Improving interoperability between microbial information and sequence databases.

abstract：BACKGROUND:Identifying diagnosis and prognosis biomarkers from expression profiling data is of great significance for achieving personalized medicine and designing therapeutic strategy in complex diseases. However, the reproducibility of identified biomarkers across tissues and experiments is still a challenge for this...

journal_title：BMC bioinformatics

authors： Zhang X,Gao L,Liu ZP,Chen L

更新日期：2015-03-18 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:PSI-BLAST, an extremely popular tool for sequence similarity search, features the utilization of Position-Specific Scoring Matrix (PSSM) constructed from a multiple sequence alignment (MSA). PSSM allows the detection of more distant homologs than a general amino acid substitution matrix does. An accurate est...

journal_title：BMC bioinformatics

authors： Oda T,Lim K,Tomii K

更新日期：2017-06-02 00:00:00

abstract：UNLABELLED: BACKGROUND:Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing...

journal_title：BMC bioinformatics

authors： Antoniw J,Beacham AM,Baldwin TK,Urban M,Rudd JJ,Hammond-Kosack KE

更新日期：2011-11-15 00:00:00

abstract：BACKGROUND:Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but require an impractical number of data points. Screening of a sparse number of doses per drug allows to sc...

journal_title：BMC bioinformatics

authors： Amzallag A,Ramaswamy S,Benes CH

更新日期：2019-02-18 00:00:00

abstract：BACKGROUND:New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. RESULTS:We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifica...

journal_title：BMC bioinformatics

authors： Hofmeister BT,Schmitz RJ

更新日期：2018-04-25 00:00:00

abstract：BACKGROUND:Identifying key components in biological processes and their associations is critical for deciphering cellular functions. Recently, numerous gene expression and molecular interaction experiments have been reported in Saccharomyces cerevisiae, and these have enabled systematic studies. Although a number of ap...

journal_title：BMC bioinformatics

authors： Hsu JT,Peng CH,Hsieh WP,Lan CY,Tang CY

更新日期：2011-07-12 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:InterPro is a collection of protein signatures for the classification and automated annotation of proteins. Interproscan is a software tool that scans protein sequences against Interpro member databases using a variety of profile-based, hidden markov model and positional specific score matrix methods. It not...

journal_title：BMC bioinformatics

authors： Kelly RJ,Vincent DE,Friedberg I

更新日期：2010-12-21 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:Glycation is a one of the post-translational modifications (PTM) where sugar molecules and residues in protein sequences are covalently bonded. It has become one of the clinically important PTM in recent times attributed to many chronic and age related complications. Being a non-enzymatic reaction, it is a g...

journal_title：BMC bioinformatics

authors： Reddy HM,Sharma A,Dehzangi A,Shigemizu D,Chandra AA,Tsunoda T

更新日期：2019-02-04 00:00:00

abstract：BACKGROUND:Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments where adjacent segments have different properties, such as different mean values. Despite dozens of algorithms developed to address this problem in genomics research, methods with...

journal_title：BMC bioinformatics

authors： Girimurugan SB,Liu Y,Lung PY,Vera DL,Dennis JH,Bass HW,Zhang J

更新日期：2018-04-11 00:00:00

abstract：BACKGROUND:Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex...

journal_title：BMC bioinformatics

authors： Gouret P,Vitiello V,Balandraud N,Gilles A,Pontarotti P,Danchin EG

更新日期：2005-08-05 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:Hierarchical Multi-Label Classification is a classification task where the classes to be predicted are hierarchically organized. Each instance can be assigned to classes belonging to more than one path in the hierarchy. This scenario is typically found in protein function prediction, considering that each pr...

journal_title：BMC bioinformatics

authors： Cerri R,Barros RC,P L F de Carvalho AC,Jin Y

更新日期：2016-09-15 00:00:00

abstract：BACKGROUND:Recently, mass spectrometry data have been mined using a genetic algorithm to produce discriminatory models that distinguish healthy individuals from those with cancer. This algorithm is the basis for claims of 100% sensitivity and specificity in two related publicly available datasets. To date, no detailed ...

