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Systems biology: new institute and applications

Jieming Chen
2011 The Yale Journal of Biology and Medicine  
This article includes a brief overview of the different topics presented at the symposium, followed by a discussion of the advantages and challenges of practical application of systems biology.  ...  The symposium served to provide Yale's scientific community with a glimpse into the wide range of research at the forefront of this interdisciplinary field.  ...  Stelling proposed application-driven approaches to study biological circuits, as opposed to a conventional knowledge-driven approach, which requires detailed hypotheses, observations, and data analyses  ... 
pmid:21451788 pmcid:PMC3064249 fatcat:6lqu7fudw5aevgpzewhwslnx6e

Size matters: network inference tackles the genome scale

Boris Hayete, Timothy S Gardner, James J Collins
2007 Molecular Systems Biology  
In network inference, three broad types of verification are possible: computational verification through cross-validation, in vivo verification, and literature-driven curation.  ...  In addition to the use of curated data sets, it may be possible to seed organisms with small synthetic in vivo networks, the connectivity of which is known by design, and to measure the success of network  ... 
doi:10.1038/msb4100118 pmid:17299414 pmcid:PMC1828748 fatcat:77z4roamjfeylgrowx5sqtq7oy

Recent development on synthetic biological devices treating bladder cancer

Zhicong Chen, Anbang He, Yuchen Liu, Weiren Huang, Zhiming Cai
2016 Synthetic and Systems Biotechnology  
We claimed that the Chinese synthetic biologists are promoting the basic research productions of tumor synthetic biology into the clinic.  ...  We expand the synthetic biology toolkits involving DNA, RNA and protein bio-parts to explore various issues in cancer research, such as elucidation of mechanisms and pathways, creation of new diagnostic  ...  By rewiring gene networks we can shed light on the treatment of bladder cancer that occurs when native networks are damaged.  ... 
doi:10.1016/j.synbio.2016.08.001 pmid:29062946 pmcid:PMC5625735 fatcat:aeukmlukffboljc7ooteuexc6y

The role of predictive modelling in rationally re-engineering biological systems

Tie Koide, Wyming Lee Pang, Nitin S. Baliga
2009 Nature Reviews Microbiology  
The integrated framework necessary for conducting such complex bioengineering requires the convergence of systems and synthetic biology.  ...  In other words, the stage is set for yet another revolutionary merger of two powerful interdisciplinary fields with fundamentally different but complementary outlooks -synthetic biology and systems biology  ...  Acknowledgments This work was supported by grants from the National Institutes of Health (NIH; P50GM076547 and 1R01GM077398-01A2), Department of Environment (DoE; DE-FG02-07ER64327 and DE-FG02-07ER64327  ... 
doi:10.1038/nrmicro2107 pmid:19252506 pmcid:PMC2734281 fatcat:bqo77xkgujhcdk4msqnubsvcie

Computer-aided whole-cell design: taking a holistic approach by integrating synthetic with systems biology [article]

Lucia Marucci, Matteo Barberis, Jonathan Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan Andreas Hoffmann, Sophie Landon, Elibio Rech, Joshua Rees-Garbutt, Richard Seabrook (+2 others)
2020 arXiv   pre-print
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models  ...  Here, we present a perspective on how whole-cell, multiscale models could transform design-build-test-learn cycles in synthetic biology.  ...  funded by the Engineering and Physical Sciences Research Council (EPSRC) within the remits of the Big Ideas initiative.  ... 
arXiv:2006.02720v1 fatcat:zyv26a5mhvfxnfm2wsmcyjn5km

Integration of Complex Data Sources to Provide Biologic Insight into Pulmonary Vascular Disease (2015 Grover Conference Series)

Evan L. Brittain, Stephen Y. Chan
2016 Pulmonary Circulation  
Here, we discuss two specific types of complex data sources-gene regulatory networks and DNA-linked electronic medical record cohorts-that illustrate the promise, challenges, and current limitations of  ...  The use of -omics platforms, in silico modeling of gene networks, and linkage of large human cohorts with DNA biobanks are beginning to bear biologic insight into pulmonary hypertension.  ...  pressure; Source of Figure 2 . 2 Illustration of hemodynamic data extraction from Vanderbilt's Synthetic Derivative.  ... 
doi:10.1086/686995 pmid:27683602 pmcid:PMC5019078 fatcat:ektohemdgngk3kwjsxp5xiwmaa

Global synthetic-lethality analysis and yeast functional profiling

Siew Loon Ooi, Xuewen Pan, Brian D. Peyser, Ping Ye, Pamela B. Meluh, Daniel S. Yuan, Rafael A. Irizarry, Joel S. Bader, Forrest A. Spencer, Jef D. Boeke
2006 Trends in Genetics  
Supplementary data Supplementary data associated with this article can be found at doi:10.1016/j.tig.2005.11.003  ...  a given pair of query genes or target genes, called a congruence network (Box 2) [23] .  ...  Although neither technique is perfect, overall there is excellent concordance in the list of target genes obtained after verification by random spore or tetrad analyses.  ... 
doi:10.1016/j.tig.2005.11.003 pmid:16309778 fatcat:whkwn5to2rh7fg4v3jepltaphu

