International Journal of Bioinformatics Research and Applications This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Predicting Pathologic Complete Response to neoadjuvant chemotherapy in breast cancer using Sparse Logistic Regression.
Abstract We utilised Sparse Logistic Regression (SLR) to build two sparse and interpretable predictors. The first one (SLR-65) was based on a signature consisting of the top 65 probe sets (59 genes) differentially expressed between Pathologic Complete Response (PCR) and Residual Disease (RD) cases, and the second one (SLR-Notch) was based on the genes involved in the Notch singling related pathways (113 genes). The two predictors produced better predictions than the predictor in a previous study. The SLR-65 selected 16 informative genes and the SLR-Notch selected 12 informative genes. PMID: 2364973...
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Hu W Tags: Int J Bioinform Res Appl Source Type: research

A discrete search algorithm for finding the structure of protein backbones and side chains.
We present an extension of the BP algorithm that can calculate not only the protein backbone, but the whole three-dimensional structure of proteins. PMID: 23649739 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Sallaume S, Martins Sde L, Ochi LS, Silva WG, Lavor C, Liberti L Tags: Int J Bioinform Res Appl Source Type: research

An ensemble learning approach for prediction of phosphorylation sites.
Abstract Protein phosphorylation plays a fundamental role in most of the cellular regulatory pathways. Experimental identification of phosphorylation sites is labour-intensive and often limited by the availability and optimisation of enzymatic reaction. An ensemble learning approach that combines different encodings using a meta-learner was developed which was catalyzed by four protein kinase families and three residues. A predictor is constructed to predict the true and false phosphorylation sites based on Support Vector Machines (SVM), and knowledge based encoding method is used for amino sequences. Diff...
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Huang J Tags: Int J Bioinform Res Appl Source Type: research

Using multivariate methods to infer knowledge from genomic data.
Abstract Since the introduction of genome sequencing techniques several methods for genomic data preprocessing and analysis have been published and applied to answer different biological questions. Rarely, multivariate methods have been used to extract knowledge about protein roles. Two of the most informative types of data are gene expression data (microarrays) and phylogenetic profiles indicating presence of genes in other organisms and therefore providing information about their co-evolution. Here we show that these two types of data, analyzed by means of principal component analysis and non parametric ...
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: López-Kleine L, Molano N, Ospina L Tags: Int J Bioinform Res Appl Source Type: research

Cytochrome Oxidase I (COI) sequence conservation and variation patterns in the yellowfin and longtail tunas.
Abstract Tunas are commercially important fishery worldwide. There are at least 13 species of tuna belonging to three genera, out of which genus Thunnus has maximum eight species. On the basis of their availability, they can be characterised as oceanic such as Thunnus albacares (yellowfin tuna) or coastal such as Thunnus tonggol (longtail tuna). Although these two are different species, morphological differentiation can only be seen in mature individuals, hence misidentification may result in erroneous data set, which ultimately affect conservation strategies. The mitochondrial DNA cytochrome oxidase c sub...
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Kunal SP, Kumar G Tags: Int J Bioinform Res Appl Source Type: research