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Feature extraction (FE) is difficult, particularly if there are more features than samples, as small sample numbers often result in biased outcomes or overfitting. Furthermore, multiple sample classes often co...
This article provides an overview of the first BioASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BioASQ as...
This report summarizes the scientific content and activities of the first edition of the Latin American Symposium organized by the Student Council of the International Society for Computational Biology (ISCB),...
Quality control is a necessary step of any Next Generation Sequencing analysis. Although customary, this step still requires manual interventions to empirically choose tuning parameters according to various qu...
Since experimental techniques are time and cost consuming, in silico protein structure prediction is essential to produce conformations of protein targets. When homologous structures are not available, fragmen...
The interpretation of the results from genome-scale experiments is a challenging and important problem in contemporary biomedical research. Biological networks that integrate experimental results with existing...
Characterization of respiratory phenotypes can enhance complex trait and genomic studies involving allergic/autoimmune and infectious diseases. Many aspects of respiration can be measured using devices known a...
RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally func...
Permutation-based gene set tests are standard approaches for testing relationships between collections of related genes and an outcome of interest in high throughput expression analyses. Using M random permutatio...
Epigenome-wide association scans (EWAS) are an increasingly powerful and widely-used approach to assess the role of epigenetic variation in human complex traits. However, this rapidly emerging field lacks dedi...
Metagenomics, the sequencing of DNA collected from an entire microbial community, enables the study of natural microbial consortia in their native habitats. Metagenomics studies produce huge volumes of data, i...
We aim to automatically extract species names of bacteria and their locations from webpages. This task is important for exploiting the vast amount of biological knowledge which is expressed in diverse natural ...
Many tree structures are found in nature and organisms. Such trees are believed to be constructed on the basis of certain rules. We have previously developed grammar-based compression methods for ordered and u...
Proteins interact with a variety of other molecules such as nucleic acids, small molecules and other proteins inside the cell. Structure-determination of protein-protein complexes is challenging due to several...
The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing r...
With the advances in high throughput technologies, increasing amounts of cancer somatic mutation data are being generated and made available. Only a small number of (driver) mutations occur in driver genes and...
G-protein-coupled receptors (GPCRs) are important drug targets and a better understanding of their molecular mechanisms would be desirable. The crystallization rate of GPCRs has accelerated in recent years as ...
Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alterative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built...
The lives of half a million children in the United States are severely affected due to the alterations in their functional and mental abilities which epilepsy causes. This study aims to introduce a novel decis...
Intracranial volume (ICV) is an important normalization measure used in morphometric analyses to correct for head size in studies of Alzheimer Disease (AD). Inaccurate ICV estimation could introduce bias in th...
The reconstruction of gene regulatory network from time course microarray data can help us comprehensively understand the biological system and discover the pathogenesis of cancer and other diseases. But how t...
Pairwise relationships extracted from biomedical literature are insufficient in formulating biomolecular interactions. Extraction of complex relations (namely, biomedical events) has become the main focus of t...
Genome assemblers to date have predominantly targeted haploid reference reconstruction from homozygous data. When applied to diploid genome assembly, these assemblers perform poorly, owing to the violation of ...
In recent years, with advances in techniques for protein structure analysis, the knowledge about protein structure and function has been published in a vast number of articles. A method to search for specific ...
Most cases of idiopathic autism spectrum disorder (ASD) likely result from unknown environmental triggers in genetically susceptible individuals. These triggers may include maternal exposure of a fetus to minu...
The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most...
Liquid chromatography-mass spectrometry is a popular technique for high-throughput protein, lipid, and metabolite comparative analysis. Such statistical comparison of millions of data points requires the gener...
High throughput sequencing technologies are able to identify the whole genomic variation of an individual. Gene-targeted and whole-exome experiments are mainly focused on coding sequence variants related to a ...
Mapping of short sequencing reads is a crucial step in the analysis of RNA sequencing (RNA-seq) data. ContextMap is an RNA-seq mapping algorithm that uses a context-based approach to identify the best alignmen...
Comparative proteomics in bacteria are often hampered by the differential nature of dataset quality and/or inherent biological deviations. Although common practice compensates by reproducing and normalizing da...
Dynamic gene-regulatory networks are complex since the interaction patterns between their components mean that it is impossible to study parts of the network in separation. This holistic character of gene-regu...
Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these anno...
Molecular docking is a widely-employed method in structure-based drug design. An essential component of molecular docking programs is a scoring function (SF) that can be used to identify the most stable bindin...
Studies on genomic sequences for classification and taxonomic identification have a leading role in the biomedical field and in the analysis of biodiversity. These studies are focusing on the so-called barcode...
This paper considers the problem of estimation and variable selection for large high-dimensional data (high number of predictors p and large sample size N, without excluding the possibility that N < p) resulting ...
Sterol glycosyltransferases (SGTs) are ubiquitous but one of the most diverse group of enzymes of glycosyltransferases family. Members of this family modulate physical and chemical properties of secondary plan...
Understanding channel structures that lead to active sites or traverse the molecule is important in the study of molecular functions such as ion, ligand, and small molecule transport. Efficient methods for ext...
Untargeted metabolomics generates a huge amount of data. Software packages for automated data processing are crucial to successfully process these data. A variety of such software packages exist, but the outco...
Unsupervised analyses such as clustering are the essential tools required to interpret time-series expression data from microarrays. Several clustering algorithms have been developed to analyze gene expression...
Point mutations can have a strong impact on protein stability. A change in stability may subsequently lead to dysfunction and finally cause diseases. Moreover, protein engineering approaches aim to deliberatel...
We recently identified two robust ovarian cancer subtypes, defined by the expression of genes involved in angiogenesis, with significant differences in clinical outcome. To identify potential regulatory mechan...
Genes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental proc...
Research in biomedical text categorization has mostly used the bag-of-words representation. Other more sophisticated representations of text based on syntactic, semantic and argumentative properties have been les...
Recent depression research has revealed a growing awareness of how to best classify depression into depressive subtypes. Appropriately subtyping depression can lead to identification of subtypes that are more ...
Comparing and aligning genomes is a key step in analyzing closely related genomes. Despite the development of many genome aligners in the last 15 years, the problem is not yet fully resolved, even when alignin...
Tandem mass spectrometry (MS/MS) acts as a key technique for peptide identification. The MS/MS-based peptide identification approaches can be categorized into two families, namely, de novo and database search. Bo...
Minimum dominating sets (MDSet) of protein interaction networks allow the control of underlying protein interaction networks through their topological placement. While essential proteins are enriched in MDSets...
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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
Speed 2023
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Submission to acceptance (median days): 146
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