Island method for estimating the statistical significance of profile-profile alignment scores.

abstract：BACKGROUND:Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presen...

journal_title：BMC bioinformatics

authors： Wenskovitch JE Jr,Harris LA,Tapia JJ,Faeder JR,Marai GE

更新日期：2014-09-25 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysa...

journal_title：BMC bioinformatics

authors： Kim JG,Park D,Kim BC,Cho SW,Kim YT,Park YJ,Cho HJ,Park H,Kim KB,Yoon KO,Park SJ,Lee BM,Bhak J

更新日期：2008-01-24 00:00:00

abstract：BACKGROUND:The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required. RESULTS:In order to improve accessibil...

journal_title：BMC bioinformatics

authors： Deng M,Brägelmann J,Schultze JL,Perner S

更新日期：2016-02-06 00:00:00

abstract：BACKGROUND:The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accurately acquiring the synaptic connectivity, and they cannot effectively alleviate the burden of synaps...

journal_title：BMC bioinformatics

authors： Xiao C,Li W,Deng H,Chen X,Yang Y,Xie Q,Han H

更新日期：2018-07-13 00:00:00

abstract：BACKGROUND:Systems biology modeling from microarray data requires the most contemporary structural and functional array annotation. However, microarray annotations, especially for non-commercial, non-traditional biomedical model organisms, are often dated. In addition, most microarray analysis tools do not readily acce...

journal_title：BMC bioinformatics

authors： van den Berg BH,Konieczka JH,McCarthy FM,Burgess SC

更新日期：2009-01-23 00:00:00

abstract：BACKGROUND:Cancer progression is caused by the sequential accumulation of mutations, but not all orders of accumulation are equally likely. When the fixation of some mutations depends on the presence of previous ones, identifying restrictions in the order of accumulation of mutations can lead to the discovery of therap...

journal_title：BMC bioinformatics

authors： Diaz-Uriarte R

更新日期：2015-02-12 00:00:00

abstract：BACKGROUND:High-throughput technology allows for genome-wide measurements at different molecular levels for the same patient, e.g. single nucleotide polymorphisms (SNPs) and gene expression. Correspondingly, it might be beneficial to also integrate complementary information from different molecular levels when building...

journal_title：BMC bioinformatics

authors： Hieke S,Benner A,Schlenl RF,Schumacher M,Bullinger L,Binder H

更新日期：2016-08-30 00:00:00

abstract：BACKGROUND:We investigate the relationships between the EC (Enzyme Commission) class, the associated chemical reaction, and the reaction mechanism by building predictive models using Support Vector Machine (SVM), Random Forest (RF) and k-Nearest Neighbours (kNN). We consider two ways of encoding the reaction mechanism ...

journal_title：BMC bioinformatics

authors： Nath N,Mitchell JB

更新日期：2012-04-24 00:00:00

abstract：BACKGROUND:While researchers have utilized versions of the Affymetrix human GeneChip for the assessment of expression patterns in non human primate (NHP) samples, there has been no comprehensive sequence analysis study undertaken to demonstrate that the probe sequences designed to detect human transcripts are reliably ...

journal_title：BMC bioinformatics

authors： Wang Z,Lewis MG,Nau ME,Arnold A,Vahey MT

更新日期：2004-10-26 00:00:00

abstract：BACKGROUND:Bioluminescent proteins (BLPs) widely exist in many living organisms. As BLPs are featured by the capability of emitting lights, they can be served as biomarkers and easily detected in biomedical research, such as gene expression analysis and signal transduction pathways. Therefore, accurate identification o...

journal_title：BMC bioinformatics

authors： Zhang J,Chai H,Yang G,Ma Z

更新日期：2017-06-05 00:00:00

abstract：BACKGROUND:Analysis of gene expression data in terms of a priori-defined gene sets has recently received significant attention as this approach typically yields more compact and interpretable results than those produced by traditional methods that rely on individual genes. The set-level strategy can also be adopted wit...

journal_title：BMC bioinformatics

authors： Holec M,Kléma J,Zelezný F,Tolar J

更新日期：2012-06-25 00:00:00

abstract：BACKGROUND:The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further proc...

