Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data.

abstract：BACKGROUND:Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families has become increasingly important. Subfunctionalization via changes in regulatory sequences followi...

journal_title：BMC bioinformatics

authors： Frank RL,Mane A,Ercal F

更新日期：2006-09-06 00:00:00

abstract：BACKGROUND:Protein aggregation is a significant problem in the biopharmaceutical industry (protein drug stability) and is associated medically with over 40 human diseases. Although a number of computational models have been developed for predicting aggregation propensity and identifying aggregation-prone regions in pro...

journal_title：BMC bioinformatics

authors： Fang Y,Gao S,Tai D,Middaugh CR,Fang J

更新日期：2013-10-28 00:00:00

abstract：BACKGROUND:Proteins are comprised of one or several building blocks, known as domains. Such domains can be classified into families according to their evolutionary origin. Whereas sequencing technologies have advanced immensely in recent years, there are no matching computational methodologies for large-scale determina...

journal_title：BMC bioinformatics

authors： Portugaly E,Harel A,Linial N,Linial M

更新日期：2006-06-02 00:00:00

abstract：BACKGROUND:Identification of transcription factors (TFs) responsible for modulation of differentially expressed genes is a key step in deducing gene regulatory pathways. Most current methods identify TFs by searching for presence of DNA binding motifs in the promoter regions of co-regulated genes. However, this strateg...

journal_title：BMC bioinformatics

authors： Roy S,Heinrich K,Phan V,Berry MW,Homayouni R

更新日期：2011-10-18 00:00:00

abstract：BACKGROUND:Transcriptome sequencing is a powerful tool for measuring gene expression, but as well as some other technologies, various artifacts and biases affect the quantification. In order to correct some of them, several normalization approaches have emerged, differing both in the statistical strategy employed and i...

journal_title：BMC bioinformatics

authors： Filloux C,Cédric M,Romain P,Lionel F,Christophe K,Dominique R,Abderrahman M,Daniel P

更新日期：2014-06-14 00:00:00

abstract：BACKGROUND:Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new m...

journal_title：BMC bioinformatics

authors： Karain WI

更新日期：2017-11-28 00:00:00

abstract：BACKGROUND:Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run a...

journal_title：BMC bioinformatics

authors： de Knikker R,Guo Y,Li JL,Kwan AK,Yip KY,Cheung DW,Cheung KH

更新日期：2004-03-10 00:00:00

abstract：BACKGROUND:Modern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functi...

journal_title：BMC bioinformatics

authors： Tchagang AB,Gawronski A,Bérubé H,Phan S,Famili F,Pan Y

更新日期：2010-05-06 00:00:00

abstract：BACKGROUND:Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microarrays does not capture all alternative splicing events. Moreover, for many species genomic data is be...

journal_title：BMC bioinformatics

authors： Sinha R,Hiller M,Pudimat R,Gausmann U,Platzer M,Backofen R

更新日期：2008-11-12 00:00:00

abstract：BACKGROUND:Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the m...

journal_title：BMC bioinformatics

authors： McQuisten KA,Peek AS

更新日期：2007-06-07 00:00:00

abstract：BACKGROUND:Inflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a long series of pathologic events that started years before. The systemic characteristics and relate...

journal_title：BMC bioinformatics

authors： Xiao H,Bartoszek K,Lio' P

更新日期：2018-11-30 00:00:00

abstract：BACKGROUND:Multiple data-analytic methods have been proposed for evaluating gene-expression levels in specific biological pathways, assessing differential expression associated with a binary phenotype. Following Goeman and Bühlmann's recent review, we compared statistical performance of three methods, namely Global Tes...

journal_title：BMC bioinformatics

authors： Liu Q,Dinu I,Adewale AJ,Potter JD,Yasui Y

更新日期：2007-11-07 00:00:00

abstract：BACKGROUND:High throughput sequencing technology provides us unprecedented opportunities to study transcriptome dynamics. Compared to microarray-based gene expression profiling, RNA-Seq has many advantages, such as high resolution, low background, and ability to identify novel transcripts. Moreover, for genes with mult...

journal_title：BMC bioinformatics

authors： Zheng W,Chung LM,Zhao H

更新日期：2011-07-19 00:00:00

abstract：BACKGROUND:Microarray technologies produced large amount of data. The hierarchical clustering is commonly used to identify clusters of co-expressed genes. However, microarray datasets often contain missing values (MVs) representing a major drawback for the use of the clustering methods. Usually the MVs are not treated,...

journal_title：BMC bioinformatics

authors： de Brevern AG,Hazout S,Malpertuy A

更新日期：2004-08-23 00:00:00

abstract：BACKGROUND:Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models requires the distinction between non-specific crystal packing contacts and biologically relevant interactions. This has been investiga...

