Page 123 of 249
Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies fo...
This article is part of a Supplement: Volume 15 Supplement 3
This article is part of a Supplement: Volume 15 Supplement 3
This article is part of a Supplement: Volume 15 Supplement 3
This report summarizes the scientific content and activities of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB), held in conjunction with the...
This article is part of a Supplement: Volume 15 Supplement 3
Recent increases in genomic studies of the developing human fetus and neonate have led to a need for widespread characterization of the functional roles of genes at different developmental stages. The Gene Ont...
Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often...
The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize th...
Next-generation sequencing (NGS) enables rapid production of billions of bases at a relatively low cost. Mapping reads from next-generation sequencers to a given reference genome is an important first step in ...
The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for...
The rapid advancements in the field of genome sequencing are aiding our understanding on many biological systems. In the last five years, computational biologists and bioinformatics specialists have come up wi...
A challenge in gene expression studies is the reliable identification of differentially expressed genes. In many high-throughput studies, genes are accepted as differentially expressed only if they satisfy sim...
New technologies for analyzing biological samples, like next generation sequencing, are producing a growing amount of data together with quality scores. Moreover, software tools (e.g., for mapping sequence rea...
Cancer subtype information is critically important for understanding tumor heterogeneity. Existing methods to identify cancer subtypes have primarily focused on utilizing generic clustering algorithms (such as...
Several small open reading frames located within the 5′ untranslated regions of mRNAs have recently been shown to be translated. In humans, about 50% of mRNAs contain at least one upstream open reading frame r...
High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases, the evolutionary history an...
Motif searching is an important step in the detection of rare events occurring in a set of DNA or protein sequences. One formulation of the problem is known as (l,d)-motif search or Planted Motif Search (PMS). In...
Under a Markov model of evolution, recoding, or lumping, of the four nucleotides into fewer groups may permit analysis under simpler conditions but may unfortunately yield misleading results unless the evoluti...
This article is part of a Supplement: Volume 15 Supplement 2
Many high throughput sequencing (HTS) approaches, such as the Roche/454 platform, produce sequences in which the quality of the sequence (as measured by a Phred-like quality scores) decreases linearly across a...
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 re...
The diagnosis and prognosis of several diseases can be shortened through the use of different large-scale genome experiments. In this context, microarrays can generate expression data for a huge set of genes. ...
Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clin...
MicroRNAs are small but biologically important RNA molecules. Although different methods can be used for quantification of microRNAs, quantitative PCR is regarded as the reference that is used to validate othe...
Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and ana...
The introduction of next-generation sequencing (NGS) technology has made it possible to detect genomic alterations within tumor cells on a large scale. However, most applications of NGS show the genetic conten...
Discovering novel interactions between HIV-1 and human proteins would greatly contribute to different areas of HIV research. Identification of such interactions leads to a greater insight into drug target pred...
Although endocrine therapy impedes estrogen-ER signaling pathway and thus reduces breast cancer mortality, patients remain at continued risk of relapse after tamoxifen or other endocrine therapies. Understandi...
This article is part of a Supplement: Volume 15 Supplement 2
Automated assignment of functions to unknown proteins is one of the most important task in computational biology. The development of experimental methods for genome scale analysis of molecular interaction netw...
This article is part of a Supplement: Volume 15 Supplement 2
Three dimensional structure prediction of a protein from its amino acid sequence, known as protein folding, is one of the most studied computational problem in bioinformatics and computational biology. Since, ...
This article is part of a Supplement: Volume 15 Supplement 2
Protein complexes play important roles in biological systems such as gene regulatory networks and metabolic pathways. Most methods for predicting protein complexes try to find protein complexes with size more ...
This article is part of a Supplement: Volume 15 Supplement 2
In Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare...
This article is part of a Supplement: Volume 15 Supplement 2
Time delays are important factors that are often neglected in gene regulatory network (GRN) inference models. Validating time delays from knowledge bases is a challenge since the vast majority of biological da...
This article is part of a Supplement: Volume 15 Supplement 2
Protein remote homology detection is one of the central problems in bioinformatics, which is important for both basic research and practical application. Currently, discriminative methods based on Support Vect...
This article is part of a Supplement: Volume 15 Supplement 2
Clustering is crucial for gene expression data analysis. As an unsupervised exploratory procedure its results can help researchers to gain insights and formulate new hypothesis about biological data from micro...
This article is part of a Supplement: Volume 15 Supplement 2
Protein function is closely intertwined with protein structure. Discovery of meaningful structure-function relationships is of utmost importance in protein biochemistry and has led to creation of high-quality,...
This article is part of a Supplement: Volume 15 Supplement 2
An ion mobility (IM) spectrometer coupled with a multi-capillary column (MCC) measures volatile organic compounds (VOCs) in the air or in exhaled breath. This technique is utilized in several biotechnological ...
The interest of the scientific community in investigating the impact of rare variants on complex traits has stimulated the development of novel statistical methodologies for association studies. The fact that ...
The methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation h...
The comparative modeling approach to protein structure prediction inherently relies on a template structure. Before building a model such a template protein has to be found and aligned with the query sequence....
Glioblastoma is the most aggressive primary central nervous tumor and carries a very poor prognosis. Invasion precludes effective treatment and virtually assures tumor recurrence. In the current study, we appl...
Structural study of retinal blood vessels provides an early indication of diseases such as diabetic retinopathy, glaucoma, and hypertensive retinopathy. These studies require accurate tracing of retinal vessel...
Automated gene-calling is still an error-prone process, particularly for the highly plastic genomes of fungal species. Improvement through quality control and manual curation of gene models is a time-consuming...
Information about genes, transcripts and proteins is spread over a wide variety of databases. Different tools have been developed using these databases to identify biological signals in gene lists from large s...
Independent data sources can be used to augment post-marketing drug safety signal detection. The vast amount of publicly available biomedical literature contains rich side effect information for drugs at all c...
Computational methods for the prediction of protein features from sequence are a long-standing focus of bioinformatics. A key observation is that several protein features are closely inter-related, that is, th...
Given the estimate that 30% of our genes are controlled by microRNAs, it is essential that we understand the precise relationship between microRNAs and their targets. OncomiRs are microRNAs (miRNAs) that have ...
Different methods have been proposed for analyzing differentially expressed (DE) genes in microarray data. Methods based on statistical tests that incorporate expression level variability are used more commonl...
Gene set analysis (GSA) is useful in deducing biological significance of gene lists using a priori defined gene sets such as gene ontology (GO) or pathways. Phenotypic annotation is sparse for human genes, but...
Interpretation of binding modes of protein–small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and ...
The Kruskal-Wallis test is a popular non-parametric statistical test for identifying expression quantitative trait loci (eQTLs) from genome-wide data due to its robustness against variations in the underlying ...
View featured videos from across the BMC-series journals
Citation Impact 2023
Journal Impact Factor: 2.9
5-year Journal Impact Factor: 3.6
Source Normalized Impact per Paper (SNIP): 0.821
SCImago Journal Rank (SJR): 1.005
Speed 2023
Submission to first editorial decision (median days): 12
Submission to acceptance (median days): 146
Usage 2023
Downloads: 5,987,678
Altmetric mentions: 4,858