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A key application area of semantic technologies is the fast-developing field of bioinformatics. Sealife was a project within this field with the aim of creating semantics-based web browsing capabilities for th...
The Brucella Bioinformatics Portal (BBP) is developed to integrate existing Brucella genome data and analysis tools with literature mining and curation. The BBP InterBru database and Brucella Genome Browser allow...
Generalized hidden Markov models (GHMMs) appear to be approaching acceptance as a de facto standard for state-of-the-art ab initio gene finding, as evidenced by the recent proliferation of GHMM implementations. W...
Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a col...
Protein ubiquitination is a critical post-translational modification (PTMs) involved in numerous cellular processes. Identifying ubiquitination sites (Ubi-sites) on proteins offers valuable insights into their...
For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encode...
Protein-amide proton hydrogen-deuterium exchange (HDX) is used to investigate protein conformation, conformational changes and surface binding sites for other molecules. To our knowledge, software tools to aut...
The increasing availability of Electronic Health Record (EHR) data and specifically free-text patient notes presents opportunities for phenotype extraction. Text-mining methods in particular can help disease m...
Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understandin...
Deep learning contributes to uncovering molecular and cellular processes with highly performant algorithms. Convolutional neural networks have become the state-of-the-art tool to provide accurate and fast ima...
We present a passage relevance model for integrating syntactic and semantic evidence of biomedical concepts and topics using a probabilistic graphical model. Component models of topics, concepts, terms, and do...
Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, ...
The competing endogenous RNA (ceRNA) regulation is a newly discovered post-transcriptional regulation mechanism and plays significant roles in physiological and pathological progress. CeRNA networks provide gl...
Extraction of associations of singular nucleotide polymorphism (SNP) and phenotypes from biomedical literature is a vital task in BioNLP. Recently, some methods have been developed to extract mutation-diseases...
A better understanding of the mechanisms of an enzyme's functionality and stability, as well as knowledge and impact of mutations is crucial for researchers working with enzymes. Though, several of the enzymes...
Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific...
The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMe...
Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology mode...
Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data conti...
Metabolomics experiments often comprise large numbers of biological samples resulting in huge amounts of data. This data needs to be inspected for plausibility before data evaluation to detect putative sources...
The biomedical domain is witnessing a rapid growth of the amount of published scientific results, which makes it increasingly difficult to filter the core information. There is a real need for support tools th...
The commercial adoption of BCI technologies for both clinical and non-clinical applications is drawing scientists to the creation of wearable devices for daily living. Emotions are essential to human existence...
The 10th and 9th revisions of the International Statistical Classification of Diseases and Related Health Problems (ICD10 and ICD9) have been adopted worldwide as a well-recognized norm to share codes for dise...
Biomedical named entity recognition is one of the most essential tasks in biomedical information extraction. Previous studies suffer from inadequate annotated datasets, especially the limited knowledge contain...
Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest futur...
The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrati...
The liquid–liquid phase separation (LLPS) of biomolecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles in cel...
In 2011, the IEEE VisWeek conferences inaugurated a symposium on Biological Data Visualization. Like other domain-oriented Vis symposia, this symposium's purpose was to explore the unique characteristics and r...
Drug-drug interaction extraction (DDI) needs assistance from automated methods to address the explosively increasing biomedical texts. In recent years, deep neural network based models have been developed to a...
Drug-target interactions (DTIs) are critical for drug repurposing and elucidation of drug mechanisms, and are manually curated by large databases, such as ChEMBL, BindingDB, DrugBank and DrugTargetCommons. How...
Extracting and visualizing of protein-protein interaction (PPI) from text literatures are a meaningful topic in protein science. It assists the identification of interactions among proteins. There is a lack of...
Like text in other domains, biomedical documents contain a range of terms with more than one possible meaning. These ambiguities form a significant obstacle to the automatic processing of biomedical texts. Pre...
Affymetrix gene expression arrays incorporate paired perfect match (PM) and mismatch (MM) probes to distinguish true signals from those arising from cross-hybridization events. A MM signal often shows greater ...
Forward-time simulations have unique advantages in power and flexibility for the simulation of genetic samples of complex human diseases because they can closely mimic the evolution of human populations carryi...
Indexing is a crucial step in any information retrieval system. In MEDLINE, a widely used database of the biomedical literature, the indexing process involves the selection of Medical Subject Headings in order to...
Enhancers are small regions of DNA that bind to proteins, which enhance the transcription of genes. The enhancer may be located upstream or downstream of the gene. It is not necessarily close to the gene to be...
To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leverag...
In recent years, biological event extraction has emerged as a key natural language processing task, aiming to address the information overload...generalization and a wider range of text types, event types, and su...
Tree-structured neural networks have shown promise in extracting lexical representations of sentence syntactic structures, particularly in the detection of event triggers using recursive neural networks.
Techniques for reconstruction of biological networks which are based on perturbation experiments often predict direct interactions between nodes that do not exist. Transitive reduction removes such relations i...
BioProspecting is a novel approach that enabled our team to mine data related to genetic markers from the New England Journal of Medicine (NEJM) utilizing SNOMED CT and the Human Gene Onotology (HUGO). The Biomed...
Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific olig...
The construction of interaction networks between proteins is central to understanding the underlying biological processes. However, since many useful relations are excluded in databases and remain hidden in ra...
Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth...
This paper describes and evaluates a sentence selection engine that extracts a GeneRiF (Gene Reference into Functions) as defined in ENTREZ-Gene based on a MEDLINE record. Inputs for this task include both a g...
Detecting homology between remotely related protein families is an important problem in computational biology since the biological properties of uncharacterized proteins can often be inferred from those of hom...
Brain Computer Interfaces (BCIs) translate the activity of the nervous system to a control signal which is interpretable for an external device. Using continuous motor BCIs, the user will be able to control a ...
Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automat...
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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