3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape.

abstract：BACKGROUND:Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional informa...

journal_title：BMC bioinformatics

authors： Peterlongo P,Noé L,Lavenier D,Nguyen VH,Kucherov G,Giraud M

更新日期：2008-12-16 00:00:00

abstract：BACKGROUND:Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has beco...

journal_title：BMC bioinformatics

authors： Zare F,Dow M,Monteleone N,Hosny A,Nabavi S

更新日期：2017-05-31 00:00:00

abstract：BACKGROUND:Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast-evolving sequences in a gene-specific manner, identifies subsets of sequences that evolve at a r...

journal_title：BMC bioinformatics

authors： Rivera-Rivera CJ,Montoya-Burgos JI

更新日期：2019-08-13 00:00:00

abstract：BACKGROUND:Many methods for species tree inference require data from a sufficiently large sample of genomic loci in order to produce accurate estimates. However, few studies have attempted to use analytical theory to quantify "sufficiently large". RESULTS:Using the multispecies coalescent model, we report a general an...

journal_title：BMC bioinformatics

authors： Uricchio LH,Warnow T,Rosenberg NA

更新日期：2016-11-11 00:00:00

abstract：BACKGROUND:In this short article, we discuss a simple method for assessing sample size requirements in microarray experiments. RESULTS:Our method starts with the output from a permutation-based analysis for a set of pilot data, e.g. from the SAM package. Then for a given hypothesized mean difference and various sample...

journal_title：BMC bioinformatics

authors： Tibshirani R

更新日期：2006-03-02 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: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:Biomedical processes can provide essential information about the (mal-) functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Process branch. These processes often need to be described and categorised in terms of their attribute...

journal_title：BMC bioinformatics

authors： Andrade AQ,Blondé W,Hastings J,Schulz S

更新日期：2012-08-28 00:00:00

abstract：BACKGROUND:Traditional algorithms for hidden Markov model decoding seek to maximize either the probability of a state path or the number of positions of a sequence assigned to the correct state. These algorithms provide only a single answer and in practice do not produce good results. RESULTS:We explore an alternative...

journal_title：BMC bioinformatics

authors： Brown DG,Golod D

更新日期：2010-01-18 00:00:00

abstract：BACKGROUND:The cost efficient two-stage design is often used in genome-wide association studies (GWASs) in searching for genetic loci underlying the susceptibility for complex diseases. Replication-based analysis, which considers data from each stage separately, often suffers from loss of efficiency. Joint test that co...

journal_title：BMC bioinformatics

authors： Pan D,Li Q,Jiang N,Liu A,Yu K

更新日期：2011-01-07 00:00:00

abstract：BACKGROUND:Typical evolutionary events like recombination, hybridization or gene transfer make necessary the use of phylogenetic networks to properly depict the evolution of DNA and protein sequences. Although several theoretical classes have been proposed to characterize these networks, they make stringent assumptions...

journal_title：BMC bioinformatics

authors： Arenas M,Patricio M,Posada D,Valiente G

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein f...

journal_title：BMC bioinformatics

authors： Arighi CN,Liu H,Natale DA,Barker WC,Drabkin H,Blake JA,Smith B,Wu CH

更新日期：2009-05-06 00:00:00

abstract：:The RNA polymerase NS5B of Hepatitis C virus (HCV) is a well-characterised drug target with an active site and four allosteric binding sites. This work presents a workflow for virtual screening and its application to Drug Bank screening targeting the Hepatitis C Virus (HCV) RNA polymerase non-nucleoside binding sites....

journal_title：BMC bioinformatics

authors： Elhefnawi M,ElGamacy M,Fares M

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many...

journal_title：BMC bioinformatics

authors： Vainshtein Y,Sanchez M,Brazma A,Hentze MW,Dandekar T,Muckenthaler MU

更新日期：2010-03-01 00:00:00

abstract：BACKGROUND:Estimation of individual ancestry from genetic data is useful for the analysis of disease association studies, understanding human population history and interpreting personal genomic variation. New, computationally efficient methods are needed for ancestry inference that can effectively utilize existing inf...

journal_title：BMC bioinformatics

authors： Bansal V,Libiger O

更新日期：2015-01-16 00:00:00

abstract：BACKGROUND:Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper ...

