A compartmentalized approach to the assembly of physical maps.

abstract：BACKGROUND:Infectious disease modeling and computational power have evolved such that large-scale agent-based models (ABMs) have become feasible. However, the increasing hardware complexity requires adapted software designs to achieve the full potential of current high-performance workstations. RESULTS:We have found l...

journal_title：BMC bioinformatics

authors： Willem L,Stijven S,Tijskens E,Beutels P,Hens N,Broeckhove J

更新日期：2015-06-02 00:00:00

abstract：BACKGROUND:Normalization in real-time qRT-PCR is necessary to compensate for experimental variation. A popular normalization strategy employs reference gene(s), which may introduce additional variability into normalized expression levels due to innate variation (between tissues, individuals, etc). To minimize this inna...

journal_title：BMC bioinformatics

authors： Chervoneva I,Li Y,Schulz S,Croker S,Wilson C,Waldman SA,Hyslop T

更新日期：2010-05-14 00:00:00

abstract：BACKGROUND:Scientific workflows management systems are increasingly used to specify and manage bioinformatics experiments. Their programming model appeals to bioinformaticians, who can use them to easily specify complex data processing pipelines. Such a model is underpinned by a graph structure, where nodes represent b...

journal_title：BMC bioinformatics

authors： Cohen-Boulakia S,Chen J,Missier P,Goble C,Williams AR,Froidevaux C

更新日期：2014-01-01 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:Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been missing is a single open-source software package to visualize standard tracking output (from software like CellProfiler) in a way that allows conve...

journal_title：BMC bioinformatics

authors： Bray MA,Carpenter AE

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI) network is a particular biological network which...

journal_title：BMC bioinformatics

authors： Turanalp ME,Can T

更新日期：2008-06-11 00:00:00

abstract：BACKGROUND:T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large proportion of the human population. The presence of clusters of promiscuous T-cell epitopes, immunolo...

journal_title：BMC bioinformatics

authors： Zhang GL,Khan AM,Srinivasan KN,Heiny A,Lee K,Kwoh CK,August JT,Brusic V

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the ...

journal_title：BMC bioinformatics

authors： González AJ,Liao L

更新日期：2010-10-29 00:00:00

abstract：BACKGROUND:Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionall...

journal_title：BMC bioinformatics

authors： Weeratunga S,Hu NJ,Simon A,Hofmann A

更新日期：2012-08-14 00:00:00

abstract：BACKGROUND:Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for th...

journal_title：BMC bioinformatics

authors： Vinayagam A,del Val C,Schubert F,Eils R,Glatting KH,Suhai S,König R

更新日期：2006-03-20 00:00:00

abstract：BACKGROUND:Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most bas...

journal_title：BMC bioinformatics

authors： Hoehndorf R,Kelso J,Herre H

更新日期：2009-11-18 00:00:00

abstract：BACKGROUND:The goal of metabolomics analyses is a comprehensive and systematic understanding of all metabolites in biological samples. Many useful platforms have been developed to achieve this goal. Gas chromatography coupled to mass spectrometry (GC/MS) is a well-established analytical method in metabolomics study, an...

journal_title：BMC bioinformatics

authors： Tsugawa H,Tsujimoto Y,Arita M,Bamba T,Fukusaki E

更新日期：2011-05-04 00:00:00

abstract：BACKGROUND:A cross-correlation (XCorr) score function is one of the most popular score functions utilized to search peptide identifications in databases, and many computer programs, such as SEQUEST, Comet, and Tide, currently use this score function. Recently, the HiXCorr algorithm was developed to speed up this score ...

journal_title：BMC bioinformatics

authors： Kim H,Han S,Um JH,Park K

更新日期：2018-12-12 00:00:00

abstract：BACKGROUND:Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major c...

journal_title：BMC bioinformatics

authors： Yue Y,Huang H,Qi Z,Dou HM,Liu XY,Han TF,Chen Y,Song XJ,Zhang YH,Tu J

更新日期：2020-07-28 00:00:00

abstract：BACKGROUND:An approach to molecular classification based on the comparative expression of protein pairs is presented. The method overcomes some of the present limitations in using peptide intensity data for class prediction for problems such as the detection of a disease, disease prognosis, or for predicting treatment ...

