A two-phase procedure for non-normal quantitative trait genetic association study.

abstract：BACKGROUND:Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to...

journal_title：BMC bioinformatics

authors： Casneuf T,Van de Peer Y,Huber W

更新日期：2007-11-26 00:00:00

abstract：BACKGROUND:The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify approximately 50% of homologies (with a false positive rate set at 1/1000). RESULTS:We present Homology Induction (HI), a new approach to inferring homology. HI uses machine learning to...

journal_title：BMC bioinformatics

authors： Karwath A,King RD

更新日期：2002-04-23 00:00:00

abstract：BACKGROUND:Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction h...

journal_title：BMC bioinformatics

authors： Su EC,Chiu HS,Lo A,Hwang JK,Sung TY,Hsu WL

更新日期：2007-09-08 00:00:00

abstract：BACKGROUND:Antibodies revolutionized cancer treatment over the past decades. Despite their successfully application, there are still challenges to overcome to improve efficacy, such as the heterogeneous distribution of antibodies within tumors. Tumor microenvironment features, such as the distribution of tumor and othe...

journal_title：BMC bioinformatics

authors： Cartaxo AL,Almeida J,Gualda EJ,Marsal M,Loza-Alvarez P,Brito C,Isidro IA

更新日期：2020-11-17 00:00:00

abstract：BACKGROUND:The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutat...

journal_title：BMC bioinformatics

authors： Santos J,Monteagudo Á

更新日期：2017-03-27 00:00:00

abstract：BACKGROUND:DNA methylation changes are associated with a wide array of biological processes. Bisulfite conversion of DNA followed by high-throughput sequencing is increasingly being used to assess genome-wide methylation at single-base resolution. The relative slowness of most commonly used aligners for processing such...

journal_title：BMC bioinformatics

authors： Ryan DP,Ehninger D

更新日期：2014-10-18 00:00:00

abstract：BACKGROUND:Cyclic nucleotides are ubiquitous intracellular messengers. Until recently, the roles of cyclic nucleotides in plant cells have proven difficult to uncover. With an understanding of the protein domains which can bind cyclic nucleotides (CNB and GAF domains) we scanned the completed genomes of the higher plan...

journal_title：BMC bioinformatics

authors： Bridges D,Fraser ME,Moorhead GB

更新日期：2005-01-11 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to that. Most proteins perform their functions by interacting with other proteins, so predicting PPIs acc...

journal_title：BMC bioinformatics

authors： Liu L,Zhu X,Ma Y,Piao H,Yang Y,Hao X,Fu Y,Wang L,Peng J

更新日期：2020-12-16 00:00:00

abstract：BACKGROUND:Identifying drug-target interaction is a key element in drug discovery. In silico prediction of drug-target interaction can speed up the process of identifying unknown interactions between drugs and target proteins. In recent studies, handcrafted features, similarity metrics and machine learning methods have...

journal_title：BMC bioinformatics

authors： Eslami Manoochehri H,Nourani M

更新日期：2020-07-06 00:00:00

abstract：BACKGROUND:Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mec...

journal_title：BMC bioinformatics

authors： Rousseau M,Fraser J,Ferraiuolo MA,Dostie J,Blanchette M

更新日期：2011-10-25 00:00:00

abstract：BACKGROUND:In template-based modeling when using a single template, inter-atomic distances of an unknown protein structure are assumed to be distributed by Gaussian probability density functions, whose center peaks are located at the distances between corresponding atoms in the template structure. The width of the Gaus...

journal_title：BMC bioinformatics

authors： Lee J,Lee K,Joung I,Joo K,Brooks BR,Lee J

更新日期：2015-03-21 00:00:00

abstract：BACKGROUND:Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole-cell scale. In such representations, the cell is considered as a system composed of interlocked sub...

journal_title：BMC bioinformatics

authors： Henry V,Saïs F,Inizan O,Marchadier E,Dibie J,Goelzer A,Fromion V

更新日期：2020-07-23 00:00:00

abstract：BACKGROUND:The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to a...

journal_title：BMC bioinformatics

authors： Green ML,Karp PD

更新日期：2004-06-09 00:00:00

abstract：BACKGROUND:Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint ...

journal_title：BMC bioinformatics

authors： Bozdag S,Close TJ,Lonardi S

更新日期：2009-07-15 00:00:00

abstract：BACKGROUND:The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB), thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based methods have been develo...

journal_title：BMC bioinformatics

authors： Li GH,Huang JF

更新日期：2010-08-27 00:00:00

abstract：BACKGROUND:Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presents a novel method to perform correlations between microarray gene expression data and clinico-pathol...

journal_title：BMC bioinformatics

authors： Corradi L,Mirisola V,Porro I,Torterolo L,Fato M,Romano P,Pfeffer U

更新日期：2009-10-15 00:00:00

abstract：BACKGROUND:Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. RESULTS:A Java program was developed for retrieval of protein and nucleic acid s...