journal_title：BMC bioinformatics

authors： Varadi M,Guharoy M,Zsolyomi F,Tompa P

更新日期：2015-05-13 00:00:00

abstract：BACKGROUND:Statistical models and methods that associate changes in the physicochemical properties of amino acids with natural selection at the molecular level typically do not take into account the correlations between such properties. We propose a Bayesian hierarchical regression model with a generalization of the Di...

journal_title：BMC bioinformatics

authors： Datta S,Rodriguez A,Prado R

更新日期：2012-10-30 00:00:00

abstract：BACKGROUND:Prognosis is of critical interest in breast cancer research. Biomedical studies suggest that genomic measurements may have independent predictive power for prognosis. Gene profiling studies have been conducted to search for predictive genomic measurements. Genes have the inherent pathway structure, where pat...

journal_title：BMC bioinformatics

authors： Ma S,Kosorok MR

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:Integrative network methods are commonly used for interpretation of high-throughput experimental biological data: transcriptomics, proteomics, metabolomics and others. One of the common approaches is finding a connected subnetwork of a global interaction network that best encompasses significant individual c...

journal_title：BMC bioinformatics

authors： Alexeev N,Isomurodov J,Sukhov V,Korotkevich G,Sergushichev A

更新日期：2020-11-18 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:A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs are identical or very similar between related (or in some cases more distant) species. Howeve...

journal_title：BMC bioinformatics

authors： Guerra-Assunção JA,Enright AJ

更新日期：2010-03-16 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：BACKGROUND:To evaluate statistical methods for genome-wide genetic analyses, one needs to be able to simulate realistic genotypes. We here describe a method, applicable to a broad range of association study designs, that can simulate autosome-wide single-nucleotide polymorphism data with realistic linkage disequilibriu...

journal_title：BMC bioinformatics

authors： Shi M,Umbach DM,Wise AS,Weinberg CR

更新日期：2018-01-02 00:00:00

abstract：BACKGROUND:The central element of each enzyme is the catalytic site, which commonly catalyzes a single biochemical reaction with high specificity. It was unclear to us how often sites that catalyze the same or highly similar reactions evolved on different, i. e. non-homologous protein folds and how similar their 3D pos...

journal_title：BMC bioinformatics

authors： Žváček C,Friedrichs G,Heizinger L,Merkl R

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:Protein-protein docking, which aims to predict the structure of a protein-protein complex from its unbound components, remains an unresolved challenge in structural bioinformatics. An important step is the ranking of docked poses using a scoring function, for which many methods have been developed. There is ...

journal_title：BMC bioinformatics

authors： Moal IH,Torchala M,Bates PA,Fernández-Recio J

更新日期：2013-10-01 00:00:00

abstract：BACKGROUND:Although many of the genic features in Mycobacterium abscessus have been fully validated, a comprehensive understanding of the regulatory elements remains lacking. Moreover, there is little understanding of how the organism regulates its transcriptomic profile, enabling cells to survive in hostile environmen...

journal_title：BMC bioinformatics

authors： Staunton PM,Miranda-CasoLuengo AA,Loftus BJ,Gormley IC

更新日期：2019-09-10 00:00:00

abstract：BACKGROUND:There are a number of different methods for generation of trees and algorithms for phylogenetic analysis in the study of bacterial taxonomy. Genotypic information, such as SSU rRNA gene sequences, now plays a more prominent role in microbial systematics than does phenotypic information. However, the integrat...

journal_title：BMC bioinformatics

authors： Tanaka N,Uchino M,Miyazaki S,Sugawara H

更新日期：2007-08-02 00:00:00

abstract：BACKGROUND:Observed levels of gene expression strongly depend on both activity of DNA binding transcription factors (TFs) and chromatin state through different histone modifications (HMs). In order to recover the functional relationship between local chromatin state, TF binding and observed levels of gene expression, r...

journal_title：BMC bioinformatics

authors： Aflakparast M,Geeven G,de Gunst MCM

更新日期：2020-01-02 00:00:00

abstract：BACKGROUND:The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accurately acquiring the synaptic connectivity, and they cannot effectively alleviate the burden of synaps...

journal_title：BMC bioinformatics

authors： Xiao C,Li W,Deng H,Chen X,Yang Y,Xie Q,Han H

更新日期：2018-07-13 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