bioinformatics and systems biology analysis

... 14593–14598, 2005 EURASIP Journal on Bioinformatics and Systems Biology [5] M R Roussel and R Zhu, “Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic ... value 60 s), and termination Its value is randomly generated from a Gaussian distribution with a mean of 102 s and a standard deviation of 14 s These values assume a lac promoter and a gene 2445 ... 2 EURASIP Journal on Bioinformatics and Systems Biology One feature in gene expression that has been proposed to influence noise in RNA and protein levels is the promoter open...

Ngày tải lên: 21/06/2014, 06:20

... phagocytosis of microbial pathogens by macrophages and neutrophils involves the integration of complex cellular systems and so lends itself well to a systems- biology approach Robert Insall (CR-UK Beatson ... this interesting and diverse sympo­ sium during a major microbiology conference helped disseminate systems- biology ideas amongst researchers in virology, bacteriology, mycology and parasitology ... Brown Genome Biology 2010, 11:302 http://genomebiology.com/2010/11/5/302 accumulation of dynein and by a phosphorylationdependent anchorage of motors This finding expands previous models...

Ngày tải lên: 09/08/2014, 20:21

... clustering analysis Gene set enrichment analysis We took the 232 human samples and classified them as basallike, luminal, HER2+/ER-, claudin-low, and normal breastlike according to a clustering analysis ... together, while the Brca1+/-;p53+/- ionizing radiation (IR) and Genome Biology 2007, 8:R76 http://genomebiology.com/2007/8/5/R76 Genome Biology 2007, Volume 8, Issue 5, Article R76 Herschkowitz ... MedroxyprogesteroneDMBA-induced 11 None Random DMBA-induced FVB [69] p53+/-irradiated None p53 heterozygous null, random IR induced BALB/cJ [70] Brca1+/-;p53+/-irradiated None Brca1 and p53 heterozygous null, random IR induced...

Ngày tải lên: 14/08/2014, 07:21

... analysis technique and can combine data obtained in different laboratories Genome Biology 2006, 7:303 Genome Biology 2006, Dynamics and topology of cellular networks Transpath network with random ... the GLYCAN database http://genomebiology.com/2006/7/1/303 a computational analysis for a precise and unbiased global mapping of p53 binding sites Experimental and statistical verification have ... by a spacer region, with one sequence being inverted and complementary to the other, and appear to play an important role in DNA replication and the generation of genomic instability Gary Benson...

Ngày tải lên: 14/08/2014, 16:20

... serve as the editor of these two volumes on Systems and Computational Biology: (I) Molecular and Cellular Experimental Systems, and (II) Bioinformatics and Computational Modeling I believe that ... data-mining approaches for efficient and accurate data analysis of various 26 Systems and Computational Biology – Bioinformatics and Computational Modeling biological systems (for reviews see, Li et ... Computational Design and Combinational Approaches for Systems Biology 75 Chapter Strengths and Weaknesses of Selected Modeling Methods Used in Systems Biology 77 Pascal Kahlem, Alessandro DiCara, Maxime...

Ngày tải lên: 28/06/2014, 10:20

... established themselves Here, the most frequently appearing ones are BMC Systems Biology, Molecular Systems Biology and PLoS Computational Biology There is a clear trend from the more engineering-oriented ... systems level On the one hand, we were surprised by the fact that only a small fraction of the publications found using the keyword systems biology actually reflect applications of systems biology ... examples of research benefitting from systems biology Thus, systems biology has been used for the prediction of drug targets (e.g see entries 84, 104 and 197 in Table 1) and for biotechnological engineering...

Ngày tải lên: 14/02/2014, 14:20

... 7.6.0.324, R2008a) with the software packages systems biology toolbox2 and the sbpd Extension Package as described in [34] Both matlab and systems biology toolbox2 are necessary for the performance ... Glob Optim 39, 197–219 34 Schmidt H & Jirstrand M (2006) Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology Bioinformatics 22, 514– 515 35 Tang X, Ruffner ... between and days, whereas the gain in tolerance was only minor during the first 24 h of cold exposure and between days and In contrast, LT50 decreased almost continuously in C24 until day and did...

Ngày tải lên: 14/02/2014, 22:20

... multidimensional, and can be described or seen in various ways, including both wet (experimental) and dry (computational and theoretical), reductionist and synthetic, qualitative and quantitative, and a systems ... for us and produce and parameterize (with linkages, equations and parameters like rate constants) candidate models of chosen parts of biological systems Single cell and single molecule biology ... suite of techniques for the largely bottom up systems biology strategies set down in Fig 2B Emergence and a true systems biology The grand problem of biology, as well as the inverse problem (Fig...

Ngày tải lên: 07/03/2014, 12:20

... errors is randomization Randomization means both, a random allocation of the experimental material and a random order in which the individual runs of the experiment are performed Randomization ... different parameter values and the optimal design for the (re)estimation of the three rates 31ị Conclusions and outlook In systems biology, experimental planning is becoming more and more crucial, because ... and parameter estimation Bioinformatics 14, 869883 Rodriguez-Fernandez M, Mendes P & Banga JR (2006) A hybrid approach for efcient and robust parameter estimation in biochemical pathways Biosystems...

Ngày tải lên: 23/03/2014, 06:20

... (2009) Systems biology: experimental design FEBS J 276, 923–942 57 Schmidt H, Jirstrand M (2006) Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology Bioinformatics ... predictions p Because over-parametrization and unidentifiability is common and usually quite substantial in systems biology models, many predictions made by a systems biology model will be highly uncertain ... than that of systems biology (i.e the type of knowledge that is sought is different) These differences are important, and also are important to clarify and agree upon if systems biology is to...

