Improved functional prediction of proteins by learning kernel combinations in multilabel settings.

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:Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserved synteny, or synteny blocks, must be precisely identified and quantified, as a prerequisite to bet...

journal_title：BMC bioinformatics

authors： Lucas JM,Muffato M,Roest Crollius H

更新日期：2014-08-08 00:00:00

abstract：BACKGROUND:Kernel-based learning algorithms are among the most advanced machine learning methods and have been successfully applied to a variety of sequence classification tasks within the field of bioinformatics. Conventional kernels utilized so far do not provide an easy interpretation of the learnt representations i...

journal_title：BMC bioinformatics

authors： Meinicke P,Tech M,Morgenstern B,Merkl R

更新日期：2004-10-28 00:00:00

abstract：BACKGROUND:The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatures of phenotypes such as clinical outcome has not been attained in almost any disease area. Here, w...

journal_title：BMC bioinformatics

authors： Smith AM,Walsh JR,Long J,Davis CB,Henstock P,Hodge MR,Maciejewski M,Mu XJ,Ra S,Zhao S,Ziemek D,Fisher CK

更新日期：2020-03-20 00:00:00

abstract：BACKGROUND:The explosive growth of biological data provides opportunities for new statistical and comparative analyses of large information sets, such as alignments comprising tens of thousands of sequences. In such studies, sequence annotations frequently play an essential role, and reliable results depend on metadata...

journal_title：BMC bioinformatics

authors： Miotto O,Tan TW,Brusic V

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Protein function in eukaryotic cells is often controlled in a cell cycle-dependent manner. Therefore, the correct assignment of cellular phenotypes to cell cycle phases is a crucial task in cell biology research. Nuclear proteins whose localization varies during the cell cycle are valuable and frequently use...

journal_title：BMC bioinformatics

authors： Schönenberger F,Deutzmann A,Ferrando-May E,Merhof D

更新日期：2015-05-29 00:00:00

abstract：BACKGROUND:The family of voltage-gated potassium channels comprises a functionally diverse group of membrane proteins. They help maintain and regulate the potassium ion-based component of the membrane potential and are thus central to many critical physiological processes. VKCDB (Voltage-gated potassium [K] Channel Dat...

journal_title：BMC bioinformatics

authors： Li B,Gallin WJ

更新日期：2004-01-09 00:00:00

abstract：BACKGROUND:Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various existing methods measure similarity between two profiles and, hence, the likelihood that the two prote...

journal_title：BMC bioinformatics

authors： Cokus S,Mizutani S,Pellegrini M

更新日期：2007-05-22 00:00:00

abstract：:The RNA polymerase NS5B of Hepatitis C virus (HCV) is a well-characterised drug target with an active site and four allosteric binding sites. This work presents a workflow for virtual screening and its application to Drug Bank screening targeting the Hepatitis C Virus (HCV) RNA polymerase non-nucleoside binding sites....

journal_title：BMC bioinformatics

authors： Elhefnawi M,ElGamacy M,Fares M

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Reproducibility of results can have a significant impact on the acceptance of new technologies in gene expression analysis. With the recent introduction of the so-called next-generation sequencing (NGS) technology and established microarrays, one is able to choose between two completely different platforms f...

journal_title：BMC bioinformatics

authors： Stiglic G,Bajgot M,Kokol P

更新日期：2010-04-08 00:00:00

abstract：BACKGROUND:Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range o...

journal_title：BMC bioinformatics

authors： Iacoangeli A,Al Khleifat A,Sproviero W,Shatunov A,Jones AR,Morgan SL,Pittman A,Dobson RJ,Newhouse SJ,Al-Chalabi A

更新日期：2019-04-27 00:00:00

abstract：BACKGROUND:The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using o...

journal_title：BMC bioinformatics

authors： von Grotthuss M,Plewczynski D,Ginalski K,Rychlewski L,Shakhnovich EI

更新日期：2006-02-06 00:00:00

abstract：BACKGROUND:Polychromatic flow cytometry is a popular technique that has wide usage in the medical sciences, especially for studying phenotypic properties of cells. The high-dimensionality of data generated by flow cytometry usually makes it difficult to visualize. The naive solution of simply plotting two-dimensional g...

journal_title：BMC bioinformatics

authors： Raj S,Hussain F,Husein Z,Torosdagli N,Turgut D,Deo N,Pattanaik S,Chang CJ,Jha SK

更新日期：2017-06-07 00:00:00

abstract：BACKGROUND:Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionall...

journal_title：BMC bioinformatics

authors： Weeratunga S,Hu NJ,Simon A,Hofmann A

更新日期：2012-08-14 00:00:00

abstract：BACKGROUND:Prognosis is of critical interest in breast cancer research. Biomedical studies suggest that genomic measurements may have independent predictive power for prognosis. Gene profiling studies have been conducted to search for predictive genomic measurements. Genes have the inherent pathway structure, where pat...

journal_title：BMC bioinformatics

authors： Ma S,Kosorok MR

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:A number of tools for the examination of linkage disequilibrium (LD) patterns between nearby alleles exist, but none are available for quickly and easily investigating LD at longer ranges (>500 kb). We have developed a web-based query tool (GLIDERS: Genome-wide LInkage DisEquilibrium Repository and Search en...

