Automated peptide mapping and protein-topographical annotation of proteomics data.

abstract：BACKGROUND:Biochemically detailed stoichiometric matrices have now been reconstructed for various bacteria, yeast, and for the human cardiac mitochondrion based on genomic and proteomic data. These networks have been manually curated based on legacy data and elementally and charge balanced. Comparative analysis of thes...

journal_title：BMC bioinformatics

authors： Becker SA,Price ND,Palsson BØ

更新日期：2006-03-06 00:00:00

abstract：BACKGROUND:Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure compariso...

journal_title：BMC bioinformatics

authors： Veeramalai M,Gilbert D,Valiente G

更新日期：2010-03-17 00:00:00

abstract：BACKGROUND:Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. Howeve...

journal_title：BMC bioinformatics

authors： Rueda AJV,Monzon AM,Ardanaz SM,Iglesias LE,Parisi G

更新日期：2018-01-30 00:00:00

abstract：BACKGROUND:The goal of class prediction studies is to develop rules to accurately predict the class membership of new samples. The rules are derived using the values of the variables available for each subject: the main characteristic of high-dimensional data is that the number of variables greatly exceeds the number o...

journal_title：BMC bioinformatics

authors： Blagus R,Lusa L

更新日期：2010-10-20 00:00:00

abstract：BACKGROUND:With the development of sequencing technologies, more and more sequence variants are available for investigation. Different classes of variants in the human genome have been identified, including single nucleotide substitutions, insertion and deletion, and large structural variations such as duplications and...

journal_title：BMC bioinformatics

authors： Liu M,Watson LT,Zhang L

更新日期：2014-01-09 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:Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has beco...

journal_title：BMC bioinformatics

authors： Zare F,Dow M,Monteleone N,Hosny A,Nabavi S

更新日期：2017-05-31 00:00:00

abstract：BACKGROUND:To further our understanding of immunopeptidomics, improved tools are needed to identify peptides presented by major histocompatibility complex class I (MHC-I). Many existing tools are limited by their reliance upon chemical affinity data, which is less biologically relevant than sampling by mass spectrometr...

journal_title：BMC bioinformatics

authors： Boehm KM,Bhinder B,Raja VJ,Dephoure N,Elemento O

更新日期：2019-01-05 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:In the last decade, a significant improvement in detecting remote similarity between protein sequences has been made by utilizing alignment profiles in place of amino-acid strings. Unfortunately, no analytical theory is available for estimating the significance of a gapped alignment of two profiles. Many exp...

journal_title：BMC bioinformatics

authors： Poleksic A

更新日期：2009-04-20 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: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:Microarray technology provides the expression level of many genes. Nowadays, an important issue is to select a small number of informative differentially expressed genes that provide biological knowledge and may be key elements for a disease. With the increasing volume of data generated by modern biomedical ...

journal_title：BMC bioinformatics

authors： Martínez-Otzeta JM,Irigoien I,Sierra B,Arenas C

更新日期：2020-04-07 00:00:00

abstract：BACKGROUND:Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint ...

journal_title：BMC bioinformatics

authors： Bozdag S,Close TJ,Lonardi S

更新日期：2009-07-15 00:00:00

abstract：BACKGROUND:X-converting enzyme (XCE) involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it's well characterized homologue endothelin-converting enzyme-1 (ECE-1) showed broad substrate specificity and acts as ...

journal_title：BMC bioinformatics

authors： Ul-Haq Z,Iqbal S,Moin ST

更新日期：2012-11-01 00:00:00

abstract：BACKGROUND:To evaluate statistical methods for genome-wide genetic analyses, one needs to be able to simulate realistic genotypes. We here describe a method, applicable to a broad range of association study designs, that can simulate autosome-wide single-nucleotide polymorphism data with realistic linkage disequilibriu...

