Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts.

abstract：BACKGROUND:Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides...

journal_title：BMC bioinformatics

authors： Haskins WE,Petritis K,Zhang J

更新日期：2011-03-15 00:00:00

abstract：BACKGROUND:Prioritizing disease genes is trying to identify potential disease causing genes for a given phenotype, which can be applied to reveal the inherited basis of human diseases and facilitate drug development. Our motivation is inspired by label propagation algorithm and the false positive protein-protein intera...

journal_title：BMC bioinformatics

authors： Zhang Y,Liu J,Liu X,Fan X,Hong Y,Wang Y,Huang Y,Xie M

更新日期：2018-02-08 00:00:00

abstract：:Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is difficult to use in practice. We introduce a series of tools for processing and analyzing RNA-Seq data...

journal_title：BMC bioinformatics

authors： Pimentel H,Sturmfels P,Bray N,Melsted P,Pachter L

更新日期：2016-12-01 00:00:00

abstract：BACKGROUND:The biological network is highly dynamic. Functional relations between genes can be activated or deactivated depending on the biological conditions. On the genome-scale network, subnetworks that gain or lose local expression consistency may shed light on the regulatory mechanisms related to the changing biol...

journal_title：BMC bioinformatics

authors： Lu J,Lu Y,Ding Y,Xiao Q,Liu L,Cai Q,Kong Y,Bai Y,Yu T

更新日期：2019-12-24 00:00:00

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: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:In addition to single-locus (main) effects of disease variants, there is a growing consensus that gene-gene and gene-environment interactions may play important roles in disease etiology. However, for the very large numbers of genetic markers currently in use, it has proven difficult to develop suitable and ...

journal_title：BMC bioinformatics

authors： Long Q,Zhang Q,Ott J

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. R...

journal_title：BMC bioinformatics

authors： Beccati A,Gerken J,Quast C,Yilmaz P,Glöckner FO

更新日期：2017-09-30 00:00:00

abstract：BACKGROUND:Finishing is the process of improving the quality and utility of draft genome sequences generated by shotgun sequencing and computational assembly. Finishing can involve targeted sequencing. Finishing reads may be incorporated by manual or automated means. One automated method uses targeted addition by local...

journal_title：BMC bioinformatics

authors： Koren S,Miller JR,Walenz BP,Sutton G

更新日期：2010-09-10 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:Endometrial cancers (ECs) are one of the most common types of malignant tumor in females. Substantial efforts had been made to identify significantly mutated genes (SMGs) in ECs and use them as biomarkers for the classification of histological subtypes and the prediction of clinical outcomes. However, the im...

journal_title：BMC bioinformatics

authors： Liu K,He L,Liu Z,Xu J,Liu Y,Kuang Q,Wen Z,Li M

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:Identifying differentially abundant features between different experimental groups is a common goal for many metabolomics and proteomics studies. However, analyzing data from mass spectrometry (MS) is difficult because the data may not be normally distributed and there is often a large fraction of zero value...

journal_title：BMC bioinformatics

authors： Li Y,Fan TWM,Lane AN,Kang WY,Arnold SM,Stromberg AJ,Wang C,Chen L

更新日期：2019-10-17 00:00:00

abstract：BACKGROUND:Next-generation sequencing technologies allow researchers to obtain millions of sequence reads in a single experiment. One important use of the technology is the sequencing of small non-coding regulatory RNAs and the identification of the genomic locales from which they originate. Currently, there is a pauci...

journal_title：BMC bioinformatics

authors： MacLean D,Moulton V,Studholme DJ

更新日期：2010-02-18 00:00:00

abstract：BACKGROUND:It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here, we describe a tool wh...

journal_title：BMC bioinformatics

authors： David MP,Lapid CM,Daria VR

更新日期：2008-04-28 00:00:00

abstract：BACKGROUND:The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologist...

journal_title：BMC bioinformatics

authors： Yin Z,Zhou X,Bakal C,Li F,Sun Y,Perrimon N,Wong ST

更新日期：2008-06-05 00:00:00

abstract：BACKGROUND:MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes ba...

journal_title：BMC bioinformatics

authors： González JR,Carrasco JL,Armengol L,Villatoro S,Jover L,Yasui Y,Estivill X

更新日期：2008-06-04 00:00:00

abstract：BACKGROUND:Multiple data-analytic methods have been proposed for evaluating gene-expression levels in specific biological pathways, assessing differential expression associated with a binary phenotype. Following Goeman and Bühlmann's recent review, we compared statistical performance of three methods, namely Global Tes...

journal_title：BMC bioinformatics

authors： Liu Q,Dinu I,Adewale AJ,Potter JD,Yasui Y

更新日期：2007-11-07 00:00:00

abstract：BACKGROUND:Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replica...

journal_title：BMC bioinformatics

authors： Zynda GJ,Song J,Concia L,Wear EE,Hanley-Bowdoin L,Thompson WF,Vaughn MW

更新日期：2017-08-07 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: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:Techniques for reconstruction of biological networks which are based on perturbation experiments often predict direct interactions between nodes that do not exist. Transitive reduction removes such relations if they can be explained by an indirect path of influences. The existing algorithms for transitive re...

journal_title：BMC bioinformatics

authors： Bošnački D,Odenbrett MR,Wijs A,Ligtenberg W,Hilbers P

更新日期：2012-10-30 00:00:00

abstract：BACKGROUND:Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties by gene express...

journal_title：BMC bioinformatics

authors： Zhang SD,Gant TW

更新日期：2008-06-02 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:Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoin...

journal_title：BMC bioinformatics

authors： Pluskal T,Castillo S,Villar-Briones A,Oresic M

更新日期：2010-07-23 00:00:00

abstract：BACKGROUND:Pseudouridylation is the most prevalent type of posttranscriptional modification in various stable RNAs of all organisms, which significantly affects many cellular processes that are regulated by RNA. Thus, accurate identification of pseudouridine (Ψ) sites in RNA will be of great benefit for understanding t...

journal_title：BMC bioinformatics

authors： He J,Fang T,Zhang Z,Huang B,Zhu X,Xiong Y

更新日期：2018-08-29 00:00:00

abstract：BACKGROUND:When constructing new biomarker or gene signature scores for time-to-event outcomes, the underlying aims are to develop a discrimination model that helps to predict whether patients have a poor or good prognosis and to identify the most influential variables for this task. In practice, this is often done fit...

journal_title：BMC bioinformatics

authors： Mayr A,Hofner B,Schmid M

更新日期：2016-07-22 00:00:00

abstract：BACKGROUND:In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image ac...

journal_title：BMC bioinformatics

authors： Hartmann A,Czauderna T,Hoffmann R,Stein N,Schreiber F

更新日期：2011-05-12 00:00:00

abstract：BACKGROUND:The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-structures with at most two mutually crossing bonds (3-noncrossing). These structures are folded by ...

journal_title：BMC bioinformatics

authors： Huang FW,Li LY,Reidys CM

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Biological data that are well-organized by an ontology, such as Gene Ontology, enables high-throughput availability of the semantic web. It can also be used to facilitate high throughput classification of biomedical information. However, to our knowledge, no evaluation has been published on automating classi...

journal_title：BMC bioinformatics

authors： Chen JL,Liu Y,Sam LT,Li J,Lussier YA

更新日期：2007-05-09 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