An automatic method to calculate heart rate from zebrafish larval cardiac videos.

abstract：BACKGROUND:In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image ac...

journal_title：BMC bioinformatics

authors： Hartmann A,Czauderna T,Hoffmann R,Stein N,Schreiber F

更新日期：2011-05-12 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:Frequent pattern mining analysis applied on microarray dataset appears to be a promising strategy for identifying relationships between gene expression levels. Unfortunately, too many itemsets (co-expressed genes) are identified by this analysis method since it does not consider the importance of each gene w...

journal_title：BMC bioinformatics

authors： Liu YC,Cheng CP,Tseng VS

更新日期：2013-07-21 00:00:00

abstract：BACKGROUND:The distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS). Applied to p...

journal_title：BMC bioinformatics

authors： Pelé J,Bécu JM,Abdi H,Chabbert M

更新日期：2012-06-15 00:00:00

abstract：:Identifying segments in the genome of different individuals that are identical-by-descent (IBD) is a fundamental element of genetics. IBD data is used for numerous applications including demographic inference, heritability estimation, and mapping disease loci. Simultaneous detection of IBD over multiple haplotypes has...

journal_title：BMC bioinformatics

authors： Park DS,Baran Y,Hormozdiari F,Eng C,Torgerson DG,Burchard EG,Zaitlen N

更新日期：2015-01-01 00:00:00

abstract：:Environmental shotgun sequencing (ESS) has potential to give greater insight into microbial communities than targeted sequencing of 16S regions, but requires much higher sequence coverage. The advent of next-generation sequencing has made it feasible for the Human Microbiome Project and other initiatives to generate E...

journal_title：BMC bioinformatics

authors： Ander C,Schulz-Trieglaff OB,Stoye J,Cox AJ

更新日期：2013-01-01 00:00:00

abstract：:DNA methylation exhibits different patterns in different cancers. DNA methylation rates at different genomic loci appear to be highly correlated in some samples but not in others. We call such phenomena conditional concordant relationships (CCRs). In this study, we explored DNA methylation patterns in 12 common cancer...

journal_title：BMC bioinformatics

authors： Qiu P,Zhang L

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public...

journal_title：BMC bioinformatics

authors： Nilsson RH,Kristiansson E,Ryberg M,Larsson KH

更新日期：2005-07-18 00:00:00

abstract：BACKGROUND:Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure compariso...

journal_title：BMC bioinformatics

authors： Veeramalai M,Gilbert D,Valiente G

更新日期：2010-03-17 00:00:00

abstract：BACKGROUND:Metabolome analysis with GC/MS has meanwhile been established as one of the "omics" techniques. Compound identification is done by comparison of the MS data with compound libraries. Mass spectral libraries in the field of metabolomics ought to connect the relevant mass traces of the metabolites to other rele...

journal_title：BMC bioinformatics

authors： Thielen B,Heinen S,Schomburg D

更新日期：2009-07-22 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:In this paper, it is proposed an optimization approach for producing reduced alphabets for peptide classification, using a Genetic Algorithm. The classification task is performed by a multi-classifier system where each classifier (Linear or Radial Basis function Support Vector Machines) is trained using feat...

journal_title：BMC bioinformatics

authors： Nanni L,Lumini A

更新日期：2008-01-24 00:00:00

abstract：BACKGROUND:The importance of biodiversity conservation has been increasing steadily due to its benefits to human beings. Recently, producing and managing biodiversity databases have become much easier because of the information technology (IT) advancement. This made the general public's participation in biodiversity co...

journal_title：BMC bioinformatics

authors： Paik IH,Lim J,Chun BS,Jin SD,Yu JP,Lee JW,Bhak J,Paek WK

更新日期：2009-12-03 00:00:00

abstract：BACKGROUND:Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presen...

journal_title：BMC bioinformatics

authors： Wenskovitch JE Jr,Harris LA,Tapia JJ,Faeder JR,Marai GE

更新日期：2014-09-25 00:00:00

abstract：BACKGROUND:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We d...

journal_title：BMC bioinformatics

authors： Bui VK,Wei C

更新日期：2020-10-20 00:00:00

abstract：BACKGROUND:Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites. Much effort has been devoted to describing known gene transcripts through the development of numerous databases. Nevertheless, owing to the...

