VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences.

abstract：BACKGROUND:Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stringent score cutoff is applied to distinguish putative homologs from possible false positive hits. As a consequence, some BLAST hits are discar...

journal_title：BMC bioinformatics

authors： Fokkens L,Botelho SM,Boekhorst J,Snel B

更新日期：2010-02-12 00:00:00

abstract：BACKGROUND:Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the prediction of complex architecture given detailed structures of its constituents. They are becoming ...

journal_title：BMC bioinformatics

authors： Setny P,Bahadur RP,Zacharias M

更新日期：2012-09-11 00:00:00

abstract：BACKGROUND:Orthologs inference is the starting point of most comparative genomics studies, and a plethora of methods have been designed in the last decade to address this challenging task. In this paper we focus on the problems of deciding consistency with a species tree (known or not) of a partial set of orthology/par...

journal_title：BMC bioinformatics

authors： Jones M,Paul C,Scornavacca C

更新日期：2016-11-11 00:00:00

abstract：BACKGROUND:PCR has the potential to detect and precisely quantify specific DNA sequences, but it is not yet often used as a fully quantitative method. A number of data collection and processing strategies have been described for the implementation of quantitative PCR. However, they can be experimentally cumbersome, the...

journal_title：BMC bioinformatics

authors： Karlen Y,McNair A,Perseguers S,Mazza C,Mermod N

更新日期：2007-04-20 00:00:00

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: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：: ...

journal_title：BMC bioinformatics

authors： Wren JD,Doerkson RJ,Toby IT,Nanduri B,Homayouni R,Manda P,Thakkar S

更新日期：2019-03-14 00:00:00

abstract：BACKGROUND:Typical evolutionary events like recombination, hybridization or gene transfer make necessary the use of phylogenetic networks to properly depict the evolution of DNA and protein sequences. Although several theoretical classes have been proposed to characterize these networks, they make stringent assumptions...

journal_title：BMC bioinformatics

authors： Arenas M,Patricio M,Posada D,Valiente G

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear ...

journal_title：BMC bioinformatics

authors： Lemieux S

更新日期：2006-08-25 00:00:00

abstract：BACKGROUND:The wide use of high-throughput DNA microarray technology provide an increasingly detailed view of human transcriptome from hundreds to thousands of genes. Although biomedical researchers typically design microarray experiments to explore specific biological contexts, the relationships between genes are hard...

journal_title：BMC bioinformatics

authors： Kong W,Mou X,Hu X

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:RNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small number of replicates. Power analysis and sample size calculation are challenging in the context of dif...

journal_title：BMC bioinformatics

authors： Bi R,Liu P

更新日期：2016-03-31 00:00:00

abstract：BACKGROUND:The ability to detect nuclei in embryos is essential for studying the development of multicellular organisms. A system of automated nuclear detection has already been tested on a set of four-dimensional (4D) Nomarski differential interference contrast (DIC) microscope images of Caenorhabditis elegans embryos...

journal_title：BMC bioinformatics

authors： Hamahashi S,Onami S,Kitano H

更新日期：2005-05-24 00:00:00

abstract：BACKGROUND:Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties by gene express...

journal_title：BMC bioinformatics

authors： Zhang SD,Gant TW

更新日期：2008-06-02 00:00:00

abstract：BACKGROUND:Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain datab...

journal_title：BMC bioinformatics

authors： Truong K,Ikura M

更新日期：2003-05-06 00:00:00

abstract：BACKGROUND:Visualization tools for deep learning models typically focus on discovering key input features without considering how such low level features are combined in intermediate layers to make decisions. Moreover, many of these methods examine a network's response to specific input examples that may be insufficien...

journal_title：BMC bioinformatics

authors： Liu G,Zeng H,Gifford DK

更新日期：2019-07-19 00:00:00

abstract：BACKGROUND:An important application of high dimensional gene expression measurements is the risk prediction and the interpretation of the variables in the resulting survival models. A major problem in this context is the typically large number of genes compared to the number of observations (individuals). Feature selec...

