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About a possible path towards the reverse engineering of quantum mechanics [article]

Alberto Ottolenghi
2011 arXiv   pre-print
variable models and we allow for the existence of an underlying network.  ...  An out of the box intellectual path exploring the foundations of quantum mechanics is discussed in some detail, in order to clarify why a possibly different way to look at the relevant fundamental questions  ...  They are the natural platforms for the new generation of communication and information sourcing and analysis.  ... 
arXiv:1111.5215v1 fatcat:3rfztrvcjva6lii6afpxvt6d4u

Path to drugging functional clones of luminal breast cancers using in-depth proteomics with spatially resolved mass spectrometry guided by MALDI imaging [article]

N. Hajjaji, S. Aboulouard, T. Cardon, D. Bertin, YM. Robin, I. Fournier, M. Salzet
2021 medRxiv   pre-print
yet known drug interactions, showing the potential for discovery.  ...  For this purpose, we performed an unsupervised, label-free, spatially resolved shotgun proteogenomic guided by MALDI mass spectrometry imaging (MSI) on 124 selected tumor clonal areas from early luminal  ...  Integrated Venn diagram analysis was performed using "the InteractiVenn": a web-based tool for the analysis of complex data sets (Heberle et al., 2015) .  ... 
doi:10.1101/2021.02.16.21251694 fatcat:vxxso3zbkjdqpo77m6mqx3sywm

Postoperative Lung Injury- The path from Initiation to Clinical Diagnosis [article]

Raluca Maltesen
2016 Ph.d.-serien for Det Teknisk-Naturvidenskabelige Fakultet, Aalborg Universitet  
Statistical methods for the analysis of high-throughput metabolomics data. Comput Struct Biotechnol J. 2013;4(5):1-9. 159. Axelson DE. Data Preprocessing for Chemometric and Metabonomic Analysis.  ...  MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res. 2009 07;37:W652-60. 163. Xia J, Wishart DS.  ... 
doi:10.5278/vbn.phd.engsci.00156 fatcat:ri3fq2cyejbdpktruzachia2ou

Learning Systems Biology: Conceptual Considerations toward a Web-Based Learning Platform

Frank Emmert-Streib, Matthias Dehmer, Fernando Lyardet
2013 Education Sciences  
This paper deals with the conceptual design of a web-based course and its content for educating students in systems biology.  ...  We discuss several learning strategies and problems when dealing with structural hypertext patterns that might occur in the context of web-based learning platforms.  ...  Acknowledgements We would like to thank Peter Hamilton, Ricardo de Matos Simoes, Shailesh Tripathi and Shu-Dong Zhang for fruitful discussions about various aspects of this paper.  ... 
doi:10.3390/educsci3020158 fatcat:bzmlk7v6fngjjdafcyw5l5mxwi

Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks

Ignat Drozdov, Christos A Ouzounis, Ajay M Shah, Sophia Tsoka
2011 BMC Research Notes  
Findings: We present Functional Genomics Assistant (FUGA) -an extensible and portable MATLAB toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network  ...  Cellular constituents such as proteins, DNA, and RNA form a complex web of interactions that regulate biochemical homeostasis and determine the dynamic cellular response to external stimuli.  ...  Acknowledgements We thank members of the King's College London Centre for Bioinformatics (KCBI), and in particular Chrysanthi Ainali, for ideas, test cases, and feedback.  ... 
doi:10.1186/1756-0500-4-462 pmid:22035155 pmcid:PMC3214203 fatcat:jnwf4zc6urbppaizrt262qgi2e

An Evaluation of China's Influenza A (H1N1) Emergency Response Measures [chapter]

Lan Xue, Guang Zeng
2018 Research Series on the Chinese Dream and China's Development Path  
Additionally, China's research and analysis of the new Influenza A (H1N1) virus' entire genome sequence garnered international recognition and played an important guiding role in the country's prevention  ...  the web-for the accurate, timely, and appropriate reporting of epidemic information and government prevention and control measures.  ... 
doi:10.1007/978-981-13-0644-0_5 fatcat:hwordvwftbbmni4xby2ewyrhia