journal_title：BMC bioinformatics

authors： de la Grange P,Dutertre M,Correa M,Auboeuf D

更新日期：2007-06-04 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

authors： Chang HC,Chu CP,Lin SJ,Hsiao CK

更新日期：2020-03-12 00:00:00

abstract：BACKGROUND:Innovations in biological and biomedical imaging produce complex high-content and multivariate image data. For decision-making and generation of hypotheses, scientists need novel information technology tools that enable them to visually explore and analyze the data and to discuss and communicate results or f...

journal_title：BMC bioinformatics

authors： Loyek C,Rajpoot NM,Khan M,Nattkemper TW

更新日期：2011-07-21 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

authors： Lawless C,Wilkinson DJ,Young A,Addinall SG,Lydall DA

更新日期：2010-05-28 00:00:00

abstract：:We developed a new computational technique called Step-Level Differential Response (SLDR) to identify genetic regulatory relationships. Our technique takes advantages of functional genomics data for the same species under different perturbation conditions, therefore complementary to current popular computational techn...

journal_title：BMC bioinformatics

authors： Yue Z,Wan P,Huang H,Xie Z,Chen JY

更新日期：2014-01-01 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:In microarray data analysis, factors such as data quality, biological variation, and the increasingly multi-layered nature of more complex biological systems complicates the modelling of regulatory networks that can represent and capture the interactions among genes. We believe that the use of multiple datas...

journal_title：BMC bioinformatics

authors： Anvar SY,'t Hoen PA,Tucker A

更新日期：2010-01-15 00:00:00

abstract：BACKGROUND:The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis by grouping thousands of genes into just several hundred pathways, but also can increase the explanatory power for the experiment by identifying...

journal_title：BMC bioinformatics

authors： Du J,Li M,Yuan Z,Guo M,Song J,Xie X,Chen Y

更新日期：2016-10-06 00:00:00

abstract：BACKGROUND:Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging vari...

journal_title：BMC bioinformatics

authors： Masino AJ,Dechene ET,Dulik MC,Wilkens A,Spinner NB,Krantz ID,Pennington JW,Robinson PN,White PS

更新日期：2014-07-21 00:00:00

abstract：BACKGROUND:Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis methods if meaningful biological conclusions are to be drawn. For example, a range of traditional s...

journal_title：BMC bioinformatics

authors： Ibrahim M,Jassim S,Cawthorne MA,Langlands K

更新日期：2014-11-04 00:00:00

abstract：BACKGROUND:The recent explosion in biological and other real-world network data has created the need for improved tools for large network analyses. In addition to well established global network properties, several new mathematical techniques for analyzing local structural properties of large networks have been develop...

journal_title：BMC bioinformatics

authors： Milenković T,Lai J,Przulj N

更新日期：2008-01-30 00:00:00

abstract：BACKGROUND:Identifying drug-target interaction is a key element in drug discovery. In silico prediction of drug-target interaction can speed up the process of identifying unknown interactions between drugs and target proteins. In recent studies, handcrafted features, similarity metrics and machine learning methods have...

journal_title：BMC bioinformatics

authors： Eslami Manoochehri H,Nourani M

更新日期：2020-07-06 00:00:00

abstract：BACKGROUND:In the analysis of networks we frequently require the statistical significance of some network statistic, such as measures of similarity for the properties of interacting nodes. The structure of the network may introduce dependencies among the nodes and it will in general be necessary to account for these de...

journal_title：BMC bioinformatics

authors： Thorne T,Stumpf MP

更新日期：2007-11-30 00:00:00

abstract：BACKGROUND:Urokinase, its receptor and the integrins are functionally associated and involved in regulation of cell signaling, migration, adhesion and proliferation. No structural information is available on this potential multimolecular complex. However, the tri-dimensional structure of urokinase, urokinase receptor a...

journal_title：BMC bioinformatics

authors： Degryse B,Fernandez-Recio J,Citro V,Blasi F,Cubellis MV

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:Detection of genomic DNA copy number variations (CNVs) can provide a complete and more comprehensive view of human disease. It is interesting to identify and represent relevant CNVs from a genome-wide data due to high data volume and the complexity of interactions. RESULTS:In this paper, we incorporate the ...

journal_title：BMC bioinformatics

authors： Liu Y,Lee YF,Ng MK

更新日期：2011-01-01 00:00:00