journal_title：BMC bioinformatics

authors： Kammers K,Lang M,Hengstler JG,Schmidt M,Rahnenführer J

更新日期：2011-12-16 00:00:00

abstract：BACKGROUND:Community structure is ubiquitous in biological networks. There has been an increased interest in unraveling the community structure of biological systems as it may provide important insights into a system's functional components and the impact of local structures on dynamics at a global scale. Choosing an a...

journal_title：BMC bioinformatics

authors： Sah P,Singh LO,Clauset A,Bansal S

更新日期：2014-06-25 00:00:00

abstract：BACKGROUND:Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptio...

journal_title：BMC bioinformatics

authors： Chevenet F,Brun C,Bañuls AL,Jacq B,Christen R

更新日期：2006-10-10 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:A standard procedure in many areas of bioinformatics is to use a multiple sequence alignment (MSA) as the basis for various types of homology-based inference. Applications include 3D structure modelling, protein functional annotation, prediction of molecular interactions, etc. These applications, however sop...

journal_title：BMC bioinformatics

authors： Vanhoutreve R,Kress A,Legrand B,Gass H,Poch O,Thompson JD

更新日期：2016-07-07 00:00:00

abstract：BACKGROUND:Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the m...

journal_title：BMC bioinformatics

authors： McQuisten KA,Peek AS

更新日期：2007-06-07 00:00:00

abstract：BACKGROUND:The challenge of classifying cortical interneurons is yet to be solved. Data-driven classification into established morphological types may provide insight and practical value. RESULTS:We trained models using 217 high-quality morphologies of rat somatosensory neocortex interneurons reconstructed by a single...

journal_title：BMC bioinformatics

authors： Mihaljević B,Larrañaga P,Benavides-Piccione R,Hill S,DeFelipe J,Bielza C

更新日期：2018-12-17 00:00:00

abstract：BACKGROUND:Predicting protein function has become increasingly demanding in the era of next generation sequencing technology. The task to assign a curator-reviewed function to every single sequence is impracticable. Bioinformatics tools, easy to use and able to provide automatic and reliable annotations at a genomic sc...

journal_title：BMC bioinformatics

authors： Falda M,Toppo S,Pescarolo A,Lavezzo E,Di Camillo B,Facchinetti A,Cilia E,Velasco R,Fontana P

更新日期：2012-03-28 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:Understanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cells cope with stress. For example, adaptation of yeast to heat shock involves a characteristic profil...

journal_title：BMC bioinformatics

authors： Vilaprinyo E,Alves R,Sorribas A

更新日期：2006-04-03 00:00:00

abstract：BACKGROUND:Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever ...

journal_title：BMC bioinformatics

authors： Sturm M,Bertsch A,Gröpl C,Hildebrandt A,Hussong R,Lange E,Pfeifer N,Schulz-Trieglaff O,Zerck A,Reinert K,Kohlbacher O

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:Amino acids in proteins are not used equally. Some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between proteins from the same species (related to protein function, expression or subcellular localization, fo...

journal_title：BMC bioinformatics

authors： Pasamontes A,Garcia-Vallve S

更新日期：2006-05-18 00:00:00

abstract：BACKGROUND:Microbial electrosynthesis and electro fermentation are techniques that aim to optimize microbial production of chemicals and fuels by regulating the cellular redox balance via interaction with electrodes. While the concept is known for decades major knowledge gaps remain, which make it hard to evaluate its ...

journal_title：BMC bioinformatics

authors： Kracke F,Krömer JO

更新日期：2014-12-30 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:MicroRNAs (miRNAs) are a kind of small noncoding RNA molecules that are direct posttranscriptional regulations of mRNA targets. Studies have indicated that miRNAs play key roles in complex diseases by taking part in many biological processes, such as cell growth, cell death and so on. Therefore, in order to ...

journal_title：BMC bioinformatics

authors： Yan C,Wu FX,Wang J,Duan G

更新日期：2020-03-18 00:00:00