Page 131 of 249
A Gene Reference Into Function (GeneRIF) describes novel functionality of genes. GeneRIFs are available from the National Center for Biotechnology Information (NCBI) Gene database. GeneRIF indexing is performe...
Machine learning techniques are becoming useful as an alternative approach to conventional medical diagnosis or prognosis as they are good for handling noisy and incomplete data, and significant results can be...
ImmunoPrecipitation (IP) efficiencies may vary largely between different antibodies and between repeated experiments with the same antibody. These differences have a large impact on the quality of ChIP-seq dat...
The de novo design of a novel protein with a particular function remains a formidable challenge with only isolated and hard-to-repeat successes to date. Due to their many structurally conserved features, antibodi...
In the past decade, bioinformatics tools have matured enough to reliably perform sophisticated primary data analysis on Next Generation Sequencing (NGS) data, such as mapping, assemblies and variant calling, h...
Genome-wide association studies have become very popular in identifying genetic contributions to phenotypes. Millions of SNPs are being tested for their association with diseases and traits using linear or log...
Two-channel (or two-color) microarrays are cost-effective platforms for comparative analysis of gene expression. They are traditionally analysed in terms of the log-ratios (M-values) of the two channel intensi...
Many models have been proposed to detect copy number alterations in chromosomal copy number profiles, but it is usually not obvious to decide which is most effective for a given data set. Furthermore, most met...
Predicting protein complexes from protein-protein interaction data is becoming a fundamental problem in computational biology. The identification and characterization of protein complexes implicated are crucia...
Calcium (Ca2+) propagates within tissues serving as an important information carrier. In particular, cilia beat frequency in oviduct cells is partially regulated by Ca2+ changes. Thus, measuring the calcium de...
Motifs are significant patterns in DNA, RNA, and protein sequences, which play an important role in biological processes and functions, like identification of open reading frames, RNA transcription, protein bi...
The k-mer counting problem, which is to build the histogram of occurrences of every k-symbol long substring in a given text, is important for many bioinformatics applications. They include developing de Bruijn gr...
Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and function...
Scientists rarely reuse expert knowledge of phylogeny, in spite of years ofeffort to assemble a great “Tree of Life” (ToL). A notableexception involves the use of Phylomatic, which provides tools togenerate custo...
In recent years there has been a growing interest in the role of copy number variations (CNV) in genetic diseases. Though there has been rapid development of technologies and statistical methods devoted to det...
Complex diseases induce perturbations to interaction and regulation networks in living systems, resulting in dynamic equilibrium states that differ for different diseases and also normal states. Thus identifyi...
This article is part of a Supplement: Volume 14 Supplement 8
Protein-protein interactions (PPIs) play crucial roles in the execution of various cellular processes and form the basis of biological mechanisms. Although large amount of PPIs data for different species has b...
This article is part of a Supplement: Volume 14 Supplement 8
Ion mobility-mass spectrometry (IMMS), an analytical technique which combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS), can rapidly separates ions on a millisecond time-scale....
This article is part of a Supplement: Volume 14 Supplement 8
Recent microbiologic studies have shown that quorum sensing mechanisms, which serve as one of the fundamental requirements for bacterial survival, exist widely in bacterial intra- and inter-species cell-cell c...
This article is part of a Supplement: Volume 14 Supplement 8
Huge numbers of genomes can now be sequenced rapidly with recent improvements in sequencing throughput. However, data analysis methods have not kept up, making it difficult to process the vast amounts of avail...
This article is part of a Supplement: Volume 14 Supplement 8
Comparison of short peptides which form amyloid-fibrils with their homologues that may form amorphous β-aggregates but not fibrils, can aid development of novel amyloid-containing nanomaterials with well defin...
This article is part of a Supplement: Volume 14 Supplement 8
Discovering the molecular targets of compounds or the cause of physiological conditions, among the multitude of known genes, is one of the major challenges of bioinformatics. One of the most common approaches ...
This article is part of a Supplement: Volume 14 Supplement 8
Understanding the localization of proteins in cells is vital to characterizing their functions and possible interactions. As a result, identifying the (sub)cellular compartment within which a protein is locate...
