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Analyzing spatial distributions of objects in images is a fundamental task in many biological studies. The relative arrangement of a set of objects with respect to another set of objects contains information a...
Protein complexes are basic cellular entities that carry out the functions of their components. It can be found that in databases of protein complexes of yeast like CYC2008, the major type of known protein com...
Disulfide engineering is an important biotechnological tool that has advanced a wide range of research. The introduction of novel disulfide bonds into proteins has been used extensively to improve protein stab...
Protein kinases are involved in relevant physiological functions and a broad number of mutations in this superfamily have been reported in the literature to affect protein function and stability. Unfortunately...
Within Flux Balance Analysis, the investigation of complex subtasks, such as finding the optimal perturbation of the network or finding an optimal combination of drugs, often requires to set up a bilevel optim...
Membrane transporters catalyze the transport of small solute molecules across biological barriers such as lipid bilayer membranes. Experimental identification of the transported substrates is very tedious. Onc...
Proteins perform their functions in associated cellular locations. Therefore, the study of protein function can be facilitated by predictions of protein location. Protein location can be predicted either from ...
A novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactat...
Gene expression profiling and other genome-scale measurement technologies provide comprehensive information about molecular changes resulting from a chemical or genetic perturbation, or disease state. A critic...
Hidden Markov models are widely used for genome analysis as they combine ease of modelling with efficient analysis algorithms. Calculating the likelihood of a model using the forward algorithm has worst case t...
Determining sample sizes for metabolomic experiments is important but due to the complexity of these experiments, there are currently no standard methods for sample size estimation in metabolomics. Since pilot...
DNA methylation has been linked to many important biological phenomena. Researchers have recently begun to sequence bisulfite treated DNA to determine its pattern of methylation. However, sequencing reads from...
Discovering functional relationships of genes through cell-based phenotyping has become an important approach in functional genomics. High-throughput imaging offers the ability to quantitatively assess complex...
Small peptides encoded as one- or two-exon genes in plants have recently been shown to affect multiple aspects of plant development, reproduction and defense responses. However, popular similarity search tools...
Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computat...
Unsupervised segmentation of multi-spectral images plays an important role in annotating infrared microscopic images and is an essential step in label-free spectral histopathology. In this context, diverse clu...
Genes located in the same chromosome region share common evolutionary events more often than other genes (e.g. a segmental duplication of this region). Their evolution may also be related if they are involved ...
Y haplogroup analyses are an important component of genealogical reconstruction, population genetic analyses, medical genetics and forensics. These fields are increasingly moving towards use of low-coverage, h...
In the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a f...
Leishmaniasis is a neglected tropical disease which affects approx. 12 million individuals worldwide and caused by parasite Leishmania. The current drugs used in the treatment of Leishmaniasis are highly toxic an...
Recently a series of algorithms have been developed, providing automatic tools for tracing C. elegans embryonic cell lineage. In these algorithms, 3D images collected from a confocal laser scanning microscope wer...
The NTF2-like superfamily is a versatile group of protein domains sharing a common fold. The sequences of these domains are very diverse and they share no common sequence motif. These domains serve a range of ...
A typical bacterial pathogen genome mapping project can identify thousands of single nucleotide polymorphisms (SNP). Interpreting SNP data is complex and it is difficult to conceptualise the data contained wit...
The common ancestor of salmonid fishes, including rainbow trout (Oncorhynchus mykiss), experienced a whole genome duplication between 20 and 100 million years ago, and many of the duplicated genes have been retai...
Phylogenetic comparative analyses usually rely on a single consensus phylogenetic tree in order to study evolutionary processes. However, most phylogenetic trees are incomplete with regard to species sampling,...
In order to access the large amount of information in biomedical literature about genes implicated in various cancers both efficiently and accurately, the aid of text mining (TM) systems is invaluable. Current...
The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux,...
Plants regulate intrinsic gene expression through transcription factors (TFs), transcriptional regulators (TRs), chromatin regulators (CRs), and the basal transcription machinery. An understanding of plant gen...
