Detecting intergene correlation changes in microarray analysis: a new approach to gene selection.

abstract：BACKGROUND:In Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare gene functional similarities at the molecular level. The existing gene similarity measures, however...

journal_title：BMC bioinformatics

authors： Peng J,Wang Y,Chen J

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:In two-channel competitive genomic hybridization microarray experiments, the ratio of the two fluorescent signal intensities at each spot on the microarray is commonly used to infer the relative amounts of the test and reference sample DNA levels. This ratio may be influenced by systematic measurement effect...

journal_title：BMC bioinformatics

authors： Khojasteh M,Lam WL,Ward RK,MacAulay C

更新日期：2005-11-18 00:00:00

abstract：BACKGROUND:During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dC...

journal_title：BMC bioinformatics

authors： Li C

更新日期：2008-05-08 00:00:00

abstract：BACKGROUND:Current malaria diagnosis relies primarily on microscopic examination of Giemsa-stained thick and thin blood films. This method requires vigorously trained technicians to efficiently detect and classify the malaria parasite species such as Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) for an appropria...

journal_title：BMC bioinformatics

authors： Kaewkamnerd S,Uthaipibull C,Intarapanich A,Pannarut M,Chaotheing S,Tongsima S

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis ...

journal_title：BMC bioinformatics

authors： Yu G

更新日期：2010-10-12 00:00:00

abstract：BACKGROUND:The abundant data available for protein interaction networks have not yet been fully understood. New types of analyses are needed to reveal organizational principles of these networks to investigate the details of functional and regulatory clusters of proteins. RESULTS:In the present work, individual cluste...

journal_title：BMC bioinformatics

authors： Sen TZ,Kloczkowski A,Jernigan RL

更新日期：2006-07-24 00:00:00

abstract：BACKGROUND:We previously introduced PCPS (Proteasome Cleavage Prediction Server), a web-based tool to predict proteasome cleavage sites using n-grams. Here, we evaluated the ability of PCPS immunoproteasome cleavage model to discriminate CD8+ T cell epitopes. RESULTS:We first assembled an epitope dataset consisting of...

journal_title：BMC bioinformatics

authors： Gomez-Perosanz M,Ras-Carmona A,Lafuente EM,Reche PA

更新日期：2020-12-14 00:00:00

abstract：BACKGROUND:Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging vari...

journal_title：BMC bioinformatics

authors： Masino AJ,Dechene ET,Dulik MC,Wilkens A,Spinner NB,Krantz ID,Pennington JW,Robinson PN,White PS

更新日期：2014-07-21 00:00:00

abstract：BACKGROUND:Orthologs inference is the starting point of most comparative genomics studies, and a plethora of methods have been designed in the last decade to address this challenging task. In this paper we focus on the problems of deciding consistency with a species tree (known or not) of a partial set of orthology/par...

journal_title：BMC bioinformatics

authors： Jones M,Paul C,Scornavacca C

更新日期：2016-11-11 00:00:00

abstract：BACKGROUND:In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorith...

journal_title：BMC bioinformatics

authors： Yang C,He Z,Yu W

更新日期：2009-01-06 00:00:00

abstract：BACKGROUND:With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or i...

journal_title：BMC bioinformatics

authors： Weinberg Z,Breaker RR

更新日期：2011-01-04 00:00:00

abstract：BACKGROUND:The median of k≥3 genomes was originally defined to find a compromise genome indicative of a common ancestor. However, in gene order comparisons, the usual definitions based on minimizing the sum of distances to the input genomes lead to degenerate medians reflecting only one of the input genomes. "Near-medi...

journal_title：BMC bioinformatics

authors： Larlee CA,Brandts A,Sankoff D

更新日期：2016-12-15 00:00:00

abstract：BACKGROUND:Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal ...

journal_title：BMC bioinformatics

authors： Wu TY,Hsieh CC,Hong JJ,Chen CY,Tsai YS

更新日期：2009-05-27 00:00:00

abstract：BACKGROUND:Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the m...

journal_title：BMC bioinformatics

authors： McQuisten KA,Peek AS

更新日期：2007-06-07 00:00:00

abstract：BACKGROUND:For the development of genome assembly tools, some comprehensive and efficiently computable validation measures are required to assess the quality of the assembly. The mostly used N50 measure summarizes the assembly results by the length of the scaffold (or contig) overlapping the midpoint of the length-orde...

journal_title：BMC bioinformatics

authors： Mäkinen V,Salmela L,Ylinen J

更新日期：2012-10-03 00:00:00

abstract：BACKGROUND:The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatures of phenotypes such as clinical outcome has not been attained in almost any disease area. Here, w...

journal_title：BMC bioinformatics

authors： Smith AM,Walsh JR,Long J,Davis CB,Henstock P,Hodge MR,Maciejewski M,Mu XJ,Ra S,Zhao S,Ziemek D,Fisher CK

