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Welcome to the Pubget Medical Subject Headings (MESH) browser. Click on a topic or subtopic below to explore related papers. In the gold box is the most recent paper about the current MESH term, and below are 20 related papers.
Systems Biology (0):
Recent article
Systems Biology
Biochemical Pharmacology (82)10 2011
Abstract
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Systems Biology, IET (5)5 2011
Abstract
Qualitative models allow understanding the relation between the structure and the dynamics of gene regulatory networks. The dynamical properties of these models can be automatically analysed by means of formal verification methods, like model checking. This facilitates the model-vali...
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PMID: 22010757
PDF is available here.
PDF is available here.
Integrative Biology (3)7 2011
Abstract
We now routinely scan cells and organisms at practically all levels, from genome to protein, metabolism, signaling and other cellular functions. This methodology allowed biological studies to move from a reductionist approach, such as isolation of specific pathways and mechanisms, to a more integrat...
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PMID: 21674097
PDF is available here.
PDF is available here.
Abstract
Molecular reductionism has failed to deliver the broad-based therapeutic insights that were initially hoped for. Simple reductionism is now being replaced by so-called "systems biology." This is a poorly defined approach and/or discipline with some versions of it relying excessively...
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PMID: 21636568
PDF is available here.
PDF is available here.
Abstract
We bring this 'bottom-up' approach alongside the current NGS-driven genetic study of genetic variations and disease aetiology. We describe experimental and computational techniques for assessing genetic variants and their deleterious effects on protein structure and function....
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PMID: 21350909
PDF is available here.
PDF is available here.
Abstract
We developed a generalized time-frequency analysis (TFA) framework to systematically explore the dynamical properties of biomolecular networks. Using TFA, we focused on two well-characterized yeast gene regulatory networks responsive to carbon-source shifts and a mammalian innate immune regulatory n...
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PMID: 21738459
PDF is available here.
PDF is available here.
Abstract
Recent years have witnessed extensive research activity in modeling biological phenomena as well as in developing intervention strategies for such phenomena. S-systems, which offer a good compromise between accuracy and mathematical flexibility, are a promising framework for modeling...
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PMID: 21172748
PDF is available here.
PDF is available here.
Abstract
We are invoking lessons learned from the broad discipline of Systems Biology research that focuses primarily on molecular and cellular networks and adapting these concepts to Systems Exposure Science which focuses on interpreting the linkage from environmental measurements and biomonitoring to the e...
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PMID: 21492901
PDF is available here.
PDF is available here.
Abstract
We suggested that the human peripheral blood mononuclear cells (PBMC) network can be delineated by cellular reconstruction to guide identification of candidate genes. Based on 285 microarrays (7370 genes) from 98 heart transplant patients enrolled in the Cardiac Allograft Rejection Gene Expression O...
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PMID: 20497491
PDF is available here.
PDF is available here.
Abstract
We compare polarization in response to a stimulus (e.g., a chemoattractant) in cells typically used in experiments (yeast, amoebae, leukocytes, keratocytes, fibroblasts, and neurons), and, in parallel, responses of several prototypical models to typical stimulation protocols. We find that the divers...
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PMID: 21552548
PDF is available here.
PDF is available here.
Abstract
Gene therapy is an exciting field that has attracted much interest since the first submission of clinical trials. Preliminary results were very encouraging and prompted many investigators and researchers. However, the ability of stem cells to differentiate into specific cell types holds immense poten...
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PMID: 21431572
PDF is available here.
PDF is available here.
Abstract
We propose a new inference algorithm that incorporates mutual information (MI), conditional mutual information (CMI), and predictive minimum description length (PMDL) principle to infer gene regulatory networks from DNA microarray data. In this algorithm, the information theoretic quantities MI and...
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PMID: 21431544
PDF is available here.
PDF is available here.