Calcium imaging in insects reveals the neural response to odours, both at the receptor level on the antenna and in the antennal lobe, the first stage of olfactory information processing in the brain. Changes o...
This article is part of a Supplement: Volume 14 Supplement 19
The internal cavities of proteins are dynamic structures and their dynamics may be associated with conformational changes which are required for the functioning of the protein. In order to study the dynamics o...
This article is part of a Supplement: Volume 14 Supplement 19
Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel techniq...
This article is part of a Supplement: Volume 14 Supplement 19
Jointly analyzing biological pathway maps and experimental data is critical for understanding how biological processes work in different conditions and why different samples exhibit certain characteristics. Th...
This article is part of a Supplement: Volume 14 Supplement 19
Mathematical models are nowadays widely used to describe biochemical reaction networks. One of the main reasons for this is that models facilitate the integration of a multitude of different data and data type...
This article is part of a Supplement: Volume 14 Supplement 19
High throughput gene expression time-course experiments provide a perspective on biological functioning recognized as having huge value for the diagnosis, treatment, and prevention of diseases. There are howev...
This article is part of a Supplement: Volume 14 Supplement 19
The production of multiple transcript isoforms from one gene is a major source of transcriptome complexity. RNA-Seq experiments, in which transcripts are converted to cDNA and sequenced, allow the resolution a...
Multi-cellular segmentation of bright field microscopy images is an essential computational step when quantifying collective migration of cells in vitro. Despite the availability of various tools and algorithm...
Constrained minimal cut sets (cMCSs) have recently been introduced as a framework to enumerate minimal genetic intervention strategies for targeted optimization of metabolic networks. Two different algorithmic...
As sequence data sets used for the investigation of pathogen transmission patterns increase in size, automated tools and standardized methods for cluster analysis have become necessary. We have developed an au...
Gene regulatory networks (GRN) inference is an important bioinformatics problem in which the gene interactions need to be deduced from gene expression data, such as microarray data. Feature selection methods c...
This article is part of a Supplement: Volume 14 Supplement 18
In the antennal lobe, a dedicated olfactory center of the honeybee brain, odours are encoded as activity patterns of coding units, the so-called glomeruli. Optical imaging with calcium-sensitive dyes allows us...
This article is part of a Supplement: Volume 14 Supplement 18
Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and ...
This article is part of a Supplement: Volume 14 Supplement 18
We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains ...
This article is part of a Supplement: Volume 14 Supplement 18
Subtypes are widely found in cancer. They are characterized with different behaviors in clinical and molecular profiles, such as survival rates, gene signature and copy number aberrations (CNAs). While cancer ...
This article is part of a Supplement: Volume 14 Supplement 18
DCE@urLAB is a software application for analysis of dynamic contrast-enhanced magnetic resonance imaging data (DCE-MRI). The tool incorporates a friendly graphical user interface (GUI) to interactively select ...
Genome annotation is a crucial component of RNA-seq data analysis. Much effort has been devoted to producing an accurate and rational annotation of the human genome. An annotated genome provides a comprehensiv...
This article is part of a Supplement: Volume 14 Supplement 11
Next generation sequencing technologies have greatly advanced many research areas of the biomedical sciences through their capability to generate massive amounts of genetic information at unprecedented rates. ...
This article is part of a Supplement: Volume 14 Supplement 11
In this work, we used the PROV-DM model to manage data provenance in workflows of genome projects. This provenance model allows the storage of details of one workflow execution, e.g., raw and produced data and...
This article is part of a Supplement: Volume 14 Supplement 11
On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool...
This article is part of a Supplement: Volume 14 Supplement 11
A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure suc...
This article is part of a Supplement: Volume 14 Supplement 11
An in silico vaccine discovery pipeline for eukaryotic pathogens typically consists of several computational tools to predict protein characteristics. The aim of the in silico approach to discovering subunit vacc...
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