MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'BioData Mining' source. Mon, 06 Feb 2012 22:09:25 +0100 http://www.medworm.com/index.php?rid=5657270&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F5%2F1%2F1 'Caipirini', a new software program, allows ranking of biomedical literature based on biological relevance to gene sets, thereby enabling data from these high-throughput experiments to be more easily accessed. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=5657270 Wed, 01 Feb 2012 05:00:00 +0100 5657270 http://www.medworm.com/index.php?rid=5418694&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F26 Machine-learning can be used to predict the resistance of HIV-1 to antiretroviral drugs like Bevirimat in order to identify which patients will benefit from these new drugs, thereby improving the provision of a personalized therapy. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=5418694 Mon, 14 Nov 2011 05:00:00 +0100 5418694 http://www.medworm.com/index.php?rid=5204981&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F25 Over the last ten years, genome-wide association studies (GWAS) have reported over 4000 single nucleotide polymorphisms associated to more than 200 traits. Despite providing us with a slightly better understanding of the genetic architecture of common diseases, generating avalanches of new hypotheses, and fostering timid progress in pharmacogenomics, genetic associations studies haven't yet revolutionized clinical practice. Hence, although such studies are still published at a remarkable pace, the notion of 'post-GWAS' functional characterization of risk loci is gradually gaining in popularity. Indeed, deciphering the function of disease-associated genetic variants is likely to get us closer to achieving an understanding of disease architecture that will ultimately be translatable into cli... BioData Mining journals http://www.medworm.com/rss/comments.php?id=5204981 Fri, 09 Sep 2011 04:00:00 +0100 5204981 http://www.medworm.com/index.php?rid=5138094&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F24 ${item.shortDescription} (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=5138094 Mon, 15 Aug 2011 23:00:00 +0100 5138094 http://www.medworm.com/index.php?rid=5085511&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F23 ${item.shortDescription} (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=5085511 Fri, 29 Jul 2011 23:00:00 +0100 5085511 http://www.medworm.com/index.php?rid=5027285&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F22 In order to characterise new bacteriocins produced by Streptococcus mutans we perform a complete bioinformatic analyses by scanning the genome sequence of strains UA159 and NN2025. By searching in the adjacent genomic context of the two-component signal transduction system we predicted the existence of many putative new bacteriocins' maturation pathways and some of them were only exclusive to a group of Streptococcus. Computational genomic and proteomic analysis combined to predictive functionnal analysis represent an alternative way for rapid identification of new putative bacteriocins as well as new potential antimicrobial drugs compared to the more traditional methods of drugs discovery using antagonism tests. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=5027285 Wed, 13 Jul 2011 23:00:00 +0100 5027285 http://www.medworm.com/index.php?rid=5007164&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F21 Conclusions: This method and the resulting datasets will allow the capabilities of novel methods to be tested without pre-specified genetic models. This allows researchers to evaluate which methods will succeed on human genetics problems where the model is not known in advance. We further make freely available to the community the entire pareto-optimal front of datasets from each run so that novel methods may be rigorously evaluated.These 76,600 datasets are available from http://discovery.dartmouth.edu/model free data/. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=5007164 Wed, 06 Jul 2011 23:00:00 +0100 5007164 http://www.medworm.com/index.php?rid=4992086&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F20 Conclusions: The trees after the evolution showed an improvement both of the fitness (based on a genetic distance matrix, then close taxa are actually genetically close), and of the biological interpretation. Samples collected in the same state or year moved close each other, making the tree easier to interpret. Biological relationships between samples are also easier to observe. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4992086 Thu, 30 Jun 2011 23:00:00 +0100 4992086 http://www.medworm.com/index.php?rid=4967988&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F19 Conclusions: These results demonstrate the importance of employing accurate statistical models and associated adjustment methods in network-based disease gene prioritization, as well as other network-based functional inference applications. DADA is implemented in Matlab and is freely available at http://compbio.case.edu/dada/. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4967988 Thu, 23 Jun 2011 23:00:00 +0100 4967988 http://www.medworm.com/index.php?rid=4959536&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F18 Conclusions: First, the data mining results might show the positive answer that there are biological basis/networks commonly existed in both RA and CHD. Second, there are basic Chinese herbs used in the treatment of both RA and CHD. Third, these commonly existed networks might be affected by the basic Chinese herbs. Forth, discrete derivative, the data slicing algorithm is feasible in mining out useful data from literature of PubMed and SinoMed. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4959536 Wed, 22 Jun 2011 23:00:00 +0100 4959536 http://www.medworm.com/index.php?rid=4944518&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F16 Conclusions: The functionality of Interpol widens the spectrum of machine learning methods that can be applied to biological sequences, and it will in many cases improve their performance in classification and regression. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4944518 Thu, 16 Jun 2011 23:00:00 +0100 4944518 http://www.medworm.com/index.php?rid=4944517&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F17 Conclusion: The predicted targets derived from approximately 20% of all human miRNAs constructed biologically meaningful molecular networks, supporting the view that a set of miRNA targets regulated by a single miRNA generally constitute the biological network of functionally-associated molecules in human cells. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4944517 Thu, 16 Jun 2011 23:00:00 +0100 4944517 http://www.medworm.com/index.php?rid=4932976&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F15 Conclusions: The results of the animation-assisted detection of changes in gene regulatory patterns make predictions about the potential roles of Hsp90 and its co-chaperone p23 in regulating whole sets of genes. The simultaneous dynamic visualization of microarray experiments, represented in networks built by integrating one's own experimental with publicly accessible data, represents a powerful discovery tool that allows the generation of new interpretations and hypotheses. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4932976 Mon, 13 Jun 2011 23:00:00 +0100 4932976 http://www.medworm.com/index.php?rid=4932977&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F14 In the late 18th century, Erasmus Darwin, Charles Darwin's grandfather, advocated evolutionary theory as a mean to "unravel the theory of disease". More than 200 years later, although Darwinian medicine is regaining some ground after having been muzzled during the second half of the 20th century, genomics has largely outcompeted evolution and has acquired a dictatorial success as a tool for studying disease etiology. From an evolution-inspired perspective, we have gradually drifted into the habit of focusing primarily on genomic data from sources such as genome-wide association studies (GWAS). As a result, understanding the how and why of human diseases and pathobiology has largely become a matter of crunching DNA sequences. Despite the popularity of GWAS, their reality remains unchanged: ... BioData Mining journals http://www.medworm.com/rss/comments.php?id=4932977 Sun, 12 Jun 2011 23:00:00 +0100 4932977 http://www.medworm.com/index.php?rid=4828363&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F13 Conclusions: It is necessary to do within-array normalization, and the two LOESS normalization methods based on specific DMH internal control probes produce more stable and relatively better results than the global LOESS normalization method. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4828363 Sun, 15 May 2011 23:00:00 +0100 4828363 http://www.medworm.com/index.php?rid=4812449&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F12 Conclusions: Since the performance of Genetic Programming is likely to be improvable compared to the out-of-the-box approach used here, and given the biological insight potentially provided by the Genetic Programming solutions, we conclude that Genetic Programming methods are worth further investigation as a tool for cancer patient classification based on gene expression data. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4812449 Tue, 10 May 2011 23:00:00 +0100 4812449 http://www.medworm.com/index.php?rid=4788554&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F11 Conclusions: Higher levels of LD begin to confound the MDR algorithm and lead to a drop in sensitivity with respect to the identification of a direct association; it does not, however, affect the ability to detect indirect association. However, careful examination of the solution models generated by MDR reveals that MDR can identify loci in the correct LD block; though it is not always the functional SNP. As such, the results of MDR analysis in datasets with LD should be carefully examined to consider the underlying LD structure of the dataset. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4788554 Wed, 04 May 2011 23:00:00 +0100 4788554 http://www.medworm.com/index.php?rid=4762425&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F10 Understanding complex systems often requires a bottom-up analysis towards a systems biology approach. The need to investigate a system, not only as individual components but as a whole, emerges. This can be done by examining the elementary constituents individually and then how these are connected. The myriad components of a system and their interactions are best characterized as networks and they are mainly represented as graphs where thousands of nodes are connected with thousands of vertices. In this article we demonstrate approaches, models and methods from the graph theory universe and we discuss ways in which they can be used to reveal hidden properties and features of a network. This network profiling combined with knowledge extraction will help us to better understand the biologica... BioData Mining journals http://www.medworm.com/rss/comments.php?id=4762425 Wed, 27 Apr 2011 23:00:00 +0100 4762425 http://www.medworm.com/index.php?rid=4733164&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F9 Conclusions: We introduce a new approach to define dynamic, statistical queries on time course data. It supports an interactive exploration of reasonably large amounts of data and enables users without expert knowledge to specify fairly complex statistical models with ease. The expressivity of the query is by its statistical nature greater and more robust with respect to amplitude and frequency fluctuation than prior deterministic approaches. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4733164 Sun, 17 Apr 2011 23:00:00 +0100 4733164 http://www.medworm.com/index.php?rid=4708866&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F8 Conclusions: In 38 independent samples, 96% of Birdsuite calls agreed with quantitative PCR. Analysis of three copy number calling programs and quantitative PCR showed Birdsuite to have the greatest agreement with quantitative PCR. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4708866 Tue, 12 Apr 2011 23:00:00 +0100 4708866 http://www.medworm.com/index.php?rid=4704122&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F6 The beginning of the 21st century has witnessed the generation of spectacular amounts of new information, ranging from marketing data to genomic sequences. As traditional statistical methods are gradually being defeated by both the amount of data and the general absence of underlying hypotheses, data mining procedures are becoming increasingly popular and user-friendly. By combining statistical-, artificial intelligence- and database management tools, those methods are tailored for processing large quantities of information and extracting interesting patterns. Since their first application, data mining procedures have progressively been tweaked to accommodate various types of information, including social science- and biological data. However, a number of features characteristic of biologi... BioData Mining journals http://www.medworm.com/rss/comments.php?id=4704122 Sat, 09 Apr 2011 23:00:00 +0100 4704122 http://www.medworm.com/index.php?rid=4704121&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F7 A common challenge of identifying meaningful patterns in high-dimensional biological data is the complexity of the relationship between genotype and phenotype. Complexity arises as a result of many environmental, genetic, genomic, metabolic and proteomic factors interacting in a nonlinear manner through time and space to influence variability in biological traits and processes. The assumptions we make about this complexity greatly influences the analytical methods we choose for data mining and, in turn, our results and inferences. For example, linear discriminant analysis assumes a linear additive relationship among the variables or attributes while support vector machine or neural network can model nonlinear relationships. Regardless, it is a useful exercise to think about where biologica... BioData Mining journals http://www.medworm.com/rss/comments.php?id=4704121 Sat, 09 Apr 2011 23:00:00 +0100 4704121 http://www.medworm.com/index.php?rid=4663506&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F5 Conclusions: The AGEP method is a widely applicable method for the rapid comprehensive interpretation of microarray data, as proven here by the definition of tissue- and disease-specific changes in gene expression as well as during cellular differentiation. The capability to quantitatively compare data from individual samples against a large-scale annotated reference database represents a widely applicable paradigm for the analysis of all types of high-throughput data. AGEP enables systematic and quantitative comparison of gene expression data from test samples against a comprehensive collection of different cell/tissue types previously studied by the entire research community. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4663506 Wed, 30 Mar 2011 23:00:00 +0100 4663506 http://www.medworm.com/index.php?rid=4535737&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F4 Conclusions: The current analyses substantiate the utility of rule based classifiers such as RIPPER, RIDOR and PART for the detection of gene-gene/gene-environment interactions in genetic association studies. These classifiers could provide a valuable new method, complementing existing approaches, in the analysis of genetic association studies. The methods provide an advantage in being able to handle both categorical and continuous variable types. Further, because the outputs of the analyses are easy to interpret, the rule based classifier approach could quickly generate testable hypotheses for additional evaluation. Since the algorithms are computationally inexpensive, they may serve as valuable tools for preselection of attributes to be used in more complex, computationally intensive app... BioData Mining journals http://www.medworm.com/rss/comments.php?id=4535737 Tue, 01 Mar 2011 00:00:00 +0100 4535737 http://www.medworm.com/index.php?rid=4371053&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F2 Conclusions: The NTI is a valuable tool in the domain of biomedical data analysis. It allows the identification of correlations between high-dimensional data and nominal labels, while at the same time a p-value measures the level of significance of the detected correlations. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4371053 Wed, 19 Jan 2011 00:00:00 +0100 4371053 http://www.medworm.com/index.php?rid=4342635&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F4%2F1%2F1 Conclusions: All together our data indicate that the quality of 3D reconstruction is unaffected by deleting up to an average 75% of the real contacts while only few percentage of randomly generated contacts in place of non-contacts are sufficient to hamper 3D reconstruction. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4342635 Thu, 13 Jan 2011 00:00:00 +0100 4342635 http://www.medworm.com/index.php?rid=4264890&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F3%2F1%2F11 Conclusions: PM compares quite favorably to CM in terms of lower FDR and much higher SP. Thus, PM can be quite effective in producing accurate signatures from large microarray data sets for differential expression between assays groups identified in a preliminary step of the PCA procedure and is, therefore, recommended for use in these applications. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4264890 Fri, 17 Dec 2010 00:00:00 +0100 4264890 http://www.medworm.com/index.php?rid=4264891&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F3%2F1%2F10 Conclusions: To truly allow a user to visually integrate multiple pieces of information typical of a genetic association study, innovative views are needed to integrate multiple pieces of information. As a result, we have created "Synthesis-View" software for the visualization of genotype-phenotype association data in multiple cohorts. Synthesis-View is freely available for non-commercial research institutions, for full details see https://chgr.mc.vanderbilt.edu/synthesisview. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4264891 Thu, 16 Dec 2010 00:00:00 +0100 4264891 http://www.medworm.com/index.php?rid=4202910&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2F Conclusions: GEDT, while still in its initial stages of development, is a promising new approach for identifying gene-gene interactions in genetic association studies. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4202910 Thu, 18 Nov 2010 00:00:00 +0100 4202910 http://www.medworm.com/index.php?rid=4182812&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F3%2F1%2F8 Conclusions: GEDT, while still in its initial stages of development, is a promising new approach for identifying gene-gene interactions in genetic association studies. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4182812 Thu, 18 Nov 2010 00:00:00 +0100 4182812 http://www.medworm.com/index.php?rid=4117711&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F3%2F1%2F7 Conclusion: My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4117711 Wed, 27 Oct 2010 23:00:00 +0100 4117711 http://www.medworm.com/index.php?rid=4012185&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F3%2F1%2F6 Conclusions: GeneWaltz will be helpful in experimental genomic studies. GeneWaltz binaries and the matrix are available online at http://en.sourceforge.jp/projects/genewaltz/. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4012185 Mon, 27 Sep 2010 23:00:00 +0100 4012185 http://www.medworm.com/index.php?rid=4012186&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F3%2F1%2F5 Conclusions: We show that a hybrid optimization procedure, alternative crossover strategies, and incorporation of domain knowledge from publicly available biological databases can result in marked increases in sensitivity and performance of the ATHENA algorithm for detecting and modelling gene-gene interactions that influence a complex human trait. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=4012186 Sun, 26 Sep 2010 23:00:00 +0100 4012186 http://www.medworm.com/index.php?rid=3861656&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F3%2F1%2F4 Conclusions: Hypothesis-free investigation of genome wide interactions allows for biological data mining at a scale never before seen. Until recently, the main focus of analysis of sequencing data has been targeted on signal patterns around transcriptional start sites which are in manageable numbers. Today, focus is shifting to a wider perspective and numerous genomic features are being studied. To this end, we provide a system allowing for fast querying in the order of hundreds of thousands of features. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=3861656 Thu, 12 Aug 2010 23:00:00 +0100 3861656 http://www.medworm.com/index.php?rid=3519070&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F3%2F1%2F2 Conclusion: The comprehensive assessment of the effects of single-base mismatches on microarrays provided in this report can be useful for improving future versions of microarray platform design and the corresponding data analysis algorithms. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=3519070 Wed, 28 Apr 2010 23:00:00 +0100 3519070 http://www.medworm.com/index.php?rid=3297980&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F3%2F1%2F1 In this study, we review tools that are currently available for the visualization of biological trees and analysis, mainly developed during the last decade. We describe the uniform and standard computer readable formats to represent tree hierarchies and we comment on the functionality and the limitations of these tools. We also discuss on how these tools can be developed further and should become integrated with various data sources. Here we focus on freely available software that offers to the users various tree-representation methodologies for biological data analysis. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=3297980 Mon, 22 Feb 2010 00:00:00 +0100 3297980 http://www.medworm.com/index.php?rid=3096373&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F2%2F1%2F9 Background: In a number of domains, like in DNA microarray data analysis, we need to cluster simultaneously rows (genes) and columns (conditions) of a data matrix to identify groups of rows coherent with groups of columns. This kind of clustering is called biclustering. Biclustering algorithms are extensively used in DNA microarray data analysis. More effective biclustering algorithms are highly desirable and needed. Methods: We introduce BiMine, a new enumeration algorithm for biclustering of DNA microarray data. The proposed algorithm is based on three original features. First, BiMine relies on a new evaluation function called Average Spearman's rho (ASR). Second, BiMine uses a new tree structure, called Bicluster Enumeration Tree (BET), to represent the different biclusters discovered d... BioData Mining journals http://www.medworm.com/rss/comments.php?id=3096373 Wed, 16 Dec 2009 00:00:00 +0100 3096373 http://www.medworm.com/index.php?rid=3056253&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F2%2F1%2F8 Conclusion: Availability of an approach to identify BRPs and a curated database of best representative PSI-BLAST derived PSSMs for 91.4% of current Pfam family will be a useful resource for the community to perform detailed and specific analysis using family-specific, best-representative PSSM profiles. 3PFDB can be accessed using the URL: http://caps.ncbs.res.in/3pfdb (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=3056253 Fri, 04 Dec 2009 00:00:00 +0100 3056253 http://www.medworm.com/index.php?rid=3051885&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F2%2F1%2F7 Conclusions: LD-Spline is an integrated database routine that quickly and effectively defines the genomic region marked by a SNP using linkage disequilibrium, with a SNP-centric block definition algorithm. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=3051885 Thu, 03 Dec 2009 00:00:00 +0100 3051885 http://www.medworm.com/index.php?rid=2882703&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F2%2F1%2F6 Gas chromatography-mass spectrometry (GC-MS) is a widely used analytical technique for the identification and quantification of trace chemicals in complex mixtures. When complex samples are analyzed by GC-MS it is common to observe co-elution of two or more components, resulting in an overlap of signal peaks observed in the total ion chromatogram. In such situations manual signal analysis is often the most reliable means for the extraction of pure component signals; however, a systematic manual analysis over a number of samples is both tedious and prone to error. In the past 30 years a number of computational approaches were proposed to assist in the process of the extraction of pure signals from co-eluting GC-MS components. This includes empirical methods, comparison with library spectra,... BioData Mining journals http://www.medworm.com/rss/comments.php?id=2882703 Sun, 11 Oct 2009 23:00:00 +0100 2882703 http://www.medworm.com/index.php?rid=2819372&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F2%2F1%2F5 Conclusions: Researchers performing genetic association studies and aiming to discover gene-gene interactions associated with increased disease susceptibility should use SURF in place of ReliefF. For instance, SURF should be used instead of ReliefF to filter a dataset before an exhaustive MDR analysis. This change increases the ability of a study to detect gene-gene interactions. The SURF algorithm is implemented in the open source Multifactor Dimensionality Reduction (MDR) software package available from www.epistasis.org. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=2819372 Mon, 21 Sep 2009 23:00:00 +0100 2819372 http://www.medworm.com/index.php?rid=2329281&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F2%2F1%2F3 Background: Genome-sequencing projects are currently producing an enormous amount of new sequences and cause the rapid increasing of protein sequence databases. The unsupervised classification of these data into functional groups or families, clustering, has become one of the principal research objectives in structural and functional genomics. Computer programs to automatically and accurately classify sequences into families become a necessity. A significant number of methods have addressed the clustering of protein sequences and most of them can be categorized in three major groups: hierarchical, graph-based and partitioning methods. Among the various sequence clustering methods in literature, hierarchical and graph-based approaches have been widely used. Although partitioning clustering ... BioData Mining journals http://www.medworm.com/rss/comments.php?id=2329281 Thu, 02 Apr 2009 04:00:00 +0100 2329281 http://www.medworm.com/index.php?rid=2329282&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F2%2F1%2F2 Background: The fidelity of DNA replication serves as the nidus for both genetic evolution and genomic instability fostering disease. Single nucleotide polymorphisms (SNPs) constitute greater than 80% of the genetic variation between individuals. A new theory regarding DNA replication fidelity has emerged in which selectivity is governed by base-pair geometry through interactions between the selected nucleotide, the complementary strand, and the polymerase active site. We hypothesize that specific nucleotide combinations in the flanking regions of SNP fragments are associated with mutation. Results: We modeled the relationship between DNA sequence and observed polymorphisms using the novel multifactor dimensionality reduction (MDR) approach. MDR was originally developed to detect synergist... BioData Mining journals http://www.medworm.com/rss/comments.php?id=2329282 Mon, 30 Mar 2009 04:00:00 +0100 2329282 http://www.medworm.com/index.php?rid=2145392&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F1%2F1%2F12 In this study we are reviewing visualization tools that are currently available for visualization of biological networks mainly invented in the latest past years. We comment on the functionality, the limitations and the specific strengths of these tools, and how these tools could be further developed in the direction of data integration and information sharing. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=2145392 Fri, 28 Nov 2008 05:00:00 +0100 2145392 http://www.medworm.com/index.php?rid=2000541&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F1%2F1%2F9 Conclusion: The HappieClust algorithm is well suited for large-scale gene expression visualization and analysis both on personal computers as well as public online web applications. The software is available from the URL http://www.quretec.com/HappieClust (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=2000541 Mon, 22 Sep 2008 04:00:00 +0100 2000541 http://www.medworm.com/index.php?rid=2000546&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F1%2F1%2F1 This editorial introduces BioData Mining, a new journal which publishes research articles related to advances in computational methods and techniques for the extraction of useful knowledge from heterogeneous biological data. We outline the aims and scope of the journal, introduce the publishing model and describe the open peer review policy, which fosters interaction within the research community. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=2000546 Thu, 17 Jul 2008 04:00:00 +0100 2000546 http://www.medworm.com/index.php?rid=2000545&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F1%2F1%2F2 Conclusion: The proposed model provides a novel hypothesis on the genetic etiology of comorbid depression with AUD, consistent with established clinical and biochemical data. This analysis also provides an example of how an integrated bioinformatics approach can maximize the use of available biomedical data to improve our understanding of complex disease. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=2000545 Thu, 17 Jul 2008 04:00:00 +0100 2000545 http://www.medworm.com/index.php?rid=2000544&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F1%2F1%2F3 During the past two decades, the field of human genetics has experienced an information explosion. The completion of the human genome project and the development of high throughput SNP technologies have created a wealth of data; however, the analysis and interpretation of these data have created a research bottleneck. While technology facilitates the measurement of hundreds or thousands of genes, statistical and computational methodologies are lacking for the analysis of these data. New statistical methods and variable selection strategies must be explored for identifying disease susceptibility genes for common, complex diseases. Neural networks (NN) are a class of pattern recognition methods that have been successfully implemented for data mining and prediction in a variety of fields. The... BioData Mining journals http://www.medworm.com/rss/comments.php?id=2000544 Thu, 17 Jul 2008 04:00:00 +0100 2000544 http://www.medworm.com/index.php?rid=2000543&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F1%2F1%2F4 Conclusion: The results validate that the CisTransMine approach is a robust method to uncover the hidden transcriptional regulatory mechanisms that can facilitate the discovery of mechanisms of transcriptional regulation. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=2000543 Thu, 17 Jul 2008 04:00:00 +0100 2000543 http://www.medworm.com/index.php?rid=2000542&cid=s_38182_79_f&fid=38182&url=http%3A%2F%2Fwww.biodatamining.org%2Fcontent%2F1%2F1%2F5 Serial analysis of gene expression (SAGE) is one of the most powerful tools for global gene expression profiling. It has led to several biological discoveries and biomedical applications, such as the prediction of new gene functions and the identification of biomarkers in human cancer research. Clustering techniques have become fundamental approaches in these applications. This paper reviews relevant clustering techniques specifically designed for this type of data. It places an emphasis on current limitations and opportunities in this area for supporting biologically-meaningful data mining and visualisation. (Source: BioData Mining) BioData Mining journals http://www.medworm.com/rss/comments.php?id=2000542 Thu, 17 Jul 2008 04:00:00 +0100 2000542