更新日期：2020-03-20 00:00:00

abstract：BACKGROUND:Different human responses to the same vaccine were frequently observed. For example, independent studies identified overlapping but different transcriptomic gene expression profiles in Yellow Fever vaccine 17D (YF-17D) immunized human subjects. Different experimental and analysis conditions were likely contr...

journal_title：BMC bioinformatics

authors： Ong E,Sun P,Berke K,Zheng J,Wu G,He Y

更新日期：2019-12-23 00:00:00

abstract：BACKGROUND:Genome imputation, admixture resolution and genome-wide association analyses are timely and computationally intensive processes with many composite and requisite steps. Analysis time increases further when building and installing the run programs required for these analyses. For scientists that may not be as...

journal_title：BMC bioinformatics

authors： Eller RJ,Janga SC,Walsh S

更新日期：2019-06-28 00:00:00

abstract：BACKGROUND:Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the current study, we describe a candidate gene prioritization method that is entirely based on protein-prot...

journal_title：BMC bioinformatics

authors： Chen J,Aronow BJ,Jegga AG

更新日期：2009-02-27 00:00:00

abstract：BACKGROUND:A professional recognition mechanism is required to encourage expedited publishing of an adequate volume of 'fit-for-use' biodiversity data. As a component of such a recognition mechanism, we propose the development of the Data Usage Index (DUI) to demonstrate to data publishers that their efforts of creatin...

journal_title：BMC bioinformatics

authors： Ingwersen P,Chavan V

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection of lncRNA-protein interactions are limited and inefficient. Many methods have been proposed to predi...

journal_title：BMC bioinformatics

authors： Deng L,Wang J,Xiao Y,Wang Z,Liu H

更新日期：2018-10-11 00:00:00

abstract：BACKGROUND:Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed. Most attempted solutions involve the production of large scale alignments, and many of these require a high stringency pre-screen for putati...

journal_title：BMC bioinformatics

authors： Stuart GW,Berry MW

更新日期：2004-12-17 00:00:00

abstract：BACKGROUND:Because common complex diseases are affected by multiple genes and environmental factors, it is essential to investigate gene-gene and/or gene-environment interactions to understand genetic architecture of complex diseases. After the great success of large scale genome-wide association (GWA) studies using th...

journal_title：BMC bioinformatics

authors： Oh S,Lee J,Kwon MS,Weir B,Ha K,Park T

更新日期：2012-06-11 00:00:00

abstract：BACKGROUND:Expression quantitative trait loci (eQTL) mapping is often used to identify genetic loci and candidate genes correlated with traits. Although usually a group of genes affect complex traits, genes in most eQTL mapping methods are considered as independent. Recently, some eQTL mapping methods have accounted fo...

journal_title：BMC bioinformatics

authors： Wang Y,Richard R,Pan Y

更新日期：2016-12-13 00:00:00

abstract：BACKGROUND:Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, t...

journal_title：BMC bioinformatics

authors： Ranjbar MR,Di Poto C,Wang Y,Ressom HW

更新日期：2015-08-19 00:00:00

abstract：BACKGROUND:DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. RESULTS:Here, we describe a method to detect copy number varia...

journal_title：BMC bioinformatics

authors： Xie C,Tammi MT

更新日期：2009-03-06 00:00:00

abstract：UNLABELLED: BACKGROUND:Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing...

journal_title：BMC bioinformatics

authors： Antoniw J,Beacham AM,Baldwin TK,Urban M,Rudd JJ,Hammond-Kosack KE

更新日期：2011-11-15 00:00:00

abstract：BACKGROUND:We introduce Approximate Entropy as a mathematical method of analysis for microarray data. Approximate entropy is applied here as a method to classify the complex gene expression patterns resultant of a clinical sample set. Since Entropy is a measure of disorder in a system, we believe that by choosing genes...

journal_title：BMC bioinformatics

authors： Botting SK,Trzeciakowski JP,Benoit MF,Salama SA,Diaz-Arrastia CR

更新日期：2009-02-20 00:00:00

abstract：BACKGROUND:Tumors have been hypothesized to be the result of a mixture of oncogenic events, some of which will be reflected in the gene expression of the tumor. Based on this hypothesis a variety of data-driven methods have been employed to decompose tumor expression profiles into component profiles, hypothetically lin...

journal_title：BMC bioinformatics

authors： van Vliet MH,Wessels LF,Reinders MJ

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in significant conflict with the plurality signal is a frequent task in comparative genomics, and especially ...

journal_title：BMC bioinformatics

authors： Mao F,Williams D,Zhaxybayeva O,Poptsova M,Lapierre P,Gogarten JP,Xu Y

更新日期：2012-06-07 00:00:00