| 1. |
- Finn, Robert D, et al.
(författare)
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Pfam : clans, web tools and services.
- 2006
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Ingår i: Nucleic Acids Res. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 34:Database issue, s. D247-51
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Lassmann, Timo
(författare)
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Algorithms for building and evaluating multiple sequence alignments
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The alignment of biological sequences is crucial for the transfer of annotation from model organisms to humans. Pairwise alignment of sequences can reveal homology while multiple alignments are used to characterize protein families and elucidate their evolutionary history. We developed several software packages to create, evaluate and visualize multiple alignments. Our alignment program Kalign combines excellent accuracy with unparalleled computational benefits. The initial publication outlines the algorithm and innovations introduced to the field, while the second introduced several key improvements and additions to the original algorithm. The accuracy of Kalign is high for both protein and nucleotide alignments and Kalign can thus be used for a wide range of applications in genomics, including homology detection, protein and RNA structure prediction, phylogenetic analysis and promoter prediction. The assessment of alignment quality is a tough problem the field. While alignment programs can be tested on benchmark sets to reveal their overall performance, determining the accuracy of individual alignments is next to impossible. We approached this problem by analyzing several alignments of the same sequences and applying a consensus principle: if different methods arrive at the same conclusion it is more likely to be correct than when methods disagree. Our program MUMSA can thus diagnose faulty alignments which is critical in high throughput genomics application. Both Kalign and Mumsa can be freely accessed at our website http://msa.cgb.ki.se which also features Kalignvu, a lightweight alignment viewer.
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| 3. |
- Lassmann, Timo, et al.
(författare)
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Automatic assessment of alignment quality.
- 2005
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Ingår i: Nucleic Acids Res. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 33:22, s. 7120-8
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Tidskriftsartikel (refereegranskat)
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| 4. |
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| 5. |
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| 6. |
- Lassmann, Timo, et al.
(författare)
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Kalign2 : high-performance multiple alignment of protein and nucleotide sequences allowing external features.
- 2009
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Ingår i: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 37:3, s. 858-65
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Tidskriftsartikel (refereegranskat)abstract
- In the growing field of genomics, multiple alignment programs are confronted with ever increasing amounts of data. To address this growing issue we have dramatically improved the running time and memory requirement of Kalign, while maintaining its high alignment accuracy. Kalign version 2 also supports nucleotide alignment, and a newly introduced extension allows for external sequence annotation to be included into the alignment procedure. We demonstrate that Kalign2 is exceptionally fast and memory-efficient, permitting accurate alignment of very large numbers of sequences. The accuracy of Kalign2 compares well to the best methods in the case of protein alignments while its accuracy on nucleotide alignments is generally superior. In addition, we demonstrate the potential of using known or predicted sequence annotation to improve the alignment accuracy. Kalign2 is freely available for download from the Kalign web site (http://msa.sbc.su.se/).
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| 7. |
- Timmons, James A, et al.
(författare)
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Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages.
- 2007
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 104:11, s. 4401-4406
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Tidskriftsartikel (refereegranskat)abstract
- Attainment of a brown adipocyte cell phenotype in white adipocytes, with their abundant mitochondria and increased energy expenditure potential, is a legitimate strategy for combating obesity. The unique transcriptional regulators of the primary brown adipocyte phenotype are unknown, limiting our ability to promote brown adipogenesis over white. In the present work, we used microarray analysis strategies to study primary preadipocytes, and we made the striking discovery that brown preadipocytes demonstrate a myogenic transcriptional signature, whereas both brown and white primary preadipocytes demonstrate signatures distinct from those found in immortalized adipogenic models. We found a plausible SIRT1-related transcriptional signature during brown adipocyte differentiation that may contribute to silencing the myogenic signature. In contrast to brown preadipocytes or skeletal muscle cells, white preadipocytes express Tcf21, a transcription factor that has been shown to suppress myogenesis and nuclear receptor activity. In addition, we identified a number of developmental genes that are differentially expressed between brown and white preadipocytes and that have recently been implicated in human obesity. The interlinkage between the myocyte and the brown preadipocyte confirms the distinct origin for brown versus white adipose tissue and also represents a plausible explanation as to why brown adipocytes ultimately specialize in lipid catabolism rather than storage, much like oxidative skeletal muscle tissue.
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