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In biomedical text mining, named entity recognition (NER) is an important task used to extract information from biomedical articles. Previously proposed methods for NER are dictionary- or rule-based methods an...
Horizontal Gene Transfer (HGT) refers to the transfer of genetic materials between organisms through mechanisms other than parent-offspring inheritance. HGTs may affect human health through a large number of m...
This article is part of a Supplement: Volume 20 Supplement 23
The main research topic in this paper is how to compare multiple biological experiments using transcriptome data, where each experiment is measured and designed to compare control and treated samples. Comparis...
This article is part of a Supplement: Volume 20 Supplement 23
With recent advances in high-throughput technologies, matrix factorization techniques are increasingly being utilized for mapping quantitative omics profiling matrix data into low-dimensional embedding space, in ...
This article is part of a Supplement: Volume 20 Supplement 23
Current technologies for understanding the transcriptional reprogramming in cells include the transcription factor (TF) chromatin immunoprecipitation (ChIP) experiments and the TF knockout experiments. The ChI...
This article is part of a Supplement: Volume 20 Supplement 23
Studying multiple microRNAs (miRNAs) synergism in gene regulation could help to understand the regulatory mechanisms of complicated human diseases caused by miRNAs. Several existing methods have been presented...
This article is part of a Supplement: Volume 20 Supplement 23
The Correction to this article has been published in BMC Bioinformatics 2020 21:32
Analysis of large genomic datasets along with their accompanying clinical information has shown great promise in cancer research over the last decade. Such datasets typically include thousands of samples, each...
Genomic prediction is an advanced method for estimating genetic values, which has been widely accepted for genetic evaluation in animal and disease-risk prediction in human. It estimates genetic values with ge...
Differences in cell-type composition across subjects and conditions often carry biological significance. Recent advancements in single cell sequencing technologies enable cell-types to be identified at the sin...
This article is part of a Supplement: Volume 20 Supplement 19
Group B streptococcus (GBS) is an important pathogen that is responsible for invasive infections, including sepsis and meningitis. GBS serotyping is an essential means for the investigation of possible infecti...
This article is part of a Supplement: Volume 20 Supplement 19
Protein structural class predicting is a heavily researched subject in bioinformatics that plays a vital role in protein functional analysis, protein folding recognition, rational drug design and other related...
This article is part of a Supplement: Volume 20 Supplement 25
Membrane proteins play an important role in the life activities of organisms. Knowing membrane protein types provides clues for understanding the structure and function of proteins. Though various computationa...
This article is part of a Supplement: Volume 20 Supplement 25
The recognition of protein interaction sites is of great significance in many biological processes, signaling pathways and drug designs. However, most sites on protein sequences cannot be defined as interface ...
This article is part of a Supplement: Volume 20 Supplement 25
Alternative splicing allows the pre-mRNAs of a gene to be spliced into various mRNAs, which greatly increases the diversity of proteins. High-throughput sequencing of mRNAs has revolutionized our ability for t...
This article is part of a Supplement: Volume 20 Supplement 25
Along with the development of precision medicine, individual heterogeneity is attracting more and more attentions in clinical research and application. Although the biomolecular reaction seems to be some vario...
This article is part of a Supplement: Volume 20 Supplement 25
Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role ...
This article is part of a Supplement: Volume 20 Supplement 25
Imbalanced datasets are commonly encountered in bioinformatics classification problems, that is, the number of negative samples is much larger than that of positive samples. Particularly, the data imbalance ph...
This article is part of a Supplement: Volume 20 Supplement 25
The interactions among proteins act as crucial roles in most cellular processes. Despite enormous effort put for identifying protein-protein interactions (PPIs) from a large number of organisms, existing first...
This article is part of a Supplement: Volume 20 Supplement 25
Glaucoma is an irreversible eye disease caused by the optic nerve injury. Therefore, it usually changes the structure of the optic nerve head (ONH). Clinically, ONH assessment based on fundus image is one of t...
This article is part of a Supplement: Volume 20 Supplement 25
The Copy Number Alterations (CNAs) are discovered to be tightly associated with cancers, so accurately detecting them is one of the most important tasks in the cancer genomics. A series of CNAs detection metho...
This article is part of a Supplement: Volume 20 Supplement 25
The association between BIN1 rs744373 variant and Alzheimer’s disease (AD) had been identified by genome-wide association studies (GWASs) as well as candidate gene studies in Caucasian populations. But in East...
This article is part of a Supplement: Volume 20 Supplement 25
2′-O-methylation (2′-O-me or Nm) is a post-transcriptional RNA methylation modified at 2′-hydroxy, which is common in mRNAs and various non-coding RNAs. Previous studies revealed the significance of Nm in mult...
This article is part of a Supplement: Volume 20 Supplement 25
Accurate identification of potential interactions between drugs and protein targets is a critical step to accelerate drug discovery. Despite many relative experimental researches have been done in the past dec...
This article is part of a Supplement: Volume 20 Supplement 25
The occurrence of cotton pests and diseases has always been an important factor affecting the total cotton production. Cotton has a great dependence on environmental factors during its growth, especially clima...
This article is part of a Supplement: Volume 20 Supplement 25
Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is...
This article is part of a Supplement: Volume 20 Supplement 25
Predicting miRNA-disease associations (MDAs) is time-consuming and expensive. It is imminent to improve the accuracy of prediction results. So it is crucial to develop a novel computing technology to predict n...
