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Although microarray studies have greatly contributed to recent genetic advances, lack of replication has been a continuing concern in this area. Complex study designs have the potential to address this concern...
Studies on multiple modalities of omics data such as transcriptomics, genomics and proteomics are growing in popularity, since they allow us to investigate complex mechanisms across molecular layers. It is wid...
Tuberculosis (TB) represents a worldwide cause of mortality (it infects one third of the world’s population) affecting mostly developing countries, including India, and recently also developed ones due to the ...
This article is part of a Supplement: Volume 20 Supplement 6
Obesity is associated with chronic activation of the immune system and an altered gut microbiome, leading to increased risk of chronic disease development. As yet, no biomarker profile has been found to distin...
This article is part of a Supplement: Volume 20 Supplement 6
Human Cytomegalovirus (HCMV) is a ubiquitous herpesvirus affecting approximately 90% of the world population. HCMV causes disease in immunologically naive and immunosuppressed patients. The prevention, diagnos...
This article is part of a Supplement: Volume 20 Supplement 6
The Correction to this article has been published in BMC Bioinformatics 2020 21:116
Principal components analysis (PCA) is often used to find characteristic patterns associated with certain diseases by reducing variable numbers before a predictive model is built, particularly when some variab...
This article is part of a Supplement: Volume 20 Supplement 6
Although targeted drugs have contributed to impressive advances in the treatment of cancer patients, their clinical benefits on tumor therapies are greatly limited due to intrinsic and acquired resistance of c...
Flow cytometry (FCM) is a powerful single-cell based measurement method to ascertain multidimensional optical properties of millions of cells. FCM is widely used in medical diagnostics and health research. The...
Dysregulated gene expression patterns have been reported in several mental disorders. Limited by the difficulty of obtaining samples, psychiatric molecular mechanism research still relies heavily on clues from...
Advances in next-generation sequencing (NGS) of antibody repertoires have led to an explosion in B cell receptor sequence data from donors with many different disease states. These data have the potential to d...
The Bacteria Biotope (BB) task is a biomedical relation extraction (RE) that aims to study the interaction between bacteria and their locations. This task is considered to pertain to fundamental knowledge in a...
In recent years, lncRNAs (long-non-coding RNAs) have been proved to be closely related to the occurrence and development of many serious diseases that are seriously harmful to human health. However, most of th...
Transcriptome analysis aims at gaining insight into cellular processes through discovering gene expression patterns across various experimental conditions. Biclustering is a standard approach to discover genes su...
A large body of evidence shows that miRNA regulates the expression of its target genes at post-transcriptional level and the dysregulation of miRNA is related to many complex human diseases. Accurately discove...
Comparative genomics has seen the development of many software performing the clustering, polymorphism and gene content analysis of genomes at different phylogenetic levels (isolates, species). These tools rel...
Cancer arises through accumulation of somatically acquired genetic mutations. An important question is to delineate the temporal order of somatic mutations during carcinogenesis, which contributes to better un...
Expression in H-sapiens plays a remarkable role when it comes to social communication. The identification of this expression by human beings is relatively easy and accurate. However, achieving the same result in ...
Viruses are closely related to bacteria and human diseases. It is of great significance to predict associations between viruses and hosts for understanding the dynamics and complex functional networks in micro...
This article is part of a Supplement: Volume 20 Supplement 16
A fundamental problem in RNA-seq data analysis is to identify genes or exons that are differentially expressed with varying experimental conditions based on the read counts. The relativeness of RNA-seq measure...
This article is part of a Supplement: Volume 20 Supplement 16
Topologically associating domains (TADs) are genomic regions with varying lengths. The interactions within TADs are more frequent than those between different TADs. TADs or sub-TADs are considered the structur...
This article is part of a Supplement: Volume 20 Supplement 16
Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, ...
This article is part of a Supplement: Volume 20 Supplement 16
The number of biomedical research articles have increased exponentially with the advancement of biomedicine in recent years. These articles have thus brought a great difficulty in obtaining the needed informat...
This article is part of a Supplement: Volume 20 Supplement 16
Predicting disease-related genes is helpful for understanding the disease pathology and the molecular mechanisms during the disease progression. However, traditional methods are not suitable for screening gene...
This article is part of a Supplement: Volume 20 Supplement 16
Integrated analysis that uses multiple sample gene expression data measured under the same stress can detect stress response genes more accurately than analysis of individual sample data. However, the integrat...
This article is part of a Supplement: Volume 20 Supplement 16
Malignant liver tumor is one of the main causes of human death. In order to help physician better diagnose and make personalized treatment schemes, in clinical practice, it is often necessary to segment and vi...
