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Imaging mass spectrometry (imaging MS) is an enabling technology for spatial metabolomics of tissue sections with rapidly growing areas of applications in biology and medicine. However, imaging MS data is poll...
Accumulated evidence shows that the abnormal regulation of long non-coding RNA (lncRNA) is associated with various human diseases. Accurately identifying disease-associated lncRNAs is helpful to study the mech...
Both intra- and inter-sentential semantic relations in biomedical texts provide valuable information for biomedical research. However, most existing methods either focus on extracting intra-sentential relation...
The notion of heme as a regulator of many physiological processes via transient binding to proteins is one that is recently being acknowledged. The broad spectrum of the effects of heme makes it important to i...
Cancer is caused by genetic mutations, but not all somatic mutations in human DNA drive the emergence or growth of cancers. While many frequently-mutated cancer driver genes have already been identified and ar...
Feature selection in class-imbalance learning has gained increasing attention in recent years due to the massive growth of high-dimensional class-imbalanced data across many scientific fields. In addition to r...
In unsupervised learning and clustering, data integration from different sources and types is a difficult question discussed in several research areas. For instance in omics analysis, dozen of clustering metho...
The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatu...
mRNA interaction with other mRNAs and other signaling molecules determine different biological pathways and functions. Gene co-expression network analysis methods have been widely used to identify correlation ...
Two-dimensional electrophoresis (2DE) is one of the most widely applied techniques in comparative proteomics. The basic task of 2DE is to identify differential protein expression by quantitative analysis of 2D...
After publication of the original article [1], we were notified that legends of Fig. 1 and Fig. 2 have been swapped.
In vertebrate genomes, CpG sites can be clustered into CpG islands, and the amount of methylation in a CpG island can change due to gene regulation processes. Thus, single regulatory events can simultaneously ...
Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix by mechanical loa...
RNA-binding proteins interact with their target RNAs at specific sites. These binding sites can be determined genome-wide through individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). Subs...
Lung cancer is the leading cause of cancer-related deaths in both men and women in the United States, and it has a much lower five-year survival rate than many other cancers. Accurate survival analysis is urge...
MicroRNAs (miRNAs) are a kind of small noncoding RNA molecules that are direct posttranscriptional regulations of mRNA targets. Studies have indicated that miRNAs play key roles in complex diseases by taking p...
With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq da...
Advanced sequencing machines dramatically speed up the generation of genomic data, which makes the demand of efficient compression of sequencing data extremely urgent and significant. As the most difficult par...
DNA methylation (DNAm) is an epigenetic regulator of gene expression programs that can be altered by environmental exposures, aging, and in pathogenesis. Traditional analyses that associate DNAm alterations wi...
Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as ...
Function genomic studies will generally result in lists of genes that may provide clues for exploring biological questions and discovering unanticipated functions, based on differential gene expression analysi...
Illumina sequencing of a marker gene is popular in metagenomic studies. However, Illumina paired-end (PE) reads sometimes cannot be merged into single reads for subsequent analysis. When mergeable PE reads are...
The selection and prioritization of drug targets is a central problem in drug discovery. Computational approaches can leverage the growing number of large-scale human genomics and proteomics data to make in-si...
Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) is a popular sequencing method for studying RNA modifications and, in particular, for N6-methyladenosine (m6A), the most abundant RNA methylation modif...
All-Food-Sequencing (AFS) is an untargeted metagenomic sequencing method that allows for the detection and quantification of food ingredients including animals, plants, and microbiota. While this approach avoi...
To identify and prioritize the influential hub genes in a gene-set or biological pathway, most analyses rely on calculation of marginal effects or tests of statistical significance. These procedures may be ina...
Chronic diseases are becoming more widespread each year in developed countries, mainly due to increasing life expectancy. Among them, diabetes mellitus (DM) and essential hypertension (EH) are two of the most ...
Screening programs use mammography as primary diagnostic tool for detecting breast cancer at an early stage. The diagnosis of some lesions, such as microcalcifications, is still difficult today for radiologist...
For optimization of microfluidic devices for the analysis of blood samples, it is useful to simulate blood cells as elastic objects in flow of blood plasma. In such numerical models, we primarily need to take ...
Phenotype prediction problems are usually considered ill-posed, as the amount of samples is very limited with respect to the scrutinized genetic probes. This fact complicates the sampling of the defective gene...
In biomedicine, infrared thermography is the most promising technique among other conventional methods for revealing the differences in skin temperature, resulting from the irregular temperature dispersion, wh...
The actual task of electrocardiographic examinations is to increase the reliability of diagnosing the condition of the heart. Within the framework of this task, an important direction is the solution of the in...
The current study’s purpose is to compare hip structural analysis variables in a group of postmenopausal women with sarcopenia and another group of postmenopausal women with normal skeletal muscle mass index. ...
In the field of protein engineering and biotechnology, the discovery and characterization of structural patterns is highly relevant as these patterns can give fundamental insights into protein-ligand interacti...
Melanoma results in the vast majority of skin cancer deaths during the last decades, even though this disease accounts for only one percent of all skin cancers’ instances. The survival rates of melanoma from e...
Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is...
Genomic micro-satellites are the genomic regions that consist of short and repetitive DNA motifs. Estimating the length distribution and state of a micro-satellite region is an important computational step in ...
The identification of all matches of a large set of position weight matrices (PWMs) in long DNA sequences requires significant computational resources for which a number of efficient yet complex algorithms hav...
Interactions between proteins and non-proteic small molecule ligands play important roles in the biological processes of living systems. Thus, the development of computational methods to support our understand...
Disease gene prediction is a critical and challenging task. Many computational methods have been developed to predict disease genes, which can reduce the money and time used in the experimental validation. Sin...
Finding the tumor location in the prostate is an essential pathological step for prostate cancer diagnosis and treatment. The location of the tumor – the laterality – can be unilateral (the tumor is affecting ...
In biomarker discovery, applying domain knowledge is an effective approach to eliminating false positive features, prioritizing functionally impactful markers and facilitating the interpretation of predictive ...
Traditional selection in livestock and crops focuses on additive genetic values or breeding values of the individuals. While traditional selection utilizes variation between individuals, differences between ga...
Bulked segregant analysis (BSA), coupled with next-generation sequencing, allows the rapid identification of both qualitative and quantitative trait loci (QTL), and this technique is referred to as BSA-Seq her...
Cancer associated copy number variation (CNV) events provide important information for identifying patient subgroups and suggesting treatment strategies. Technical and logistical issues, however, make it chall...
With the rapid development of whole exome sequencing (WES), an increasing number of tools are being proposed for copy number variation (CNV) detection based on this technique. However, no comprehensive guide i...
Duplex sequencing is the most accurate approach for identification of sequence variants present at very low frequencies. Its power comes from pooling together multiple descendants of both strands of original D...
Many cancers arise from mutations in cells within epithelial tissues. Mutations manifesting at the subcellular level influence the structure and function of the tissue resulting in cancer. Previous work has pr...
The systems-scale analysis of cellular metabolites, “metabolomics,” provides data ideal for applications in metabolic engineering. However, many of the computational tools for strain design are built around Fl...
Cancer prognosis prediction is valuable for patients and clinicians because it allows them to appropriately manage care. A promising direction for improving the performance and interpretation of expression-bas...
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Citation Impact 2023
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