This article is part of a Supplement: Volume 20 Supplement 25
Protein structure prediction has always been an important issue in bioinformatics. Prediction of the two-dimensional structure of proteins based on the hydrophobic polarity model is a typical non-deterministic...
This article is part of a Supplement: Volume 20 Supplement 25
RNA secondary structure prediction is an important issue in structural bioinformatics, and RNA pseudoknotted secondary structure prediction represents an NP-hard problem. Recently, many different machine-learn...
This article is part of a Supplement: Volume 20 Supplement 25
In ab initio protein-structure predictions, a large set of structural decoys are often generated, with the requirement to select best five or three candidates from the decoys. The clustered central structures ...
This article is part of a Supplement: Volume 20 Supplement 25
Protein complexes are the cornerstones of many biological processes and gather them to form various types of molecular machinery that perform a vast array of biological functions. In fact, a protein may belong...
This article is part of a Supplement: Volume 20 Supplement 25
Cost-sensitive algorithm is an effective strategy to solve imbalanced classification problem. However, the misclassification costs are usually determined empirically based on user expertise, which leads to uns...
This article is part of a Supplement: Volume 20 Supplement 25
Protein comparative analysis and similarity searches play essential roles in structural bioinformatics. A couple of algorithms for protein structure alignments have been developed in recent years. However, fac...
This article is part of a Supplement: Volume 20 Supplement 19
Drug-drug interactions (DDIs) are a major concern in patients’ medication. It’s unfeasible to identify all potential DDIs using experimental methods which are time-consuming and expensive. Computational method...
This article is part of a Supplement: Volume 20 Supplement 19
Single-cell RNA-sequencing (scRNA-seq) is a transformative technology, allowing global transcriptomes of individual cells to be profiled with high accuracy. An essential task in scRNA-seq data analysis is the ...
This article is part of a Supplement: Volume 20 Supplement 19
Accurate classification of diffuse gliomas, the most common tumors of the central nervous system in adults, is important for appropriate treatment. However, detection of isocitrate dehydrogenase (IDH) mutation an...
This article is part of a Supplement: Volume 20 Supplement 19
Studying structural and functional morphology of small organisms such as monogenean, is difficult due to the lack of visualization in three dimensions. One possible way to resolve this visualization issue is t...
This article is part of a Supplement: Volume 20 Supplement 19
Synthetic lethality has attracted a lot of attentions in cancer therapeutics due to its utility in identifying new anticancer drug targets. Identifying synthetic lethal (SL) interactions is the key step toward...
This article is part of a Supplement: Volume 20 Supplement 19
A survey of presences and absences of specific species across multiple biogeographic units (or bioregions) are used in a broad area of biological studies from ecology to microbiology. Using binary presence-abs...
This article is part of a Supplement: Volume 20 Supplement 15
Super-enhancers (SEs) are clusters of transcriptional active enhancers, which dictate the expression of genes defining cell identity and play an important role in the development and progression of tumors and ...
This article is part of a Supplement: Volume 20 Supplement 15
Traditional drug research and development is high cost, time-consuming and risky. Computationally identifying new indications for existing drugs, referred as drug repositioning, greatly reduces the cost and attra...
This article is part of a Supplement: Volume 20 Supplement 15
A drug-drug interaction (DDI) is defined as a drug effect modified by another drug, which is very common in treating complex diseases such as cancer. Many studies have evidenced that some DDIs could be an incr...
This article is part of a Supplement: Volume 20 Supplement 15
Antimicrobial resistance (AMR) is a major threat to global public health because it makes standard treatments ineffective and contributes to the spread of infections. It is important to understand AMR’s biolog...
This article is part of a Supplement: Volume 20 Supplement 15
Chromatin immunoprecipitation sequencing (ChIP-seq) is a technology that combines chromatin immunoprecipitation (ChIP) with next generation of sequencing technology (NGS) to analyze protein interactions with D...
This article is part of a Supplement: Volume 20 Supplement 15
Cluster analysis is a core task in modern data-centric computation. Algorithmic choice is driven by factors such as data size and heterogeneity, the similarity measures employed, and the type of clusters sough...
This article is part of a Supplement: Volume 20 Supplement 15
The biological network is highly dynamic. Functional relations between genes can be activated or deactivated depending on the biological conditions. On the genome-scale network, subnetworks that gain or lose l...
This article is part of a Supplement: Volume 20 Supplement 15
Protein-protein interaction plays a key role in a multitude of biological processes, such as signal transduction, de novo drug design, immune responses, and enzymatic activities. Gaining insights of various bi...
This article is part of a Supplement: Volume 20 Supplement 15
Gene is a key step in genome annotation. Ab initio gene prediction enables gene annotation of new genomes regardless of availability of homologous sequences. There exist a number of ab initio gene prediction tool...
This article is part of a Supplement: Volume 20 Supplement 15
Cognitive decline has emerged as a significant threat to both public health and personal welfare, and mild cognitive decline/impairment (MCI) can further develop into Dementia/Alzheimer’s disease. While treatm...
This article is part of a Supplement: Volume 20 Supplement 15
A perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For exampl...
This Editorial first introduces the background of the vaccine and drug relations and how biomedical terminologies and ontologies have been used to support their studies. The history of the seven workshops, ini...
This article is part of a Supplement: Volume 20 Supplement 21
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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
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