This article is part of a Supplement: Volume 20 Supplement 16
Sleep is a complex and dynamic biological process characterized by different sleep patterns. Comprehensive sleep monitoring and analysis using multivariate polysomnography (PSG) records has achieved significan...
This article is part of a Supplement: Volume 20 Supplement 16
Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT...
This article is part of a Supplement: Volume 20 Supplement 16
In order to isolate an individual’s genotype from a sample of biological material, most laboratories use PCR and Capillary Electrophoresis (CE) to construct a genetic profile based on polymorphic loci known as...
This article is part of a Supplement: Volume 20 Supplement 16
Microbes have been shown to play a crucial role in various ecosystems. Many human diseases have been proved to be associated with bacteria, so it is essential to extract the interaction between bacteria for me...
This article is part of a Supplement: Volume 20 Supplement 16
Over the past decades, a large number of long non-coding RNAs (lncRNAs) have been identified. Growing evidence has indicated that the mutation and dysregulation of lncRNAs play a critical role in the developme...
This article is part of a Supplement: Volume 20 Supplement 16
Protein-protein interactions(PPIs) engage in dynamic pathological and biological procedures constantly in our life. Thus, it is crucial to comprehend the PPIs thoroughly such that we are able to illuminate the...
This article is part of a Supplement: Volume 20 Supplement 16
Essential proteins are crucial for cellular life and thus, identification of essential proteins is an important topic and a challenging problem for researchers. Recently lots of computational approaches have b...
This article is part of a Supplement: Volume 20 Supplement 16
Understanding cellular responses via signal transduction is a core focus in systems biology. Tools to automatically reconstruct signaling pathways from protein-protein interactions (PPIs) can help biologists g...
This article is part of a Supplement: Volume 20 Supplement 16
In recent years, deep learning methods have been applied to many natural language processing tasks to achieve state-of-the-art performance. However, in the biomedical domain, they have not out-performed superv...
This article is part of a Supplement: Volume 20 Supplement 16
The kinase pocket structural information is important for drug discovery targeting cancer or other diseases. Although some kinase sequence, structure or drug databases have been developed, the databases cannot...
Following publication of the original article [1], the author explained that there are several errors in the original article
The original article was published in BMC Bioinformatics 2019 20:537
Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellula...
Untargeted metabolomics of host-associated samples has yielded insights into mechanisms by which microbes modulate health. However, data interpretation is challenged by the complexity of origins of the small m...
Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and ...
Automatic signal-feature extraction algorithms are crucial for profile processing in bioinformatics. Both baseline drift and noise seriously affect the position and peak area of signals. An efficient algorithm...
Over the last 10 years, there have been over 3300 genome-wide association studies (GWAS). Almost every GWAS study provides a Manhattan plot either as a main figure or in the supplement. Several software packag...
Recurrent neural network(RNN) is a good way to process sequential data, but the capability of RNN to compute long sequence data is inefficient. As a variant of RNN, long short term memory(LSTM) solved the prob...
Microarray datasets consist of complex and high-dimensional samples and genes, and generally the number of samples is much smaller than the number of genes. Due to this data imbalance, gene selection is a dema...
To study cell biological phenomena which depend on diffusion, active transport processes, or the locations of species, modeling and simulation studies need to take space into account. To describe the system as...
Influenza is an infectious respiratory disease that can cause serious public health hazard. Due to its huge threat to the society, precise real-time forecasting of influenza outbreaks is of great value to our ...
This article is part of a Supplement: Volume 20 Supplement 18
The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. Since the beginning of GO project, various tools have been developed to perform GO enrichment analys...
This article is part of a Supplement: Volume 20 Supplement 18
Collective cell migration is a significant and complex phenomenon that affects many basic biological processes. The coordination between leader cell and follower cell affects the rate of collective cell migrat...
This article is part of a Supplement: Volume 20 Supplement 18
Alzheimer’s disease (AD) imposes a heavy burden on society and every family. Therefore, diagnosing AD in advance and discovering new drug targets are crucial, while these could be achieved by identifying AD-re...
This article is part of a Supplement: Volume 20 Supplement 18
Lung cancer is one of the most malignant tumors, causing over 1,000,000 deaths each year worldwide. Deep learning has brought success in many domains in recent years. DNA methylation, an epigenetic factor, is ...
This article is part of a Supplement: Volume 20 Supplement 18
With the development of e-Health, it plays a more and more important role in predicting whether a doctor’s answer can be accepted by a patient through online healthcare community. Unlike the previous work whic...
This article is part of a Supplement: Volume 20 Supplement 18
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