Evolutionary Pareto-optimization of stably folding peptides.

abstract：BACKGROUND:A common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biological systems, particularly when these tools offer analysis capabilities. However, most published networ...

journal_title：BMC bioinformatics

authors： Macpherson JI,Pinney JW,Robertson DL

更新日期：2009-03-26 00:00:00

abstract：BACKGROUND:Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoin...

journal_title：BMC bioinformatics

authors： Pluskal T,Castillo S,Villar-Briones A,Oresic M

更新日期：2010-07-23 00:00:00

abstract：BACKGROUND:Over the last two decades, an innovative technology called Tissue Microarray (TMA), which combines multi-tissue and DNA microarray concepts, has been widely used in the field of histology. It consists of a collection of several (up to 1000 or more) tissue samples that are assembled onto a single support - ty...

journal_title：BMC bioinformatics

authors： Nguyen HN,Paveau V,Cauchois C,Kervrann C

更新日期：2018-04-19 00:00:00

abstract：BACKGROUND:We investigate the relationships between the EC (Enzyme Commission) class, the associated chemical reaction, and the reaction mechanism by building predictive models using Support Vector Machine (SVM), Random Forest (RF) and k-Nearest Neighbours (kNN). We consider two ways of encoding the reaction mechanism ...

journal_title：BMC bioinformatics

authors： Nath N,Mitchell JB

更新日期：2012-04-24 00:00:00

abstract：BACKGROUND:RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence o...

journal_title：BMC bioinformatics

authors： Li B,Dewey CN

更新日期：2011-08-04 00:00:00

abstract：BACKGROUND:The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been im...

journal_title：BMC bioinformatics

authors： Podell S,Gaasterland T,Allen EE

更新日期：2008-10-07 00:00:00

abstract：BACKGROUND:Orthologs inference is the starting point of most comparative genomics studies, and a plethora of methods have been designed in the last decade to address this challenging task. In this paper we focus on the problems of deciding consistency with a species tree (known or not) of a partial set of orthology/par...

journal_title：BMC bioinformatics

authors： Jones M,Paul C,Scornavacca C

更新日期：2016-11-11 00:00:00

abstract：BACKGROUND:We introduce Approximate Entropy as a mathematical method of analysis for microarray data. Approximate entropy is applied here as a method to classify the complex gene expression patterns resultant of a clinical sample set. Since Entropy is a measure of disorder in a system, we believe that by choosing genes...

journal_title：BMC bioinformatics

authors： Botting SK,Trzeciakowski JP,Benoit MF,Salama SA,Diaz-Arrastia CR

更新日期：2009-02-20 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：BACKGROUND:Tumors have been hypothesized to be the result of a mixture of oncogenic events, some of which will be reflected in the gene expression of the tumor. Based on this hypothesis a variety of data-driven methods have been employed to decompose tumor expression profiles into component profiles, hypothetically lin...

journal_title：BMC bioinformatics

authors： van Vliet MH,Wessels LF,Reinders MJ

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Pre-processing methods for two-sample long oligonucleotide arrays, specifically the Agilent technology, have not been extensively studied. The goal of this study is to quantify some of the sources of error that affect measurement of expression using Agilent arrays and to compare Agilent's Feature Extraction ...

journal_title：BMC bioinformatics

authors： Zahurak M,Parmigiani G,Yu W,Scharpf RB,Berman D,Schaeffer E,Shabbeer S,Cope L

更新日期：2007-05-01 00:00:00

abstract：BACKGROUND:Gene expression data can be analyzed by summarizing groups of individual gene expression profiles based on GO annotation information. The mean expression profile per group can then be used to identify interesting GO categories in relation to the experimental settings. However, the expression profiles present...

journal_title：BMC bioinformatics

authors： De Haan JR,Piek E,van Schaik RC,de Vlieg J,Bauerschmidt S,Buydens LM,Wehrens R

更新日期：2010-03-26 00:00:00

abstract：BACKGROUND:The identification of protein coding regions (exons) in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing. In this paper, a new method is presented for the identification of exonic regions in DNA sequences. This method is based on th...

journal_title：BMC bioinformatics

authors： Abbasi O,Rostami A,Karimian G

更新日期：2011-11-03 00:00:00

abstract：BACKGROUND:Current network-based microarray analysis uses the information of interactions among concerned genes/gene products, but still considers each gene expression individually. We propose an organized knowledge-supervised approach - Integrative eXpression Profiling (IXP), to improve microarray classification accur...

journal_title：BMC bioinformatics

authors： Wu X,Huang H,Sonachalam M,Reinhard S,Shen J,Pandey R,Chen JY

更新日期：2012-03-13 00:00:00

abstract：BACKGROUND:The developments of high-throughput genotyping technologies, which enable the simultaneous genotyping of hundreds of thousands of single nucleotide polymorphisms (SNP) have the potential to increase the benefits of genetic epidemiology studies. Although the enhanced resolution of these platforms increases th...

