A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships.

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: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:Sequence comparison is one of the most prominent tools in biological research, and is instrumental in studying gene function and evolution. The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in prote...

journal_title：BMC bioinformatics

authors： Shlomi T,Segal D,Ruppin E,Sharan R

更新日期：2006-04-10 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:Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microarrays does not capture all alternative splicing events. Moreover, for many species genomic data is be...

journal_title：BMC bioinformatics

authors： Sinha R,Hiller M,Pudimat R,Gausmann U,Platzer M,Backofen R

更新日期：2008-11-12 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding the mechanisms of post-transcriptional regulation. Hu...

journal_title：BMC bioinformatics

authors： Huang TH,Fan B,Rothschild MF,Hu ZL,Li K,Zhao SH

更新日期：2007-09-17 00:00:00

abstract：BACKGROUND:The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear ...

journal_title：BMC bioinformatics

authors： Lemieux S

更新日期：2006-08-25 00:00:00

abstract：BACKGROUND:PacBio sequencing platform offers longer read lengths than the second-generation sequencing technologies. It has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. Due to its extremely wide range of application areas, fast sequencing simulation syste...

journal_title：BMC bioinformatics

authors： Wei ZG,Zhang SW

更新日期：2018-05-22 00:00:00

abstract：BACKGROUND:The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-d...

journal_title：BMC bioinformatics

authors： Wang Q,Tang B,Song L,Ren B,Liang Q,Xie F,Zhuo Y,Liu X,Zhang L

更新日期：2013-11-14 00:00:00

abstract：BACKGROUND:An increasing number of researchers have released novel RNA structure analysis and prediction algorithms for comparative approaches to structure prediction. Yet, independent benchmarking of these algorithms is rarely performed as is now common practice for protein-folding, gene-finding and multiple-sequence-...

journal_title：BMC bioinformatics

authors： Gardner PP,Giegerich R

更新日期：2004-09-30 00:00:00

abstract：BACKGROUND:Recently, measuring phenotype similarity began to play an important role in disease diagnosis. Researchers have begun to pay attention to develop phenotype similarity measurement. However, existing methods ignore the interactions between phenotype-associated proteins, which may lead to inaccurate phenotype s...

journal_title：BMC bioinformatics

authors： Peng J,Hui W,Shang X

更新日期：2018-04-11 00:00:00

abstract：:Identifying segments in the genome of different individuals that are identical-by-descent (IBD) is a fundamental element of genetics. IBD data is used for numerous applications including demographic inference, heritability estimation, and mapping disease loci. Simultaneous detection of IBD over multiple haplotypes has...

journal_title：BMC bioinformatics

authors： Park DS,Baran Y,Hormozdiari F,Eng C,Torgerson DG,Burchard EG,Zaitlen N

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Proteins are comprised of one or several building blocks, known as domains. Such domains can be classified into families according to their evolutionary origin. Whereas sequencing technologies have advanced immensely in recent years, there are no matching computational methodologies for large-scale determina...

journal_title：BMC bioinformatics

authors： Portugaly E,Harel A,Linial N,Linial M

更新日期：2006-06-02 00:00:00

abstract：BACKGROUND:The large gap between the number of protein sequences in databases and the number of functionally characterized proteins calls for the development of a fast computational tool for the prediction of subnuclear and subcellular localizations generally applicable to protein sequences. The information on localiza...

journal_title：BMC bioinformatics

authors： Lei Z,Dai Y

更新日期：2005-12-07 00:00:00

abstract：BACKGROUND:Melanoma results in the vast majority of skin cancer deaths during the last decades, even though this disease accounts for only one percent of all skin cancers' instances. The survival rates of melanoma from early to terminal stages is more than fifty percent. Therefore, having the right information at the r...

journal_title：BMC bioinformatics

authors： Nasiri S,Helsper J,Jung M,Fathi M

更新日期：2020-03-11 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:High throughput DNA/RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine ...

