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Translation efficiency of certain mRNAs can be regulated through a cytoplasmic polyadenylation process at the pre-initiation phase. A translational regulator controls the polyadenylation process and this regul...
Expression of the two transcription factors microphthalmia-associated transcription factor (MITF) and signal transducer and activator of transcription 3 (STAT3) are tightly connected to cell proliferation and ...
We consider the possibility of engineering metabolic pathways in a chassis organism in order to synthesize novel target compounds that are heterologous to the chassis. For this purpose, we model metabolic netw...
Carbon-13 (13C) analysis is a commonly used method for estimating reaction rates in biochemical networks. The choice of carbon labeling pattern is an important consideration when designing these experiments. We p...
The creation and modification of genome-scale metabolic models is a task that requires specialized software tools. While these are available, subsequently running or visualizing a model often relies on disjoin...
Transcription networks define the core of the regulatory machinery of cellular life and are largely responsible for information processing and decision making. At the small scale, interaction motifs have been ...
In System Biology, iterations of wet-lab experiments followed by modelling approaches and model-inspired experiments describe a cyclic workflow. This approach is especially useful for the inference of gene reg...
Drug resistance has now posed more severe and emergent threats to human health and infectious disease treatment. However, wet-lab approaches alone to counter drug resistance have so far still achieved limited ...
Control of growth rate is mediated by tight regulation mechanisms in all free-living organisms since long-term survival depends on adaptation to diverse environmental conditions. The yeast, Saccharomyces cerevisi...
Ovarian cancer causes more deaths than any other gynecological cancer. Identifying the molecular mechanisms that drive disease progress in ovarian cancer is a critical step in providing therapeutics, improving...
Toxins A and B (TcdA and TcdB) are Clostridium difficile's principal virulence factors, yet the pathways by which they lead to inflammation and severe diarrhea remain unclear. Also, the relative role of either to...
The WHO considers leishmaniasis as one of the six most important tropical diseases worldwide. It is caused by parasites of the genus Leishmania that are passed on to humans and animals by the phlebotomine sandfly...
Apoptosis is a form of programmed cell death essential for the maintenance of homeostasis and the removal of potentially damaged cells in multicellular organisms. By binding its cognate membrane receptor, TNF ...
To understand how infectious agents disseminate throughout a population it is essential to capture the social model in a realistic manner. This paper presents a novel approach to modeling the propagation of th...
This article is part of a Supplement: Volume 5 Supplement 3
The primary objectives of this paper are: 1.) to apply Statistical Learning Theory (SLT), specifically Partial Least Squares (PLS) and Kernelized PLS (K-PLS), to the universal "feature-rich/case-poor" (also kn...
This article is part of a Supplement: Volume 5 Supplement 3
Numerous genetic and genomic datasets related to complex diseases have been made available during the last decade. It is now a great challenge to assess such heterogeneous datasets to prioritize disease genes ...
This article is part of a Supplement: Volume 5 Supplement 3
Currently, several systems have been proposed to classify viruses and indicate the relationships between different ones, though each system has its limitations because of the complexity of viral origins and th...
This article is part of a Supplement: Volume 5 Supplement 3
Various gene-expression signatures for breast cancer are available for the prediction of clinical outcome. However due to small overlap between different signatures, it is challenging to integrate existing dis...
This article is part of a Supplement: Volume 5 Supplement 3
The availability of temporal measurements on biological experiments has significantly promoted research areas in systems biology. To gain insight into the interaction and regulation of biological systems, math...
This article is part of a Supplement: Volume 5 Supplement 3
To understand transcriptional regulatory networks (TRNs), especially the coordinated dynamic regulation between transcription factors (TFs) and their corresponding target genes during development, computationa...
This article is part of a Supplement: Volume 5 Supplement 3
Bone cells can sense physical forces and convert mechanical stimulation conditions into biochemical signals that lead to expression of mechanically sensitive genes and proteins. However, it is still poorly und...
This article is part of a Supplement: Volume 5 Supplement 3
Breast cancer is one of the leading causes of cancer death for women all over the world and mammography is thought of as one of the main tools for early detection of breast cancer. In order to detect the breas...
This article is part of a Supplement: Volume 5 Supplement 3
Molecular level of biological data can be constructed into system level of data as biological networks. Network motifs are defined as over-represented small connected subgraphs in networks and they have been u...
This article is part of a Supplement: Volume 5 Supplement 3
Many groups, including our own, have proposed the use of DNA methylation profiles as biomarkers for various disease states. While much research has been done identifying DNA methylation signatures in cancer vs...