journal_title：BMC bioinformatics

authors： Chai HS,Sicotte H,Bailey KR,Turner ST,Asmann YW,Kocher JP

更新日期：2009-04-03 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:Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inferen...

journal_title：BMC bioinformatics

authors： Lu G,Jiang L,Helikar RM,Rowley TW,Zhang L,Chen X,Moriyama EN

更新日期：2006-12-12 00:00:00

abstract：BACKGROUND:High-throughput methods can directly detect the set of interacting proteins in model species but the results are often incomplete and exhibit high false positive and false negative rates. A number of researchers have recently presented methods for integrating direct and indirect data for predicting interacti...

journal_title：BMC bioinformatics

authors： Qi Y,Klein-Seetharaman J,Bar-Joseph Z

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. RESULTS:We present a data structure called a history graph that offers a practical ba...

journal_title：BMC bioinformatics

authors： Paten B,Zerbino DR,Hickey G,Haussler D

更新日期：2014-06-19 00:00:00

abstract：:Selected reaction monitoring (SRM)-based proteomics approaches enable highly sensitive and reproducible assays for profiling of thousands of peptides in one experiment. The development of such assays involves the determination of retention time, detectability and fragmentation properties of peptides, followed by an op...

journal_title：BMC bioinformatics

authors： Nahnsen S,Kohlbacher O

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entiti...

journal_title：BMC bioinformatics

authors： Henriques R,Ferreira FL,Madeira SC

更新日期：2017-02-02 00:00:00

abstract：BACKGROUND:Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional natur...

journal_title：BMC bioinformatics

authors： Arakawa K,Tamaki S,Kono N,Kido N,Ikegami K,Ogawa R,Tomita M

更新日期：2009-01-23 00:00:00

abstract：BACKGROUND:Circular RNAs (circRNAs) are a newly appreciated class of non-coding RNA molecules. Numerous tools have been developed for the detection of circRNAs, however computational tools to perform downstream functional analysis of circRNAs are scarce. RESULTS:We present circRNAprofiler, an R-based computational fra...

journal_title：BMC bioinformatics

authors： Aufiero S,Reckman YJ,Tijsen AJ,Pinto YM,Creemers EE

更新日期：2020-04-29 00:00:00

abstract：BACKGROUND:The central element of each enzyme is the catalytic site, which commonly catalyzes a single biochemical reaction with high specificity. It was unclear to us how often sites that catalyze the same or highly similar reactions evolved on different, i. e. non-homologous protein folds and how similar their 3D pos...

journal_title：BMC bioinformatics

authors： Žváček C,Friedrichs G,Heizinger L,Merkl R

更新日期：2015-11-04 00:00:00

abstract：:Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these ca...

journal_title：BMC bioinformatics

authors： Schlitt T,Brazma A

更新日期：2007-09-27 00:00:00

abstract：BACKGROUND:Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mec...

journal_title：BMC bioinformatics

authors： Rousseau M,Fraser J,Ferraiuolo MA,Dostie J,Blanchette M

更新日期：2011-10-25 00:00:00

abstract：BACKGROUND:The analysis of mass spectra suggests that the existence of derivative peaks is strongly dependent on the intensity of the primary peaks. Peak selection from tandem mass spectrum is used to filter out noise and contaminant peaks. It is widely accepted that a valid primary peak tends to have high intensity an...

journal_title：BMC bioinformatics

authors： Zhang S,Wang Y,Bu D,Zhang H,Sun S

更新日期：2011-08-17 00:00:00

abstract：BACKGROUND:Lung adenocarcinoma is the most common type of lung cancer, with high mortality worldwide. Its occurrence and development were thoroughly studied by high-throughput expression microarray, which produced abundant data on gene expression, DNA methylation, and miRNA quantification. However, the hub genes, which...

journal_title：BMC bioinformatics

authors： Fan X,Wang Y,Tang XQ

更新日期：2019-05-01 00:00:00

abstract：BACKGROUND:Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA fragments. Although typically used in small RNA sequencing, adapter trimming is also used widely in other applications, such as genome DNA sequencing and transcriptome...

journal_title：BMC bioinformatics

authors： Jiang H,Lei R,Ding SW,Zhu S

更新日期：2014-06-12 00:00:00

abstract：BACKGROUND:Protein-protein docking, which aims to predict the structure of a protein-protein complex from its unbound components, remains an unresolved challenge in structural bioinformatics. An important step is the ranking of docked poses using a scoring function, for which many methods have been developed. There is ...

journal_title：BMC bioinformatics

authors： Moal IH,Torchala M,Bates PA,Fernández-Recio J

更新日期：2013-10-01 00:00:00