Graph-representation of oxidative folding pathways.

abstract：BACKGROUND:Amplified fragment length polymorphism (AFLP) is a PCR-based technique that involves restriction of genomic DNA followed by ligation of adaptors to the fragments generated and selective PCR amplification of a subset of these fragments. The amplified fragments are separated on a sequencing gel and visualized ...

journal_title：BMC bioinformatics

authors： Hong Y,Chuah A

更新日期：2003-02-25 00:00:00

abstract：BACKGROUND:Analysis of cellular processes with microscopic bright field defocused imaging has the advantage of low phototoxicity and minimal sample preparation. However bright field images lack the contrast and nuclei reporting available with florescent approaches and therefore present a challenge to methods that segme...

journal_title：BMC bioinformatics

authors： Mohamadlou H,Shope JC,Flann NS

更新日期：2014-01-30 00:00:00

abstract：BACKGROUND:REX1 and REX2 are protein components of the RNA editing complex (the editosome) and function as exouridylylases. The exact roles of REX1 and REX2 in the editosome are unclear and the consequences of the presence of two related proteins are not fully understood. Here, a variety of computational studies were p...

journal_title：BMC bioinformatics

authors： Mian IS,Worthey EA,Salavati R

更新日期：2006-06-16 00:00:00

abstract：BACKGROUND:Protein-protein interactions play a key role in biological processes of proteins within a cell. Recent high-throughput techniques have generated protein-protein interaction data in a genome-scale. A wide range of computational approaches have been applied to interactome network analysis for uncovering functi...

journal_title：BMC bioinformatics

authors： Cho YR,Zhang A

更新日期：2010-04-29 00:00:00

abstract：BACKGROUND:The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where seq...

journal_title：BMC bioinformatics

authors： Konopka BM,Marciniak M,Dyrka W

更新日期：2017-07-17 00:00:00

abstract：BACKGROUND:Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like ...

journal_title：BMC bioinformatics

authors： Stoma S,Fröhlich M,Gerber S,Klipp E

更新日期：2011-04-28 00:00:00

abstract：BACKGROUND:Polymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence of aberrant splicing causing Mendelian diseases, the implication of such events in multi-genic disorders is yet to be well understood. We...

journal_title：BMC bioinformatics

authors： Churbanov A,Vorechovský I,Hicks C

更新日期：2010-01-12 00:00:00

abstract：BACKGROUND:The human immunodeficiency virus type 1 (HIV-1) aspartic protease is an important enzyme owing to its imperative part in viral development and a causative agent of deadliest disease known as acquired immune deficiency syndrome (AIDS). Development of HIV-1 protease inhibitors can help understand the specifici...

journal_title：BMC bioinformatics

authors： Singh O,Su EC

更新日期：2016-12-23 00:00:00

abstract：BACKGROUND:Severity gradation of missense mutations is a big challenge for exome annotation. Predictors of deleteriousness that are most frequently used to filter variants found by next generation sequencing, produce qualitative predictions, but also numerical scores. It has never been tested if these scores correlate ...

journal_title：BMC bioinformatics

authors： Cimmaruta C,Citro V,Andreotti G,Liguori L,Cubellis MV,Hay Mele B

更新日期：2018-11-30 00:00:00

abstract：BACKGROUND:Recently, measuring phenotype similarity began to play an important role in disease diagnosis. Researchers have begun to pay attention to develop phenotype similarity measurement. However, existing methods ignore the interactions between phenotype-associated proteins, which may lead to inaccurate phenotype s...

journal_title：BMC bioinformatics

authors： Peng J,Hui W,Shang X

更新日期：2018-04-11 00:00:00

abstract：BACKGROUND:The challenge of classifying cortical interneurons is yet to be solved. Data-driven classification into established morphological types may provide insight and practical value. RESULTS:We trained models using 217 high-quality morphologies of rat somatosensory neocortex interneurons reconstructed by a single...

journal_title：BMC bioinformatics

authors： Mihaljević B,Larrañaga P,Benavides-Piccione R,Hill S,DeFelipe J,Bielza C

更新日期：2018-12-17 00:00:00

abstract：BACKGROUND:Scaffolding is an important step in genome assembly that orders and orients the contigs produced by assemblers. However, repetitive regions in contigs usually prevent scaffolding from producing accurate results. How to solve the problem of repetitive regions has received a great deal of attention. In the pas...

