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For over sixty years, it has been known that mammalian spermatozoa immediately after ejaculation are virtually infertile. They became able to fertilize only after they reside for long time (hours to days) with...
Time course measurement of single molecules on a cell surface provides detailed information about the dynamics of the molecules that would otherwise be inaccessible. To extract the quantitative information, si...
This article is part of a Supplement: Volume 12 Supplement 1
Drug-drug interactions (DDIs) always cause unexpected and even adverse drug reactions. It is important to identify DDIs before drugs are used in the market. However, preclinical identification of DDIs requires...
This article is part of a Supplement: Volume 12 Supplement 1
Alzheimer’s disease (AD) is a progressive neurological disorder, recognized as the most common cause of dementia affecting people aged 65 and above. AD is characterized by an increase in amyloid metabolism, an...
This article is part of a Supplement: Volume 12 Supplement 1
Signaling pathways can be reconstructed by identifying ‘effect types’ (i.e. activation/inhibition) of protein-protein interactions (PPIs). Effect types are composed of ‘directions’ (i.e. upstream/downstream) a...
This article is part of a Supplement: Volume 12 Supplement 1
Breast cancer and ovarian cancer are hormone driven and are known to have some predisposition genes in common such as the two well known cancer genes BRCA1 and BRCA2. The objective of this study is to compare ...
This article is part of a Supplement: Volume 12 Supplement 1
A network motif is a sub-network that occurs frequently in a given network. Detection of such motifs is important since they uncover functions and local properties of the given biological network. Finding moti...
This article is part of a Supplement: Volume 12 Supplement 1
Cell death as a result of ischemic injury triggers powerful mechanisms regulated by germline-encoded Pattern Recognition Receptors (PRRs) with shared specificity that recognize invading pathogens and endogenou...
Controlling complex molecular regulatory networks is getting a growing attention as it can provide a systematic way of driving any cellular state to a desired cell phenotypic state. A number of recent studies ...
Kinase inhibition in the mitogen activated protein kinase (MAPK) pathway is a standard therapy for cancer patients with activating BRAF mutations. However, the anti-tumorigenic effect and clinical benefit are ...
Progesterone plays an essential role in mammalian ovulation. Although much is known about this process, the gene networks involved in ovulation have yet to be established. When analyze the mechanisms of ovulat...
Existing experimental data have shown hypoxia to be an important factor affecting the proliferation of mesenchymal stromal cells (MSCs), but the contrasting observations made at various hypoxic levels raise th...
Melanoma can be diagnosed by identifying nests of cells on the skin surface. Understanding the processes that drive nest formation is important as these processes could be potential targets for new cancer drug...
The integration of gene expression profiles (GEPs) and large-scale biological networks derived from pathways databases is a subject which is being widely explored. Existing methods are based on network distanc...
This article is part of a Supplement: Volume 12 Supplement 3
Decomposing a protein-protein interaction network (PPI network) into non-overlapping clusters or communities, sometimes called “network modules,” is an important way to explore functional roles of sets of gene...
This article is part of a Supplement: Volume 12 Supplement 3
The Retraction Note to this article has been published in BMC Systems Biology 2018 12:113
Expression-based phenotype classification using either microarray or RNA-Seq measurements suffers from a lack of specificity because pathway timing is not revealed and expressions are averaged across groups of...
This article is part of a Supplement: Volume 12 Supplement 3
The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary r...
This article is part of a Supplement: Volume 12 Supplement 2
Regeneration is an important biological process for the restoration of organ mass, structure, and function after damage, and involves complex bio-physiological mechanisms including cell differentiation and imm...
This article is part of a Supplement: Volume 12 Supplement 2
Transcriptomic datasets often contain undeclared heterogeneity arising from biological variation such as diversity of disease subtypes, treatment subgroups, time-series gene expression, nested experimental con...
This article is part of a Supplement: Volume 12 Supplement 2
Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Pan...
This article is part of a Supplement: Volume 12 Supplement 2
Identifying gene regulatory networks is an important task for understanding biological systems. Time-course measurement data became a valuable resource for inferring gene regulatory networks. Various methods h...
This article is part of a Supplement: Volume 12 Supplement 2
With the rapid advancement of array-based genotyping techniques, genome-wide association studies (GWAS) have successfully identified common genetic variants associated with common complex diseases. However, it...
This article is part of a Supplement: Volume 12 Supplement 2
Gene Ontology (GO) is one of the most popular bioinformatics resources. In the past decade, Gene Ontology-based gene semantic similarity has been effectively used to model gene-to-gene interactions in multiple...
This article is part of a Supplement: Volume 12 Supplement 2
Cell surface proteins have provided useful targets and biomarkers for advanced cancer therapies. The recent clinical success of antibody-drug conjugates (ADCs) highlights the importance of finding selective su...
This article is part of a Supplement: Volume 12 Supplement 2
Drug combination therapy, which is considered as an alternative to single drug therapy, can potentially reduce resistance and toxicity, and have synergistic efficacy. As drug combination therapies are widely u...
