Identification of exonic regions in DNA sequences using cross-correlation and noise suppression by discrete wavelet transform.

abstract：BACKGROUND:Community structure is ubiquitous in biological networks. There has been an increased interest in unraveling the community structure of biological systems as it may provide important insights into a system's functional components and the impact of local structures on dynamics at a global scale. Choosing an a...

journal_title：BMC bioinformatics

authors： Sah P,Singh LO,Clauset A,Bansal S

更新日期：2014-06-25 00:00:00

abstract：BACKGROUND:The computation of phylogenetic trees on the same set of species that are based on different orthologous genes can lead to incongruent trees. One possible explanation for this behavior are interspecific hybridization events recombining genes of different species. An important approach to analyze such events ...

journal_title：BMC bioinformatics

authors： Albrecht B

更新日期：2015-07-30 00:00:00

abstract：BACKGROUND:Biological resources are essential tools for biomedical research. Their availability is promoted through on-line catalogues. Common Access to Biological Resources and Information (CABRI) is a service for distribution of biological resources and related data collected by 28 European culture collections. Linki...

journal_title：BMC bioinformatics

authors： Romano P,Dawyndt P,Piersigilli F,Swings J

更新日期：2005-12-01 00:00:00

abstract：BACKGROUND:The low success rate and high cost of drug discovery requires the development of new paradigms to identify molecules of therapeutic value. The Anatomical Therapeutic Chemical (ATC) Code System is a World Health Organization (WHO) proposed classification that assigns multi-level codes to compounds based on th...

journal_title：BMC bioinformatics

authors： Olson T,Singh R

更新日期：2017-06-07 00:00:00

abstract：BACKGROUND:Genes occurring co-localized in multiple genomes can be strong indicators for either functional constraints on the genome organization or remnant ancestral gene order. The computational detection of these patterns, which are usually referred to as gene clusters, has become increasingly sensitive over the pas...

journal_title：BMC bioinformatics

authors： Jahn K,Winter S,Stoye J,Böcker S

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interest include simple moti...

journal_title：BMC bioinformatics

authors： Mangalam HJ

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:The challenge of classifying cortical interneurons is yet to be solved. Data-driven classification into established morphological types may provide insight and practical value. RESULTS:We trained models using 217 high-quality morphologies of rat somatosensory neocortex interneurons reconstructed by a single...

journal_title：BMC bioinformatics

authors： Mihaljević B,Larrañaga P,Benavides-Piccione R,Hill S,DeFelipe J,Bielza C

更新日期：2018-12-17 00:00:00

abstract：BACKGROUND:Recent studies have shown that N6-methyladenosine (m6A) plays a critical role in numbers of biological processes and complex human diseases. However, the regulatory mechanisms of most methylation sites remain uncharted. Thus, in-depth study of the epi-transcriptomic patterns of m6A may provide insights into ...

journal_title：BMC bioinformatics

authors： Zhang L,Chen S,Zhu J,Meng J,Liu H

更新日期：2020-10-09 00:00:00

abstract：BACKGROUND:Microarray devices permit a genome-scale evaluation of gene function. This technology has catalyzed biomedical research and development in recent years. As many important diseases can be traced down to the gene level, a long-standing research problem is to identify specific gene expression patterns linking t...

journal_title：BMC bioinformatics

authors： Fu LM,Fu-Liu CS

更新日期：2005-03-22 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) are central to many biological processes. Considering that the experimental methods for identifying PPIs are time-consuming and expensive, it is important to develop automated computational methods to better predict PPIs. Various machine learning methods have been proposed...

journal_title：BMC bioinformatics

authors： Yang F,Fan K,Song D,Lin H

更新日期：2020-07-21 00:00:00

abstract：BACKGROUND:Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq and microarray are two main technologies for profiling gene expression levels. However, considerable discrepancy has been found between DEGs detected using the t...

journal_title：BMC bioinformatics

authors： Lyu Y,Li Q

更新日期：2016-01-11 00:00:00

abstract：BACKGROUND:Knowledge of subcellular localization of proteins is crucial to proteomics, drug target discovery and systems biology since localization and biological function are highly correlated. In recent years, numerous computational prediction methods have been developed. Nevertheless, there is still a need for predi...

journal_title：BMC bioinformatics

authors： Blum T,Briesemeister S,Kohlbacher O

更新日期：2009-09-01 00:00:00

abstract：BACKGROUND:Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data sources for exploiting m...

journal_title：BMC bioinformatics

authors： Mei S,Fei W,Zhou S

更新日期：2011-02-02 00:00:00

abstract：BACKGROUND:A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal gen...

