A sensitive short read homology search tool for paired-end read sequencing data.

abstract：BACKGROUND:Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure ...

journal_title：BMC bioinformatics

authors： Tharatipyakul A,Numnark S,Wichadakul D,Ingsriswang S

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Pattern recognition receptors of the immune system have key roles in the regulation of pathways after the recognition of microbial- and danger-associated molecular patterns in vertebrates. Members of NOD-like receptor (NLR) family typically function intracellularly. The NOD-like receptor family CARD domain c...

journal_title：BMC bioinformatics

authors： Mótyán JA,Bagossi P,Benkő S,Tőzsér J

更新日期：2013-09-17 00:00:00

abstract：BACKGROUND:The Triplex cell vaccine is a cancer cellular vaccine that can prevent almost completely the mammary tumor onset in HER-2/neu transgenic mice. In a translational perspective, the activity of the Triplex vaccine was also investigated against lung metastases showing that the vaccine is an effective treatment a...

journal_title：BMC bioinformatics

authors： Pennisi M,Pappalardo F,Palladini A,Nicoletti G,Nanni P,Lollini PL,Motta S

更新日期：2010-10-15 00:00:00

abstract：BACKGROUND:Membrane transport proteins (transporters) play an essential role in every living cell by transporting hydrophilic molecules across the hydrophobic membranes. While the sequences of many membrane proteins are known, their structure and function is still not well characterized and understood, owing to the imm...

journal_title：BMC bioinformatics

authors： Alballa M,Butler G

更新日期：2020-04-23 00:00:00

abstract：BACKGROUND:Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. In order to fully capture the intrinsic value and knowledge expressed within them, we need to take advantage of their inner structure, which implicitly co...

journal_title：BMC bioinformatics

authors： Groza T,Hunter J,Zankl A

更新日期：2012-10-15 00:00:00

abstract：BACKGROUND:Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations acco...

journal_title：BMC bioinformatics

authors： Lloyd S,Snell QO

更新日期：2011-12-07 00:00:00

abstract：BACKGROUND:The central element of each enzyme is the catalytic site, which commonly catalyzes a single biochemical reaction with high specificity. It was unclear to us how often sites that catalyze the same or highly similar reactions evolved on different, i. e. non-homologous protein folds and how similar their 3D pos...

journal_title：BMC bioinformatics

authors： Žváček C,Friedrichs G,Heizinger L,Merkl R

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding the mechanisms of post-transcriptional regulation. Hu...

journal_title：BMC bioinformatics

authors： Huang TH,Fan B,Rothschild MF,Hu ZL,Li K,Zhao SH

更新日期：2007-09-17 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:It is now well established that nearly 20% of human cancers are caused by infectious agents, and the list of human oncogenic pathogens will grow in the future for a variety of cancer types. Whole tumor transcriptome and genome sequencing by next-generation sequencing technologies presents an unparalleled opp...

journal_title：BMC bioinformatics

authors： Borozan I,Wilson S,Blanchette P,Laflamme P,Watt SN,Krzyzanowski PM,Sircoulomb F,Rottapel R,Branton PE,Ferretti V

更新日期：2012-08-17 00:00:00

abstract：:In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a re...

journal_title：BMC bioinformatics

authors： Aganezov S Jr,Alekseyev MA

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:The reconstruction of reliable graphical models from observational data is important in bioinformatics and other computational fields applying network reconstruction methods to large, yet finite datasets. The main network reconstruction approaches are either based on Bayesian scores, which enable the ranking...

journal_title：BMC bioinformatics

authors： Affeldt S,Verny L,Isambert H

更新日期：2016-01-20 00:00:00

abstract：BACKGROUND:Cryo-electron tomography (cryo-ET) enables the 3D visualization of cellular organization in near-native state which plays important roles in the field of structural cell biology. However, due to the low signal-to-noise ratio (SNR), large volume and high content complexity within cells, it remains difficult a...

journal_title：BMC bioinformatics

authors： Li R,Zeng X,Sigmund SE,Lin R,Zhou B,Liu C,Wang K,Jiang R,Freyberg Z,Lv H,Xu M

更新日期：2019-03-29 00:00:00

abstract：BACKGROUND:Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling ...

journal_title：BMC bioinformatics

authors： Chelaru F,Corrada Bravo H

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:To understand biology and differences among various tissues or cell types, one typically searches for molecular features that display characteristic abundance patterns. Several specificity metrics have been introduced to identify tissue-specific molecular features, but these either require an equal number of...

journal_title：BMC bioinformatics

authors： Everaert C,Volders PJ,Morlion A,Thas O,Mestdagh P

更新日期：2020-02-17 00:00:00

abstract：BACKGROUND:Inference of sequence homology is inherently an evolutionary question, dependent upon evolutionary divergence. However, the insertion and deletion penalties in the most widely used methods for inferring homology by sequence alignment, including BLAST and profile hidden Markov models (profile HMMs), are not b...

