Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays.

abstract：BACKGROUND:The rapid pace of bioscience research makes it very challenging to track relevant articles in one's area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million citations with three-quarters of a million new ones added each year. Thus it is not surprising to se...

journal_title：BMC bioinformatics

authors： Srinivasan P,Zhang XN,Bouten R,Chang C

更新日期：2015-06-20 00:00:00

abstract：BACKGROUND:Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analyses of their RNA and DNA profiles are challenging, because they comprise reads not only from the grafted human cancer but also from t...

journal_title：BMC bioinformatics

authors： Kluin RJC,Kemper K,Kuilman T,de Ruiter JR,Iyer V,Forment JV,Cornelissen-Steijger P,de Rink I,Ter Brugge P,Song JY,Klarenbeek S,McDermott U,Jonkers J,Velds A,Adams DJ,Peeper DS,Krijgsman O

更新日期：2018-10-04 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: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:The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required. RESULTS:In order to improve accessibil...

journal_title：BMC bioinformatics

authors： Deng M,Brägelmann J,Schultze JL,Perner S

更新日期：2016-02-06 00:00:00

abstract：BACKGROUND:Over the last two decades, an innovative technology called Tissue Microarray (TMA), which combines multi-tissue and DNA microarray concepts, has been widely used in the field of histology. It consists of a collection of several (up to 1000 or more) tissue samples that are assembled onto a single support - ty...

journal_title：BMC bioinformatics

authors： Nguyen HN,Paveau V,Cauchois C,Kervrann C

更新日期：2018-04-19 00:00:00

abstract：BACKGROUND:Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune sup...

journal_title：BMC bioinformatics

authors： Ammari M,McCarthy FM,Nanduri B,Pinchuk LM

更新日期：2010-10-07 00:00:00

abstract：BACKGROUND:The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortunately, efforts to annotate, classify, and analyze these chemical entities have largely remained in ...

journal_title：BMC bioinformatics

authors： Chepelev LL,Riazanov A,Kouznetsov A,Low HS,Dumontier M,Baker CJ

更新日期：2011-07-26 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:The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. RESULTS:...

journal_title：BMC bioinformatics

authors： Müller HM,Van Auken KM,Li Y,Sternberg PW

更新日期：2018-03-09 00:00:00

abstract：BACKGROUND:Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expressed in microarray experiments is challenging because of their potentially high type I error rate. Me...

journal_title：BMC bioinformatics

authors： Tan YD,Fornage M,Xu H

更新日期：2008-03-06 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:RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence o...

journal_title：BMC bioinformatics

authors： Li B,Dewey CN

更新日期：2011-08-04 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: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:Transcription factors are known to play key roles in carcinogenesis and therefore, are gaining popularity as potential therapeutic targets in drug development. A 'master regulator' transcription factor often appears to control most of the regulatory activities of the other transcription factors and the assoc...

journal_title：BMC bioinformatics

authors： Sikdar S,Datta S

更新日期：2017-02-02 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: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:A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes. Si...

journal_title：BMC bioinformatics

authors： Alanko J,Cunial F,Belazzougui D,Mäkinen V

更新日期：2017-03-14 00:00:00

abstract：BACKGROUND:The efficient and robust statistical analysis of the shape of plant organs of different cultivars is an important investigation issue in plant breeding and enables a robust cultivar description within the breeding progress. Laserscanning is a highly accurate and high resolution technique to acquire the 3D sh...

journal_title：BMC bioinformatics

authors： Heeren B,Paulus S,Goldbach H,Kuhlmann H,Mahlein AK,Rumpf M,Wirth B

更新日期：2020-07-29 00:00:00

abstract：BACKGROUND:One of the major challenges in biology is the correct identification of promoter regions. Computational methods based on motif searching have been the traditional approach taken. Recent studies have shown that DNA structural properties, such as curvature, stacking energy, and stress-induced duplex destabiliz...

journal_title：BMC bioinformatics

authors： Bland C,Newsome AS,Markovets AA

更新日期：2010-10-07 00:00:00

abstract：BACKGROUND:Circular RNAs (circRNAs) are a newly appreciated class of non-coding RNA molecules. Numerous tools have been developed for the detection of circRNAs, however computational tools to perform downstream functional analysis of circRNAs are scarce. RESULTS:We present circRNAprofiler, an R-based computational fra...

journal_title：BMC bioinformatics

authors： Aufiero S,Reckman YJ,Tijsen AJ,Pinto YM,Creemers EE

更新日期：2020-04-29 00:00:00

abstract：BACKGROUND:Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run a...

journal_title：BMC bioinformatics

authors： de Knikker R,Guo Y,Li JL,Kwan AK,Yip KY,Cheung DW,Cheung KH

更新日期：2004-03-10 00:00:00

abstract：BACKGROUND:DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene function over a period of time. Temporal gene expression curves can be treated as functional data s...

journal_title：BMC bioinformatics

authors： Kim J,Kim H

更新日期：2017-10-12 00:00:00

abstract：BACKGROUND:PCR clonal artefacts originating from NGS library preparation can affect both genomic as well as RNA-Seq applications when protocols are pushed to their limits. In RNA-Seq however the artifactual reads are not easy to tell apart from normal read duplication due to natural over-sequencing of highly expressed ...

journal_title：BMC bioinformatics

authors： Sayols S,Scherzinger D,Klein H

更新日期：2016-10-21 00:00:00

abstract：BACKGROUND:Gene expression microarray experiments are expensive to conduct and guidelines for acceptable quality control at intermediate steps before and after the samples are hybridised to chips are vague. We conducted an experiment hybridising RNA from human brain to 117 U133A Affymetrix GeneChips and used these data...

journal_title：BMC bioinformatics

authors： Jones L,Goldstein DR,Hughes G,Strand AD,Collin F,Dunnett SB,Kooperberg C,Aragaki A,Olson JM,Augood SJ,Faull RL,Luthi-Carter R,Moskvina V,Hodges AK

更新日期：2006-04-19 00:00:00

abstract：BACKGROUND:The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics...

journal_title：BMC bioinformatics

authors： Widmer C,Toussaint NC,Altun Y,Rätsch G

更新日期：2010-10-26 00:00:00

abstract：BACKGROUND:Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling ...

journal_title：BMC bioinformatics

authors： Chelaru F,Corrada Bravo H

更新日期：2015-01-01 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:Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in co...

journal_title：BMC bioinformatics

authors： Pravda L,Berka K,Svobodová Vařeková R,Sehnal D,Banáš P,Laskowski RA,Koča J,Otyepka M

更新日期：2014-11-18 00:00:00