Conclusions:
A-MADMAN allows i) the batch retrieval from Gene Expression Omnibus and the local organization of raw data files and of any related meta-information, ii) the re-annotation of samples to fix incomplete, or otherwise inadequate, metadata and to create user-defined batches of data, iii) the integrative analysis of data obtained from different Affymetrix platforms through custom chip definition files and meta-normalization. Software and documentation are available on-line at http://compgen.bio.unipd.it/bioinfo/amadman/. (Source: BMC Bioinformatics – Latest articles)

Conclusion:
This tool provides a new pathway-level analysis scheme for integrative and comparative analysis of data derived from different but relevant systems. The tool is freely available as a Pathway Pattern Extraction Pipeline implemented in our existing software package WPS, which can be obtained at http://www.abcc.ncifcrf.gov/wps/wps_index.php (Source: BMC Bioinformatics – Latest articles)

Conclusions:
Here we illustrate the capabilities and performance of DOTcvpSB by solving several challenging optimization problems related with bioreactor optimization, optimal drug infusion to a patient and the minimization of intracellular oscillations. The results illustrate how the suite of solvers available allows the efficient solution of a wide class of dynamic optimization problems, including challenging multimodal ones. The toolbox is freely available for academic use. (Source: BMC Bioinformatics – Latest articles)

Authors: Carroll H, Teichert AR, Krein J, Sundberg K, Snell Q, Clement M
PSODA is a comprehensive phylogenetics package, including alignment, phylogenetic search under both parsimony and maximum likelihood, and visualisation and analysis tools. PSODA offers performance comparable to PAUP* in an open source package that aims to provide a foundation for researchers examining new phylogenetic algorithms. A key new feature is PsodaScript, an extension to the nearly ubiquitous NEXUS format, that includes conditional and loop constructs; thereby allowing complex meta-search techniques like the parsimony ratchet to be easily and compactly implemented. PSODA promises to be a valuable tool in the future development of novel phylogenetic techniques. This paper seeks to familiarise researchers wi…

Authors: Loganantharaj R
Microarray technology provides an opportunity to view transcriptions at genomic level under different experimental conditions. Generally, co-expressed genes, which are members of the same cluster, are expected to have similar function, but unfortunately it is not true due to various reasons including co-expression does not necessarily imply co-regulation. To improve the results of clustering, we investigate a method based on singular value decomposition (SVD) for integrating diverse data sources. We also introduce a new cluster evaluation method based on mutual information. Using time series data sets on yeast, we have empirically demonstrated the effectiveness of SVD as a data integrator.
PMID: 19525204 [PubMed - in process] (Source: International Journal …

Authors: Das R, Kalita J, Bhattacharyya DK
Identifying groups of genes that manifest similar expression patterns is crucial in the analysis of gene expression time series data. Choosing a similarity measure to determine the similarity or distance between profiles is an important task. This paper proposes a suitable dissimilarity measure for gene expression time series data sets. It also presents a graph-based clustering method for finding clusters in gene expression time series data using the new dissimilarity measure. A comparison with other similarity measures used for gene expression data is presented; the new dissimilarity measure is found effective. The clustering method is used in experiments that use real-life datasets and has been found to perform satisfactorily.
PMID: 1952…

Authors: Opiyo SO, Moriyama EN
Cyclophilins, which possess peptidyl-prolyl isomerase activity, are cellular targets of immunosuppressant drugs and involved in a wide variety of functions. While the Arabidopsis thaliana genome contains the largest number of cyclophilins, the number of plant cyclophilins available in databases is small compared to that of other organisms. It implies that many cyclophilins are yet to be identified in plants. In order to identify cyclophilin candidates from available plant sequence data, we examined alignment-free methods based on Partial Least Squares (PLS). PLS classifier performed better than profile hidden Markov models and PSI-BLAST in identifying cyclophilins from the Arabidopsis and rice genomes.
PMID: 19525202 [PubMed - in process] (Source: Int…

Authors: Duax WL, Huether R, Pletnev V, Umland TC,
beta-ketoacyl (acyl carrier protein) reductase (beta-k-ACPR) enzymes are essential to fatty acid synthesis in bacteria. The analyses revealed the most primitive member of the beta-k-ACPRs family was a NADP reductase where NADP was recognised by a Thr residue in the beta2alpha3 turn. Aromatic residue stacking at the dimer interface and a previously undetected conserved sequence at the C-terminus, stabilise the oligomeric assembly of these proteins. Our analysis indicates that the primordial members of the beta-k-ACPR family probably arose in the alpha-proteobacteria and are characterised by the presence of multiple open reading frames and an extreme codon and amino acid bias.
PMID: 19525201 [PubMed - in process] (Source: Internatio…

Authors: Zhang S, Du-Cuny L
We have developed a High-Performance Computing (HPC)-based molecular docking scheme, termed HiPCDock, for drug discovery and development. To improve the statistical significance of our screening results, a bioinformatics approach, motivated by a sequence alignment package BLAST, was implemented. The statistical model was validated with ten known Thymidine Kinase (TK) binders and the real inhibitors showed significant statistics, in terms of low probabilities and expectation values. Our HiPCDock has been implemented to be used by both computational experts and experimental scientists. Thus it is an automated, easy-to-use, and efficient package for molecular docking-based high-throughput virtual screening in drug discovery.
PMID: 19525200 [PubMed – in proc…

Authors: Cai X, Koduru P, Das S, Welch SM
This paper presents a hybrid algorithm based on Genetic Programming (GP) and Particle Swarm Optimisation (PSO) for the automated recovery of gene network structure. It uses gene expression time series data as well as phenotypic data pertaining to plant flowering time as its input data. The algorithm then attempts to discover simple structures to approximate the plant gene regulatory networks that produce model gene expressions and flowering times that closely resemble the input data. To show the efficacy of the proposed approach, simulation results applied to flowering time control in Arabidopsis thaliana are demonstrated and discussed.
PMID: 19525199 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applic…