GenNon-h: generating multiple sequence alignments on nonhomogeneous phylogenetic trees.

abstract：BACKGROUND:In two-channel competitive genomic hybridization microarray experiments, the ratio of the two fluorescent signal intensities at each spot on the microarray is commonly used to infer the relative amounts of the test and reference sample DNA levels. This ratio may be influenced by systematic measurement effect...

journal_title：BMC bioinformatics

authors： Khojasteh M,Lam WL,Ward RK,MacAulay C

更新日期：2005-11-18 00:00:00

abstract：BACKGROUND:Continuous enzyme kinetic assays are often used in high-throughput applications, as they allow rapid acquisition of large amounts of kinetic data and increased confidence compared to discontinuous assays. However, data analysis is often rate-limiting in high-throughput enzyme assays, as manual inspection and...

journal_title：BMC bioinformatics

authors： Olp MD,Kalous KS,Smith BC

更新日期：2020-05-14 00:00:00

abstract：BACKGROUND:DNA methylation changes are associated with a wide array of biological processes. Bisulfite conversion of DNA followed by high-throughput sequencing is increasingly being used to assess genome-wide methylation at single-base resolution. The relative slowness of most commonly used aligners for processing such...

journal_title：BMC bioinformatics

authors： Ryan DP,Ehninger D

更新日期：2014-10-18 00:00:00

abstract：BACKGROUND:Supervised learning and many stochastic methods for predicting protein-protein interactions require both negative and positive interactions in the training data set. Unlike positive interactions, negative interactions cannot be readily obtained from interaction data, so these must be generated. In protein-pr...

journal_title：BMC bioinformatics

authors： Kim J,Huang DS,Han K

更新日期：2009-01-30 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:We develop a probabilistic model for combining kernel matrices to predict the function of proteins. It extends previous approaches in that it can handle multiple labels which naturally appear in the context of protein function. RESULTS:Explicit modeling of multilabels significantly improves the capability o...

journal_title：BMC bioinformatics

authors： Roth V,Fischer B

更新日期：2007-05-03 00:00:00

abstract：BACKGROUND:Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error ...

journal_title：BMC bioinformatics

authors： Skums P,Dimitrova Z,Campo DS,Vaughan G,Rossi L,Forbi JC,Yokosawa J,Zelikovsky A,Khudyakov Y

更新日期：2012-06-25 00:00:00

abstract：BACKGROUND:Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene regulatory, and metabolic pathways. Among these, metabolic networks are probably the most studied, as t...

journal_title：BMC bioinformatics

authors： Manipur I,Granata I,Maddalena L,Guarracino MR

更新日期：2020-08-21 00:00:00

abstract：BACKGROUND:Molecular docking is a widely-employed method in structure-based drug design. An essential component of molecular docking programs is a scoring function (SF) that can be used to identify the most stable binding pose of a ligand, when bound to a receptor protein, from among a large set of candidate poses. Des...

journal_title：BMC bioinformatics

authors： Ashtawy HM,Mahapatra NR

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of post-genomic research. We present a novel method called MergeAlign which constructs consensus MSAs fro...

journal_title：BMC bioinformatics

authors： Collingridge PW,Kelly S

更新日期：2012-05-30 00:00:00

abstract：BACKGROUND:SNP genotyping microarrays have revolutionized the study of complex disease. The current range of commercially available genotyping products contain extensive catalogues of low frequency and rare variants. Existing SNP calling algorithms have difficulty dealing with these low frequency variants, as the under...

journal_title：BMC bioinformatics

authors： Liu R,Dai Z,Yeager M,Irizarry RA,Ritchie ME

更新日期：2014-05-23 00:00:00

abstract：BACKGROUND:A professional recognition mechanism is required to encourage expedited publishing of an adequate volume of 'fit-for-use' biodiversity data. As a component of such a recognition mechanism, we propose the development of the Data Usage Index (DUI) to demonstrate to data publishers that their efforts of creatin...

