Bioinformatics

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Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data
Bioinformatics - Tập 21 Số 13 - Trang 3001-3008 - 2005
Jiang Gui, Hongzhe Li
Two-stage designs for experiments with a large number of hypotheses
Bioinformatics - Tập 21 Số 19 - Trang 3771-3777 - 2005
Sonja Zehetmayer, Péter Bauer, Martin Posch
QuickGO: a web-based tool for Gene Ontology searching
Bioinformatics - Tập 25 Số 22 - Trang 3045-3046 - 2009
David Binns, Emily Dimmer, Rachael P. Huntley, Daniel Barrell, Claire O’Donovan, Rolf Apweiler
Abstract Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups QuickGO has been a popular GO browser for many years, but after a recent redevelopment it is now able to offer a greater range of facilities including...... hiện toàn bộ
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
Bioinformatics - Tập 26 Số 19 - Trang 2455-2457 - 2010
Wayne Delport, Art F. Y. Poon, Simon D. W. Frost, Sergei L. Kosakovsky Pond
Abstract Summary: Datamonkey is a popular web-based suite of phylogenetic analysis tools for use in evolutionary biology. Since the original release in 2005, we have expanded the analysis options to include recently developed algorithmic methods for recombination detection, evolutionary fingerprinting of genes, codon model selection, co-evolution bet...... hiện toàn bộ
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Bioinformatics - Tập 30 Số 9 - Trang 1312-1313 - 2014
Alexandros Stamatakis
Abstract Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of la...... hiện toàn bộ
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
Bioinformatics - Tập 21 Số 9 - Trang 1908-1916 - 2005
Alasdair T. R. Laurie, Robert M. Jackson
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Bioinformatics - Tập 22 Số 21 - Trang 2688-2690 - 2006
Alexandros Stamatakis
Abstract Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Γ yiel...... hiện toàn bộ
MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans
Bioinformatics - Tập 29 Số 11 - Trang 1458-1460 - 2013
Yupeng Wang, Jingping Li, Andrew H. Paterson
Abstract Summary: Gene duplication occurs via different modes such as segmental and single-gene duplications. Transposed gene duplication, a specific form of single-gene duplication, ‘copies’ a gene from an ancestral chromosomal location to a novel location. MCScanX is a toolkit for detection and evolutionary analysis of gene colinearity. We have dev...... hiện toàn bộ
Using GOstats to test gene lists for GO term association
Bioinformatics - Tập 23 Số 2 - Trang 257-258 - 2007
Seth Falcon, Robert Gentleman
AbstractMotivation: Functional analyses based on the association of Gene Ontology (GO) terms to genes in a selected gene list are useful bioinformatic tools and the GOstats package has been widely used to perform such computations. In this paper we report significant improvements and extensions such as support for conditional testing.Results: We di...... hiện toàn bộ
Multistructural hot spot characterization with FTProd
Bioinformatics - Tập 29 Số 3 - Trang 393-394 - 2013
Lane Votapka, Rommie E. Amaro
Abstract Summary: Computational solvent fragment mapping is typically performed on a single structure of a protein to identify and characterize binding sites. However, the simultaneous analysis of several mutant structures or frames of a molecular dynamics simulation may provide more realistic detail about the behavior of the sites. Here we present a...... hiện toàn bộ
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