SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

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

authors： Bertolazzi P,Guerra C,Liuzzi G

更新日期：2010-09-29 00:00:00

abstract：BACKGROUND:Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, t...

journal_title：BMC bioinformatics

authors： Ranjbar MR,Di Poto C,Wang Y,Ressom HW

更新日期：2015-08-19 00:00:00

abstract：BACKGROUND:Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and m...

journal_title：BMC bioinformatics

authors： Rios D,McLaren WM,Chen Y,Birney E,Stabenau A,Flicek P,Cunningham F

更新日期：2010-05-11 00:00:00

abstract：BACKGROUND:Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and metagenomes. However, deep coverage variations in short-read data sets and high sequencing error rates o...

journal_title：BMC bioinformatics

authors： McCorrison JM,Venepally P,Singh I,Fouts DE,Lasken RS,Methé BA

更新日期：2014-11-19 00:00:00

abstract：BACKGROUND:We introduce the decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information (ProCKSI). ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs the Universal Simila...

journal_title：BMC bioinformatics

authors： Barthel D,Hirst JD,Błazewicz J,Burke EK,Krasnogor N

更新日期：2007-10-26 00:00:00

abstract：BACKGROUND:As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective. RESULTS:We reconstruct...

journal_title：BMC bioinformatics

authors： Zhang Y,Li S,Skogerbø G,Zhang Z,Zhu X,Zhang Z,Sun S,Lu H,Shi B,Chen R

更新日期：2006-05-09 00:00:00

abstract：BACKGROUND:Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabolic networks are constructed from the genome sequence of an organism, and the graphs can be used to s...

journal_title：BMC bioinformatics

authors： Weber Zendrera A,Sokolovska N,Soula HA

更新日期：2019-10-15 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:Formal classification of a large collection of protein structures aids the understanding of evolutionary relationships among them. Classifications involving manual steps, such as SCOP and CATH, face the challenge of increasing volume of available structures. Automatic methods such as FSSP or Dali Domain Dict...

journal_title：BMC bioinformatics

authors： Sam V,Tai CH,Garnier J,Gibrat JF,Lee B,Munson PJ

更新日期：2008-01-31 00:00:00

abstract：BACKGROUND:Numerical solutions of the chemical master equation (CME) are important for understanding the stochasticity of biochemical systems. However, solving CMEs is a formidable task. This task is complicated due to the nonlinear nature of the reactions and the size of the networks which result in different realizat...

journal_title：BMC bioinformatics

authors： Kosarwal R,Kulasiri D,Samarasinghe S

更新日期：2020-11-11 00:00:00

abstract：BACKGROUND:Scaffolding is an important step in genome assembly that orders and orients the contigs produced by assemblers. However, repetitive regions in contigs usually prevent scaffolding from producing accurate results. How to solve the problem of repetitive regions has received a great deal of attention. In the pas...

journal_title：BMC bioinformatics

authors： Luo J,Lyu M,Chen R,Zhang X,Luo H,Yan C

更新日期：2019-10-30 00:00:00

abstract：BACKGROUND:Failure on Highly Active Anti-Retroviral Treatment is often accompanied with development of antiviral resistance to one or more drugs included in the treatment. In general, the virus is more likely to develop resistance to drugs with a lower genetic barrier. Previously, we developed a method to reverse engin...

journal_title：BMC bioinformatics

authors： Theys K,Deforche K,Beheydt G,Moreau Y,van Laethem K,Lemey P,Camacho RJ,Rhee SY,Shafer RW,Van Wijngaerden E,Vandamme AM

更新日期：2010-08-03 00:00:00

abstract：BACKGROUND:RNA secondary structure prediction, or folding, is a classic problem in bioinformatics: given a sequence of nucleotides, the aim is to predict the base pairs formed in its three dimensional conformation. The inverse problem of designing a sequence folding into a particular target structure has only more rece...

journal_title：BMC bioinformatics

authors： Lyngsø RB,Anderson JW,Sizikova E,Badugu A,Hyland T,Hein J

更新日期：2012-10-09 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

authors： Borile C,Labarre M,Franz S,Sola C,Refrégier G

更新日期：2011-06-02 00:00:00

abstract：BACKGROUND:While biomedical text mining is emerging as an important research area, practical results have proven difficult to achieve. We believe that an important first step towards more accurate text-mining lies in the ability to identify and characterize text that satisfies various types of information needs. We rep...