journal_title：BMC bioinformatics

authors： Ingwersen P,Chavan V

更新日期：2011-01-01 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:Over the last few years transcriptome sequencing (RNA-Seq) has almost completely taken over microarrays for high-throughput studies of gene expression. Currently, the most popular use of RNA-Seq is to identify genes which are differentially expressed between two or more conditions. Despite the importance of ...

journal_title：BMC bioinformatics

authors： Rahmatallah Y,Emmert-Streib F,Glazko G

更新日期：2014-12-05 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:The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues. Such periodicity is usually not observed in introns and intergenic regions. If a DNA sequence is d...

journal_title：BMC bioinformatics

authors： Wang L,Stein LD

更新日期：2010-11-08 00:00:00

abstract：BACKGROUND:In addition to single-locus (main) effects of disease variants, there is a growing consensus that gene-gene and gene-environment interactions may play important roles in disease etiology. However, for the very large numbers of genetic markers currently in use, it has proven difficult to develop suitable and ...

journal_title：BMC bioinformatics

authors： Long Q,Zhang Q,Ott J

更新日期：2009-01-30 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：: ...

journal_title：BMC bioinformatics

authors： Wren JD,Doerkson RJ,Toby IT,Nanduri B,Homayouni R,Manda P,Thakkar S

更新日期：2019-03-14 00:00:00

abstract：BACKGROUND:Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal ...

journal_title：BMC bioinformatics

authors： Wu TY,Hsieh CC,Hong JJ,Chen CY,Tsai YS

更新日期：2009-05-27 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: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：: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:Modern plant taxonomy reflects phylogenetic relationships among taxa based on proposed morphological and genetic similarities. However, taxonomical relation is not necessarily reflected by close overall resemblance, but rather by commonality of very specific morphological characters or similarity on the mole...

journal_title：BMC bioinformatics

authors： Seeland M,Rzanny M,Boho D,Wäldchen J,Mäder P

更新日期：2019-01-03 00:00:00

abstract：BACKGROUND:Horizontal gene transfer, i.e. the acquisition of genetic material from nonparent organism, is considered an important force driving species evolution. Many cases of horizontal gene transfer from prokaryotes to eukaryotes have been registered, but no transfer mechanism has been deciphered so far, although vi...

journal_title：BMC bioinformatics

authors： Daugavet MA,Shabelnikov SV,Podgornaya OI

更新日期：2020-07-24 00:00:00

abstract：BACKGROUND:Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area is assigned to each spot and the sum of the pixel intensities in that area, the so-called volume, is ...

journal_title：BMC bioinformatics

authors： Brauner JM,Groemer TW,Stroebel A,Grosse-Holz S,Oberstein T,Wiltfang J,Kornhuber J,Maler JM

更新日期：2014-06-11 00:00:00

abstract：BACKGROUND:Molecular biology (MB) is a dynamic research domain that benefits greatly from the use of modern software technology in preparing experiments, analyzing acquired data, and even performing "in-silico" analyses. As ever new findings change the face of this domain, software for MB has to be sufficiently flexibl...

journal_title：BMC bioinformatics

authors： Busch N,Wedemann G

更新日期：2009-03-27 00:00:00

abstract：BACKGROUND:As a novel cancer diagnostic paradigm, mass spectroscopic serum proteomic pattern diagnostics was reported superior to the conventional serologic cancer biomarkers. However, its clinical use is not fully validated yet. An important factor to prevent this young technology to become a mainstream cancer diagnos...

journal_title：BMC bioinformatics

authors： Han H

更新日期：2010-01-18 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:In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences. As the number of software packages increases, it becomes more important to identify the tools with ...

journal_title：BMC bioinformatics

authors： Quest D,Dempsey K,Shafiullah M,Bastola D,Ali H

更新日期：2008-08-12 00:00:00