This article is part of a Supplement: Volume 12 Supplement 2
One of the crucial steps toward understanding the associations among molecular interactions, pathways, and diseases in a cell is to investigate detailed atomic protein-protein interactions (PPIs) in the struct...
This article is part of a Supplement: Volume 12 Supplement 2
Recently, there have been several attempts to produce long-chain dicarboxylic acids (DCAs) in various microbial hosts. Of these, Yarrowia lipolytica has great potential due to its oleaginous characteristics and u...
This article is part of a Supplement: Volume 12 Supplement 2
Blood transfusions are an important part of modern medicine, delivering approximately 85 million blood units to patients annually. Recently, the field of transfusion medicine has started to benefit from the “o...
Muscle atrophy, an involuntary loss of muscle mass, is involved in various diseases and sometimes leads to mortality. However, therapeutics for muscle atrophy thus far have had limited effects. Here, we presen...
The efficacy of antibiotics against M. tuberculosis has been shown to be influenced by experimental media conditions. Investigations of M. tuberculosis growth in physiological conditions have described an environ...
Heterogeneous gene expressions of cells are widely observed in self-renewing pluripotent stem cells, suggesting possible coexistence of multiple cellular states with distinct characteristics. Though the elemen...
After publication of the article [1], it has been brought to our attention that an author’s name was spelt incorrectly in the original published article. Yonghua Wang was previously spelt “Yonghua Wan”. This h...
The original article was published in BMC Systems Biology 2018 12:2
Transfection of NF κB synthetic decoy Oligodeoxynucleotides (ODNs) has been proposed as a promising therapeutic strategy for a variety of diseases arising from constitutive activation of the eukaryotic transcript...
With the global emergence of multi-drug resistant strains of Mycobacterium tuberculosis, new strategies to treat tuberculosis are urgently needed such as therapeutics targeting potential human host factors.
Dengue virus (DENV) is an increasing global health threat and associated with induction of both a long-lived protective immune response and immune-suppression. So far, the potency of treatment of DENV via anti...
The Correction to this article has been published in BMC Systems Biology 2018 12:21
Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substanti...
Photosynthetic (PS) gene expression in Rhodobacter sphaeroides is regulated in response to changes in light and redox conditions mainly by PrrB/A, FnrL and AppA/PpsR systems. The PrrB/A and FnrL systems activate ...
Inflammatory bowel diseases (IBD), which include ulcerative colitis and Crohn’s disease, cause chronic inflammation of the digestive tract in approximately 1.6 million Americans. A signature of IBD is dysbiosi...
Osmanthus fragrans has been used as folk medicine for thousands of years. The extracts of Osmanthus fragrans flowers were reported to have various bioactivities including free radical ...
We propose OptPipe - a Pipeline for Optimizing Metabolic Engineering Targets, based on a consensus approach. The method generates consensus hypotheses for metabolic engineering applications by combining severa...
Breast cancer is one of the leading causes of deaths for women. It is of great necessity to develop effective methods for breast cancer detection and diagnosis. Recent studies have focused on gene-based signat...
This article is part of a Supplement: Volume 11 Supplement 7
Carbonylation, which takes place through oxidation of reactive oxygen species (ROS) on specific residues, is an irreversibly oxidative modification of proteins. It has been reported that the carbonylation is r...
This article is part of a Supplement: Volume 11 Supplement 7
Effectively predicting protein complexes not only helps to understand the structures and functions of proteins and their complexes, but also is useful for diagnosing disease and developing new drugs. Up to now...
This article is part of a Supplement: Volume 11 Supplement 7
Genome-scale metabolic models provide an opportunity for rational approaches to studies of the different reactions taking place inside the cell. The integration of these models with gene regulatory networks is...
This article is part of a Supplement: Volume 11 Supplement 7
Identification of novel gene-gene relations is a crucial issue to understand system-level biological phenomena. To this end, many methods based on a correlation analysis of gene expressions or structural analy...
This article is part of a Supplement: Volume 11 Supplement 7
Drug development considering individual varieties among patients becomes crucial to improve clinical development success rates and save healthcare costs. As a useful tool to predict individual phenomena and co...
This article is part of a Supplement: Volume 11 Supplement 7
Detecting causality for short time-series data such as gene regulation data is quite important but it is usually very difficult. This can be used in many fields especially in biological systems. Recently, seve...
This article is part of a Supplement: Volume 11 Supplement 7
In recent years, the integration of ‘omics’ technologies, high performance computation, and mathematical modeling of biological processes marks that the systems biology has started to fundamentally impact the ...
This article is part of a Supplement: Volume 11 Supplement 7
Cell fate regulation directly affects tissue homeostasis and human health. Research on cell fate decision sheds light on key regulators, facilitates understanding the mechanisms, and suggests novel strategies ...
This article is part of a Supplement: Volume 11 Supplement 7
Biological networks consisting of molecular components and interactions are represented by a graph model. There have been some studies based on that model to analyze a relationship between structural character...
This article is part of a Supplement: Volume 11 Supplement 7