemiplegia显示文摘 | Totta M Beneck S | 1991 | Phys Med Rehabil Clin N Am1991，2，： | 1 |
| 18 | Therapy with introvenous immunoglobulin:com-plications and side-effects显示文摘 | WITTSTOCK M BENECKE R ZETTL U K | 2003 | Eur Neurol2003，50，： | 1 |
| 19 | Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs显示文摘 | A. Benecke | 2006 | The European Physical Journal E2006，，3： | 1 |
| 20 | Gene locus FPD1 of the dystonic Mount - Bebaeck type of autosomal - dominant paroxysmal choreoathetosis显示文摘 | Hofele K Benecke R Auburger G | 1997 | Neurology1997，49，5： | 1 |
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