Quantitative Biology

http://link.springer.com/journal/40484

List of Papers (Total 128)

Geometric and amino acid type determinants for protein-protein interaction interfaces

BackgroundProtein-protein interactions are essential to many biological processes. The binding site information of protein-protein complexes is extremely useful to obtain their structures from biochemical experiments. Geometric description of protein structures is the precondition of protein binding site prediction and protein-protein interaction analysis. The previous...

BMTK: a toolkit for determining modules in biological bipartite networks

BackgroundModule detection is widely used to analyze and visualize biological networks. A number of methods and tools have been developed to achieve it. Meanwhile, bipartite module detection is also very useful for mining and analyzing bipartite biological networks and a few methods have been developed for it. However, there is few user-friendly toolkit for this task.MethodsTo...

Biclustering by sparse canonical correlation analysis

BackgroundDeveloping appropriate computational tools to distill biological insights from large-scale gene expression data has been an important part of systems biology. Considering that gene relationships may change or only exist in a subset of collected samples, biclustering that involves clustering both genes and samples has become increasingly important, especially when the...

Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway’s involvement in juvenile myelomonocytic leukemia

BackgroundClinical studies and genetic analyses have revealed that juvenile myelomonocytic leukemia (JMML) is caused by somatic and/or germline mutations of genes involved in the RAS/MAPK signalling pathway. Given the vastly different clinical prognosis among individual patients that have had this disease, mutations in genes of other pathways may be involved.MethodsIn this study...

The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines

Background The community-based Ontology of Biological and Clinical Statistics (OBCS) represents and standardizes biological and clinical data and statistical methods. Methods Both OBCS and the Vaccine Ontology (VO) were used to ontologically model various components and relations in a typical host response to vaccination study. Such a model was then applied to represent and...

Transcription regulation by DNA methylation under stressful conditions in human cancer

Background We aim to address one question: do cancer vs. normal tissue cells execute their transcription regulation essentially the same or differently, and why? Methods We utilized an integrated computational study of cancer epigenomes and transcriptomes of 10 cancer types, by using penalized linear regression models to evaluate the regulatory effects of DNA methylations on gene...

PMTDS: a computational method based on genetic interaction networks for Precision Medicine Target-Drug Selection in cancer

Background Precision medicine attempts to tailor the right therapy for the right patient. Recent progress in large-scale collection of patents’ tumor molecular profiles in The Cancer Genome Atlas (TCGA) provides a foundation for systematic discovery of potential drug targets specific to different types of cancer. However, we still lack powerful computational methods to...

Towards integrated oncogenic marker recognition through mutual information-based statistically significant feature extraction: an association rule mining based study on cancer expression and methylation profiles

Background Marker detection is an important task in complex disease studies. Here we provide an association rule mining (ARM) based approach for identifying integrated markers through mutual information (MI) based statistically significant feature extraction, and apply it to acute myeloid leukemia (AML) and prostate carcinoma (PC) gene expression and methylation profiles. Methods...

On the use of kernel machines for Mendelian randomization

Background Properly adjusting for unmeasured confounders is critical for health studies in order to achieve valid testing and estimation of the exposure’s causal effect on outcomes. The instrumental variable (IV) method has long been used in econometrics to estimate causal effects while accommodating the effect of unmeasured confounders. Mendelian randomization (MR), which uses...

Cap-seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse

Background MicroRNAs (miRNAs) regulate target gene expression at post-transcriptional level. Intense research has been conducted for miRNA identification and the target finding. However, much less is known about the transcriptional regulation of miRNA genes themselves. Recently, a special group of pre-miRNAs that are produced directly by transcription without Drosha processing...

Variable importance-weighted random forests

Background Random Forests is a popular classification and regression method that has proven powerful for various prediction problems in biological studies. However, its performance often deteriorates when the number of features increases. To address this limitation, feature elimination Random Forests was proposed that only uses features with the largest variable importance scores...

Systems and synthetic biology approaches in understanding biological oscillators

Background Self-sustained oscillations are a ubiquitous and vital phenomenon in living systems. From primitive single-cellular bacteria to the most sophisticated organisms, periodicities have been observed in a broad spectrum of biological processes such as neuron firing, heart beats, cell cycles, circadian rhythms, etc. Defects in these oscillators can cause diseases from...

Transcriptome assembly strategies for precision medicine

BackgroundPrecision medicine approach holds great promise to tailored diagnosis, treatment and prevention. Individuals can be vastly different in their genomic information and genetic mechanisms hence having unique transcriptomic signatures. The development of precision medicine has demanded moving beyond DNA sequencing (DNA-Seq) to much more pointed RNA-sequencing (RNA-Seq...

Strategic planning for national biomedical big data infrastructure in China

The promise that big data will revolutionize scientific discovery and technology innovation is now being widely recognized. With the explosive growth of biomedical data, life science is being transformed into a digital science in which novel insights are gained from in-depth data analysis and modeling. Extensive and innovative utilization of biomedical big data is a key to the...

Metabolic pathway databases and model repositories

BackgroundThe number of biological Knowledge bases/databases storing metabolic pathway information and models has been growing rapidly. These resources are diverse in the type of information/data, the analytical tools, and objectives. Here we present a review of the most popular metabolic pathway databases and model repositories, focusing on their scope, content including...

The system capacity view of aging and longevity

Background Aging is a complex systems level problem that needs a systems level solution. However, system models of aging and longevity, although urgently needed, are still lacking, largely due to the paucity of conceptual frameworks for modeling such a complex process. Results We propose that aging can be viewed as a decline in system capacity, defined as the maximum level of...

Models, methods and tools for ancestry inference and admixture analysis

Background Genetic admixture refers to the process or consequence of interbreeding between two or more previously isolated populations within a species. Compared to many other evolutionary driving forces such as mutations, genetic drift, and natural selection, genetic admixture is a quick mechanism for shaping population genomic diversity. In particular, admixture results in...

Decoding nervous system by single-cell RNA sequencing

Background Mammalian brain are composed of a large number of specialized cell types with diverse molecular composition, functions and differentiation potentials. The application of recently developed single-cell RNA sequencing (scRNA-seq) technology in this filed has provided us new insights about this sophisticated system, deepened our understanding of the cell type diversity...

ePlant for quantitative and predictive plant science research in the big data era

Background The increase in global population, climate change and stagnancy in crop yield on unit land area basis in recent decades urgently call for a new approach to support contemporary crop improvements. ePlant is a mathematical model of plant growth and development with a high level of mechanistic details to meet this challenge. Results ePlant integrates modules developed for...

Multifaceted roles of complementary sequences on circRNA formation

Background Circular RNAs (circRNAs) from back-spliced exon(s) are characterized by the covalently closed loop feature with neither 5′ to 3′ polarity nor polyadenylated tail. By using specific computational approaches that identify reads mapped to back-splice junctions with a reversed genomic orientation, ten thousands of circRNAs have been recently re-identified in various cell...