journal_title：BMC bioinformatics

authors： Jeffries NO

更新日期：2004-11-19 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:Phenotype prediction problems are usually considered ill-posed, as the amount of samples is very limited with respect to the scrutinized genetic probes. This fact complicates the sampling of the defective genetic pathways due to the high number of possible discriminatory genetic networks involved. In this re...

journal_title：BMC bioinformatics

authors： Cernea A,Fernández-Martínez JL,deAndrés-Galiana EJ,Fernández-Ovies FJ,Alvarez-Machancoses O,Fernández-Muñiz Z,Saligan LN,Sonis ST

更新日期：2020-03-11 00:00:00

abstract：BACKGROUND:Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presents a novel method to perform correlations between microarray gene expression data and clinico-pathol...

journal_title：BMC bioinformatics

authors： Corradi L,Mirisola V,Porro I,Torterolo L,Fato M,Romano P,Pfeffer U

更新日期：2009-10-15 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:Infections are often associated to comorbidity that increases the risk of medical conditions which can lead to further morbidity and mortality. SARS is a threat which is similar to MERS virus, but the comorbidity is the key aspect to underline their different impacts. One UK doctor says "I'd rather have HIV ...

journal_title：BMC bioinformatics

authors： Moni MA,Liò P

更新日期：2014-10-24 00:00:00

abstract：BACKGROUND:Intrinsically Disordered Proteins (IDPs) lack an ordered three-dimensional structure and are enriched in various biological processes. The Molecular Recognition Features (MoRFs) are functional regions within IDPs that undergo a disorder-to-order transition on binding to a partner protein. Identifying MoRFs i...

journal_title：BMC bioinformatics

authors： Sharma R,Kumar S,Tsunoda T,Patil A,Sharma A

更新日期：2016-12-22 00:00:00

abstract：BACKGROUND:Analysis of cellular processes with microscopic bright field defocused imaging has the advantage of low phototoxicity and minimal sample preparation. However bright field images lack the contrast and nuclei reporting available with florescent approaches and therefore present a challenge to methods that segme...

journal_title：BMC bioinformatics

authors： Mohamadlou H,Shope JC,Flann NS

更新日期：2014-01-30 00:00:00

abstract：BACKGROUND:With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other...

journal_title：BMC bioinformatics

authors： Bergmann FT,Adams R,Moodie S,Cooper J,Glont M,Golebiewski M,Hucka M,Laibe C,Miller AK,Nickerson DP,Olivier BG,Rodriguez N,Sauro HM,Scharm M,Soiland-Reyes S,Waltemath D,Yvon F,Le Novère N

更新日期：2014-12-14 00:00:00

abstract：BACKGROUND:Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entiti...

journal_title：BMC bioinformatics

authors： Henriques R,Ferreira FL,Madeira SC

更新日期：2017-02-02 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:Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing "outliers" among the objects being clustered. Few clustering algorithms currently deal directly with the outlier pro...

journal_title：BMC bioinformatics

authors： Wang M,Abrams ZB,Kornblau SM,Coombes KR

更新日期：2018-01-08 00:00:00

abstract：BACKGROUND:Accurate somatic mutation-calling is essential for insightful mutation analyses in cancer studies. Several mutation-callers are publicly available and more are likely to appear. Nonetheless, mutation-calling is still challenging and there is unlikely to be one established caller that systematically outperfor...

journal_title：BMC bioinformatics

authors： Kim SY,Jacob L,Speed TP

更新日期：2014-05-21 00:00:00

abstract：BACKGROUND:In this short article, we discuss a simple method for assessing sample size requirements in microarray experiments. RESULTS:Our method starts with the output from a permutation-based analysis for a set of pilot data, e.g. from the SAM package. Then for a given hypothesized mean difference and various sample...

journal_title：BMC bioinformatics

authors： Tibshirani R

更新日期：2006-03-02 00:00:00

abstract：BACKGROUND:Leishmaniasis is a virulent parasitic infection that causes a worldwide disease burden. Most treatments have toxic side-effects and efficacy has decreased due to the emergence of resistant strains. The outlook is worsened by the absence of promising drug targets for this disease. We have taken a computationa...

journal_title：BMC bioinformatics

authors： Flórez AF,Park D,Bhak J,Kim BC,Kuchinsky A,Morris JH,Espinosa J,Muskus C

更新日期：2010-09-27 00:00:00