Partitioning of functional gene expression data using principal points.

abstract：BACKGROUND:Meta-analysis (MA) is widely used to pool genome-wide association studies (GWASes) in order to a) increase the power to detect strong or weak genotype effects or b) as a result verification method. As a consequence of differing SNP panels among genotyping chips, imputation is the method of choice within GWAS...

journal_title：BMC bioinformatics

authors： Meesters C,Leber M,Herold C,Angisch M,Mattheisen M,Drichel D,Lacour A,Becker T

更新日期：2012-09-12 00:00:00

abstract：BACKGROUND:Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compound...

journal_title：BMC bioinformatics

authors： Le Guilloux V,Schmidtke P,Tuffery P

更新日期：2009-06-02 00:00:00

abstract：BACKGROUND:Processing and analysis of DNA sequences obtained from next-generation sequencing (NGS) face some difficulties in terms of the correct prediction of DNA sequencing outcomes without the implementation of bioinformatics approaches. However, algorithms based on NGS perform inefficiently due to the generation of...

journal_title：BMC bioinformatics

authors： Shityakov S,Bencurova E,Förster C,Dandekar T

更新日期：2020-04-03 00:00:00

abstract：BACKGROUND:Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effective prevention and control measures for blood pressure diseases. Traditional blood pressure measure...

journal_title：BMC bioinformatics

authors： Zhang B,Ren H,Huang G,Cheng Y,Hu C

更新日期：2019-02-28 00:00:00

abstract：BACKGROUND:The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can h...

journal_title：BMC bioinformatics

authors： Zampieri G,Tran DV,Donini M,Navarin N,Aiolli F,Sperduti A,Valle G

更新日期：2018-01-25 00:00:00

abstract：BACKGROUND:An important application of high dimensional gene expression measurements is the risk prediction and the interpretation of the variables in the resulting survival models. A major problem in this context is the typically large number of genes compared to the number of observations (individuals). Feature selec...

journal_title：BMC bioinformatics

authors： Kammers K,Lang M,Hengstler JG,Schmidt M,Rahnenführer J

更新日期：2011-12-16 00:00:00

abstract：BACKGROUND:Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology all...

journal_title：BMC bioinformatics

authors： Aubry M,Monnier A,Chicault C,de Tayrac M,Galibert MD,Burgun A,Mosser J

更新日期：2006-05-04 00:00:00

abstract：BACKGROUND:Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational and systems biology is to go beyond identification towards an explana...

journal_title：BMC bioinformatics

authors： Samal A,Singh S,Giri V,Krishna S,Raghuram N,Jain S

更新日期：2006-03-08 00:00:00

abstract：BACKGROUND:The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×10(84) possible genetic codes. The main question related to the organization of the genetic code is why ...

journal_title：BMC bioinformatics

authors： de Oliveira LL,de Oliveira PS,Tinós R

更新日期：2015-02-19 00:00:00

abstract：BACKGROUND:Clinical studies often track dose-response curves of subjects over time. One can easily model the dose-response curve at each time point with Hill equation, but such a model fails to capture the temporal evolution of the curves. On the other hand, one can use Gompertz equation to model the temporal behaviors...

journal_title：BMC bioinformatics

authors： Dhruba SR,Rahman A,Rahman R,Ghosh S,Pal R

更新日期：2019-06-20 00:00:00

abstract：BACKGROUND:Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing "outliers" among the objects being clustered. Few clustering algorithms currently deal directly with the outlier pro...

journal_title：BMC bioinformatics

authors： Wang M,Abrams ZB,Kornblau SM,Coombes KR

更新日期：2018-01-08 00:00:00

abstract：BACKGROUND:To understand biology and differences among various tissues or cell types, one typically searches for molecular features that display characteristic abundance patterns. Several specificity metrics have been introduced to identify tissue-specific molecular features, but these either require an equal number of...

journal_title：BMC bioinformatics

authors： Everaert C,Volders PJ,Morlion A,Thas O,Mestdagh P

更新日期：2020-02-17 00:00:00

abstract：BACKGROUND:DNA methylation patterns have been shown to significantly correlate with different tissue types and disease states. High-throughput methylation arrays enable large-scale DNA methylation analysis to identify informative DNA methylation biomarkers. The identification of disease-specific methylation signatures ...

journal_title：BMC bioinformatics

authors： Meng H,Murrelle EL,Li G

更新日期：2008-10-27 00:00:00

abstract：BACKGROUND:We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples ...

journal_title：BMC bioinformatics

authors： Seoighe C,Korir PK

更新日期：2011-10-05 00:00:00

abstract：BACKGROUND:The definition of a distance measure plays a key role in the evaluation of different clustering solutions of gene expression profiles. In this empirical study we compare different clustering solutions when using the Mutual Information (MI) measure versus the use of the well known Euclidean distance and Pears...

