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The impact of a perturbation, over-expression, or repression of a key node on an organism, can be modelled based on a regulatory and/or metabolic network. Integration of these two networks could improve our gl...
Quantitative analysis of neurite growth and morphology is essential for understanding the determinants of neural development and regeneration, however, it is complicated by the labor-intensive process of measu...
Hashimoto’s thyroiditis is an autoimmune disorder characterized by the destruction of thyroid cells through immune-mediated mechanisms involving cells and antibodies. The condition can trigger disturbances in ...
Single-cell RNA sequencing (scRNA-seq) technology has enabled assessment of transcriptome-wide changes at single-cell resolution. Due to the heterogeneity in environmental exposure and genetic background acros...
Transposable elements (TEs) are short, mobile DNA elements that are known to play important roles in the genomes of many eukaryotic species. The identification and categorization of these elements is a critica...
Biologists are faced with an ever-changing array of complex software tools with steep learning curves, often run on High Performance Computing platforms. To resolve the tradeoff between analytical sophisticati...
Two types of non-invasive, radiation-free, and inexpensive imaging technologies that are widely employed in medical applications are ultrasound (US) and infrared thermography (IRT). The ultrasound image obtain...
Existing methods for generating synthetic genotype data are ill-suited for replicating the effects of assortative mating (AM). We propose rb_dplr, a novel and computationally efficient algorithm for generating hi...
Antibiotic resistance is a major public health concern around the globe. As a result, researchers always look for new compounds to develop new antibiotic drugs for combating antibiotic-resistant bacteria. Bact...
Accurate case report data are essential to understand arbovirus dynamics, including spread and evolution of arboviruses such as Zika, dengue and chikungunya viruses. Giving the multi-country nature of arboviru...
Single-cell sequencing (sc-Seq) experiments are producing increasingly large data sets. However, large data sets do not necessarily contain large amounts of information.
Visualizing genome coverage is of vital importance to inspect and interpret various next-generation sequencing (NGS) data. Besides genome coverage, genome annotations are also crucial in the visualization. Whi...
With the continuous advances in third-generation sequencing technology and the increasing affordability of next-generation sequencing technology, sequencing data from different sequencing technology platforms ...
Proteins often assemble into higher-order complexes to perform their biological functions. Such protein–protein interactions (PPI) are often experimentally measured for pairs of proteins and summarized in a we...
Since the introduction of next-generation sequencing (NGS) techniques, whole-exome sequencing (WES) and whole-genome sequencing (WGS) have not only revolutionized research, but also diagnostics. The gradual sw...
Integrating multi-omics data is fast becoming a powerful approach for predicting disease progression and treatment outcomes. In light of that, we introduce a modified version of the NetRank algorithm, a networ...
The growing power and ever decreasing cost of RNA sequencing (RNA-Seq) technologies have resulted in an explosion of RNA-Seq data production. Comparing gene expression values within RNA-Seq datasets is relativ...
Single-cell RNA sequencing (scRNA-seq) enables the high-throughput profiling of gene expression at the single-cell level. However, overwhelming dropouts within data may obscure meaningful biological signals. V...
The identification of tumor T cell antigens (TTCAs) is crucial for providing insights into their functional mechanisms and utilizing their potential in anticancer vaccines development. In this context, TTCAs a...
Modern genome sequencing leads to an ever-growing collection of genomic annotations. Combining these elements with a set of input regions (e.g. genes) would yield new insights in genomic associations, such as ...
An updated version of the mwtab Python package for programmatic access to the Metabolomics Workbench (MetabolomicsWB) data repository was released at the beginning of 2021. Along with updating the package to m...
Protein biomarkers of cancer progression and response to therapy are increasingly important for improving personalized medicine. Advanced quantitative pathology platforms enable measurement of protein expressi...
Protein engineering aims to improve the functional properties of existing proteins to meet people’s needs. Current deep learning-based models have captured evolutionary, functional, and biochemical features co...
