Measure of synonymous codon usage diversity among genes in bacteria.

abstract：BACKGROUND:Many models have been proposed to detect copy number alterations in chromosomal copy number profiles, but it is usually not obvious to decide which is most effective for a given data set. Furthermore, most methods have a smoothing parameter that determines the number of breakpoints and must be chosen using v...

journal_title：BMC bioinformatics

authors： Hocking TD,Schleiermacher G,Janoueix-Lerosey I,Boeva V,Cappo J,Delattre O,Bach F,Vert JP

更新日期：2013-05-22 00:00:00

abstract：BACKGROUND:The nonparametric trend test (NPT) is well suitable for identifying the genetic variants associated with quantitative traits when the trait values do not satisfy the normal distribution assumption. If the genetic model, defined according to the mode of inheritance, is known, the NPT derived under the given g...

journal_title：BMC bioinformatics

authors： Zhang W,Li H,Li Z,Li Q

更新日期：2016-01-28 00:00:00

abstract：BACKGROUND:Parametric feature selection methods for machine learning and association studies based on genetic data are not robust with respect to outliers or influential observations. While rank-based, distribution-free statistics offer a robust alternative to parametric methods, their practical utility can be limited,...

journal_title：BMC bioinformatics

authors： Lin J,Sibley A,Shterev I,Nixon A,Innocenti F,Chan C,Owzar K

更新日期：2019-06-13 00:00:00

abstract：BACKGROUND:Zebrafish is a widely used model organism for studying heart development and cardiac-related pathogenesis. With the ability of surviving without a functional circulation at larval stages, strong genetic similarity between zebrafish and mammals, prolific reproduction and optically transparent embryos, zebrafi...

journal_title：BMC bioinformatics

authors： Kang CP,Tu HC,Fu TF,Wu JM,Chu PH,Chang DT

更新日期：2018-05-09 00:00:00

abstract：BACKGROUND:The identification of prognostic genes that can distinguish the prognostic risks of cancer patients remains a significant challenge. Previous works have proven that functional gene sets were more reliable for this task than the gene signature. However, few works have considered the cross-talk among functiona...

journal_title：BMC bioinformatics

authors： Zhou XH,Chu XY,Xue G,Xiong JH,Zhang HY

更新日期：2019-02-18 00:00:00

abstract：:Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughp...

journal_title：BMC bioinformatics

authors： Li YF,Radivojac P

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:The search for enriched features has become widely used to characterize a set of genes or proteins. A key aspect of this technique is its ability to identify correlations amongst heterogeneous data such as Gene Ontology annotations, gene expression data and genome location of genes. Despite the rapid growth ...

journal_title：BMC bioinformatics

authors： Barriot R,Sherman DJ,Dutour I

更新日期：2007-09-11 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:A large number of experimental studies show that the mutation and regulation of long non-coding RNAs (lncRNAs) are associated with various human diseases. Accurate prediction of lncRNA-disease associations can provide a new perspective for the diagnosis and treatment of diseases. The main function of many ln...

journal_title：BMC bioinformatics

authors： Zhang Y,Ye F,Xiong D,Gao X

更新日期：2020-09-03 00:00:00

abstract：BACKGROUND:Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for network enrichment analysis deal only with undirected networks, they can be computationally slow and a...

journal_title：BMC bioinformatics

authors： Signorelli M,Vinciotti V,Wit EC

更新日期：2016-09-05 00:00:00

abstract：BACKGROUND:Antibacterial peptides are one of the effecter molecules of innate immune system. Over the last few decades several antibacterial peptides have successfully approved as drug by FDA, which has prompted an interest in these antibacterial peptides. In our recent study we analyzed 999 antibacterial peptides, whi...

journal_title：BMC bioinformatics

authors： Lata S,Mishra NK,Raghava GP

更新日期：2010-01-18 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：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:Heritability of a phenotypic or molecular trait measures the proportion of variance that is attributable to genotypic variance. It is an important concept in breeding and genetics. Few methods are available for calculating heritability for traits derived from high-throughput sequencing. RESULTS:We propose s...

journal_title：BMC bioinformatics

authors： Rudra P,Shi WJ,Vestal B,Russell PH,Odell A,Dowell RD,Radcliffe RA,Saba LM,Kechris K

