Affiliation: National Institutes of Health
- Getting a tree fast: Neighbor Joining, FastME, and distance-based methodsRichard Desper
Department of Biology, University College, London, United Kingdom
Curr Protoc Bioinformatics . 2006..It also describes how to estimate evolutionary distances from DNA and proteins, how to perform bootstrap analysis, and how to use CLUSTAL to compute both a sequence alignment and a phylogenetic tree...
- Tumor classification using phylogenetic methods on expression dataRichard Desper
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bldg 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
J Theor Biol 228:477-96. 2004..We tested this method on the SRBCT data set, and classified each tumor successfully...
- Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fittingRichard Desper
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
Mol Biol Evol 21:587-98. 2004..Interestingly, the covarion parameter has little effect on the tree quality for any of the algorithms. FASTME is freely available on the web...
- A comprehensive continuous-time model for the appearance of CGH signal due to chromosomal missegregations during mitosisRichard Desper
Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Building 38A, Room 6S608, 8600 Rockville Pike, Bethesda, MD, USA
Math Biosci 197:67-87. 2005..This allows the user to test hypotheses regarding the effect chromosomal aberrations have upon the cell cycle, cell growth rates, and time to population dominance...
- Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principleRichard Desper
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
J Comput Biol 9:687-705. 2002..Moreover, this BME scheme yields a very significant improvement over NJ and other distance-based algorithms, especially with large trees, in terms of topological accuracy...
- A newly discovered human alpha-globin geneSung Ho Goh
Molecular Medicine Branch, National Institute of Diabetes, Digestive and Kidney Disease, National Institutes of Health, Bldg 10 Rm 9B17, 10 Center Dr, Bethesda, MD 20892, USA
Blood 106:1466-72. 2005..These results suggest the human genome encodes a previously unrecognized globin member of the avian alpha-D family that is transcribed in a highly regulated pattern in erythroid cells...
- Construction and analysis of tree models for chromosomal classification of diffuse large B-cell lymphomasHui Yong Jiang
Department of General Surgery, General Hospital of Shenyang Military Region, Shenyang, China
World J Gastroenterol 13:1737-42. 2007....