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Detecting and visualizing nonlinear interaction effects of single nucleotide polymorphisms (SNPs) or epistatic interactions are important topics in bioinformatics since they play an important role in unravelin...
Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for larg...
The underlying molecular processes representing stress responses to low-dose ionising radiation (LDIR) in mammals are just beginning to be understood. In particular, LDIR effects on the brain and their possibl...
Gene expression connectivity mapping has gained much popularity recently with a number of successful applications in biomedical research testifying its utility and promise. Previously methodological research i...
MicroRNAs (miRNAs) impact various biological processes within animals and plants. They complementarily bind target mRNAs, effecting a post-transcriptional negative regulation on mRNA level. The investigation o...
Genomics and proteomics are nowadays the dominant techniques for novel biomarker discovery. However, histopathology images contain a wealth of information related to the tumor histology, morphology and tumor-h...
Trimming of adapter sequences from short read data is a common preprocessing step during NGS data analysis. When performing paired-end sequencing, the overlap between forward and reverse read can be used to id...
Several tools are available for visualizing genomic data. Some, such as Gbrowse and Jbrowse, are very efficient for small genomic regions, but they are not suitable for entire genomes. Others, like Phenogram a...
RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequence...
The targeting of disease-related proteins is important for drug discovery, and yet target-based discovery has not been fruitful. Contextualizing overall biological processes is critical to formulating successf...
SomaLogic’s SOMAscan™ assay platform allows the analysis of the relative abundance of over 1300 proteins directly from biological matrices such as blood plasma and serum. The data resulting from the assay is p...
Non-negative linear combinations of elementary flux modes (EMs) describe all feasible reaction flux distributions for a given metabolic network under the quasi steady state assumption. However, only a small su...
TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for ...
Gene expression connectivity mapping has proven to be a powerful and flexible tool for research. Its application has been shown in a broad range of research topics, most commonly as a means of identifying pote...
Single particle tracking (SPT) is nowadays one of the most popular technique to probe spatio-temporal dynamics of proteins diffusing within the plasma membrane. Indeed membrane components of eukaryotic cells a...
Endocytosis is regarded as a mechanism of attenuating the epidermal growth factor receptor (EGFR) signaling and of receptor degradation. There is increasing evidence becoming available showing that breast canc...
G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and m...
The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S rRNA gene amplicon sequencing). Denoising,...
MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6–8 nucleotide long target sites, usually located wi...
BLOSUM matrices belong to the most commonly used substitution matrix series for protein homology search and sequence alignments since their publication in 1992. In 2008, Styczynski et al. discovered miscalcula...
Detection of tandem duplication within coding exons, referred to as internal tandem duplication (ITD), remains challenging due to inefficiencies in alignment of ITD-containing reads to the reference genome. Th...
We have previously presented a formal language for describing population dynamics based on environment-dependent Stochastic Tree Grammars (eSTG). The language captures in broad terms the effect of the changing...
Recently, high-throughput experimental techniques have generated a large amount of protein-protein interaction (PPI) data which can construct large complex PPI networks for numerous organisms. System biology a...
Network visualization and analysis tools aid in better understanding of complex biological systems. Furthermore, to understand the differences in behaviour of system(s) under various environmental conditions (...
Proteins are the important molecules which participate in virtually every aspect of cellular function within an organism in pairs. Although high-throughput technologies have generated considerable protein-prot...
Cell culture on printed micropatterns slides combined with automated fluorescent microscopy allows for extraction of tens of thousands of videos of small isolated growing cell clusters. The analysis of such la...
There is growing evidence that DNA methylation alterations may contribute to carcinogenesis. Recent data also suggest that DNA methylation field defects in normal pre-neoplastic tissue represent infrequent sto...
Next-generation sequencing has been used by investigators to address a diverse range of biological problems through, for example, polymorphism and mutation discovery and microRNA profiling. However, compared t...
Amplicon pyrosequencing targets a known genetic region and thus inherently produces reads highly anticipated to have certain features, such as conserved nucleotide sequence, and in the case of protein coding D...
Plate readers can measure the growth curves of many microbial strains in a high-throughput fashion. The hundreds of absorbance readings collected simultaneously for hundreds of samples create technical hurdles...
The immune system is multifaceted, structured by diverse components that interconnect using multilayered dynamic cellular processes. Genomic technologies provide a means for investigating, at the molecular lev...
The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. W...
Trellis graphics are a visualization method that splits data by one or more categorical variables and displays subsets of the data in a grid of panels. Trellis graphics are broadly used in genomic data analysi...
The α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. The barrel architecture of these proteins is formed by either homo-/hetero-...
MicroRNAs (miRNAs) are about 22 nucleotides, non-coding RNAs that affect various cellular functions, and play a regulatory role in different organisms including human. Until now, more than 2500 mature miRNAs i...
Many popular dengue forecasting techniques have been used by several researchers to extrapolate dengue incidence rates, including the K-H model, support vector machines (SVM), and artificial neural networks (A...
Previously, we described ROVER, a DNA variant caller which identifies genetic variants from PCR-targeted massively parallel sequencing (MPS) datasets generated by the Hi-Plex protocol. ROVER permits stringent ...
The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for anal...
Entity coreference is common in biomedical literature and it can affect text understanding systems that rely on accurate identification of named entities, such as relation extraction and automatic summarizatio...
The importance of the material properties of membranes for diverse cellular processes is well established. Notably, the elastic properties of the membrane, which depend on its composition, can directly influen...
In the context of drug discovery, drug target interactions (DTIs) can be predicted based on observed topological features of a semantic network across the chemical and biological space. In a semantic network, ...
Accurate adjustment for the amplification efficiency (AE) is an important part of real-time quantitative polymerase chain reaction (qPCR) experiments. The most commonly used correction strategy is to estimate ...
Existing feature selection methods typically do not consider prior knowledge in the form of structural relationships among features. In this study, the features are structured based on prior knowledge into gro...
Biological research increasingly relies on network models to study complex phenomena. Signal Transduction Pathways are molecular circuits that model how cells receive, process, and respond to information from ...
Compound Heterozygosity (CH) in classical genetics is the presence of two different recessive mutations at a particular gene locus. A relaxed form of CH alleles may account for an essential proportion of the m...
Understanding the interactions between antibodies and the linear epitopes that they recognize is an important task in the study of immunological diseases. We present a novel computational method for the design...
Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another. However, they have been developed...
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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
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