journal_title：BMC bioinformatics

authors： Shi M,Umbach DM,Wise AS,Weinberg CR

更新日期：2018-01-02 00:00:00

abstract：BACKGROUND:The main goal of the whole transcriptome analysis is to correctly identify all expressed transcripts within a specific cell/tissue--at a particular stage and condition--to determine their structures and to measure their abundances. RNA-seq data promise to allow identification and quantification of transcript...

journal_title：BMC bioinformatics

authors： Angelini C,De Canditiis D,De Feis I

更新日期：2014-05-09 00:00:00

abstract：BACKGROUND:High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key for drawing meaningful and accurate conclusions from the massive and complex datasets generat...

journal_title：BMC bioinformatics

authors： Bullard JH,Purdom E,Hansen KD,Dudoit S

更新日期：2010-02-18 00:00:00

abstract：BACKGROUND:Protein solvent accessibility prediction is a pivotal intermediate step towards modeling protein tertiary structures directly from one-dimensional sequences. It also plays an important part in identifying protein folds and domains. Although some methods have been presented to the protein solvent accessibilit...

journal_title：BMC bioinformatics

authors： Fan C,Liu D,Huang R,Chen Z,Deng L

更新日期：2016-01-11 00:00:00

abstract：BACKGROUND:The amount of gene expression data available in public repositories has grown exponentially in the last years, now requiring new data mining tools to transform them in information easily accessible to biologists. RESULTS:By exploiting expression data publicly available in the Gene Expression Omnibus (GEO) d...

journal_title：BMC bioinformatics

authors： Cremaschi P,Rovida S,Sacchi L,Lisa A,Calvi F,Montecucco A,Biamonti G,Bione S,Sacchi G

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The detection of bias due to cryptic population structure is an important step in the evaluation of findings of genetic association studies. The standard method of measuring this bias in a genetic association study is to compare the observed median association test statistic to the expected median test stati...

journal_title：BMC bioinformatics

authors： Pirie A,Wood A,Lush M,Tyrer J,Pharoah PD

更新日期：2015-02-20 00:00:00

abstract：BACKGROUND:Proton Magnetic Resonance (MR) Spectroscopy (MRS) is a widely available technique for those clinical centres equipped with MR scanners. Unlike the rest of MR-based techniques, MRS yields not images but spectra of metabolites in the tissues. In pathological situations, the MRS profile changes and this has bee...

journal_title：BMC bioinformatics

authors： Pérez-Ruiz A,Julià-Sapé M,Mercadal G,Olier I,Majós C,Arús C

更新日期：2010-11-29 00:00:00

abstract：BACKGROUND:To interpret microarray experiments, several ontological analysis tools have been developed. However, current tools are limited to specific organisms. RESULTS:We developed a bioinformatics system to assign the probe set sequences of any organism to a hierarchical functional classification modelled on KEGG o...

journal_title：BMC bioinformatics

authors： Goffard N,Weiller G

更新日期：2007-03-12 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

abstract：BACKGROUND:The Codon Adaptation Index (CAI) is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a...

journal_title：BMC bioinformatics

authors： Puigbò P,Bravo IG,Garcia-Vallvé S

更新日期：2008-01-29 00:00:00

abstract：BACKGROUND:A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to a...

journal_title：BMC bioinformatics

authors： Yue F,Shi J,Tang J

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Identifying key components in biological processes and their associations is critical for deciphering cellular functions. Recently, numerous gene expression and molecular interaction experiments have been reported in Saccharomyces cerevisiae, and these have enabled systematic studies. Although a number of ap...

journal_title：BMC bioinformatics

authors： Hsu JT,Peng CH,Hsieh WP,Lan CY,Tang CY

更新日期：2011-07-12 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:In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein structure prediction methods. It is also observed that for almost all globular proteins, the quality of co...

journal_title：BMC bioinformatics

authors： Adhikari B,Nowotny J,Bhattacharya D,Hou J,Cheng J

更新日期：2016-12-07 00:00:00

abstract：BACKGROUND:In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorith...

journal_title：BMC bioinformatics

authors： Yang C,He Z,Yu W

更新日期：2009-01-06 00:00:00