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In most mammals, a vast array of genes coding for chemosensory receptors mediates olfaction. Odorant receptor (OR) genes generally constitute the largest multifamily (> 1100 intact members in the mouse). From ...
HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which rep...
Nucleus or cell detection is a fundamental task in microscopy image analysis and supports many other quantitative studies such as object counting, segmentation, tracking, etc. Deep neural networks are emerging...
Neurogenesis in the murine cerebral cortex involves the coordinated divisions of two main types of progenitor cells, whose numbers, division modes and cell cycle durations set up the final neuronal output. To ...
Long-chain non-coding RNA (lncRNA) is closely related to many biological activities. Since its sequence structure is similar to that of messenger RNA (mRNA), it is difficult to distinguish between the two base...
MiRNAs play significant roles in many fundamental and important biological processes, and predicting potential miRNA-disease associations makes contributions to understanding the molecular mechanism of human d...
Cytogenetic nomenclature is used to describe chromosomal aberrations (or lack thereof) in a collection of cells, referred to as the cells’ karyotype. The nomenclature identifies locations on chromosomes using ...
Although many of the genic features in Mycobacterium abscessus have been fully validated, a comprehensive understanding of the regulatory elements remains lacking. Moreover, there is little understanding of how t...
Atomic force microscopy (AFM) allows the mechanical characterization of single cells and live tissue by quantifying force-distance (FD) data in nano-indentation experiments. One of the main problems when deali...
The function of oligomeric proteins is inherently linked to their quaternary structure. In the absence of high-resolution data, low-resolution information in the form of spatial restraints can significantly co...
The Human Protein Atlas (HPA) aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics. Access of the HPA data is mainly via web-based interface allowing views of ...
Determining the association between tumor sample and the gene is demanding because it requires a high cost for conducting genetic experiments. Thus, the discovered association between tumor sample and gene fur...
The efficient biological production of industrially and economically important compounds is a challenging problem. Brute-force determination of the optimal pathways to efficient production of a target chemical...
Uncovering the evolutionary principles of gene coexpression network is important for our understanding of the network topological property of new genes. However, most existing evolutionary models only consider...
Automatic extraction of biomedical events from literature is an important task in the understanding biological systems, allowing for faster update of the latest discoveries automatically. Detecting trigger wor...
Despite the availability of many ready-made testing software, reliable detection of differentially expressed genes in RNA-seq data is not a trivial task. Even though the data collection is considered high-thro...
Mathematics and Phy sics-based simulation models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form. Similarly, comprehensive descriptions of such m...
Background In the search for therapeutic peptides for disease treatments, many efforts have been made to identify various functional peptides from large numbers of peptide sequence databases. In this paper, we...
Evolutionary information contained in the amino acid sequences of proteins specifies the biological function and fold, but exactly what information contained in the protein sequence drives both of these proces...
As genome sequencing projects grow rapidly, the diversity of organisms with recently assembled genome sequences peaks at an unprecedented scale, thereby highlighting the need to make gene functional annotation...
Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis...
Streptomycetes are filamentous microorganisms of high biotechnological relevance, especially for the production of antibiotics. In submerged cultures, the productivity of these microorganisms is closely linked...
High-throughput gene expression technologies provide complex datasets reflecting mechanisms perturbed in an experiment, typically in a treatment versus control design. Analysis of these information-rich data c...
Mutational signatures are specific patterns of somatic mutations introduced into the genome by oncogenic processes. Several mutational signatures have been identified and quantified from multiple cancer studie...
Hodgkin Lymphoma (HL) is a type of aggressive malignancy in lymphoma that has high incidence in young adults and elderly patients. Identification of reliable diagnostic markers and efficient therapeutic target...
Multiplexed in-situ fluorescent imaging offers several advantages over single-cell assays that do not preserve the spatial characteristics of biological samples. This spatial information, in addition to morpho...
Metabolic coupling of product synthesis and microbial growth is a prominent approach for maximizing production performance. Growth-coupling (GC) also helps stabilizing target production and allows the selectio...
Protein interaction databases often provide confidence scores for each recorded interaction based on the available experimental evidence. Protein interaction networks (PINs) are then built by thresholding on t...
Due to the recent advances in deep learning, this model attracted researchers who have applied it to medical image analysis. However, pathological image analysis based on deep learning networks faces a number ...
Mining epistatic loci which affects specific phenotypic traits is an important research issue in the field of biology. Bayesian network (BN) is a graphical model which can express the relationship between gene...
Cryo-electron tomography (Cryo-ET) is an imaging technique used to generate three-dimensional structures of cellular macromolecule complexes in their native environment. Due to developing cryo-electron microsc...
Contemporary biological observations have revealed a large variety of mechanisms acting during the expansion of a tumor. However, there are still many qualitative and quantitative aspects of the phenomenon tha...
Although a few comparison methods based on the biological meaning of gene lists have been developed, the goProfiles approach is one of the few that are being used for that purpose. It consists of projecting li...
With every new genome that is sequenced, thousands of species-specific genes (orphans) are found, some originating from ultra-rapid mutations of existing genes, many others originating de novo from non-genic r...
Following publication of the original article [1], the author noticed that the following lines were missing from the published article. The original article has been corrected.
One of the most important steps in peptide identification is to estimate the false discovery rate (FDR). The most commonly used method for estimating FDR is the target-decoy search strategy (TDS). While this m...
Batch effects were not accounted for in most of the studies of computational drug repositioning based on gene expression signatures. It is unknown how batch effect removal methods impact the results of signatu...
Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant da...
Gene and protein interaction data are often represented as interaction networks, where nodes stand for genes or gene products and each edge stands for a relationship between a pair of gene nodes. Commonly, tha...
The epidermal growth factor receptor (EGFR) is a major regulator of proliferation in tumor cells. Elevated expression levels of EGFR are associated with prognosis and clinical outcomes of patients in a variety...
Host immune response is coordinated by a variety of different specialized cell types that vary in time and location. While host immune response can be studied using conventional low-dimensional approaches, adv...
Relationships between specific microbes and proper immune system development, composition, and function have been reported in a number of studies. However, researchers have discovered only a fraction of the li...
Protein pulldown using Methyl-CpG binding domain (MBD) proteins followed by high-throughput sequencing is a common method to determine DNA methylation. Algorithms have been developed to estimate absolute methy...
Background Consisting of dictated free-text documents such as discharge summaries, medical narratives are widely used in medical natural language processing. Relationships between anatomical entities and human...
Diagnosis and treatment decisions in cancer increasingly depend on a detailed analysis of the mutational status of a patient’s genome. This analysis relies on previously published information regarding the ass...
With the advent of array-based techniques to measure methylation levels in primary tumor samples, systematic investigations of methylomes have widely been performed on a large number of tumor entities. Most of...
Biomedical named entity recognition (BioNER) is a fundamental and essential task for biomedical literature mining, which affects the performance of downstream tasks. Most BioNER models rely on domain-specific ...
Advances in medical technology have allowed for customized prognosis, diagnosis, and treatment regimens that utilize multiple heterogeneous data sources. Multiple kernel learning (MKL) is well suited for the i...
Literature Based Discovery (LBD) produces more potential hypotheses than can be manually reviewed, making automatically ranking these hypotheses critical. In this paper, we introduce the indirect association m...
High throughput DNA/RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies...
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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