| 1. |
- Nilsson, Björn, et al.
(författare)
-
An improved method for detecting and delineating genomic regions with altered gene expression in cancer
- 2008
-
Ingår i: GENOME BIOL. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 9:1, s. R13-
-
Tidskriftsartikel (refereegranskat)abstract
- Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method combines top-notch detection performance with an ability to delineate relevant regions without excessive over-segmentation, making it a significant advance over existing methods. Software (Rendersome) is provided.
|
|
| 2. |
- Nilsson, Björn, et al.
(författare)
-
Cross-platform classification in microarray-based leukemia diagnostics
- 2006
-
Ingår i: Haematologica. - 1592-8721 .- 0390-6078. ; 91:6, s. 821-824
-
Tidskriftsartikel (refereegranskat)abstract
- Gene expression profiling is a powerful technique for classifying hematologic malignancies. Its clinical use is, however, currently hindered by the need to collect large sets of expression profiles at each diagnostic facility. To overcome this limitation, we introduced cross-platform classification, allowing classifier construction using pre-existing microarray datasets. As proof-of-principle, we performed cross-platform classification of acute myeloid leukemia and childhood acute lymphoblastic leukemia using expression data from four different facilities. We show that cross-platform classification of these disorders is achievable, and, strikingly, that the diagnostic accuracy can be retained. We conclude that cross-platform classification constitutes an effective and convenient way to implement microarray diagnostics.
|
|
| 3. |
- Nilsson, Björn, et al.
(författare)
-
Threshold-free high-power methods for the ontological analysis of genome-wide gene expression studies
- 2007
-
Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 8:5, s. R74-
-
Tidskriftsartikel (refereegranskat)abstract
- Ontological analysis facilitates microarray data interpretation. We describe new ontological analysis methods which, unlike existing approaches, are threshold-free and statistically powerful. We perform extensive evaluations and introduce a new concept, detection spectra, to characterize methods. We show that different ontological analysis methods exhibit distinct detection spectra, and that it is critical to account for this diversity. Our results argue strongly against the continued use of existing methods, and provide directions towards an enhanced approach.
|
|
| 4. |
- Nilsson, Björn, et al.
(författare)
-
Ultrasome : efficient aberration caller for copy number studies of ultra-high resolution
- 2009
-
Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 25:8, s. 1078-1079
-
Tidskriftsartikel (refereegranskat)abstract
- Motivation: Multimillion-probe microarrays allow detection of gains and losses of chromosomal material at unprecedented resolution. However, the data generated by these arrays are several-fold larger than data from earlier platforms, creating a need for efficient analysis tools that scale robustly with data size. Results: We developed a new aberration caller, Ultrasome, that delineates genomic changes-of-interest with dramatically improved efficiency. Ultrasome shows near-linear computational complexity and processes latest generation copy number arrays about 10 000 times faster than standard methods with preserved analytic accuracy.
|
|