更新日期：2017-03-02 00:00:00

abstract：:Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these ca...

journal_title：BMC bioinformatics

authors： Schlitt T,Brazma A

更新日期：2007-09-27 00:00:00

abstract：BACKGROUND:While technological advances have made it possible to profile the immune system at high resolution, translating high-throughput data into knowledge of immune mechanisms has been challenged by the complexity of the interactions underlying immune processes. Tools to explore the immune network are critical for ...

journal_title：BMC bioinformatics

authors： Atallah MB,Tandon V,Hiam KJ,Boyce H,Hori M,Atallah W,Spitzer MH,Engleman E,Mallick P

更新日期：2020-08-10 00:00:00

abstract：BACKGROUND:The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This makes it difficult to keep track of available bioinformatics software, let alone the most suitable proto...

journal_title：BMC bioinformatics

authors： Eales JM,Pinney JW,Stevens RD,Robertson DL

更新日期：2008-09-01 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6-8 nucleotide long target sites, usually located within the mRNA 3' untranslated region. A common approach to validate and probe microRNA-mRNA interact...

journal_title：BMC bioinformatics

authors： Ryan BC,Werner TS,Howard PL,Chow RL

更新日期：2016-04-27 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: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:Computational discovery of transcription factor binding sites (TFBS) is a challenging but important problem of bioinformatics. In this study, improvement of a Gibbs sampling based technique for TFBS discovery is attempted through an approach that is widely known, but which has never been investigated before:...

journal_title：BMC bioinformatics

authors： Shida K

更新日期：2006-11-04 00:00:00

abstract：BACKGROUND:Protein remote homology detection is one of the central problems in bioinformatics, which is important for both basic research and practical application. Currently, discriminative methods based on Support Vector Machines (SVMs) achieve the state-of-the-art performance. Exploring feature vectors incorporating...

journal_title：BMC bioinformatics

authors： Liu B,Xu J,Zou Q,Xu R,Wang X,Chen Q

更新日期：2014-01-01 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:Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map con...

journal_title：BMC bioinformatics

authors： Dias Z,Dias U,Setubal JC

更新日期：2012-05-14 00:00:00

abstract：BACKGROUND:Text mining tools have gained popularity to process the vast amount of available research articles in the biomedical literature. It is crucial that such tools extract information with a sufficient level of detail to be applicable in real life scenarios. Studies of mining non-causal molecular relations attrib...

journal_title：BMC bioinformatics

authors： Van Landeghem S,Björne J,Abeel T,De Baets B,Salakoski T,Van de Peer Y

更新日期：2012-06-26 00:00:00

abstract：BACKGROUND:Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale va...

journal_title：BMC bioinformatics

authors： Aganezov S,Zban I,Aksenov V,Alexeev N,Schatz MC

更新日期：2019-12-17 00:00:00

abstract：BACKGROUND:One of the most powerful methods for the prediction of protein structure from sequence information alone is the iterative construction of profile-type models. Because profiles are built from sequence alignments, the sequences included in the alignment and the method used to align them will be important to th...

journal_title：BMC bioinformatics

authors： Scheeff ED,Bourne PE

更新日期：2006-09-14 00:00:00

abstract：BACKGROUND:Many statistical methods have been proposed to identify disease biomarkers from gene expression profiles. However, from gene expression profile data alone, statistical methods often fail to identify biologically meaningful biomarkers related to a specific disease under study. In this paper, we develop a nove...

journal_title：BMC bioinformatics

authors： Chen L,Xuan J,Wang C,Shih IeM,Wang Y,Zhang Z,Hoffman E,Clarke R

更新日期：2008-10-06 00:00:00

abstract：BACKGROUND:Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as si...

journal_title：BMC bioinformatics

authors： Alexopoulou D,Andreopoulos B,Dietze H,Doms A,Gandon F,Hakenberg J,Khelif K,Schroeder M,Wächter T

更新日期：2009-01-21 00:00:00

abstract：BACKGROUND:Many proteins contain conserved sequence patterns (motifs) that contribute to their functionality. The process of experimentally identifying and validating novel protein motifs can be difficult, expensive, and time consuming. A means for helping to identify in advance the possible function of a novel motif i...

journal_title：BMC bioinformatics

authors： Bristow F,He R,Van Domselaar G

更新日期：2011-09-26 00:00:00