Abstract
I = Hmax-H. Genetic networks are composed of a relative low and fluctuating amount of molecules and this characteristic, together with the effect of noise, produces a genetic response at time t with a probability p(t) of being correct with respect to the input message, and a probability 1-p(t) of be...
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PMID: 21368577
PDF is available here.
PDF is available here.
Abstract
We show that the model manifolds of a large class of models, known as sloppy models, have many universal features; they are characterized by a geometric series of widths, extrinsic curvatures, and parameter-effect curvatures, which we describe as a hyper-ribbon. A number of common difficulties in op...
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PMID: 21517619
PDF is available here.
PDF is available here.
Abstract
We will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays, and lectin microarrays. We will also discuss the challenges and f...
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PMID: 21257623
PDF is available here.
PDF is available here.
Abstract
Cancer begins to be recognized as a highly complex disease, and advanced knowledge of the carcinogenic process claims to be acquired by means of supragenomic strategies. Experimental data evidence that tumor emerges from disruption of tissue architecture, and it is therefore conseque...
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PMID: 21319994
PDF is available here.
PDF is available here.
Abstract
We demonstrate that machine learning of multiple CPIs can not only assess drug polypharmacology but can also efficiently identify novel bioactive scaffold-hopping compounds. Through a machine-learning technique that uses multiple CPIs, we have successfully identified novel lead compounds for two pha...
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PMID: 21364574
PDF is available here.
PDF is available here.
Systems Biology, IET (5)2 2011
Abstract
Many methods had been developed on inferring transcriptional network from gene expression. However, it is still necessary to design new method that discloses more detailed and exact network information. Using network-assisted regression, the authors combined the averaged three-way mu...
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PMID: 21405197
PDF is available here.
PDF is available here.
Abstract
Systems biology provides an integrative platform by which to account for the biological complexity related to cardiac health and disease. In this way, consequences of ATP-sensitive K(+) (K(ATP)) channel deficiency for heart failure prediction, diagnosis, and therapy were resolved recently at a proteo...
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PMID: 21321057
PDF is available here.
PDF is available here.
Proteomics (11)4 2011
Abstract
The ability to sequence DNA rapidly, inexpensively and in a high-throughput fashion provides a unique opportunity to sequence whole genomes of a large number of species. The cataloging of protein-coding genes from these species, however, remains a non-trivial task with the majority o...
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PMID: 21246734
PDF is available here.
PDF is available here.
Abstract
Abstract
Biomedical systems involve a large number of entities and intricate interactions between these. Their direct analysis is, therefore, difficult, and it is often necessary to rely on computational models. These models require significant resources and parallel computing solutions. These approaches are...
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PMID: 21431578
PDF is available here.
PDF is available here.
Abstract
Here we present a Bayesian method that identifies which known transcriptional relationships in a regulatory network are consistent with a given body of static gene expression data by eliminating the non-relevant ones. The Partially Observed Bipartite Network (POBN) approach developed here is tested...
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PMID: 21619639
PDF is available here.
PDF is available here.
Abstract
The availability of gene network inference algorithms with known inferential properties opens a new era of large-scale screening experiments that could be equally beneficial for basic biological and biomedical research with auspicious prospects. The availability of our easy to use software package c...
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PMID: 21696592
PDF is available here.
PDF is available here.
Abstract
The proposed methods are capable of distinguishing metabolic time trends resulting from different treatments and associate significance levels to these differences. Among several nonlinear mixed-effects regression models tested, a three-parameter logistic function represents the data with highest ac...
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PMID: 21518445
PDF is available here.
PDF is available here.
Abstract
The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organ...
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PMID: 21569493
PDF is available here.
PDF is available here.
Abstract
We focus on one of the most important mechanisms underpinning tumor robustness and degeneracy, the cellular heterogeneity that is the hallmark of most solid tumors. Based on a combination of computational, experimental and clinical studies we argue that stochastic noise is an underlying cause of tum...
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PMID: 20944865
PDF is available here.
PDF is available here.