Ngày tải lên: 23/03/2014, 06:20

... Automotive Waste Heat Recovery Systems Part I: Numerical Modeling and Baseline Model Analysis Fig Representation of a TE couple (one n- and one p-leg) with fins at the hot side and coolant at the cold ... Vinning and D M Rowe, CRC Handbook of Thermoelectrics, (CRC Press, 1995), pp 329–337 11 M.S Dresselhaus, Y.M Lin, T Koga, S.B Cronin, O Rabin, M.R Blackand, and G Dresselhaus, in Semiconductors and ... thermoelectric leg (n or p), and A denotes the cross-sectional area Subscripts ‘‘n’’ and ‘‘p’’ denote the corresponding n or p thermoelectric materials k and q are thermal conductivity and electrical resistivity,...

Ngày tải lên: 06/05/2014, 08:54

... in systems biology and computational biology and practitioners in industry, (2) researchers and graduate students in computer science and mathematics who are interested in systems biology, and ... understand the state-of-the-art techniques in bioinformatics and systems biology, particularly the theory and application of biomolecular networks The potential readers are (1) specialists and advanced ... closely to systems biology, network biology emphasizes local interactions and global networks of molecules that characterize various biological systems, and attempts to understand biology from the...

Ngày tải lên: 29/05/2014, 14:34

... Introduction Random variables 2.1 2.2 2.3 2.4 2.5 2.6 Probability theory and set theory Discrete random variables Continuous random variables The conditional probability Several random variables and independence ... 0) and where function dened below in (2.59) (2.51) (and similarly for continuous random ( ) is the joint probability density 2.5 Several random variables and independence 2.5.1 Discrete random ... ) and = 2( ) and the transformed random variables = 1( denote the inverse transform by = ( ) and = ( ), then ( where the Jacobian )= ( ( 1( ) 1( )) ( ) ) is ( If ) = det and are independent and...

Ngày tải lên: 01/06/2014, 11:02

... yeast, Fischbach and Krogan Genome Biology 2010, 11:208 http://genomebiology.com/2010/11/5/208 Higher-order experiments as a future focal point of systems biology If modern systems biology is only ... response to an extracellular growth factor - and so another form of higher-dimension systems biology will be the study of how cellular modules change over space and time Another area in which dimensionality ... difficult than analyzing a small subset, and robotics and high-throughput screening techniques are now within the reach of most labs Second, the costs of systems biology scale sub-linearly while the...

Ngày tải lên: 09/08/2014, 20:21

... Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave, New Haven, CT 06511, USA Authors’ contributions TG designed the experiments and completed the analysis AA and TG developed ... drugs labeled as high and low, and the denominator is simply the difference between the standard error for high and low Welch’s t-statistic was used to compute P values, and proteins with P < ... for both AR and ABsensitive proteins and in DNA binding for AR and hydrophilicity-sensitive proteins In addition, charge-sensitive proteins showed an enrichment in transferase activity and MlogP...

Ngày tải lên: 09/08/2014, 22:24

... regulation within Populus and between Populus and Arabidopsis, and (3) to understand the regulatory complexity in leaves by comparing systems biology and traditional bioinformatics as methods ... frontier of systems biology: higherorder and interspecies interactions Genome Biol 11(5):208 Gatherer D: So what we really mean when we say that systems biology is holistic BMC Systems Biology 2010, ... modules (and in parenthesis the number of genes) regulated by the factor in our systems biology- based network and in the co-expression network, respectively Transcription factors in our systems biology- based...

Ngày tải lên: 11/08/2014, 11:21

... clear boundary exists between systems biology and systems medicine, it could be stated that systems biology is aimed at a fundamental understanding of biologic processes and ultimately at an exhaustive ... essential roles in discovery and validation in systems biology and medicine [7] Study design is often the weakest point of complex molecular studies in systems biology and medicine For example, ... tissues, organs, and all the way to individuals, environmental factors, populations, and ecosystems, systems medicine aims to discover and select the key factors at each level and integrate them...

Ngày tải lên: 11/08/2014, 12:20

... manufacturomes and relational biology: analogies between systems biology and manufacturing systems Theoretical Biology and Medical Modelling 2011 8:19 Submit your next manuscript to BioMed Central and take ... manufacturing systems [15-17] Armbruster et al [18] outline and describe the similarities between networks of interacting machines in factory production systems and cell biology, and Iglesias and Ingalls ... analogies between control theory and systems biology Casti [20,21] makes mathematical analogies between factory systems, control theory and connects it to cellular biology via a set of mathematical...

Ngày tải lên: 13/08/2014, 16:20

... theory and network statistics are Newman et al [32] and Albert and Barabasi [33] Godsil and Royle [34] and Chung [35] are good references that go beyond the statistical analysis of network graphs and ... predictions and propose new hypotheses The motivation of this paper is to examine an alternative set of mathematical abstractions applied to biology, and in particular systems biology Symmetry and symmetry ... Rietman et al.: Review and application of group theory to molecular systems biology Theoretical Biology and Medical Modelling 2011 8:21 Submit your next manuscript to BioMed Central and take full advantage...

Ngày tải lên: 13/08/2014, 16:20

... Theoretical Biology and Medical Modelling 2005, 2:34 http://www.tbiomed.com/content/2/1/34 techniques and their practical applications are well described – and would be better placed ... it stands I expect to consult it regularly over the foreseeable future, and I am confident that biologists everywhere will benefit from having a copy to hand Publish with Bio Med Central and every ... thermodynamics and enzymology, surely elementary for most readers, and ends with the same amount of text – a mere 20 pages – on metabolic control theory, which is less likely to be familiar and is far...

Ngày tải lên: 13/08/2014, 23:20