journal_title：BMC bioinformatics

authors： Lawrence R,Day-Williams AG,Mott R,Broxholme J,Cardon LR,Zeggini E

更新日期：2009-10-31 00:00:00

abstract：BACKGROUND:One of the most powerful methods for the prediction of protein structure from sequence information alone is the iterative construction of profile-type models. Because profiles are built from sequence alignments, the sequences included in the alignment and the method used to align them will be important to th...

journal_title：BMC bioinformatics

authors： Scheeff ED,Bourne PE

更新日期：2006-09-14 00:00:00

abstract：BACKGROUND:An approach to molecular classification based on the comparative expression of protein pairs is presented. The method overcomes some of the present limitations in using peptide intensity data for class prediction for problems such as the detection of a disease, disease prognosis, or for predicting treatment ...

journal_title：BMC bioinformatics

authors： Kaur P,Schlatzer D,Cooke K,Chance MR

更新日期：2012-08-07 00:00:00

abstract：BACKGROUND:Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers. Over 95% of human genes are estimated to be alternatively spliced as a powerful means of producing functionally diverse proteins from a single gene. The emergence of next-generation sequencing technologies, e...

journal_title：BMC bioinformatics

authors： Zhang F,Deng CK,Wang M,Deng B,Barber R,Huang G

更新日期：2020-12-03 00:00:00

abstract：BACKGROUND:High-throughput "omics" based data analysis play emerging roles in life sciences and molecular diagnostics. This emphasizes the urgent need for user-friendly windows-based software interfaces that could process the diversity of large tab-delimited raw data files generated by these methods. Depending on the s...

journal_title：BMC bioinformatics

authors： Schwager C,Wirkner U,Abdollahi A,Huber PE

更新日期：2009-07-29 00:00:00

abstract：BACKGROUND:With the advent of high-throughput proteomic experiments such as arrays of purified proteins comes the need to analyse sets of proteins as an ensemble, as opposed to the traditional one-protein-at-a-time approach. Although there are several publicly available tools that facilitate the analysis of protein set...

journal_title：BMC bioinformatics

authors： Wolting C,McGlade CJ,Tritchler D

更新日期：2006-07-12 00:00:00

abstract：BACKGROUND:Sequence mutations represent a driving force of adaptive evolution in bacterial pathogens. It is especially evident in reductive genome evolution where bacteria underwent lifestyles shifting from a free-living to a strictly intracellular or host-depending life. It resulted in loss-of-function mutations and/o...

journal_title：BMC bioinformatics

authors： Yu GX

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The wide usage of protein sequence analysis in par with the growth of databases signifies the importance...

journal_title：BMC bioinformatics

authors： Giri AV,Anishetty S,Gautam P

更新日期：2004-09-09 00:00:00

abstract：BACKGROUND:Different human responses to the same vaccine were frequently observed. For example, independent studies identified overlapping but different transcriptomic gene expression profiles in Yellow Fever vaccine 17D (YF-17D) immunized human subjects. Different experimental and analysis conditions were likely contr...

journal_title：BMC bioinformatics

authors： Ong E,Sun P,Berke K,Zheng J,Wu G,He Y

更新日期：2019-12-23 00:00:00

abstract：BACKGROUND:Gene expression microarray experiments are expensive to conduct and guidelines for acceptable quality control at intermediate steps before and after the samples are hybridised to chips are vague. We conducted an experiment hybridising RNA from human brain to 117 U133A Affymetrix GeneChips and used these data...

journal_title：BMC bioinformatics

authors： Jones L,Goldstein DR,Hughes G,Strand AD,Collin F,Dunnett SB,Kooperberg C,Aragaki A,Olson JM,Augood SJ,Faull RL,Luthi-Carter R,Moskvina V,Hodges AK

更新日期：2006-04-19 00:00:00

abstract：BACKGROUND:Microarray technology is commonly used as a simple screening tool with a focus on selecting genes that exhibit extremely large differential expressions between different phenotypes. It lacks the ability to select genes that change their relationships with other genes in different biological conditions (diffe...

journal_title：BMC bioinformatics

authors： Hu R,Qiu X,Glazko G,Klebanov L,Yakovlev A

更新日期：2009-01-15 00:00:00

abstract：BACKGROUND:Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff bet...

journal_title：BMC bioinformatics

authors： Nashta-Ali D,Aliyari A,Ahmadian Moghadam A,Edrisi MA,Motahari SA,Hossein Khalaj B

更新日期：2017-02-23 00:00:00

abstract：BACKGROUND:During evolution, large-scale genome rearrangements of chromosomes shuffle the order of homologous genome sequences ("synteny blocks") across species. Some years ago, a controversy erupted in genome rearrangement studies over whether rearrangements recur, causing breakpoints to be reused. METHODS:We investi...

journal_title：BMC bioinformatics

authors： Attie O,Darling AE,Yancopoulos S

更新日期：2011-10-05 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6-8 nucleotide long target sites, usually located within the mRNA 3' untranslated region. A common approach to validate and probe microRNA-mRNA interact...

journal_title：BMC bioinformatics

authors： Ryan BC,Werner TS,Howard PL,Chow RL

更新日期：2016-04-27 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