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A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematica...
Systems approaches in studying disease relationship have wide applications in biomedical discovery, such as disease mechanism understanding and drug discovery. The FDA Adverse Event Reporting System (FAERS) co...
Electronic Medical Record (EMR) comprises patients’ medical information gathered by medical stuff for providing better health care. Named Entity Recognition (NER) is a sub-field of information extraction aimed...
Identifying local recurrences in breast cancer from patient data sets is important for clinical research and practice. Developing a model using natural language processing and machine learning to identify loca...
In precision medicine, scarcity of suitable biological data often hinders the design of an appropriate predictive model. In this regard, large scale pharmacogenomics studies, like CCLE and GDSC hold the promis...
Hi-C data have been widely used to reconstruct chromosomal three-dimensional (3D) structures. One of the key limitations of Hi-C is the unclear relationship between spatial distance and the number of Hi-C cont...
Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, en...
Top-down mass spectrometry has unique advantages in identifying proteoforms with multiple post-translational modifications and/or unknown alterations. Most software tools in this area search top-down mass spec...
In genomic studies, to investigate how the structure of a genetic network differs between two experiment conditions is a very interesting but challenging problem, especially in high-dimensional setting. Existi...
The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held on June 10–12, 2018, in Los Angeles, California, USA. The conference consisted of a total of eleven scientific sessio...
Adverse drug reactions (ADRs) are unintended and harmful reactions caused by normal uses of drugs. Predicting and preventing ADRs in the early stage of the drug development pipeline can help to enhance drug sa...
Noises and artifacts may arise in several steps of the next-generation sequencing (NGS) process. Recently, an NGS library preparation method called SMART, or Switching Mechanism At the 5′ end of the RNA Transcrip...
The neutral theory of Motoo Kimura stipulates that evolution is mostly driven by neutral mutations. However adaptive pressure eventually leads to changes in phenotype that involve non-neutral mutations. The re...
As a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase ...
Biomedical literature is expanding rapidly, and tools that help locate information of interest are needed. To this end, a multitude of different approaches for classifying sentences in biomedical publications ...
DNA methylation of CpG dinucleotides is an essential epigenetic modification that plays a key role in transcription. Widely used DNA enrichment-based methods offer high coverage for measuring methylated CpG di...
Molecular profiles change in response to perturbations. These changes are coordinated into functional modules via regulatory interactions. The genes and their products within a functional module are expected to b...
Pathway enrichment techniques are useful for understanding experimental metabolomics data. Their purpose is to give context to the affected metabolites in terms of the prior knowledge contained in metabolic pa...
Sequencing highly-variable 16S regions is a common and often effective approach to the study of microbial communities, and next-generation sequencing (NGS) technologies provide abundant quantities of data for ...
With applications in cancer, drug metabolism, and disease etiology, understanding structural variation in the human genome is critical in advancing the thrusts of individualized medicine. However, structural v...
In biomedical information extraction, event extraction plays a crucial role. Biological events are used to describe the dynamic effects or relationships between biological entities such as proteins and genes. ...
Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solv...
The traditional methods of visualizing high-dimensional data objects in low-dimensional metric spaces are subject to the basic limitations of metric space. These limitations result in multidimensional scaling ...
The majority of cancer-related deaths are due to lung cancer, and there is a need for reliable diagnostic biomarkers to predict stages in non-small cell lung cancer cases. Recently, microRNAs were found to hav...
Bacterial small non-coding RNAs (sRNAs) have emerged as important elements in diverse physiological processes, including growth, development, cell proliferation, differentiation, metabolic reactions and carbon...
Biomedical semantic indexing is important for information retrieval and many other research fields in bioinformatics. It annotates biomedical citations with Medical Subject Headings. In face of unbalanced cate...
Current multi-petaflop supercomputers are powerful systems, but present challenges when faced with problems requiring large machine learning workflows. Complex algorithms running at system scale, often with di...
Real-time analysis of patient data during medical procedures can provide vital diagnostic feedback that significantly improves chances of success. With sensors becoming increasingly fast, frameworks such as De...
Histopathology images of tumor biopsies present unique challenges for applying machine learning to the diagnosis and treatment of cancer. The pathology slides are high resolution, often exceeding 1GB, have non...
Deep Learning (DL) has advanced the state-of-the-art capabilities in bioinformatics applications which has resulted in trends of increasingly sophisticated and computationally demanding models trained by large...
The National Cancer Institute drug pair screening effort against 60 well-characterized human tumor cell lines (NCI-60) presents an unprecedented resource for modeling combinational drug activity.
Manual extraction of information from electronic pathology (epath) reports to populate the Surveillance, Epidemiology, and End Result (SEER) database is labor intensive. Systematizing the data extraction autom...
We examine the problem of clustering biomolecular simulations using deep learning techniques. Since biomolecular simulation datasets are inherently high dimensional, it is often necessary to build low dimensio...
Cancer is a complex, multiscale dynamical system, with interactions between tumor cells and non-cancerous host systems. Therapies act on this combined cancer-host system, sometimes with unexpected results. Sys...
Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins,...
The deployment of Genome-wide association studies (GWASs) requires genomic information of a large population to produce reliable results. This raises significant privacy concerns, making people hesitate to con...
Advances in Illumina DNA sequencing technology have produced longer paired-end reads that increasingly have sequence overlaps. These reads can be merged into a single read that spans the full length of the ori...
Identifying protein complexes from protein-protein interaction (PPI) network is one of the most important tasks in proteomics. Existing computational methods try to incorporate a variety of biological evidence...
RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially for biologists. We aim to streamline the bioinformatic a...
Almost 16,000 human long non-coding RNA (lncRNA) genes have been identified in the GENCODE project. However, the function of most of them remains to be discovered. The function of lncRNAs and other novel genes...
Virus genome sequences, generated in ever-higher volumes, can provide new scientific insights and inform our responses to epidemics and outbreaks. To facilitate interpretation, such data must be organised and ...
Various algorithms have been developed to predict fetal trisomies using cell-free DNA in non-invasive prenatal testing (NIPT). As basis for prediction, a control group of non-trisomy samples is needed. Predict...
After publication of the original article [1], it was noticed that the dagger symbol indicating equal contribution wasn’t added next to the names of all authors.
Selection for feed efficiency is crucial for overall profitability and sustainability in dairy cattle production. Key regulator genes and genetic markers derived from co-expression networks underlying feed eff...
For analyzing these gene expression data sets under different samples, clustering and visualizing samples and genes are important methods. However, it is difficult to integrate clustering and visualizing techn...
The challenge of classifying cortical interneurons is yet to be solved. Data-driven classification into established morphological types may provide insight and practical value.
Predicting prognosis in patients from large-scale genomic data is a fundamentally challenging problem in genomic medicine. However, the prognosis still remains poor in many diseases. The poor prognosis may be ...
The current versions of reference genome assemblies still contain gaps represented by stretches of Ns. Since high throughput sequencing reads cannot be mapped to those gap regions, the regions are depleted of ...
A cross-correlation (XCorr) score function is one of the most popular score functions utilized to search peptide identifications in databases, and many computer programs, such as SEQUEST, Comet, and Tide, curr...
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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
Submission to first editorial decision (median days): 12
Submission to acceptance (median days): 146
Usage 2023
Downloads: 5,987,678
Altmetric mentions: 4,858