Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.

abstract：BACKGROUND:Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five...

journal_title：BMC bioinformatics

authors： Rangarajan A,Schedl T,Yook K,Chan J,Haenel S,Otis L,Faelten S,DePellegrin-Connelly T,Isaacson R,Skrzypek MS,Marygold SJ,Stefancsik R,Cherry JM,Sternberg PW,Müller HM

更新日期：2011-05-19 00:00:00

abstract：BACKGROUND:Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper ...

journal_title：BMC bioinformatics

authors： Varadi M,Guharoy M,Zsolyomi F,Tompa P

更新日期：2015-05-13 00:00:00

abstract：BACKGROUND:Knowledge of subcellular localization of proteins is crucial to proteomics, drug target discovery and systems biology since localization and biological function are highly correlated. In recent years, numerous computational prediction methods have been developed. Nevertheless, there is still a need for predi...

journal_title：BMC bioinformatics

authors： Blum T,Briesemeister S,Kohlbacher O

更新日期：2009-09-01 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:Analyses of molecular high-throughput data often lack in robustness, i.e. results are very sensitive to the addition or removal of a single observation. Therefore, the identification of extreme observations is an important step of quality control before doing further data analysis. Standard outlier detection...

journal_title：BMC bioinformatics

authors： Kruppa J,Jung K

更新日期：2017-05-02 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:Detecting local correlations in expression between neighboring genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to illustrate the role of mechanisms such as copy number variation (CNV) or epigene...

journal_title：BMC bioinformatics

authors： Delatola EI,Lebarbier E,Mary-Huard T,Radvanyi F,Robin S,Wong J

更新日期：2017-07-11 00:00:00

abstract：BACKGROUND:During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public...

journal_title：BMC bioinformatics

authors： Nilsson RH,Kristiansson E,Ryberg M,Larsson KH

更新日期：2005-07-18 00:00:00

abstract：:Following publication of the original article [1], the author reported that there are several errors in the original article. ...

journal_title：BMC bioinformatics

authors： Ranjard L,Wong TKF,Rodrigo AG

更新日期：2020-01-22 00:00:00

abstract：BACKGROUND:The imputation of missing values is necessary for the efficient use of DNA microarray data, because many clustering algorithms and some statistical analysis require a complete data set. A few imputation methods for DNA microarray data have been introduced, but the efficiency of the methods was low and the va...

journal_title：BMC bioinformatics

authors： Kim KY,Kim BJ,Yi GS

更新日期：2004-10-26 00:00:00

abstract：BACKGROUND:Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. DESCRIPTION:Here we present...

journal_title：BMC bioinformatics

authors： Birkland A,Yona G

更新日期：2006-02-15 00:00:00

abstract：BACKGROUND:Many models have been proposed to detect copy number alterations in chromosomal copy number profiles, but it is usually not obvious to decide which is most effective for a given data set. Furthermore, most methods have a smoothing parameter that determines the number of breakpoints and must be chosen using v...

journal_title：BMC bioinformatics

authors： Hocking TD,Schleiermacher G,Janoueix-Lerosey I,Boeva V,Cappo J,Delattre O,Bach F,Vert JP

更新日期：2013-05-22 00:00:00

abstract：BACKGROUND:Heart disease (HD) is one of the most common diseases nowadays, and an early diagnosis of such a disease is a crucial task for many health care providers to prevent their patients for such a disease and to save lives. In this paper, a comparative analysis of different classifiers was performed for the classi...

journal_title：BMC bioinformatics

authors： Almustafa KM

更新日期：2020-07-02 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:Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential ...

journal_title：BMC bioinformatics

authors： Li X,Fu Y,Wang X,Qiu W

更新日期：2018-05-18 00:00:00

abstract：BACKGROUND:In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein-small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (MC) and REMC sampling methods, these methods use multi-objective optimization Pareto front informatio...

journal_title：BMC bioinformatics

authors： Wang H,Liu H,Cai L,Wang C,Lv Q

更新日期：2017-07-10 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:Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many...

journal_title：BMC bioinformatics

authors： Vainshtein Y,Sanchez M,Brazma A,Hentze MW,Dandekar T,Muckenthaler MU

更新日期：2010-03-01 00:00:00

abstract：BACKGROUND:A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes. Si...

journal_title：BMC bioinformatics

authors： Alanko J,Cunial F,Belazzougui D,Mäkinen V

更新日期：2017-03-14 00:00:00

abstract：BACKGROUND:The misregulation of microRNA (miRNA) has been shown to cause diseases. Recently, we have proposed a computational method based on a random walk framework on a miRNA-target gene network to predict disease-associated miRNAs. The prediction performance of our method is better than that of some existing state-o...

journal_title：BMC bioinformatics

authors： Le DH,Tran TTH

更新日期：2020-06-15 00:00:00

abstract：BACKGROUND:Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant data. Shared data science infrastructures like Boag is needed to efficiently process and parse data co...

journal_title：BMC bioinformatics

authors： Bagheri H,Muppirala U,Masonbrink RE,Severin AJ,Rajan H

更新日期：2019-08-22 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 distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS). Applied to p...

journal_title：BMC bioinformatics

authors： Pelé J,Bécu JM,Abdi H,Chabbert M

更新日期：2012-06-15 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:Text mining tools have gained popularity to process the vast amount of available research articles in the biomedical literature. It is crucial that such tools extract information with a sufficient level of detail to be applicable in real life scenarios. Studies of mining non-causal molecular relations attrib...

journal_title：BMC bioinformatics

authors： Van Landeghem S,Björne J,Abeel T,De Baets B,Salakoski T,Van de Peer Y

更新日期：2012-06-26 00:00:00

abstract：BACKGROUND:Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematica...

journal_title：BMC bioinformatics

authors： Chain B,Bowen H,Hammond J,Posch W,Rasaiyaah J,Tsang J,Noursadeghi M

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure eleme...

journal_title：BMC bioinformatics

authors： Kolbeck B,May P,Schmidt-Goenner T,Steinke T,Knapp EW

更新日期：2006-11-21 00:00:00

abstract：BACKGROUND:Nearly all cellular processes involve proteins structurally rearranging to accommodate molecular partners. The energy landscape underscores the inherent nature of proteins as dynamic molecules interconverting between structures with varying energies. In principle, reconstructing a protein's energy landscape ...

journal_title：BMC bioinformatics

authors： Morris D,Maximova T,Plaku E,Shehu A

更新日期：2019-06-06 00:00:00

abstract：BACKGROUND:Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, integrative analysis have been performed by using genomics, transcriptomics, epigenomics, proteomics an...

journal_title：BMC bioinformatics

authors： Zengin T,Önal-Süzek T

更新日期：2020-09-30 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