journal_title：BMC bioinformatics

authors： Chanumolu SK,Albahrani M,Otu HH

更新日期：2019-08-15 00:00:00

abstract：BACKGROUND:Periodogram analysis of time-series is widespread in biology. A new challenge for analyzing the microarray time series data is to identify genes that are periodically expressed. Such challenge occurs due to the fact that the observed time series usually exhibit non-idealities, such as noise, short length, an...

journal_title：BMC bioinformatics

authors： Liew AW,Xian J,Wu S,Smith D,Yan H

更新日期：2007-04-24 00:00:00

abstract：BACKGROUND:We introduce a novel method, called PuFFIN, that takes advantage of paired-end short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes and higher accuracy than existing tools. In contrast to other approaches that require users to optimize several parameters according to t...

journal_title：BMC bioinformatics

authors： Polishko A,Bunnik EM,Le Roch KG,Lonardi S

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Many practical tasks in biomedicine require accessing specific types of information in scientific literature; e.g. information about the results or conclusions of the study in question. Several schemes have been developed to characterize such information in scientific journal articles. For example, a simple ...

journal_title：BMC bioinformatics

authors： Guo Y,Korhonen A,Liakata M,Silins I,Hogberg J,Stenius U

更新日期：2011-03-08 00:00:00

abstract：BACKGROUND:Severity gradation of missense mutations is a big challenge for exome annotation. Predictors of deleteriousness that are most frequently used to filter variants found by next generation sequencing, produce qualitative predictions, but also numerical scores. It has never been tested if these scores correlate ...

journal_title：BMC bioinformatics

authors： Cimmaruta C,Citro V,Andreotti G,Liguori L,Cubellis MV,Hay Mele B

更新日期：2018-11-30 00:00:00

abstract：BACKGROUND:Copy number variants (CNVs) have been demonstrated to occur at a high frequency and are now widely believed to make a significant contribution to the phenotypic variation in human populations. Array-based comparative genomic hybridization (array-CGH) and newly developed read-depth approach through ultrahigh ...

journal_title：BMC bioinformatics

authors： Zhang ZD,Gerstein MB

更新日期：2010-10-31 00:00:00

abstract：BACKGROUND:Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks. RESULTS:Based on a homogeneity assumptio...

journal_title：BMC bioinformatics

authors： Hu GQ,Zheng X,Ju LN,Zhu H,She ZS

更新日期：2008-03-25 00:00:00

abstract：BACKGROUND:Current microRNA (miRNA) research in progress has engendered rapid accumulation of expression data evolving from microarray experiments. Such experiments are generally performed over different tissues belonging to a specific species of metazoan. For disease diagnosis, microarray probes are also prepared with...

journal_title：BMC bioinformatics

authors： Bandyopadhyay S,Bhattacharyya M

更新日期：2009-05-28 00:00:00

abstract：BACKGROUND:Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionall...

journal_title：BMC bioinformatics

authors： Weeratunga S,Hu NJ,Simon A,Hofmann A

更新日期：2012-08-14 00:00:00

abstract：BACKGROUND:A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinform...

journal_title：BMC bioinformatics

authors： Santamaria M,Vicario S,Pappadà G,Scioscia G,Scazzocchio C,Saccone C

更新日期：2009-06-16 00:00:00

abstract：:We developed a new computational technique called Step-Level Differential Response (SLDR) to identify genetic regulatory relationships. Our technique takes advantages of functional genomics data for the same species under different perturbation conditions, therefore complementary to current popular computational techn...

journal_title：BMC bioinformatics

authors： Yue Z,Wan P,Huang H,Xie Z,Chen JY

更新日期：2014-01-01 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:Knowledge of when and in which cells each gene is expressed across multicellular organisms is critical in understanding both gene function and regulation of cell type diversity. However, methods for measuring expression typically involve a trade-off between imaging-based methods, which give the precise locat...

journal_title：BMC bioinformatics

authors： Burdick JT,Murray JI

更新日期：2013-06-22 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