Improving clustering with metabolic pathway data.

abstract：BACKGROUND:Molecular recognition in proteins occurs due to appropriate arrangements of physical, chemical, and geometric properties of an atomic surface. Similar surface regions should create similar binding interfaces. Effective methods for comparing surface regions can be used in identifying similar regions, and to p...

journal_title：BMC bioinformatics

authors： Cipriano GM,Phillips GN Jr,Gleicher M

更新日期：2012-11-24 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: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：:We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists work...

journal_title：BMC bioinformatics

authors： Ranganathan S,Gribskov M,Tan TW

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Recent studies in computational primary protein sequence analysis have leveraged the power of unlabeled data. For example, predictive models based on string kernels trained on sequences known to belong to particular folds or superfamilies, the so-called labeled data set, can attain significantly improved acc...

journal_title：BMC bioinformatics

authors： Kuksa P,Huang PH,Pavlovic V

更新日期：2009-04-29 00:00:00

abstract：BACKGROUND:Identifying protein complexes from protein-protein interaction (PPI) network is one of the most important tasks in proteomics. Existing computational methods try to incorporate a variety of biological evidences to enhance the quality of predicted complexes. However, it is still a challenge to integrate diffe...

journal_title：BMC bioinformatics

authors： Xu B,Li K,Zheng W,Liu X,Zhang Y,Zhao Z,He Z

更新日期：2018-12-20 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:The large increase in the size of patent collections has led to the need of efficient search strategies. But the development of advanced text-mining applications dedicated to patents of the biomedical field remains rare, in particular to address the needs of the pharmaceutical & biotech industry, which inten...

journal_title：BMC bioinformatics

authors： Pasche E,Gobeill J,Kreim O,Oezdemir-Zaech F,Vachon T,Lovis C,Ruch P

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides...

journal_title：BMC bioinformatics

authors： Haskins WE,Petritis K,Zhang J

更新日期：2011-03-15 00:00:00

abstract：BACKGROUND:Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic seq...

journal_title：BMC bioinformatics

authors： Zamani N,Sundström G,Meadows JR,Höppner MP,Dainat J,Lantz H,Haas BJ,Grabherr MG

更新日期：2014-06-30 00:00:00

abstract：BACKGROUND:The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in significant conflict with the plurality signal is a frequent task in comparative genomics, and especially ...

journal_title：BMC bioinformatics

authors： Mao F,Williams D,Zhaxybayeva O,Poptsova M,Lapierre P,Gogarten JP,Xu Y

更新日期：2012-06-07 00:00:00

abstract：BACKGROUND:Knowledge of when and in which cells each gene is expressed across multicellular organisms is critical in understanding both gene function and regulation of cell type diversity. However, methods for measuring expression typically involve a trade-off between imaging-based methods, which give the precise locat...

journal_title：BMC bioinformatics

authors： Burdick JT,Murray JI

更新日期：2013-06-22 00:00:00

abstract：BACKGROUND:In bioinformatics community, many tasks associate with matching a set of protein query sequences in large sequence datasets. To conduct multiple queries in the database, a common used method is to run BLAST on each original querey or on the concatenated queries. It is inefficient since it doesn't exploit the...

journal_title：BMC bioinformatics

authors： Ge H,Sun L,Yu J

更新日期：2017-11-21 00:00:00

abstract：BACKGROUND:Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among transcription factors (TFs) and their target genes, with a method able to handle both the high number...

journal_title：BMC bioinformatics

authors： Sauta E,Demartini A,Vitali F,Riva A,Bellazzi R

更新日期：2020-05-29 00:00:00

abstract：BACKGROUND:Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks. RESULTS:Based on a homogeneity assumptio...

journal_title：BMC bioinformatics

authors： Hu GQ,Zheng X,Ju LN,Zhu H,She ZS

更新日期：2008-03-25 00:00:00

abstract：BACKGROUND:Biological data that are well-organized by an ontology, such as Gene Ontology, enables high-throughput availability of the semantic web. It can also be used to facilitate high throughput classification of biomedical information. However, to our knowledge, no evaluation has been published on automating classi...

journal_title：BMC bioinformatics

authors： Chen JL,Liu Y,Sam LT,Li J,Lussier YA

更新日期：2007-05-09 00:00:00

abstract：BACKGROUND:In metabolomics experiments, spectral fingerprints of metabolites with no known structural identity are detected routinely. Computer-assisted structure elucidation (CASE) has been used to determine the structural identities of unknown compounds. It is generally accepted that a single 1D NMR spectrum or mass ...

journal_title：BMC bioinformatics

authors： Jayaseelan KV,Steinbeck C

更新日期：2014-07-05 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:The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics...

journal_title：BMC bioinformatics

authors： Widmer C,Toussaint NC,Altun Y,Rätsch G

更新日期：2010-10-26 00:00:00

abstract：BACKGROUND:In recent years, protein-protein interaction (PPI) networks have been well recognized as important resources to elucidate various biological processes and cellular mechanisms. In this paper, we address the problem of predicting protein complexes from a PPI network. This problem has two difficulties. One is r...

journal_title：BMC bioinformatics

authors： Maruyama O,Kuwahara Y

更新日期：2017-12-06 00:00:00

abstract：BACKGROUND:Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree constructi...

journal_title：BMC bioinformatics

authors： Sievers F,Hughes GM,Higgins DG

更新日期：2014-10-04 00:00:00

abstract：BACKGROUND:Although both conservation and correlated mutation (CM) are important information reflecting the different sorts of context in multiple sequence alignment, most of alignment methods use sequence profiles that only represent conservation. There is no general way to represent correlated mutation and incorporat...

journal_title：BMC bioinformatics

authors： Jeong CS,Kim D

更新日期：2010-04-16 00:00:00

abstract：BACKGROUND:The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to use the "Lightweight DAS" server (LDAS). Onto this type of server, annotations can be uploaded as fl...

journal_title：BMC bioinformatics

authors： Negre V,Grunau C

更新日期：2004-05-07 00:00:00

abstract：BACKGROUND:Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV da...

journal_title：BMC bioinformatics

authors： Vandeweyer G,Reyniers E,Wuyts W,Rooms L,Kooy RF

更新日期：2011-01-05 00:00:00

abstract：BACKGROUND:It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here, we describe a tool wh...

journal_title：BMC bioinformatics

authors： David MP,Lapid CM,Daria VR

更新日期：2008-04-28 00:00:00

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:Detecting patterns in high-dimensional multivariate datasets is non-trivial. Clustering and dimensionality reduction techniques often help in discerning inherent structures. In biological datasets such as microbial community composition or gene expression data, observations can be generated from a continuous...

journal_title：BMC bioinformatics

authors： Nguyen LH,Holmes S

更新日期：2017-09-13 00:00:00

abstract：:Selected reaction monitoring (SRM)-based proteomics approaches enable highly sensitive and reproducible assays for profiling of thousands of peptides in one experiment. The development of such assays involves the determination of retention time, detectability and fragmentation properties of peptides, followed by an op...

journal_title：BMC bioinformatics

authors： Nahnsen S,Kohlbacher O

更新日期：2012-01-01 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:The diagnosis of many diseases can be often formulated as a decision problem; uncertainty affects these problems so that many computerized Diagnostic Decision Support Systems (in the following, DDSSs) have been developed to aid the physician in interpreting clinical data and thus to improve the quality of th...

journal_title：BMC bioinformatics

authors： d'Acierno A,Esposito M,De Pietro G

更新日期：2013-01-01 00:00:00