Identifying metabolic enzymes with multiple types of association evidence.

abstract：BACKGROUND:Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carboh...

journal_title：BMC bioinformatics

authors： Ranzinger R,Herget S,Wetter T,von der Lieth CW

更新日期：2008-09-19 00:00:00

abstract：BACKGROUND:Protein structure prediction has achieved a lot of progress during the last few decades and a greater number of models for a certain sequence can be predicted. Consequently, assessing the qualities of predicted protein models in perspective is one of the key components of successful protein structure predict...

journal_title：BMC bioinformatics

authors： Jing X,Dong Q

更新日期：2017-05-25 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:The low success rate and high cost of drug discovery requires the development of new paradigms to identify molecules of therapeutic value. The Anatomical Therapeutic Chemical (ATC) Code System is a World Health Organization (WHO) proposed classification that assigns multi-level codes to compounds based on th...

journal_title：BMC bioinformatics

authors： Olson T,Singh R

更新日期：2017-06-07 00:00:00

abstract：BACKGROUND:The use of classification algorithms is becoming increasingly important for the field of computational biology. However, not only the quality of the classification, but also its biological interpretation is important. This interpretation may be eased if interacting elements can be identified and visualized, ...

journal_title：BMC bioinformatics

authors： Bornelöv S,Marillet S,Komorowski J

更新日期：2014-05-12 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:A major goal of the analysis of high-dimensional RNA expression data from tumor tissue is to identify prognostic signatures for discriminating patient subgroups. For this purpose genome-wide identification of bimodally expressed genes from gene array data is relevant because distinguishability of high and lo...

journal_title：BMC bioinformatics

authors： Hellwig B,Hengstler JG,Schmidt M,Gehrmann MC,Schormann W,Rahnenführer J

更新日期：2010-05-25 00:00:00

abstract：BACKGROUND:Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment. Former benchmark studies revealed drawbacks of MSA methods on nucleo...

journal_title：BMC bioinformatics

authors： Wang Y,Wu H,Cai Y

更新日期：2018-12-31 00:00:00

abstract：BACKGROUND:Cryo-electron microscopy (Cryo-EM) is widely used in the determination of the three-dimensional (3D) structures of macromolecules. Particle picking from 2D micrographs remains a challenging early step in the Cryo-EM pipeline due to the diversity of particle shapes and the extremely low signal-to-noise ratio ...

journal_title：BMC bioinformatics

authors： Al-Azzawi A,Ouadou A,Max H,Duan Y,Tanner JJ,Cheng J

更新日期：2020-11-09 00:00:00

abstract：BACKGROUND:One of key issues in the post-genomic era is to assign functions to uncharacterized proteins. Since proteins seldom act alone; rather, they must interact with other biomolecular units to execute their functions. Thus, the functions of unknown proteins may be discovered through studying their interactions wit...

journal_title：BMC bioinformatics

authors： Hu P,Jiang H,Emili A

更新日期：2010-01-18 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:Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection of lncRNA-protein interactions are limited and inefficient. Many methods have been proposed to predi...

journal_title：BMC bioinformatics

authors： Deng L,Wang J,Xiao Y,Wang Z,Liu H

更新日期：2018-10-11 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

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:Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright ...

journal_title：BMC bioinformatics

authors： Prlić A,Martinez MA,Dimitropoulos D,Beran B,Yukich BT,Rose PW,Bourne PE,Fink JL

更新日期：2010-04-29 00:00:00

abstract：BACKGROUND:Sparse principal component analysis (PCA) is a popular tool for dimensionality reduction, pattern recognition, and visualization of high dimensional data. It has been recognized that complex biological mechanisms occur through concerted relationships of multiple genes working in networks that are often repre...

journal_title：BMC bioinformatics

authors： Li Z,Safo SE,Long Q

更新日期：2017-07-11 00:00:00

abstract：BACKGROUND:The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologist...

journal_title：BMC bioinformatics

authors： Yin Z,Zhou X,Bakal C,Li F,Sun Y,Perrimon N,Wong ST

更新日期：2008-06-05 00:00:00

abstract：BACKGROUND:Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solving protein-DNA complex structures, protein-DNA docking can be used to predict native or near-native...