Abstract
We have used an engineered poly(dimethylsiloxane) (PDMS) microwell array as a reductionist approach to study the effect of environmental parameters, independently of each other. It is observed for MCF-7 breast cancer cells, that culture within the three-dimensional (3D) environment of the microwells...
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PMID: 21049126
PDF is available here.
PDF is available here.
Abstract
Neurons are highly polarized cells with extensive sub-cellular compartmentalization to accommodate diverse local needs. Information flows between the pre-synaptic (axon) and post-synaptic (dendrite) compartments, as well as between the soma and the nerve termini. It is critical that a neuron control...
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PMID: 21116543
PDF is available here.
PDF is available here.
Abstract
We propose a module-detection algorithm through defining network activity measures and associating them through a weighted clustering approach. We verify our method on diverse models and it provides a unique perspective for analysing model dynamics and expression data, especially with consideration...
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PMID: 21712564
PDF is available here.
PDF is available here.
B M B Reports (44)1 2011
Abstract
We briefly review and compare the major srRNA pathways, and argue that the impact of srRNA is always at the system level. We demonstrate how a simple mathematical model can ease the discussion of governing principles. To demonstrate these points we review a few examples from bacteria and animals....
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PMID: 21266101
PDF is available here.
PDF is available here.
Abstract
We investigated possible cooperative deregulation of microRNAs (miRNAs) and transcription factors (TFs) in glioblastoma, under the hypothesis that miRNAs and TFs might have a combinational regulatory effect on glioblastoma genes. We searched glioblastoma-specific regulatory networks by integrating g...
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PMID: 21712563
PDF is available here.
PDF is available here.
Integration of clustering and biclustering procedures for analysis of large DNA microarray datasets.
Abstract
In this paper, a new biclustering method is introduced based on a geometric method. The Hough Transform (HT) in column-pair space is used to find sub-biclusters and the k-means method is used to optimise the combining process. The experiment results show that the K-means Based Geomet...
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PMID: 21712567
PDF is available here.
PDF is available here.
Abstract
We propose an Answer Set Programming (ASP)-based approach to model interaction networks. We build a general ASP framework that describes the network semantics and allows modelling specific networks with little effort. ASP provides a rich and flexible toolbox that allows expanding the framework with...
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PMID: 21544955
PDF is available here.
PDF is available here.
Abstract
Abstract
We have entered an era of systems modeling, experimental testing, and refinement. This approach, coupled with advances from the genetic and biochemical analyses of clock function, is accelerating our progress towards a comprehensive understanding of the plant circadian clock network.
Copyright © 20...
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PMID: 20889330
PDF is available here.
PDF is available here.
Abstract
Our understanding of outputs that regulate behavior and physiology has been enhanced through gene expression profiling and proteomic analyses. Systems approaches uncovered underlying principles of transcriptional regulation and robustness of the oscillator through perturbation analysis and synthetic...
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PMID: 20926286
PDF is available here.
PDF is available here.
Proteomics (10)24 2010
Abstract
We used an in-depth, 3-D protein level, comparative proteome analysis of two genetically, very closely related melanoma cell lines with low- and high-metastatic potentials to identify proteins and key pathways involved in tumor progression. This proteome comparison utilized fluorescent tagging of ce...
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PMID: 21136598
PDF is available here.
PDF is available here.
Abstract
The autotrophic nitrogen removal process (partial nitritation combined with the Anammox process) is a new and sustainable nitrogen removal technique for nitrogen-rich streams. A modelling study has been performed to define optimal process conditions (temperature, oxygen supply, pH and biomass retent...
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PMID: 21121455
PDF is available here.
PDF is available here.
Abstract
We remain largely ignorant of the mechanisms by which successful vaccines stimulate protective immunity. Two recent advances are beginning to illuminate such mechanisms: realization of the pivotal role of the innate immune system in sensing microbes and stimulating adaptive immunity, and advances in...
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PMID: 21029962
PDF is available here.
PDF is available here.
