SLDR: a computational technique to identify novel genetic regulatory relationships.

abstract：BACKGROUND:In the last decade, a significant improvement in detecting remote similarity between protein sequences has been made by utilizing alignment profiles in place of amino-acid strings. Unfortunately, no analytical theory is available for estimating the significance of a gapped alignment of two profiles. Many exp...

journal_title：BMC bioinformatics

authors： Poleksic A

更新日期：2009-04-20 00:00:00

abstract：BACKGROUND:The identification of genes responsible for human inherited diseases is one of the most challenging tasks in human genetics. Recent studies based on phenotype similarity and gene proximity have demonstrated great success in prioritizing candidate genes for human diseases. However, most of these methods rely ...

journal_title：BMC bioinformatics

authors： Zhang W,Sun F,Jiang R

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository has been used extensively to characterize changes in gene expression between biological samples, but h...

journal_title：BMC bioinformatics

authors： Robinson TJ,Dinan MA,Dewhirst M,Garcia-Blanco MA,Pearson JL

更新日期：2010-02-25 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: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:Knowing the subcellular location of proteins provides clues to their function as well as the interconnectivity of biological processes. Dozens of tools are available for predicting protein location in the eukaryotic cell. Each tool performs well on certain data sets, but their predictions often disagree for ...

journal_title：BMC bioinformatics

authors： Shen YQ,Burger G

更新日期：2007-10-29 00:00:00

abstract：BACKGROUND:Gene expression microarray experiments are expensive to conduct and guidelines for acceptable quality control at intermediate steps before and after the samples are hybridised to chips are vague. We conducted an experiment hybridising RNA from human brain to 117 U133A Affymetrix GeneChips and used these data...

journal_title：BMC bioinformatics

authors： Jones L,Goldstein DR,Hughes G,Strand AD,Collin F,Dunnett SB,Kooperberg C,Aragaki A,Olson JM,Augood SJ,Faull RL,Luthi-Carter R,Moskvina V,Hodges AK

更新日期：2006-04-19 00:00:00

abstract：BACKGROUND:Genes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental processes. Transcription factors control the expression of their downstream target genes by interacting ...

journal_title：BMC bioinformatics

authors： Wang K,Nishida H

更新日期：2015-04-10 00:00:00

abstract：BACKGROUND:In many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported. However, no quantitative attempt has been made to compare the diversity levels among different genomes. Here, we introduce a mean dissimilarity-based index (Dmean) for quantifying the level of diversity in synon...

journal_title：BMC bioinformatics

authors： Suzuki H,Saito R,Tomita M

更新日期：2009-06-01 00:00:00

abstract：BACKGROUND:The detection of genomic copy number alterations (CNA) in cancer based on SNP arrays requires methods that take into account tumour specific factors such as normal cell contamination and tumour heterogeneity. A number of tools have been recently developed but their performance needs yet to be thoroughly asse...

journal_title：BMC bioinformatics

authors： Mosén-Ansorena D,Aransay AM,Rodríguez-Ezpeleta N

更新日期：2012-08-07 00:00:00

abstract：BACKGROUND:The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common tar...

journal_title：BMC bioinformatics

authors： Hanzlik RP,Koen YM,Theertham B,Dong Y,Fang J

更新日期：2007-03-16 00:00:00

abstract：BACKGROUND:Genome and metagenome studies have identified thousands of protein families whose functions are poorly understood and for which techniques for functional characterization provide only partial information. For such proteins, the genome context can give further information about their functional context. RESU...

journal_title：BMC bioinformatics

authors： Konietzny SG,Dietz L,McHardy AC

更新日期：2011-05-09 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:Bioinformatics software quality assurance is essential in genomic medicine. Systematic verification and validation of bioinformatics software is difficult because it is often not possible to obtain a realistic "gold standard" for systematic evaluation. Here we apply a technique that originates from the softw...

journal_title：BMC bioinformatics

authors： Giannoulatou E,Park SH,Humphreys DT,Ho JW

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function i...

journal_title：BMC bioinformatics

authors： Bray T,Chan P,Bougouffa S,Greaves R,Doig AJ,Warwicker J

更新日期：2009-11-18 00:00:00

abstract：BACKGROUND:Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, ...

journal_title：BMC bioinformatics

authors： Thakur S,Guttman DS

更新日期：2016-06-30 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 traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootst...

journal_title：BMC bioinformatics

authors： Cai B,Yang X,Tuskan GA,Cheng ZM

更新日期：2011-03-18 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:Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for network enrichment analysis deal only with undirected networks, they can be computationally slow and a...

journal_title：BMC bioinformatics

authors： Signorelli M,Vinciotti V,Wit EC

更新日期：2016-09-05 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:The identification of prognostic genes that can distinguish the prognostic risks of cancer patients remains a significant challenge. Previous works have proven that functional gene sets were more reliable for this task than the gene signature. However, few works have considered the cross-talk among functiona...

journal_title：BMC bioinformatics

authors： Zhou XH,Chu XY,Xue G,Xiong JH,Zhang HY

更新日期：2019-02-18 00:00:00

abstract：BACKGROUND:Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, integrative analysis have been performed by using genomics, transcriptomics, epigenomics, proteomics an...

journal_title：BMC bioinformatics

authors： Zengin T,Önal-Süzek T

更新日期：2020-09-30 00:00:00

abstract：BACKGROUND:Meta-analysis (MA) is widely used to pool genome-wide association studies (GWASes) in order to a) increase the power to detect strong or weak genotype effects or b) as a result verification method. As a consequence of differing SNP panels among genotyping chips, imputation is the method of choice within GWAS...

journal_title：BMC bioinformatics

authors： Meesters C,Leber M,Herold C,Angisch M,Mattheisen M,Drichel D,Lacour A,Becker T

更新日期：2012-09-12 00:00:00

abstract：:Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughp...

journal_title：BMC bioinformatics

authors： Li YF,Radivojac P

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here, we describe a tool wh...

journal_title：BMC bioinformatics

authors： David MP,Lapid CM,Daria VR

更新日期：2008-04-28 00:00:00

abstract：BACKGROUND:Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a 'molecular picture' of the cell state. On the other hand, the genomic responses to a pharmacological or hormonal stimulus are dynamic molecular processes, where t...

journal_title：BMC bioinformatics

authors： Mutarelli M,Cicatiello L,Ferraro L,Grober OM,Ravo M,Facchiano AM,Angelini C,Weisz A

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:Bioluminescent proteins (BLPs) widely exist in many living organisms. As BLPs are featured by the capability of emitting lights, they can be served as biomarkers and easily detected in biomedical research, such as gene expression analysis and signal transduction pathways. Therefore, accurate identification o...

journal_title：BMC bioinformatics

authors： Zhang J,Chai H,Yang G,Ma Z

更新日期：2017-06-05 00:00:00

abstract：BACKGROUND:Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings i...

journal_title：BMC bioinformatics

authors： Camacho C,Coulouris G,Avagyan V,Ma N,Papadopoulos J,Bealer K,Madden TL

更新日期：2009-12-15 00:00:00

abstract：:Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic networks has been considered in the past, the computational complexity of the existing solutions has so far lim...

journal_title：BMC bioinformatics

authors： Ay F,Dang M,Kahveci T

更新日期：2012-03-21 00:00:00