journal_title：BMC bioinformatics

authors： Corona RI,Sudarshan S,Aluru S,Guo JT

更新日期：2018-12-21 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:MicroRNAs (miRNAs) are single-stranded non-coding RNAs known to regulate a wide range of cellular processes by silencing the gene expression at the protein and/or mRNA levels. Computational prediction of miRNA targets is essential for elucidating the detailed functions of miRNA. However, the prediction speci...

journal_title：BMC bioinformatics

authors： Liu H,Yue D,Chen Y,Gao SJ,Huang Y

更新日期：2010-09-22 00:00:00

abstract：BACKGROUND:The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advance...

journal_title：BMC bioinformatics

authors： Matey-Hernandez ML,Danish Pan Genome Consortium.,Brunak S,Izarzugaza JMG

更新日期：2018-06-25 00:00:00

abstract：BACKGROUND:Traditional algorithms for hidden Markov model decoding seek to maximize either the probability of a state path or the number of positions of a sequence assigned to the correct state. These algorithms provide only a single answer and in practice do not produce good results. RESULTS:We explore an alternative...

journal_title：BMC bioinformatics

authors： Brown DG,Golod D

更新日期：2010-01-18 00:00:00

abstract：BACKGROUND:Activities of drug molecules can be predicted by QSAR (quantitative structure activity relationship) models, which overcomes the disadvantages of high cost and long cycle by employing the traditional experimental method. With the fact that the number of drug molecules with positive activity is rather fewer t...

journal_title：BMC bioinformatics

authors： Li GZ,Meng HH,Lu WC,Yang JY,Yang MQ

更新日期：2008-05-28 00:00:00

abstract：BACKGROUND:Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be ...

journal_title：BMC bioinformatics

authors： Andrieu O,Fiston AS,Anxolabéhère D,Quesneville H

更新日期：2004-07-13 00:00:00

abstract：BACKGROUND:This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulatio...

journal_title：BMC bioinformatics

authors： Barros RC,Winck AT,Machado KS,Basgalupp MP,de Carvalho AC,Ruiz DD,de Souza ON

更新日期：2012-11-21 00:00:00

abstract：BACKGROUND:DNA methylation is an important heritable epigenetic mark that plays a crucial role in transcriptional regulation and the pathogenesis of various human disorders. The commonly used DNA methylation measurement approaches, e.g., Illumina Infinium HumanMethylation-27 and -450 BeadChip arrays (27 K and 450 K arr...

journal_title：BMC bioinformatics

authors： Yu F,Xu C,Deng HW,Shen H

更新日期：2020-12-01 00:00:00

abstract：BACKGROUND:The cost of DNA sequencing has undergone a dramatical reduction in the past decade. As a result, sequencing technologies have been increasingly applied to genomic research. RNA-Seq is becoming a common technique for surveying gene expression based on DNA sequencing. As it is not clear how increased sequencin...

journal_title：BMC bioinformatics

authors： Cai G,Li H,Lu Y,Huang X,Lee J,Müller P,Ji Y,Liang S

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Time- and dose-to-event phenotypes used in basic science and translational studies are commonly measured imprecisely or incompletely due to limitations of the experimental design or data collection schema. For example, drug-induced toxicities are not reported by the actual time or dose triggering the event, ...

journal_title：BMC bioinformatics

authors： Li Z,Lin J,Sibley AB,Truong T,Chua KC,Jiang Y,McCarthy J,Kroetz DL,Allen A,Owzar K

更新日期：2019-05-28 00:00:00

abstract：BACKGROUND:Data are the evidentiary basis for scientific hypotheses, analyses and publication, for policy formation and for decision-making. They are essential to the evaluation and testing of results by peer scientists both present and future. There is broad consensus in the scientific and conservation communities tha...

journal_title：BMC bioinformatics

authors： Moritz T,Krishnan S,Roberts D,Ingwersen P,Agosti D,Penev L,Cockerill M,Chavan V,Data Publishing Framework Task Group.

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. RESULTS:...

journal_title：BMC bioinformatics

authors： Müller HM,Van Auken KM,Li Y,Sternberg PW

更新日期：2018-03-09 00:00:00