Proteomics (10)22 2010
Abstract
We attempt to summarize the most recent advancements in the proteomic study of microbial phagosomes, especially those originating from mouse or human cells. We also briefly describe the proteomics of latex bead-containing phagosomes because they are often used as model phagosomes for study. We provi...
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PMID: 21080496
PDF is available here.
PDF is available here.
Abstract
Molecular Interventions (10)5 2010
Abstract
Abstract
We show, by developing mathematical tools that merge control and information theory with physical chemistry, that seemingly mild constraints on these rates place severe limits on the ability to suppress molecular fluctuations. Specifically, the minimum standard deviation in abundances decreases with...
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PMID: 20829788
PDF is available here.
PDF is available here.
Journal of Biotechnology (149)3 2010
Abstract
Photosynthesis produces the basic building block for crop biomass and yields; however, improving photosynthesis has not been effectively used as a breeding goal. More and more evidences suggested that improving photosynthesis can substantially increase crop yields. The complexity of photosynthesis h...
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PMID: 20036701
PDF is available here.
PDF is available here.
Abstract
We also describe strategies that could lead to achievement of this goal.
Using the yellow fever vaccine as a benchmark of an efficient vaccine, recent studies identified factors of immune protection and more importantly innate immune pathways needed for the establishment of long-term...
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PMID: 20978376
PDF is available here.
PDF is available here.
Systems Biology, IET (4)5 2010
Abstract
Epigenetics is the study of regulatory mechanisms that are not accompanied by the action of genetic elements. Recently, a system-wide extension of epigenetics has been driven by the rapid evolution of genomics technology. This means not simply profiling multiple genes together as gen...
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PMID: 20831342
PDF is available here.
PDF is available here.
Proteomics (10)17 2010
Abstract
We try to shed light on what these definitions mean, how large-scale proteomics such as a HPP can insert into the larger omics chorus, and what we can reasonably expect from a HPP in the way it has been proposed so far....
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PMID: 20648483
PDF is available here.
PDF is available here.
Abstract
The use of computational applications in biological research is significantly lagging behind other scientific research areas such as physics, mathematics, and geology; more in silico tools are needed. The increasing complexity of biological data makes it more and more difficult for s...
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PMID: 20865508
PDF is available here.
PDF is available here.
Experimental Dermatology (19)8 2010
Abstract
We argue that the hair follicle (HF), one of the signature features of mammals, is a perfect and clinically relevant model for systems biology research. The HF represents a stem cell-rich, essentially autonomous mini-organ, whose cyclic transformations follow a hypothetical intrafollicular "hair cyc...
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PMID: 20590819
PDF is available here.
PDF is available here.
Abstract
We review recent progress made in understanding the molecular mechanisms of copper transport in cells by analyzing structural features of copper proteins, their mode of interaction, and their thermodynamic and kinetic parameters, thus contributing to systems biology of copper within the cell....
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PMID: 20333435
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)30 2010
Abstract
We tested the ability of a library of small peptidomimetics to induce phenotypic effects with functional implications on a panel of strains of the budding yeast Saccharomyces cerevisiae, both wild type and mutants, for respiratory function and multidrug resistance. Further elucidation of the functio...
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PMID: 20501664
PDF is available here.
PDF is available here.
Abstract
We characterize the integrated response of a rat host to the liver fluke Fasciola hepatica using a combination of (1)H nuclear magnetic resonance spectroscopic profiles (liver, kidney, intestine, brain, spleen, plasma, urine, feces) and multiplex cytokine markers of systemic inflammation. Multivaria...
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PMID: 20664642
PDF is available here.
PDF is available here.
Abstract
Life is a dynamic process driven by the complex interplay between physical constraints and selection pressures, ranging from nutrient limitation to inhibitory substances to predators. These stressors are not mutually exclusive; microbes have faced concurrent challenges for eons. Genome-enabled syste...
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PMID: 20637598
PDF is available here.
PDF is available here.
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