A Method For Analysing A Gene Expression Data Sequence Using Probabilistic Boolean Networks

Stephen Marshall, Le Yu
2006 Zenodo  
Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006  ...  Ghazal at Scottish Centre for Genomic Technology and Informatics, University of Edinburgh for their support and help in this research.  ...  VERIFICATION WITH SIMULATED DATA The simulated data is modelled by a PBN [3] consisting of M Boolean Networks (BNs) BN 1 …BN M .  ... 
doi:10.5281/zenodo.53462 fatcat:zhoejzj6n5eolavsy5teqbqfte

Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components

Christopher Y. Park, David C. Hess, Curtis Huttenhower, Olga G. Troyanskaya, Ernest Fraenkel
2010 PLoS Computational Biology  
One goal of systems biology is to bridge three aspects of this complexity: the growing body of high-throughput data assaying these interactions; the specific interactions in which individual genes participate  ...  This compendium of physical, synthetic, regulatory, and functional interaction networks has been made publicly available through an interactive web interface for investigators to utilize in future research  ...  Analyzed the data: CYP DCH CH OGT. Wrote the paper: CYP DCH CH OGT.  ... 
doi:10.1371/journal.pcbi.1001009 pmid:21124865 pmcid:PMC2991250 fatcat:3iera7cfcvdctebizsfk7xsqi4

Integrative metabolic engineering

George H McArthur IV, Pooja P Nanjannavar, Emily H Miller, Stephen S Fong
2015 AIMS Bioengineering  
The integration of synthetic biology and metabolic engineering within an iterative design-build-test framework will improve the practice of metabolic engineering by relying more on efficient design strategies  ...  In this review, we highlight computational synthetic biology tools relevant to metabolic engineering, organized in the context of the design-build-test cycle.  ...  Fisher and other members of the Fong Lab for helpful discussions and for comments on the manuscript.  ... 
doi:10.3934/bioeng.2015.3.93 fatcat:2s26fw57nzauphsmyz2iledite

Understanding biological functions through molecular networks

Jing-Dong Jackie Han
2008 Cell Research  
Physics and mathematics have provided important tools for network biology on data mining, network metrics and modeling techniques, and will be driven by new challenges and requirements of network biology  ...  Such results are naturally expected if the selections on network motifs within a species are driven by function rather than driven by structure.  ... 
doi:10.1038/cr.2008.16 pmid:18227860 fatcat:zskbcrtc6bbphovy344auhn4uu

Diversity-based, model-guided construction of synthetic gene networks with predicted functions

Tom Ellis, Xiao Wang, James J Collins
2009 Nature Biotechnology  
Engineering artificial gene networks from modular components is a major goal of synthetic biology.  ...  We then expand our method to produce a synthetic gene network acting as a predictable timer, modifiable by component choice.  ...  AUTHOR CONTRIBUTIONS T.E., X.W. and J.J.C. designed the study; T.E. performed the experiments; X.W. conducted the modeling work; T.E., X.W. and J.J.C. analyzed the data and wrote the paper.  ... 
doi:10.1038/nbt.1536 pmid:19377462 pmcid:PMC2680460 fatcat:eszl5obrqba5pa67nrxpbiecou

Sensitivity of Biological Models to Errors in Parameter Estimates

Robert S. Erb, George S. Michaels
1998 Biocomputing '99  
Continued laboratory study and recent improvements in measurement capabilities have provided an immense quantity of raw gene expression data.  ...  The level of data now available demands the development of well-characterized and tested computational tools.  ...  Boolean networks propose that gene control networks can be solved by considering only the "on" or "off" state of a particular gene. [e.g. Somogyi 7 ].  ... 
doi:10.1142/9789814447300_0006 fatcat:zmanghwzibguzlokuyvmscdt3y

Metabolic systems analysis to advance algal biotechnology

Brian J. Schmidt, Xiefan Lin-Schmidt, Austin Chamberlin, Kourosh Salehi-Ashtiani, Jason A. Papin
2010 Biotechnology Journal  
Metabolic network reconstruction of C. reinhardtii with transcript verification Manichaikul et al.  ...  The experimental verification improved the original structural annotation of the sequence, refining 5% of the ORFs. An additional round of expansion and verification was then applied to the network.  ... 
doi:10.1002/biot.201000129 pmid:20665641 fatcat:qrqi2dq54rbqziupu3azyh37ca

Spectrum of Advancements and Developments in Multidisciplinary Domains for Generative Adversarial Networks (GANs)

Syed Khurram Jah Rizvi, Muhammad Ajmal Azad, Muhammad Moazam Fraz
2021 Archives of Computational Methods in Engineering  
GANs is one of the most highlighted research avenue due to its synthetic data generation capabilities and benefits of representations comprehended irrespective of the application.  ...  The survey paper summarizes the recent applications and developments in the domain of Generative Adversarial Networks (GANs) i.e. a back propagation based neural network architecture for generative modeling  ...  Acknowledgements The authors would like to express their gratitude for the institutional support and research grant of Higher Education Commission (HEC) of Pakistan under International Research Support  ... 
doi:10.1007/s11831-021-09543-4 pmid:33824572 pmcid:PMC8017345 fatcat:efjw24635vdlbgj26bezu4y5sq
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