journal_title：BMC bioinformatics

authors： Kaur P,Schlatzer D,Cooke K,Chance MR

更新日期：2012-08-07 00:00:00

abstract：BACKGROUND:Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phase...

journal_title：BMC bioinformatics

authors： Verdi KK,Ellis HJ,Gryk MR

更新日期：2007-01-30 00:00:00

abstract：BACKGROUND:Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematica...

journal_title：BMC bioinformatics

authors： Chain B,Bowen H,Hammond J,Posch W,Rasaiyaah J,Tsang J,Noursadeghi M

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:Human triosephosphate isomerase (HsTIM) deficiency is a genetic disease caused often by the pathogenic mutation E104D. This mutation, located at the side of an abnormally large cluster of water in the inter-subunit interface, reduces the thermostability of the enzyme. Why and how these water molecules are di...

journal_title：BMC bioinformatics

authors： Li Z,He Y,Liu Q,Zhao L,Wong L,Kwoh CK,Nguyen H,Li J

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:RNA-seq is a powerful tool for measuring transcriptomes, especially for identifying differentially expressed genes or transcripts (DEGs) between sample groups. A number of methods have been developed for this task, and several evaluation studies have also been reported. However, those evaluations so far have...

journal_title：BMC bioinformatics

authors： Tang M,Sun J,Shimizu K,Kadota K

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for...

journal_title：BMC bioinformatics

authors： Needhamsen M,Ewing E,Lund H,Gomez-Cabrero D,Harris RA,Kular L,Jagodic M

更新日期：2017-11-15 00:00:00

abstract：BACKGROUND:Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics...

journal_title：BMC bioinformatics

authors： Menolascina F,Bellomo D,Maiwald T,Bevilacqua V,Ciminelli C,Paradiso A,Tommasi S

更新日期：2009-10-15 00:00:00

abstract：BACKGROUND:Mammalian germ cells undergo meiosis to produce sperm or eggs, haploid cells that are primed to meet and propagate life. Meiosis is initiated by retinoic acid and meiotic prophase is the first and most complex stage of meiosis when homologous chromosomes pair to exchange genetic information. Errors in meiosi...

journal_title：BMC bioinformatics

authors： Li Y,Ray D,Ye P

更新日期：2013-02-27 00:00:00

abstract：BACKGROUND:Discovering patterns from gene expression levels is regarded as a classification problem when tissue classes of the samples are given and solved as a discrete-data problem by discretizing the expression levels of each gene into intervals maximizing the interdependence between that gene and the class labels. ...

journal_title：BMC bioinformatics

authors： Wu GP,Chan KC,Wong AK

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:We aim to solve the problem of determining word senses for ambiguous biomedical terms with minimal human effort. METHODS:We build a fully automated system for Word Sense Disambiguation by designing a system that does not require manually-constructed external resources or manually-labeled training examples e...

journal_title：BMC bioinformatics

authors： Duan W,Song M,Yates A

更新日期：2009-03-19 00:00:00

abstract：BACKGROUND:Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating ...

journal_title：BMC bioinformatics

authors： Doran AG,Creevey CJ

更新日期：2013-02-08 00:00:00

abstract：BACKGROUND:Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct reprogramming from an original cell to target cell type needs the cell similarity and cell specific regu...

journal_title：BMC bioinformatics

authors： Li L,Che D,Wang X,Zhang P,Rahman SU,Zhao J,Yu J,Tao S,Lu H,Liao M

更新日期：2019-03-04 00:00:00

abstract：BACKGROUND:We present the algorithm PFClust (Parameter Free Clustering), which is able automatically to cluster data and identify a suitable number of clusters to group them into without requiring any parameters to be specified by the user. The algorithm partitions a dataset into a number of clusters that share some co...

journal_title：BMC bioinformatics

authors： Mavridis L,Nath N,Mitchell JB

更新日期：2013-07-03 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:Guanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as "molecular switches" in the second messenger cascades and are found in all organisms between yeast and humans. They form the single, biggest drug-target family due to their versatility of action and...

journal_title：BMC bioinformatics

authors： Sarkar A,Kumar S,Sundar D

更新日期：2011-02-15 00:00:00

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

authors： Yu GX

更新日期：2009-01-30 00:00:00