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Many methods have been developed to test the enrichment of genes related to certain phenotypes or cell states in gene sets. These approaches usually combine gene expression data with functionally related gene ...
In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, the interpretation of each single p-valu...
There has been recent concern regarding the inability of predictive modeling approaches to generalize to new data. Some of the problems can be attributed to improper methods for model selection and assessment....
The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This make...
Protein structure analysis and comparison are major challenges in structural bioinformatics. Despite the existence of many tools and algorithms, very few of them have managed to capture the intuitive understan...
The problem of accurate prediction of protein secondary structure continues to be one of the challenging problems in Bioinformatics. It has been previously suggested that amino acid relative solvent accessibil...
Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, ar...
The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments.
This paper addresses key biological problems and statistical issues in the analysis of large gene expression data sets that describe systemic temporal response cascades to therapeutic doses in multiple tissues...
Despite significant improvements in computational annotation of genomes, sequences of abnormal, incomplete or incorrectly predicted genes and proteins remain abundant in public databases. Since the majority of...
Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies...
In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently ...
In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Mos...
Structural similarities among proteins can provide valuable insight into their functional mechanisms and relationships. As the number of available three-dimensional (3D) protein structures increases, a greater...
Microarray experiments measure changes in the expression of thousands of genes. The resulting lists of genes with changes in expression are then searched for biologically related sets using several divergent m...
Rejection of false positive peptide matches in database searches of shotgun proteomic experimental data is highly desirable. Several methods have been developed to use the peptide retention time as to refine a...
The acceptor photobleaching fluorescence resonance energy transfer (FRET) method is widely used for monitoring molecular interactions in cells. This method of FRET, while among those with the simplest mathemat...
Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Repbase already has software for entering new sequen...
Understanding how proteins fold is essential to our quest in discovering how life works at the molecular level. Current computation power enables researchers to produce a huge amount of folding simulation data...
Tiling arrays are an important tool for the study of transcriptional activity, protein-DNA interactions and chromatin structure on a genome-wide scale at high resolution. Although hidden Markov models have bee...
It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for ...
Slow-fast analysis is a simple and effective method to reduce the influence of substitution saturation, one of the causes of phylogenetic noise and long branch attraction (LBA) artifacts. In several steps of i...
The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA s...
Innumerable biological investigations require comparing collections of molecules, cells or organisms to one another with respect to one or more of their properties. Almost all of these comparisons are performe...
Quasi-steady state approximation (QSSA) based on time-scale analysis is known to be an effective method for simplifying metabolic reaction system, but the conventional analysis becomes time-consuming and tedio...
In studies that use DNA arrays to assess changes in gene expression, it is preferable to measure the significance of treatment effects on a group of genes from a pathway or functional category such as gene ont...
This article is part of a Supplement: Volume 9 Supplement 9
Biological systems can be modeled as complex network systems with many interactions between the components. These interactions give rise to the function and behavior of that system. For example, the protein-pr...
This article is part of a Supplement: Volume 9 Supplement 9
Circadian rhythm is a crucial factor in orchestration of plant physiology, keeping it in synchrony with the daylight cycle. Previous studies have reported that up to 16% of plant transcriptome are circadially ...
This article is part of a Supplement: Volume 9 Supplement 9
Genome-wide association studies (GWAS) aim to identify genetic variants (usually single nucleotide polymorphisms [SNPs]) across the entire human genome that are associated with phenotypic traits such as diseas...
This article is part of a Supplement: Volume 9 Supplement 9
Biological chemistry is very stereospecific. Nonetheless, the diastereotopic oxygen atoms of diphosphate-containing molecules in the Protein Data Bank (PDB) are often given names that do not uniquely distingui...
This article is part of a Supplement: Volume 9 Supplement 9
Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector ...
This article is part of a Supplement: Volume 9 Supplement 9
Over the past decade, many investigators have used sophisticated time series tools for the analysis of genomic sequences. Specifically, the correlation of the nucleotide chain has been studied by examining the...
This article is part of a Supplement: Volume 9 Supplement 9
Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties with potential implications for DNA sequencing. The α-Hemolysin transmembr...
This article is part of a Supplement: Volume 9 Supplement 9
In this paper we present preliminary results stemming from a novel application of Markov Models and Support Vector Machines to splice site classification of Intron-Exon and Exon-Intron (5' and 3') splice sites...
This article is part of a Supplement: Volume 9 Supplement 9
Relationships between entities such as genes, chemicals, metabolites, phenotypes and diseases in MEDLINE are often directional. That is, one may affect the other in a positive or negative manner. Detection of ...
This article is part of a Supplement: Volume 9 Supplement 9
Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not repr...
This article is part of a Supplement: Volume 9 Supplement 9
Advances in DNA microarray technology portend that molecular signatures from which microarray will eventually be used in clinical environments and personalized medicine. Derivation of biomarkers is a large ste...
This article is part of a Supplement: Volume 9 Supplement 9
Metastases are responsible for the majority of cancer fatalities. The molecular mechanisms governing metastasis are poorly understood, hindering early diagnosis and treatment. Previous studies of gene expressi...
This article is part of a Supplement: Volume 9 Supplement 9
Most existing transcriptional databases like Comprehensive Systems-Biology Database (CSB.DB) and Arabidopsis Microarray Database and Analysis Toolbox (GENEVESTIGATOR) help to seek a shared biological role (sim...
This article is part of a Supplement: Volume 9 Supplement 9
In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences....
This article is part of a Supplement: Volume 9 Supplement 9
New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many soft...
This article is part of a Supplement: Volume 9 Supplement 9
A statistically robust and biologically-based approach for analysis of microarray data is described that integrates independent biological knowledge and data with a global F-test for finding genes of interest ...
This article is part of a Supplement: Volume 9 Supplement 9
Single Nucleotide Polymorphisms (SNPs) are the most abundant form of genomic variation and can cause phenotypic differences between individuals, including diseases. Bases are subject to various levels of selec...
This article is part of a Supplement: Volume 9 Supplement 9
Gene family identification from ESTs can be a valuable resource for analysis of genome evolution but presents unique challenges in organisms for which the entire genome is not yet sequenced. We have developed ...
This article is part of a Supplement: Volume 9 Supplement 9
This article is part of a Supplement: Volume 9 Supplement 9
Hypermethylation of promoter CpG islands is strongly correlated to transcriptional gene silencing and epigenetic maintenance of the silenced state. As well as its role in tumor development, CpG island methylat...
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...
Both microarrays and quantitative real-time PCR are convenient tools for studying the transcriptional levels of genes. The former is preferable for large scale studies while the latter is a more targeted techn...
Data mining in large DNA sequences is a major challenge in microbial genomics and bioinformatics. Oligonucleotide usage (OU) patterns provide a wealth of information for large scale sequence analysis and visua...
Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been prop...
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