BMC Bioinformatics

Items from 1 to 20 out of 3,155 results

article

Benchmarking tools for the alignment of functional noncoding DNA

Daniel A Pollard, Casey M Bergman, Jens Stoye, Susan E Celniker, more

BMC Bioinformatics > 2004 > 5 > 1 > 1-17

Background Numerous tools have been developed to align genomic sequences. However, their relative performance in specific applications remains poorly characterized. Alignments of protein-coding sequences typically have been benchmarked against "correct" alignments inferred from structural data. For noncoding sequences, where such independent validation is lacking, simulation provides an...

article

Determination of the differentially expressed genes in microarray experiments using local FDR

J Aubert, A Bar-Hen, J-J Daudin, S Robin

BMC Bioinformatics > 2004 > 5 > 1 > 1-9

Background Thousands of genes in a genomewide data set are tested against some null hypothesis, for detecting differentially expressed genes in microarray experiments. The expected proportion of false positive genes in a set of genes, called the False Discovery Rate (FDR), has been proposed to measure the statistical significance of this set. Various procedures exist for controlling the FDR. However...

article

Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment

Tomokazu Konishi

BMC Bioinformatics > 2004 > 5 > 1 > 1-17

Background To cancel experimental variations, microarray data must be normalized prior to analysis. Where an appropriate model for statistical data distribution is available, a parametric method can normalize a group of data sets that have common distributions. Although such models have been proposed for microarray data, they have not always fit the distribution of real data and thus have been inappropriate...

article

Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity

Fran Supek, Kristian Vlahoviček

BMC Bioinformatics > 2005 > 6 > 1 > 1-15

Background There are a number of methods (also called: measures) currently in use that quantify codon usage in genes. These measures are often influenced by other sequence properties, such as length. This can introduce strong methodological bias into measurements; therefore we attempted to develop a method free from such dependencies. One of the common applications of codon usage analyses is to quantitatively...

article

Versatile and declarative dynamic programming using pair algebras

Peter Steffen, Robert Giegerich

BMC Bioinformatics > 2005 > 6 > 1 > 1-13

Background Dynamic programming is a widely used programming technique in bioinformatics. In sharp contrast to the simplicity of textbook examples, implementing a dynamic programming algorithm for a novel and non-trivial application is a tedious and error prone task. The algebraic dynamic programming approach seeks to alleviate this situation by clearly separating the dynamic programming recurrences...

article

Genetic algorithm learning as a robust approach to RNA editing site prediction

James Thompson, Shuba Gopal

BMC Bioinformatics > 2006 > 7 > 1 > 1-12

Background RNA editing is one of several post-transcriptional modifications that may contribute to organismal complexity in the face of limited gene complement in a genome. One form, known as C → U editing, appears to exist in a wide range of organisms, but most instances of this form of RNA editing have been discovered serendipitously. With the large amount of genomic and transcriptomic data now...

article

Splice site identification using probabilistic parameters and SVM classification

Akma Baten, Bch Chang, Sk Halgamuge, Jason Li

BMC Bioinformatics > 2006 > 7 > 5 > 1-15

Background Recent advances and automation in DNA sequencing technology has created a vast amount of DNA sequence data. This increasing growth of sequence data demands better and efficient analysis methods. Identifying genes in this newly accumulated data is an important issue in bioinformatics, and it requires the prediction of the complete gene structure. Accurate identification of splice sites in...

article

Inference of miRNA targets using evolutionary conservation and pathway analysis

Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan

BMC Bioinformatics > 2007 > 8 > 1 > 1-22

Background MicroRNAs have emerged as important regulatory genes in a variety of cellular processes and, in recent years, hundreds of such genes have been discovered in animals. In contrast, functional annotations are available only for a very small fraction of these miRNAs, and even in these cases only partially. Results We developed a general Bayesian method for the inference of miRNA target sites,...

article

PatternLab for proteomics: a tool for differential shotgun proteomics

Paulo C Carvalho, Juliana Sg Fischer, Emily I Chen, John R Yates, more

BMC Bioinformatics > 2008 > 9 > 1 > 1-14

Background A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with its abundance in a mixture; however, two issues...

article

AtPIN: Arabidopsis thaliana Protein Interaction Network

Marcelo M Brandão, Luiza L Dantas, Marcio C Silva-Filho

BMC Bioinformatics > 2009 > 10 > 1 > 1-7

Background Protein-protein interactions (PPIs) constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. Description All interactions were divided into experimentally demonstrated...

article

Integrative approaches to the prediction of protein functions based on the feature selection