journal_title：BMC bioinformatics

authors： Luo J,Lyu M,Chen R,Zhang X,Luo H,Yan C

更新日期：2019-10-30 00:00:00

abstract：BACKGROUND:There are a number of different methods for generation of trees and algorithms for phylogenetic analysis in the study of bacterial taxonomy. Genotypic information, such as SSU rRNA gene sequences, now plays a more prominent role in microbial systematics than does phenotypic information. However, the integrat...

journal_title：BMC bioinformatics

authors： Tanaka N,Uchino M,Miyazaki S,Sugawara H

更新日期：2007-08-02 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:Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as p...

journal_title：BMC bioinformatics

authors： Nagar A,Hahsler M

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. RESULTS:We developed a...

journal_title：BMC bioinformatics

authors： Condon DE,Tran PV,Lien YC,Schug J,Georgieff MK,Simmons RA,Won KJ

更新日期：2018-02-05 00:00:00

abstract：BACKGROUND:Protein structure comparison is a fundamental task in structural biology. While the number of known protein structures has grown rapidly over the last decade, searching a large database of protein structures is still relatively slow using existing methods. There is a need for new techniques which can rapidly...

journal_title：BMC bioinformatics

authors： Zhang L,Bailey J,Konagurthu AS,Ramamohanarao K

更新日期：2010-01-18 00:00:00

abstract：BACKGROUND:Novel sequence motifs detection is becoming increasingly essential in computational biology. However, the high computational cost greatly constrains the efficiency of most motif discovery algorithms. RESULTS:In this paper, we accelerate MEME algorithm targeted on Intel Many Integrated Core (MIC) Architectur...

journal_title：BMC bioinformatics

authors： Peng S,Cheng M,Huang K,Cui Y,Zhang Z,Guo R,Zhang X,Yang S,Liao X,Lu Y,Zou Q,Shi B

更新日期：2018-08-13 00:00:00

abstract：BACKGROUND:During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dC...

journal_title：BMC bioinformatics

authors： Li C

更新日期：2008-05-08 00:00:00

abstract：BACKGROUND:Somatic copy number alternation (SCNA) is a common feature of the cancer genome and is associated with cancer etiology and prognosis. The allele-specific SCNA analysis of a tumor sample aims to identify the allele-specific copy numbers of both alleles, adjusting for the ploidy and the tumor purity. Next gene...

journal_title：BMC bioinformatics

authors： Choo-Wosoba H,Albert PS,Zhu B

更新日期：2018-11-14 00:00:00

abstract：BACKGROUND:The NTF2-like superfamily is a versatile group of protein domains sharing a common fold. The sequences of these domains are very diverse and they share no common sequence motif. These domains serve a range of different functions within the proteins in which they are found, including both catalytic and non-ca...

journal_title：BMC bioinformatics

authors： Eberhardt RY,Chang Y,Bateman A,Murzin AG,Axelrod HL,Hwang WC,Aravind L

更新日期：2013-11-19 00:00:00

abstract：BACKGROUND:The most common method of identifying groups of functionally related genes in microarray data is to apply a clustering algorithm. However, it is impossible to determine which clustering algorithm is most appropriate to apply, and it is difficult to verify the results of any algorithm due to the lack of a gol...

journal_title：BMC bioinformatics

authors： Hibbs MA,Dirksen NC,Li K,Troyanskaya OG

更新日期：2005-05-12 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:Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput sequencing technologies, new protein sequences are becoming available at an extraordinary rate. The ra...

journal_title：BMC bioinformatics

authors： Abnousi A,Broschat SL,Kalyanaraman A

更新日期：2018-03-05 00:00:00

abstract：BACKGROUND:In the last decade, there have been many applications of formal language theory in bioinformatics such as RNA structure prediction and detection of patterns in DNA. However, in the field of proteomics, the size of the protein alphabet and the complexity of relationship between amino acids have mainly limited...

journal_title：BMC bioinformatics

authors： Dyrka W,Nebel JC

更新日期：2009-10-08 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: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: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

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:With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other...

journal_title：BMC bioinformatics

authors： Bergmann FT,Adams R,Moodie S,Cooper J,Glont M,Golebiewski M,Hucka M,Laibe C,Miller AK,Nickerson DP,Olivier BG,Rodriguez N,Sauro HM,Scharm M,Soiland-Reyes S,Waltemath D,Yvon F,Le Novère N

更新日期：2014-12-14 00:00:00