| 1. |
- Carninci, P, et al.
(författare)
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The transcriptional landscape of the mammalian genome
- 2005
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 309:5740, s. 1559-1563
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Tidskriftsartikel (refereegranskat)abstract
- This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5′ and 3′ boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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| 2. |
- Argyropoulos, C., et al.
(författare)
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Operational criteria for selecting a cDNA microarray data normalization algorithm
- 2006
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Ingår i: Oncology Reports. - 1021-335X .- 1791-2431. ; 15:4, s. 983-996
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Tidskriftsartikel (refereegranskat)abstract
- Microarray technology allows gene expression profiling at a global level. Many algorithms for the normalization of raw microarray data have been proposed, but no attempt has yet been made to propose operationally verifiable criteria for their comparative evaluation, which is necessary for the selection of the most appropriate method for a given dataset. This study develops a set of operational criteria for assessing the impact of various normalization algorithms in terms of accuracy (bias), precision (variance) and over-fitting (information reduction). The use of these criteria is illustrated by applying the three most widely used algorithms (global median normalization, spiked-in based normalization and lowess) on a specifically designed, multiply-controlled dataset.
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| 3. |
- Wilm, B. J., et al.
(författare)
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Reduced field-of-view MRI using outer volume suppression for spinal cord diffusion imaging
- 2007
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Ingår i: Magnetic Resonance in Medicine. - : Wiley. - 1522-2594 .- 0740-3194. ; 57:3, s. 625-630
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Tidskriftsartikel (refereegranskat)abstract
- A spin-echo single-shot echo-planar imaging (SS-EPI) technique with a reduced field of view (FOV) in the phase-encoding direction is presented that simultaneously reduces susceptibility effects and motion artifacts in diffusion-weighted (DW) imaging (DWI) of the spinal cord at a high field strength (3T). To minimize aliasing, an outer volume suppression (OVS) sequence was implemented. Effective fat suppression was achieved with the use of a slice-selection gradient-reversal technique. The OVS was optimized by numerical simulations with respect to T-1 relaxation times and B-1 variations. The optimized sequence was evaluated in vitro and in vivo. In simulations the optimized OVS showed suppression to < 0.25% and similar to 3% in an optimal and worst-case scenario, respectively. In vitro measurements showed a mean residual signal of < 0.95% +/- 0.42 for all suppressed areas. In vivo acquisition with 0.9 x 1.05 mm(2) in-plane resolution resulted in artifact-free images. The short imaging time of this technique makes it promising for clinical studies.
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