journal_title：BMC bioinformatics

authors： Priness I,Maimon O,Ben-Gal I

更新日期：2007-03-30 00:00:00

abstract：BACKGROUND:Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models requires the development of effective statistical methods to calibrat...

journal_title：BMC bioinformatics

authors： Komorowski M,Finkenstädt B,Harper CV,Rand DA

更新日期：2009-10-19 00:00:00

abstract：BACKGROUND:Time-course microarray experiments are being increasingly used to characterize dynamic biological processes. In these experiments, the goal is to identify genes differentially expressed in time-course data, measured between different biological conditions. These differentially expressed genes can reveal the ...

journal_title：BMC bioinformatics

authors： Jonnalagadda S,Srinivasan R

更新日期：2008-06-06 00:00:00

abstract：BACKGROUND:The identification of genes responsible for human inherited diseases is one of the most challenging tasks in human genetics. Recent studies based on phenotype similarity and gene proximity have demonstrated great success in prioritizing candidate genes for human diseases. However, most of these methods rely ...

journal_title：BMC bioinformatics

authors： Zhang W,Sun F,Jiang R

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks of the cell. The available methods to identify functional domain combinations are limited in their scope, e.g. to the identification of combinations falling within individual...

journal_title：BMC bioinformatics

authors： McLaughlin WA,Chen K,Hou T,Wang W

更新日期：2007-10-16 00:00:00

abstract：BACKGROUND:Designing small-molecule kinase inhibitors with desirable selectivity profiles is a major challenge in drug discovery. A high-throughput screen for inhibitors of a given kinase will typically yield many compounds that inhibit more than one kinase. A series of chemical modifications are usually required befor...

journal_title：BMC bioinformatics

authors： Caffrey DR,Lunney EA,Moshinsky DJ

更新日期：2008-11-25 00:00:00

abstract：BACKGROUND:Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of transcription factor binding sites. RESULTS:We propose to identify and group similar profiles using tw...

journal_title：BMC bioinformatics

authors： Kielbasa SM,Gonze D,Herzel H

更新日期：2005-09-28 00:00:00

abstract：BACKGROUND:A cross-correlation (XCorr) score function is one of the most popular score functions utilized to search peptide identifications in databases, and many computer programs, such as SEQUEST, Comet, and Tide, currently use this score function. Recently, the HiXCorr algorithm was developed to speed up this score ...

journal_title：BMC bioinformatics

authors： Kim H,Han S,Um JH,Park K

更新日期：2018-12-12 00:00:00

abstract：BACKGROUND:Analyses of molecular high-throughput data often lack in robustness, i.e. results are very sensitive to the addition or removal of a single observation. Therefore, the identification of extreme observations is an important step of quality control before doing further data analysis. Standard outlier detection...

journal_title：BMC bioinformatics

authors： Kruppa J,Jung K

更新日期：2017-05-02 00:00:00

abstract：BACKGROUND:Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene regulatory, and metabolic pathways. Among these, metabolic networks are probably the most studied, as t...

journal_title：BMC bioinformatics

authors： Manipur I,Granata I,Maddalena L,Guarracino MR

更新日期：2020-08-21 00:00:00

abstract：BACKGROUND:In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching techniq...

journal_title：BMC bioinformatics

authors： Bhattacharya S,Bhattacharyya C,Chandra NR

更新日期：2006-12-18 00:00:00

abstract：BACKGROUND:Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interest include simple moti...

journal_title：BMC bioinformatics

authors： Mangalam HJ

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:Detecting patterns in high-dimensional multivariate datasets is non-trivial. Clustering and dimensionality reduction techniques often help in discerning inherent structures. In biological datasets such as microbial community composition or gene expression data, observations can be generated from a continuous...

journal_title：BMC bioinformatics

authors： Nguyen LH,Holmes S

更新日期：2017-09-13 00:00:00

abstract：BACKGROUND:One of the most important goals of the mathematical modeling of gene regulatory networks is to alter their behavior toward desirable phenotypes. Therapeutic techniques are derived for intervention in terms of stationary control policies. In large networks, it becomes computationally burdensome to derive an o...

journal_title：BMC bioinformatics

authors： Ghaffari N,Ivanov I,Qian X,Dougherty ER

更新日期：2011-10-18 00:00:00

abstract：BACKGROUND:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We d...

journal_title：BMC bioinformatics

authors： Bui VK,Wei C

更新日期：2020-10-20 00:00:00

abstract：BACKGROUND:We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, ma...

journal_title：BMC bioinformatics

authors： Cherkasov A,Ho Sui SJ,Brunham RC,Jones SJ

更新日期：2004-07-26 00:00:00