journal_title：BMC bioinformatics

authors： Zhu H,Domingues FS,Sommer I,Lengauer T

更新日期：2006-01-19 00:00:00

abstract：BACKGROUND:Formal classification of a large collection of protein structures aids the understanding of evolutionary relationships among them. Classifications involving manual steps, such as SCOP and CATH, face the challenge of increasing volume of available structures. Automatic methods such as FSSP or Dali Domain Dict...

journal_title：BMC bioinformatics

authors： Sam V,Tai CH,Garnier J,Gibrat JF,Lee B,Munson PJ

更新日期：2008-01-31 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:Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of ...

journal_title：BMC bioinformatics

authors： Spirito G,Mangoni D,Sanges R,Gustincich S

更新日期：2019-11-22 00:00:00

abstract：BACKGROUND:Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis ...

journal_title：BMC bioinformatics

authors： Yu G

更新日期：2010-10-12 00:00:00

abstract：BACKGROUND:Transcription factor binding sites (TFBSs) are crucial in the regulation of gene transcription. Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used to identify potential regulatory sequences, but the procedure can only map the probable protein-DNA...

journal_title：BMC bioinformatics

authors： Lu CC,Yuan WH,Chen TM

更新日期：2008-12-12 00:00:00

abstract：BACKGROUND:Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introd...

journal_title：BMC bioinformatics

authors： Block A,Debode F,Grohmann L,Hulin J,Taverniers I,Kluga L,Barbau-Piednoir E,Broeders S,Huber I,Van den Bulcke M,Heinze P,Berben G,Busch U,Roosens N,Janssen E,Žel J,Gruden K,Morisset D

更新日期：2013-08-22 00:00:00

abstract：BACKGROUND:S-glutathionylation is the formation of disulfide bonds between the tripeptide glutathione and cysteine residues of the protein, protecting them from irreversible oxidation and in some cases causing change in their functions. Regulatory glutathionylation of proteins is a controllable and reversible process a...

journal_title：BMC bioinformatics

authors： Anashkina AA,Poluektov YM,Dmitriev VA,Kuznetsov EN,Mitkevich VA,Makarov AA,Petrushanko IY

更新日期：2020-09-14 00:00:00

abstract：BACKGROUND:Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations acco...

journal_title：BMC bioinformatics

authors： Lloyd S,Snell QO

更新日期：2011-12-07 00:00:00

abstract：BACKGROUND:The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-rea...

journal_title：BMC bioinformatics

authors： Donaldson I,Martin J,de Bruijn B,Wolting C,Lay V,Tuekam B,Zhang S,Baskin B,Bader GD,Michalickova K,Pawson T,Hogue CW

更新日期：2003-03-27 00:00:00

abstract：BACKGROUND:Biomedical processes can provide essential information about the (mal-) functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Process branch. These processes often need to be described and categorised in terms of their attribute...

journal_title：BMC bioinformatics

authors： Andrade AQ,Blondé W,Hastings J,Schulz S

更新日期：2012-08-28 00:00:00

abstract：BACKGROUND:Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between species and groups of species, and classical matrices such as those in the BLOSUM series fail to ac...

journal_title：BMC bioinformatics

authors： Lemaitre C,Barré A,Citti C,Tardy F,Thiaucourt F,Sirand-Pugnet P,Thébault P

更新日期：2011-11-24 00:00:00

abstract：BACKGROUND:Finishing is the process of improving the quality and utility of draft genome sequences generated by shotgun sequencing and computational assembly. Finishing can involve targeted sequencing. Finishing reads may be incorporated by manual or automated means. One automated method uses targeted addition by local...

journal_title：BMC bioinformatics

authors： Koren S,Miller JR,Walenz BP,Sutton G

更新日期：2010-09-10 00:00:00

abstract：BACKGROUND:Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks of the cell. The available methods to identify functional domain combinations are limited in their scope, e.g. to the identification of combinations falling within individual...

journal_title：BMC bioinformatics

authors： McLaughlin WA,Chen K,Hou T,Wang W

更新日期：2007-10-16 00:00:00

abstract：BACKGROUND:Many Bioinformatics studies begin with a multiple sequence alignment as the foundation for their research. This is because multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence structure relationships. RESULTS:In this paper, we have proposed a Vertical...

journal_title：BMC bioinformatics

authors： Naznin F,Sarker R,Essam D

更新日期：2011-08-25 00:00:00

abstract：BACKGROUND:Melanoma results in the vast majority of skin cancer deaths during the last decades, even though this disease accounts for only one percent of all skin cancers' instances. The survival rates of melanoma from early to terminal stages is more than fifty percent. Therefore, having the right information at the r...

journal_title：BMC bioinformatics

authors： Nasiri S,Helsper J,Jung M,Fathi M

更新日期：2020-03-11 00:00:00