Seokha Ko, Hyunju Lee

BMC Bioinformatics > 2009 > 10 > 1 > 1-19

Background Protein function prediction has been one of the most important issues in functional genomics. With the current availability of various genomic data sets, many researchers have attempted to develop integration models that combine all available genomic data for protein function prediction. These efforts have resulted in the improvement of prediction quality and the extension of prediction...

article

Disease candidate gene identification and prioritization using protein interaction networks

Jing Chen, Bruce J Aronow, Anil G Jegga

BMC Bioinformatics > 2009 > 10 > 1 > 1-14

Background Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the current study, we describe a candidate gene prioritization method that is entirely based on protein-protein interaction network (PPIN) analyses. Results For the first time, extended...

article

In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase

Sayak Ganguli, Manjita Mazumder, Protip Basu, Paushali Roy, more

BMC Bioinformatics > 2010 > 11 > 1 > 1-1

This article has been withdrawn from the public domain because of significant plagiarism. In the light of this situation, BioMed Central regrets that this article is no longer available. The authors apologise to all affected parties for the inconvenience.

article

A two-step site and mRNA-level model for predicting microRNA targets

Takaya Saito, Pål Sætrom

BMC Bioinformatics > 2010 > 11 > 1 > 1-10

Background Despite experiments showing that the number of microRNA (miRNA) target sites is critical for miRNA targeting, most existing methods focus on identifying individual miRNA target sites and do not model contributions of multiple target sites to miRNA regulation. To address this possible fault, we developed a miRNA target prediction model that recognizes the individual characteristics of functional...

article

Erratum to: PathEx: A novel multi factors based datasets selector web tool

Eric Bareke, Michael Pierre, Anthoula Gaigneaux, Bertrand De Meulder, more

BMC Bioinformatics > 2010 > 11 > 1 > 1-1

article

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

Aaron M Newman, James B Cooper

BMC Bioinformatics > 2010 > 11 > 1 > 1-15

Background Clustering the information content of large high-dimensional gene expression datasets has widespread application in "omics" biology. Unfortunately, the underlying structure of these natural datasets is often fuzzy, and the computational identification of data clusters generally requires knowledge about cluster number and geometry. Results We integrated strategies from machine...

article

MINE: Module Identification in Networks

Kahn Rhrissorrakrai, Kristin C Gunsalus

BMC Bioinformatics > 2011 > 12 > 1 > 1-10

Background Graphical models of network associations are useful for both visualizing and integrating multiple types of association data. Identifying modules, or groups of functionally related gene products, is an important challenge in analyzing biological networks. However, existing tools to identify modules are insufficient when applied to dense networks of experimentally derived interaction data...

article

The G protein-coupled receptors in the pufferfish Takifugu rubripes

Anita Sarkar, Sonu Kumar, Durai Sundar

BMC Bioinformatics > 2011 > 12 > 1 > 1-9

Background Guanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as “molecular switches” in the second messenger cascades and are found in all organisms between yeast and humans. They form the single, biggest drug-target family due to their versatility of action and their role in several physiological functions, being active players in detecting...

article

An automated homology-based approach for identifying transposable elements

Ryan C Kennedy, Maria F Unger, Scott Christley, Frank H Collins, more

BMC Bioinformatics > 2011 > 12 > 1 > 1-10

Background Transposable elements (TEs) are mobile sequences found in nearly all eukaryotic genomes. They have the ability to move and replicate within a genome, often influencing genome evolution and gene expression. The identification of TEs is an important part of every genome project. The number of sequenced genomes is rapidly rising, and the need to identify TEs within them is also growing. The...

article

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li, Colin N Dewey

BMC Bioinformatics > 2011 > 12 > 1 > 1-16

Background RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms...

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MACHINE LEARNING (122)
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TRANSCRIPTOMICS (12)
COPY NUMBER VARIATION (11)
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INFONA - science communication portal

BMC Bioinformatics

Benchmarking tools for the alignment of functional noncoding DNA

Determination of the differentially expressed genes in microarray experiments using local FDR

Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment

Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity

Versatile and declarative dynamic programming using pair algebras

Genetic algorithm learning as a robust approach to RNA editing site prediction

Splice site identification using probabilistic parameters and SVM classification

Inference of miRNA targets using evolutionary conservation and pathway analysis

PatternLab for proteomics: a tool for differential shotgun proteomics

AtPIN: Arabidopsis thaliana Protein Interaction Network

Integrative approaches to the prediction of protein functions based on the feature selection

Disease candidate gene identification and prioritization using protein interaction networks

In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase

A two-step site and mRNA-level model for predicting microRNA targets

Erratum to: PathEx: A novel multi factors based datasets selector web tool

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

MINE: Module Identification in Networks

The G protein-coupled receptors in the pufferfish Takifugu rubripes

An automated homology-based approach for identifying transposable elements

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

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