This article is part of a Supplement: Volume 14 Supplement 8
How to identify a set of genes that are relevant to a key biological process is an important issue in current molecular biology. In this paper, we propose a novel method to discover differentially expressed ge...
This article is part of a Supplement: Volume 14 Supplement 8
A weighted biological sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. We attempt to locate all the tandem repeats in a weighted sequen...
This article is part of a Supplement: Volume 14 Supplement 8
The HLA (human leukocyte antigen) class I is a kind of molecule encoded by a large family of genes and is characteristic of high polymorphism. Now the number of the registered HLA-I molecules has exceeded 3000...
This article is part of a Supplement: Volume 14 Supplement 8
Vibrational spectroscopic imaging is now used in several fields to acquire molecular information from microscopically heterogeneous systems. Recent advances have led to promising applications in tissue analysi...
Glycoproteins are involved in a diverse range of biochemical and biological processes. Changes in protein glycosylation are believed to occur in many diseases, particularly during cancer initiation and progres...
We can describe protein-protein interactions (PPIs) as sets of distinct domain-domain interactions (DDIs) that mediate the physical interactions between proteins. Experimental data confirm that DDIs are more c...
Many gene expression normalization algorithms exist for Affymetrix GeneChip microarrays. The most popular of these is RMA, primarily due to the precision and low noise produced during the process. A significan...
Many content-based statistical features of secondary structural elements (CBF-PSSEs) have been proposed and achieved promising results in protein structural class prediction, but until now position distributio...
Complex traits may be defined by a range of different criteria. It would result in a loss of information to perform analyses simply on the basis of a final clinical dichotomized affected / unaffected variable.
Copy number variation (CNV) is an important structural variation (SV) in human genome. Various studies have shown that CNVs are associated with complex diseases. Traditional CNV detection methods such as fluor...
With the advancement of next-generation sequencing and transcriptomics technologies, regulatory effects involving RNA, in particular RNA structural changes are being detected. These results often rely on RNA s...
High-throughput sequencing can identify numerous potential genomic targets for microbial strain typing, but identification of the most informative combinations requires the use of computational screening tools...
The use of tissue microarrays (TMA) and advances in digital scanning microscopy has enabled the collection of thousands of tissue images. There is a need for software tools to annotate, query and share this da...
Most of the institutional and research information in the biomedical domain is available in the form of English text. Even in countries where English is an official language, such as the United States, languag...
Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed...
Analysis and interpretation of biological networks is one of the primary goals of systems biology. In this context identification of sub-networks connecting sets of seed proteins or seed genes plays a crucial ...
Reliability and Reproducibility of differentially expressed genes (DEGs) are essential for the biological interpretation of microarray data. The microarray quality control (MAQC) project launched by US Food an...
RNAalifold, a popular computational method for RNA consensus structure prediction, incorporates covarying mutations into a thermodynamic model to fold the aligned RNA sequences. When quantifying covariance, it...
Comparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under...
The binding of transcription factors to DNA plays an essential role in the regulation of gene expression. Numerous experiments elucidated binding sequences which subsequently have been used to derive statistic...
Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile app...
Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved translation efforts of...
Biological networks tend to have high interconnectivity, complex topologies and multiple types of interactions. This renders difficult the identification of sub-networks that are involved in condition- specifi...
Perturbations in intestinal microbiota composition have been associated with a variety of gastrointestinal tract-related diseases. The alleviation of symptoms has been achieved using treatments that alter the ...
Pairing of samples arises naturally in many genomic experiments; for example, gene expression in tumour and normal tissue from the same patients. Methods for analysing high-throughput sequencing data from such...
Microscopy image segmentation lays the foundation for shape analysis, motion tracking, and classification of biological objects. Despite its importance, automated segmentation remains challenging for several w...
The BITS2012 meeting, held in Catania on May 2-4, 2012, brought together almost 100 Italian researchers working in the field of Bioinformatics, as well as students in the same or related disciplines. About 90 ...
This article is part of a Supplement: Volume 14 Supplement 7
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