journal_title：BMC bioinformatics

authors： Rivas E,Eddy SR

更新日期：2015-12-10 00:00:00

abstract：BACKGROUND:Failure on Highly Active Anti-Retroviral Treatment is often accompanied with development of antiviral resistance to one or more drugs included in the treatment. In general, the virus is more likely to develop resistance to drugs with a lower genetic barrier. Previously, we developed a method to reverse engin...

journal_title：BMC bioinformatics

authors： Theys K,Deforche K,Beheydt G,Moreau Y,van Laethem K,Lemey P,Camacho RJ,Rhee SY,Shafer RW,Van Wijngaerden E,Vandamme AM

更新日期：2010-08-03 00:00:00

abstract：BACKGROUND:In this paper, it is proposed an optimization approach for producing reduced alphabets for peptide classification, using a Genetic Algorithm. The classification task is performed by a multi-classifier system where each classifier (Linear or Radial Basis function Support Vector Machines) is trained using feat...

journal_title：BMC bioinformatics

authors： Nanni L,Lumini A

更新日期：2008-01-24 00:00:00

abstract：BACKGROUND:The identification of protein coding regions (exons) in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing. In this paper, a new method is presented for the identification of exonic regions in DNA sequences. This method is based on th...

journal_title：BMC bioinformatics

authors： Abbasi O,Rostami A,Karimian G

更新日期：2011-11-03 00:00:00

abstract：BACKGROUND:Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating ...

journal_title：BMC bioinformatics

authors： Doran AG,Creevey CJ

更新日期：2013-02-08 00:00:00

abstract：BACKGROUND:A new algorithm has been developed for generating conservation profiles that reflect the evolutionary history of the subfamily associated with a query sequence. It is based on n-gram patterns (NP{n,m}) which are sets of n residues and m wildcards in windows of size n+m. The generation of conservation profile...

journal_title：BMC bioinformatics

authors： Vries JK,Liu X

更新日期：2008-01-30 00:00:00

abstract：BACKGROUND:Because loops connect regular secondary structures, analysis of the former depends directly on the definition of the latter. The numerous assignment methods, however, can offer different definitions. In a previous study, we defined a structural alphabet composed of 16 average protein fragments, which we call...

journal_title：BMC bioinformatics

authors： Fourrier L,Benros C,de Brevern AG

更新日期：2004-05-12 00:00:00

abstract：BACKGROUND:We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce a coding of the shape of the coverage depth function as a tree and explain how thi...

journal_title：BMC bioinformatics

authors： Evans SN,Hower V,Pachter L

更新日期：2010-08-18 00:00:00

abstract：BACKGROUND:The advent of RNA interference techniques enables the selective silencing of biologically interesting genes in an efficient way. In combination with DNA microarray technology this enables researchers to gain insights into signaling pathways by observing downstream effects of individual knock-downs on gene ex...

journal_title：BMC bioinformatics

authors： Froehlich H,Fellmann M,Sueltmann H,Poustka A,Beissbarth T

更新日期：2007-10-15 00:00:00

abstract：BACKGROUND:Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) is a powerful technique which has gained increasing attention over the last two decades. The GC × GC-MS provides much increased separation capacity, chemical selectivity and sensitivity for complex sample analysis an...

journal_title：BMC bioinformatics

authors： Kim S,Koo I,Fang A,Zhang X

更新日期：2011-06-15 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:Although protein-protein interaction networks determined with high-throughput methods are incomplete, they are commonly used to infer the topology of the complete interactome. These partial networks often show a scale-free behavior with only a few proteins having many and the majority having only a few conne...

journal_title：BMC bioinformatics

authors： Friedel CC,Zimmer R

更新日期：2006-11-30 00:00:00

abstract：BACKGROUND:Discovering patterns from gene expression levels is regarded as a classification problem when tissue classes of the samples are given and solved as a discrete-data problem by discretizing the expression levels of each gene into intervals maximizing the interdependence between that gene and the class labels. ...

journal_title：BMC bioinformatics

authors： Wu GP,Chan KC,Wong AK

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:A professional recognition mechanism is required to encourage expedited publishing of an adequate volume of 'fit-for-use' biodiversity data. As a component of such a recognition mechanism, we propose the development of the Data Usage Index (DUI) to demonstrate to data publishers that their efforts of creatin...

journal_title：BMC bioinformatics

authors： Ingwersen P,Chavan V

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Biologists often conduct multiple but different cDNA microarray studies that all target the same biological system or pathway. Within each study, replicate slides within repeated identical experiments are often produced. Pooling information across studies can help more accurately identify true target genes. ...

journal_title：BMC bioinformatics

authors： Conlon EM,Song JJ,Liu JS

更新日期：2006-05-05 00:00:00