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 throughput genomic sequencing both provide rapid, robust, and comprehensive methods to identify CNVs on a whole-genome scale. RESULTS:We developed a Bayesian statistical analysis algorithm for the detection of CNVs from both types of genomic data. The algorithm can analyze such data obtained from PCR-based bacterial artificial chromosome arrays, high-density oligonucleotide arrays, and more recently developed high-throughput DNA sequencing. Treating parameters--e.g., the number of CNVs, the position of each CNV, and the data noise level--that define the underlying data generating process as random variables, our approach derives the posterior distribution of the genomic CNV structure given the observed data. Sampling from the posterior distribution using a Markov chain Monte Carlo method, we get not only best estimates for these unknown parameters but also Bayesian credible intervals for the estimates. We illustrate the characteristics of our algorithm by applying it to both synthetic and experimental data sets in comparison to other segmentation algorithms. CONCLUSIONS:In particular, the synthetic data comparison shows that our method is more sensitive than other approaches at low false positive rates. Furthermore, given its Bayesian origin, our method can also be seen as a technique to refine CNVs identified by fast point-estimate methods and also as a framework to integrate array-CGH and sequencing data with other CNV-related biological knowledge, all through informative priors.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Zhang ZD,Gerstein MBdoi
10.1186/1471-2105-11-539subject
Has Abstractpub_date
2010-10-31 00:00:00pages
539issn
1471-2105pii
1471-2105-11-539journal_volume
11pub_type
杂志文章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
pub_type： 杂志文章
doi：10.1186/1471-2105-10-S1-S3
更新日期：2009-01-30 00:00:00
abstract：BACKGROUND:The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to a...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-5-76
更新日期：2004-06-09 00:00:00
abstract：BACKGROUND:Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain datab...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-4-16
更新日期：2003-05-06 00:00:00
abstract：BACKGROUND:FREGENE simulates sequence-level data over large genomic regions in large populations. Because, unlike coalescent simulators, it works forwards through time, it allows complex scenarios of selection, demography, and recombination to be modelled simultaneously. Detailed tracking of sites under selection is im...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-364
更新日期：2008-09-08 00:00:00
abstract：BACKGROUND:The imputation of genotypes increases the power of genome-wide association studies. However, the imputation quality should be assessed in each particular case. Nevertheless, not all imputation softwares control the error of output, e.g., the last release of fastPHASE program (1.4.8) lacks such an option. In ...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-020-03589-0
更新日期：2020-07-24 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
pub_type： 杂志文章
doi：10.1186/s12859-020-03654-8
更新日期：2020-07-29 00:00:00
abstract：BACKGROUND:Affymetrix microarrays are used by many laboratories to generate gene expression profiles. Generally, only large differences (> 1.7-fold) between conditions have been reported. Computational methods to reduce inter-array variability might be of value when attempting to detect smaller differences. We examined...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-3-23
更新日期：2002-08-30 00:00:00
abstract：BACKGROUND:Abundant information about gene products is stored in online searchable databases such as annotation or literature. To efficiently obtain and digest such information, there is a pressing need for automated information-summarization and functional-similarity clustering of genes. RESULTS:We have developed a n...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-7-392
更新日期：2006-08-29 00:00:00
abstract：BACKGROUND:Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objectiv...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-4-51
更新日期：2003-10-28 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
pub_type： 杂志文章
doi：10.1186/1471-2105-11-268
更新日期：2010-05-20 00:00:00
abstract：BACKGROUND:Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-019-3293-4
更新日期：2019-12-27 00:00:00
abstract：BACKGROUND:Scaffold proteins are known for being crucial regulators of various cellular functions by assembling multiple proteins involved in signaling and metabolic pathways. Identification of scaffold proteins and the study of their molecular mechanisms can open a new aspect of cellular systemic regulation and the re...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-016-1079-5
更新日期：2016-07-28 00:00:00
abstract：:After publication of this supplement article. ...
journal_title：BMC bioinformatics
pub_type： 已发布勘误
doi：10.1186/s12859-019-2776-7
更新日期：2019-05-15 00:00:00
abstract：BACKGROUND:Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations fo...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-018-2073-x
更新日期：2018-05-08 00:00:00
abstract：BACKGROUND:Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures. RESULTS:MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic ma...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-014-0394-y
更新日期：2014-12-14 00:00:00
abstract：BACKGROUND:Gene expression measurements from breast cancer (BrCa) tumors are established clinical predictive tools to identify tumor subtypes, identify patients showing poor/good prognosis, and identify patients likely to have disease recurrence. However, diverse breast cancer datasets in conjunction with diagnostic cl...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-63
更新日期：2008-01-28 00:00:00
abstract：BACKGROUND:Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptio...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-7-439
更新日期：2006-10-10 00:00:00
abstract：BACKGROUND:To identify and prioritize the influential hub genes in a gene-set or biological pathway, most analyses rely on calculation of marginal effects or tests of statistical significance. These procedures may be inappropriate since hub nodes are common connection points and therefore may interact with other nodes ...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-020-3444-7
更新日期：2020-03-12 00:00:00
abstract：BACKGROUND:Sparse principal component analysis (PCA) is a popular tool for dimensionality reduction, pattern recognition, and visualization of high dimensional data. It has been recognized that complex biological mechanisms occur through concerted relationships of multiple genes working in networks that are often repre...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-017-1740-7
更新日期：2017-07-11 00:00:00
abstract：BACKGROUND:A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for ...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-11-488
更新日期：2010-09-29 00:00:00
abstract：BACKGROUND:Classification and naming is a key step in the analysis, understanding and adequate management of living organisms. However, where to set limits between groups can be puzzling especially in clonal organisms. Within the Mycobacterium tuberculosis complex (MTC), the etiological agent of tuberculosis (TB), expe...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-12-224
更新日期：2011-06-02 00:00:00
abstract：BACKGROUND:Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs oft...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-8-102
更新日期：2007-03-26 00:00:00
abstract：BACKGROUND:Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understanding the differences in drug response. In this regard, it is of particular interest to study the effect...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-10-S8-S6
更新日期：2009-08-27 00:00:00
abstract：BACKGROUND:The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae trnL-F sequences and compare them with 533 previously determined sequences. It is supplied with input files design...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-5-173
更新日期：2004-10-29 00:00:00
abstract：BACKGROUND:One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PTMs) that occur in the PPIR can either interfere with or facilitate the interaction between proteins....
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-016-1165-8
更新日期：2016-08-17 00:00:00
abstract：BACKGROUND:New "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioi...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-11-100
更新日期：2010-02-22 00:00:00
abstract：:We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists work...
journal_title：BMC bioinformatics
pub_type：
doi：10.1186/1471-2105-9-S1-S1
更新日期：2008-01-01 00:00:00
abstract：BACKGROUND:High-throughput screens comparing growth rates of arrays of distinct micro-organism cultures on solid agar are useful, rapid methods of quantifying genetic interactions. Growth rate is an informative phenotype which can be estimated by measuring cell densities at one or more times after inoculation. Precise ...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-11-287
更新日期：2010-05-28 00:00:00
abstract：BACKGROUND:X-converting enzyme (XCE) involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it's well characterized homologue endothelin-converting enzyme-1 (ECE-1) showed broad substrate specificity and acts as ...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-13-285
更新日期：2012-11-01 00:00:00
abstract：BACKGROUND:Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression tra...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-014-0421-z
更新日期：2015-01-16 00:00:00