journal_title：BMC bioinformatics

authors： Choo KH,Tan TW,Ranganathan S

更新日期：2005-10-13 00:00:00

abstract：BACKGROUND:With the advent of Next-Generation Sequencing technologies (NGS), a large amount of short read data has been generated. If a reference genome is not available, the assembly of a template sequence is usually challenging because of repeats and the short length of reads. When NGS reads cannot be mapped onto a r...

journal_title：BMC bioinformatics

authors： Comin M,Schimd M

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Event sequences where different types of events often occur close together arise, e.g., when studying potential transcription factor binding sites (TFBS, events) of certain transcription factors (TF, types) in a DNA sequence. These events tend to occur in bursts: in some genomic regions there are more genes ...

journal_title：BMC bioinformatics

authors： Haiminen N,Mannila H,Terzi E

更新日期：2008-08-08 00:00:00

abstract：BACKGROUND:Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a 'molecular picture' of the cell state. On the other hand, the genomic responses to a pharmacological or hormonal stimulus are dynamic molecular processes, where t...

journal_title：BMC bioinformatics

authors： Mutarelli M,Cicatiello L,Ferraro L,Grober OM,Ravo M,Facchiano AM,Angelini C,Weisz A

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:This study addresses a recurrent biological problem, that is to define a formal clustering structure for a set of tissues on the basis of the relative abundance of multiple alternatively spliced isoforms mRNAs generated by the same gene. To this aim, we have used a model-based clustering approach, based on a...

journal_title：BMC bioinformatics

authors： Pelosi M,Alfò M,Martella F,Pappalardo E,Musarò A

更新日期：2015-09-15 00:00:00

abstract：BACKGROUND:The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical treatment and medicine research. However, current mainstream variant caller tools have a serious pro...

journal_title：BMC bioinformatics

authors： Xiao A,Wu Z,Dong S

更新日期：2019-02-14 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: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: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：BACKGROUND:Dynamic programming algorithms provide exact solutions to many problems in computational biology, such as sequence alignment, RNA folding, hidden Markov models (HMMs), and scoring of phylogenetic trees. Structurally analogous algorithms compute optimal solutions, evaluate score distributions, and perform sto...

journal_title：BMC bioinformatics

authors： zu Siederdissen CH,Prohaska SJ,Stadler PF

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Observed co-expression of a group of genes is frequently attributed to co-regulation by shared transcription factors. This assumption has led to the hypothesis that promoters of co-expressed genes should share common regulatory motifs, which forms the basis for numerous computational tools that search for th...

journal_title：BMC bioinformatics

authors： Meng G,Mosig A,Vingron M

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:Genetic interaction profiles are highly informative and helpful for understanding the functional linkages between genes, and therefore have been extensively exploited for annotating gene functions and dissecting specific pathway structures. However, our understanding is rather limited to the relationship bet...

journal_title：BMC bioinformatics

authors： You ZH,Yin Z,Han K,Huang DS,Zhou X

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole-cell scale. In such representations, the cell is considered as a system composed of interlocked sub...

journal_title：BMC bioinformatics

authors： Henry V,Saïs F,Inizan O,Marchadier E,Dibie J,Goelzer A,Fromion V

更新日期：2020-07-23 00:00:00

abstract：BACKGROUND:This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulatio...

journal_title：BMC bioinformatics

authors： Barros RC,Winck AT,Machado KS,Basgalupp MP,de Carvalho AC,Ruiz DD,de Souza ON

更新日期：2012-11-21 00:00:00

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: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

abstract：BACKGROUND:Interpretation of gene expression microarray data in the light of external information on both columns and rows (experimental variables and gene annotations) facilitates the extraction of pertinent information hidden in these complex data. Biologists classically interpret genes of interest after retrieving f...

journal_title：BMC bioinformatics

authors： Baty F,Rüdiger J,Miglino N,Kern L,Borger P,Brutsche M

更新日期：2013-06-06 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:MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes ba...

journal_title：BMC bioinformatics

authors： González JR,Carrasco JL,Armengol L,Villatoro S,Jover L,Yasui Y,Estivill X

更新日期：2008-06-04 00:00:00