journal_title：BMC bioinformatics

authors： Khan A,Liu Q,Wang K

更新日期：2018-12-28 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：BACKGROUND:The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the simila...

journal_title：BMC bioinformatics

authors： Zhang M,Yang L,Ren J,Ahlgren NA,Fuhrman JA,Sun F

更新日期：2017-03-14 00:00:00

abstract：BACKGROUND:Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. RESULTS:PubFocus w...

journal_title：BMC bioinformatics

authors： Plikus MV,Zhang Z,Chuong CM

更新日期：2006-10-02 00:00:00

abstract：BACKGROUND:Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant data. Shared data science infrastructures like Boag is needed to efficiently process and parse data co...

journal_title：BMC bioinformatics

authors： Bagheri H,Muppirala U,Masonbrink RE,Severin AJ,Rajan H

更新日期：2019-08-22 00:00:00

abstract：BACKGROUND:Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an important first step toward understanding cellular function and machinery of a proteome. Solely deri...

journal_title：BMC bioinformatics

authors： Wu X,Zhu L,Guo J,Fu C,Zhou H,Dong D,Li Z,Zhang DY,Lin K

更新日期：2006-12-18 00:00:00

abstract：BACKGROUND:Protein sequence profile-profile alignment is an important approach to recognizing remote homologs and generating accurate pairwise alignments. It plays an important role in protein sequence database search, protein structure prediction, protein function prediction, and phylogenetic analysis. RESULTS:In thi...

journal_title：BMC bioinformatics

authors： Deng X,Cheng J

更新日期：2014-07-25 00:00:00

abstract：BACKGROUND:Replication origins are considered important sites for understanding the molecular mechanisms involved in DNA replication. Many computational methods have been developed for predicting their locations in archaeal, bacterial and eukaryotic genomes. However, a prediction method designed for a particular kind o...

journal_title：BMC bioinformatics

authors： Chew DS,Leung MY,Choi KP

更新日期：2007-05-21 00:00:00

abstract：BACKGROUND:Detection of periodically expressed genes from microarray data without use of known periodic and non-periodic training examples is an important problem, e.g. for identifying genes regulated by the cell-cycle in poorly characterised organisms. Commonly the investigator is only interested in genes expressed at...

journal_title：BMC bioinformatics

authors： Andersson CR,Isaksson A,Gustafsson MG

更新日期：2006-02-09 00:00:00

abstract：BACKGROUND:Modules of interacting components arranged in specific network topologies have evolved to perform a diverse array of cellular functions. For a network with a constant topological structure, its function within a cell may still be tuned by changing the number of instances of a particular component (e.g., gene...

journal_title：BMC bioinformatics

authors： Shah NA,Sarkar CA

更新日期：2019-05-14 00:00:00

abstract：BACKGROUND:This paper summarises the lessons and experiences gained from a case study of the application of semantic web technologies to the integration of data from the bacterial species Francisella tularensis novicida (Fn). Fn data sources are disparate and heterogeneous, as multiple laboratories across the world, us...

journal_title：BMC bioinformatics

authors： Anwar N,Hunt E

更新日期：2009-10-01 00:00:00

abstract：BACKGROUND:The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×10(84) possible genetic codes. The main question related to the organization of the genetic code is why ...

journal_title：BMC bioinformatics

authors： de Oliveira LL,de Oliveira PS,Tinós R

更新日期：2015-02-19 00:00:00

abstract：BACKGROUND:As whole-genome sequencing is becoming a routine technique, it is important to identify a cost-effective depth of sequencing for such studies. However, the relationship between sequencing depth and biological results from the aspects of whole-genome coverage, variant discovery power and the quality of varian...

journal_title：BMC bioinformatics

authors： Jiang Y,Jiang Y,Wang S,Zhang Q,Ding X

更新日期：2019-11-08 00:00:00

abstract：BACKGROUND:Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcriptome data with pathway based interpretation. Over the years, the amount of omics data has become hu...

journal_title：BMC bioinformatics

authors： Kim I,Choi S,Kim S

更新日期：2018-02-19 00:00:00

abstract：BACKGROUND:In metabolomics experiments, spectral fingerprints of metabolites with no known structural identity are detected routinely. Computer-assisted structure elucidation (CASE) has been used to determine the structural identities of unknown compounds. It is generally accepted that a single 1D NMR spectrum or mass ...

journal_title：BMC bioinformatics

authors： Jayaseelan KV,Steinbeck C

更新日期：2014-07-05 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

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