This article is part of a Supplement: Volume 5 Supplement 3
State Space Model (SSM) is a relatively new approach to inferring gene regulatory networks. It requires less computational time than Dynamic Bayesian Networks (DBN). There are two types of variables in the lin...
This article is part of a Supplement: Volume 5 Supplement 3
A phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches (dichotomies) for simplicity, although polytomies (multifurcating br...
This article is part of a Supplement: Volume 5 Supplement 3
For RNA-seq data, the aggregated counts of the short reads from the same gene is used to approximate the gene expression level. The count data can be modelled as samples from Poisson distributions with possibl...
This article is part of a Supplement: Volume 5 Supplement 3
We present a report of the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology and other related work in the area of systems biology.
This article is part of a Supplement: Volume 5 Supplement 3
Constructing predictive dynamic models of interacting signalling networks remains one of the great challenges facing systems biology. While detailed dynamical data exists about individual pathways, the task of...
During respiratory viral infections host injury occurs due in part to inappropriate host responses. In this study we sought to uncover the host transcriptional responses underlying differences between high- an...
In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined...
Hereditary Hemorrhagic Telangiectasia (HHT) is an autosomal dominant disease with a varying range of phenotypes involving abnormal vasculature primarily manifested as arteriovenous malformations in various org...
MicroRNA (miRNA) is a class of small RNAs of ~22nt which play essential roles in many crucial biological processes and numerous human diseases at post-transcriptional level of gene expression. It has been reve...
The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum In...
The pyruvate dehydrogenase regulator protein (PdhR) of Escherichia coli acts as a transcriptional regulator in a pyruvate dependent manner to control central metabolic fluxes. However, the complete PdhR regulon h...
The increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association netw...
This article is part of a Supplement: Volume 5 Supplement 2
Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their pr...
This article is part of a Supplement: Volume 5 Supplement 2
Current Genome-Wide Association Studies (GWAS) are performed in a single trait framework without considering genetic correlations between important disease traits. Hence, the GWAS have limitations in discoveri...
This article is part of a Supplement: Volume 5 Supplement 2
Drugs that bind to common targets likely exert similar activities. In this target-centric view, the inclusion of richer target information may better represent the relationships between drugs and their activit...
This article is part of a Supplement: Volume 5 Supplement 2
The current genome-wide association (GWA) analysis mainly focuses on the single genetic variant, which may not reveal some the genetic variants that have small individual effects but large joint effects. Consi...
This article is part of a Supplement: Volume 5 Supplement 2
To understand how stroke risk factors mechanistically contribute to stroke, the genetic components regulating each risk factor need to be integrated and evaluated with respect to biological function and throug...
This article is part of a Supplement: Volume 5 Supplement 2
In recent years, a number of tools have been developed to explore microRNAs (miRNAs) by analyzing their target genes. However, a reverse problem, that is, inferring patterns of protein-coding genes through the...
This article is part of a Supplement: Volume 5 Supplement 2
Somatic cells can be reprogrammed to induced-pluripotent stem cells (iPSCs) by introducing few reprogramming factors, which challenges the long held view that cell differentiation is irreversible. However, the...
This article is part of a Supplement: Volume 5 Supplement 2
Deficiency of the transcription factor MafB, which is normally expressed in macrophages, can underlie cellular dysfunction associated with a range of autoimmune diseases and arteriosclerosis. MafB has importan...
This article is part of a Supplement: Volume 5 Supplement 2
Microarray technology has enabled the measurement of comprehensive transcriptomic information. However, each data entry may reflect trivial individual differences among samples and also contain technical noise...
This article is part of a Supplement: Volume 5 Supplement 2
Although mass spectrometry based proteomics demonstrates an exciting promise in complex diseases diagnosis, it remains an important research field rather than an applicable clinical routine for its diagnostic ...
This article is part of a Supplement: Volume 5 Supplement 2
Lymph node invasion is one of the most powerful clinical factors in cancer prognosis. However, molecular level signatures of their correlation are remaining poorly understood. Here, we propose a new approach, ...
This article is part of a Supplement: Volume 5 Supplement 2
Chromatin immunoprecipitation combined with the next-generation DNA sequencing technologies (ChIP-seq) becomes a key approach for detecting genome-wide sets of genomic sites bound by proteins, such as transcri...
This article is part of a Supplement: Volume 5 Supplement 2
The inference of genes that are truly associated with inherited human diseases from a set of candidates resulting from genetic linkage studies has been one of the most challenging tasks in human genetics. Alth...
This article is part of a Supplement: Volume 5 Supplement 2
Microarray analyses based on differentially expressed genes (DEGs) have been widely used to distinguish samples across different cellular conditions. However, studies based on DEGs have not been able to clearl...
This article is part of a Supplement: Volume 5 Supplement 2