Statistical correlation analysis is currently the most typically used approach for investigating the risk factors of type 2 diabetes mellitus (T2DM). However, this approach does not readily reveal the causal r...
To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers. A common approach is to perform a gene-tree / species-tree ...
Identifying variants associated with diseases is a challenging task in medical genetics research. Current studies that prioritize variants within individual genomes generally rely on known variants, evidence f...
Accurate prediction of molecular property holds significance in contemporary drug discovery and medical research. Recent advances in AI-driven molecular property prediction have shown promising results. Due to...
The accelerating pace of biomedical publication has made it impractical to manually, systematically identify papers containing specific information and extract this information. This is especially challenging ...
The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the grow...
The growing recognition of the microbiome’s impact on human health and well-being has prompted extensive research into discovering the links between microbiome dysbiosis and disease (healthy) states. However, ...
Cancer subtype classification is helpful for personalized cancer treatment. Although, some approaches have been developed to classifying caner subtype based on high dimensional gene expression data, it is diff...
PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous...
Next-generation sequencing technologies yield large numbers of genetic alterations, of which a subset are missense variants that alter an amino acid in the protein product. These variants can have a potentiall...
Integration site (IS) analysis is a fundamental analytical platform for evaluating the safety and efficacy of viral vector based preclinical and clinical Gene Therapy (GT). A handful of groups have developed s...
Deep learning-based medical image segmentation has made great progress over the past decades. Scholars have proposed many novel transformer-based segmentation networks to solve the problems of building long-ra...
Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele re...
Quantitative descriptions of multi-cellular structures from optical microscopy imaging are prime to understand the variety of three-dimensional (3D) shapes in living organisms. Experimental models of vertebrat...
Kernel methods have been proven to be a powerful tool for the integration and analysis of high-throughput technologies generated data. Kernels offer a nonlinear version of any linear algorithm solely based on ...
Network analysis is a powerful tool for studying gene regulation and identifying biological processes associated with gene function. However, constructing gene co-expression networks can be a challenging task,...
Uveal melanoma arises from stromal melanocytes and is the most prevalent primary intraocular tumor in adults. It poses a significant diagnostic and therapeutic challenge due to its high malignancy and early on...
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) displays significant potential for applications in cancer research, especially in tumor typing and subtyping. Lung cancer is th...
Accurate identification of Drug-Target Interactions (DTIs) plays a crucial role in many stages of drug development and drug repurposing. (i) Traditional methods do not consider the use of multi-source data and...
Molecular interaction networks have become an important tool in providing context to the results of various omics experiments. For example, by integrating transcriptomic data and protein–protein interaction (P...
In many applications of bioinformatics, data stem from distinct heterogeneous sources. One of the well-known examples is the identification of drug–target interactions (DTIs), which is of significant importanc...
P4 medicine (predict, prevent, personalize, and participate) is a new approach to diagnosing and predicting diseases on a patient-by-patient basis. For the prevention and treatment of diseases, prediction play...
N6-methyladenosine (m6A) and 5-methylcytosine (m5C) are the main RNA methylation modifications involved in the oncogenesis of cancer. However, it remains obscure whether m6A/m5C-related long non-coding RNAs (l...
Pathogenic bacteria present a major threat to human health, causing various infections and illnesses, and in some cases, even death. The accurate identification of these bacteria is crucial, but it can be chal...
Dealing with the high dimension of both neuroimaging data and genetic data is a difficult problem in the association of genetic data to neuroimaging. In this article, we tackle the latter problem with an eye t...
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2022 Citation Impact
3.0 - 2-year Impact Factor
4.3 - 5-year Impact Factor
0.938 - SNIP (Source Normalized Impact per Paper)
1.100 - SJR (SCImago Journal Rank)
2023 Speed
19 days submission to first editorial decision for all manuscripts (Median)
146 days submission to accept (Median)
2023 Usage
5,987,678 downloads
4,858 Altmetric mentions