journal_title：BMC bioinformatics

authors： Büssow K,Hoffmann S,Sievert V

更新日期：2002-12-19 00:00:00

abstract：BACKGROUND:The main goal of the whole transcriptome analysis is to correctly identify all expressed transcripts within a specific cell/tissue--at a particular stage and condition--to determine their structures and to measure their abundances. RNA-seq data promise to allow identification and quantification of transcript...

journal_title：BMC bioinformatics

authors： Angelini C,De Canditiis D,De Feis I

更新日期：2014-05-09 00:00:00

abstract：BACKGROUND:Sequence mutations represent a driving force of adaptive evolution in bacterial pathogens. It is especially evident in reductive genome evolution where bacteria underwent lifestyles shifting from a free-living to a strictly intracellular or host-depending life. It resulted in loss-of-function mutations and/o...

journal_title：BMC bioinformatics

authors： Yu GX

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations acco...

journal_title：BMC bioinformatics

authors： Lloyd S,Snell QO

更新日期：2011-12-07 00:00:00

abstract：BACKGROUND:Systematic mutagenesis studies have shown that only a few interface residues termed hot spots contribute significantly to the binding free energy of protein-protein interactions. Therefore, hot spots prediction becomes increasingly important for well understanding the essence of proteins interactions and hel...

journal_title：BMC bioinformatics

authors： Chen R,Chen W,Yang S,Wu D,Wang Y,Tian Y,Shi Y

更新日期：2011-07-29 00:00:00

abstract：BACKGROUND:Reverse transcription followed by real-time PCR is widely used for quantification of specific mRNA, and with the use of double-stranded DNA binding dyes it is becoming a standard for microarray data validation. Despite the kinetic information generated by real-time PCR, most popular analysis methods assume c...

journal_title：BMC bioinformatics

authors： Alvarez MJ,Vila-Ortiz GJ,Salibe MC,Podhajcer OL,Pitossi FJ

更新日期：2007-03-09 00:00:00

abstract：BACKGROUND:In the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functional antibody sequences to their sourcing germline gene segments is vital not only for understanding...

journal_title：BMC bioinformatics

authors： Wang X,Wu D,Zheng S,Sun J,Tao L,Li Y,Cao Z

更新日期：2008-12-12 00:00:00

abstract：BACKGROUND:Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear...

journal_title：BMC bioinformatics

authors： Bieri M,Gooley PR

更新日期：2011-10-27 00:00:00

abstract：BACKGROUND:Discovering patterns from gene expression levels is regarded as a classification problem when tissue classes of the samples are given and solved as a discrete-data problem by discretizing the expression levels of each gene into intervals maximizing the interdependence between that gene and the class labels. ...

journal_title：BMC bioinformatics

authors： Wu GP,Chan KC,Wong AK

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Research related to cancer is vast, and continues in earnest in many directions. Due to the complexity of cancer, a better understanding of tumor growth dynamics can be gleaned from a dynamic computational model. We present a comprehensive, fully executable, spatial and temporal 3D computational model of the...

journal_title：BMC bioinformatics

authors： Bloch N,Harel D

更新日期：2016-08-24 00:00:00

abstract：BACKGROUND:DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it rema...

journal_title：BMC bioinformatics

authors： Bulla I,Aliaga B,Lacal V,Bulla J,Grunau C,Chaparro C

更新日期：2018-03-27 00:00:00

abstract：BACKGROUND:The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data. Typically, the genome is divided into tiling windows and windowed read-count data is generated for the entire geno...

journal_title：BMC bioinformatics

authors： Wang W,Sun W,Wang W,Szatkiewicz J

更新日期：2018-03-01 00:00:00

abstract：BACKGROUND:Accurately prioritizing candidate disease genes is an important and challenging problem. Various network-based methods have been developed to predict potential disease genes by utilizing the disease similarity network and molecular networks such as protein interaction or gene co-expression networks. Although...

journal_title：BMC bioinformatics

authors： Ni J,Koyuturk M,Tong H,Haines J,Xu R,Zhang X

更新日期：2016-11-10 00:00:00

abstract：BACKGROUND:Activation of naïve B lymphocytes by extracellular ligands, e.g. antigen, lipopolysaccharide (LPS) and CD40 ligand, induces a combination of common and ligand-specific phenotypic changes through complex signal transduction pathways. For example, although all three of these ligands induce proliferation, only ...

journal_title：BMC bioinformatics

authors： Lee JA,Sinkovits RS,Mock D,Rab EL,Cai J,Yang P,Saunders B,Hsueh RC,Choi S,Subramaniam S,Scheuermann RH,Alliance for Cellular Signaling.

更新日期：2006-05-02 00:00:00