journal_title：BMC bioinformatics

authors： Wilbur WJ,Rzhetsky A,Shatkay H

更新日期：2006-07-25 00:00:00

abstract：BACKGROUND:We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so ...

journal_title：BMC bioinformatics

authors： Saunders NF,Brinkworth RI,Huber T,Kemp BE,Kobe B

更新日期：2008-05-26 00:00:00

abstract：BACKGROUND:The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appea...

journal_title：BMC bioinformatics

authors： Tatusov RL,Fedorova ND,Jackson JD,Jacobs AR,Kiryutin B,Koonin EV,Krylov DM,Mazumder R,Mekhedov SL,Nikolskaya AN,Rao BS,Smirnov S,Sverdlov AV,Vasudevan S,Wolf YI,Yin JJ,Natale DA

更新日期：2003-09-11 00:00:00

abstract：BACKGROUND:The efficiency of lymph nodes depends on tissue structure and organization, which allow the coordination of lymphocyte traffic. Despite their essential role, our understanding of lymph node specific mechanisms is still incomplete and currently a topic of intense research. RESULTS:In this paper, we present a...

journal_title：BMC bioinformatics

authors： Baldazzi V,Paci P,Bernaschi M,Castiglione F

更新日期：2009-11-25 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

authors： Chiang JH,Shin JW,Liu HH,Chin CL

更新日期：2006-08-29 00:00:00

abstract：BACKGROUND:This paper presents a novel approach for Generative Anatomy Modeling Language (GAML). This approach automatically detects the geometric partitions in 3D anatomy that in turn speeds up integrated non-linear optimization model in GAML for 3D anatomy modeling with constraints (e.g. joints). This integrated non-...

journal_title：BMC bioinformatics

authors： Demirel D,Cetinsaya B,Halic T,Kockara S,Ahmadi S

更新日期：2019-03-14 00:00:00

abstract：BACKGROUND:The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and ass...

journal_title：BMC bioinformatics

authors： Meehan TF,Masci AM,Abdulla A,Cowell LG,Blake JA,Mungall CJ,Diehl AD

更新日期：2011-01-05 00:00:00

abstract：BACKGROUND:Clustering techniques are routinely used in gene expression data analysis to organize the massive data. Clustering techniques arrange a large number of genes or assays into a few clusters while maximizing the intra-cluster similarity and inter-cluster separation. While clustering of genes facilitates learnin...

journal_title：BMC bioinformatics

authors： Jonnalagadda S,Srinivasan R

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Intrinsically Disordered Proteins (IDPs) lack an ordered three-dimensional structure and are enriched in various biological processes. The Molecular Recognition Features (MoRFs) are functional regions within IDPs that undergo a disorder-to-order transition on binding to a partner protein. Identifying MoRFs i...

journal_title：BMC bioinformatics

authors： Sharma R,Kumar S,Tsunoda T,Patil A,Sharma A

更新日期：2016-12-22 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:Under conditions of no strand bias the number of Gs is equal to that of Cs for each DNA strand; similarly, the total number of Ts is equal to that of As. However, within each strand there are considerable local deviations from the A = T and G = C equality. These asymmetries in nucleotide composition have bee...

journal_title：BMC bioinformatics

authors： Thomas JM,Horspool D,Brown G,Tcherepanov V,Upton C

更新日期：2007-01-23 00:00:00

abstract：BACKGROUND:We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, ma...

journal_title：BMC bioinformatics

authors： Cherkasov A,Ho Sui SJ,Brunham RC,Jones SJ

更新日期：2004-07-26 00:00:00

abstract：BACKGROUND:Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results...

journal_title：BMC bioinformatics

authors： Gautier L,Møller M,Friis-Hansen L,Knudsen S

更新日期：2004-08-14 00:00:00

abstract：BACKGROUND:The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cryo-EM data analysis. Template-based particle picking by an objective function using fast local corre...

journal_title：BMC bioinformatics

authors： Wang WL,Yu Z,Castillo-Menendez LR,Sodroski J,Mao Y

更新日期：2019-04-03 00:00:00

abstract：BACKGROUND:Recently, revealing the function of proteins with protein-protein interaction (PPI) networks is regarded as one of important issues in bioinformatics. With the development of experimental methods such as the yeast two-hybrid method, the data of protein interaction have been increasing extremely. Many databas...

journal_title：BMC bioinformatics

authors： Monji H,Koizumi S,Ozaki T,Ohkawa T

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model...

journal_title：BMC bioinformatics

authors： Cobbs G

更新日期：2012-08-16 00:00:00