Cancer Commons: Biomedicine in the Internet Age [chapter]

Jeff Shrager, Jay M. Tenenbaum, Michael Travers
2011 Collaborative Computational Technologies for Biomedical Research  
ACKNOWLEDGMENTS The Cancer Commons platform was built by the CollabRx engineering team led by Mike Travers, Randy Gobbel, and Jay Bartels.  ...  Steve Bagley, Sean Ekins, Gavin Gordon, and George Lundberg provided helpful comments on various drafts of this chapter.  ...  An initial disease model may be created top down, for example, by a panel of recognized disease experts, or bottom up, for example, via a statistical analysis of clinically annotated genomic data.  ... 
doi:10.1002/9781118026038.ch11 fatcat:u2f5heqjmbh67cdi5lhphoum2e

AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis

P. Li, W. Zang, Y. Li, F. Xu, J. Wang, T. Shi
2010 Nucleic Acids Research  
Ignorance of these features will bring much bias to the network analysis and application.  ...  With improvements in experimental techniques and progress in research, the overall protein interaction network frameworks of several model organisms have been created through data collection and integration  ...  We also plan to carry out quantification analysis for protein interaction network via statistical approaches; at the same time, we will dynamically display the network based on time course data on developmental  ... 
doi:10.1093/nar/gkq959 pmid:21036873 pmcid:PMC3013798 fatcat:f5tjljj6dvaapkqgws5khwwm54

designGG: an R-package and web tool for the optimal design of genetical genomics experiments

Yang Li, Morris A Swertz, Gonzalo Vera, Jingyuan Fu, Rainer Breitling, Ritsert C Jansen
2009 BMC Bioinformatics  
High-dimensional biomolecular profiling of genetically different individuals in one or more environmental conditions is an increasingly popular strategy for exploring the functioning of complex biological  ...  Results: This paper presents designGG, an R package for designing optimal genetical genomics experiments. A web implementation for designGG is available at http://gbic.biol.rug.nl/designGG.  ...  Acknowledgements This work was supported by the Netherlands Organization for Scientific Research, NWO-86504001. We thank Danny Arends for help in implementing the web tool.  ... 
doi:10.1186/1471-2105-10-188 pmid:19538731 pmcid:PMC2706229 fatcat:xe5y7cktkjbq3n64vothanvkgy

Incorporating computational resources in a cancer research program

Nicholas T. Woods, Ankita Jhuraney, Alvaro N. A. Monteiro
2014 Human Genetics  
Abbreviations AP-MS affinity purification coupled to mass spectrometry ENCODE Encyclopedia of DNA Elements FANTOM Functional Annotation of the Mammalian Genome HCIP high confidence interacting proteins  ...  Thus, one of the most pressing issues facing an experimental cancer biology research program in genetics is incorporating data from multiple sources to annotate, visualize, and analyze the system under  ...  This tool provides an interactive platform to aid in genome analysis.  ... 
doi:10.1007/s00439-014-1496-3 pmid:25324189 pmcid:PMC4401625 fatcat:gkrgo3kbsnag3hadp67q3pzqcq

Network Biology in Medicine and Beyond

B. Zhang, Y. Tian, Z. Zhang
2014 Circulation: Cardiovascular Genetics  
It is challenging to discern patterns and distill knowledge from massive amount of data in a high-dimensional space.  ...  However, because of differences in these technology platforms, data sets are often heterogeneous in nature.  ...  Sources of Funding Disclosures None.  ... 
doi:10.1161/circgenetics.113.000123 pmid:25140061 pmcid:PMC4333150 fatcat:bobjv3d5xzcttgtvng5vcf7x2a

Proteogenomic convergence for understanding cancer pathways and networks

Emily S Boja, Henry Rodriguez
2014 Clinical Proteomics  
With a critical link to genotypes (i.e., high throughput genomics and transcriptomics data), new and complementary information can be gleaned from multi-dimensional omics data to (1) assess the effect  ...  Recent technological advances in high throughput, deep sequencing for the human genomes and proteomic technologies to comprehensively characterize the human proteomes in conjunction with multiplexed targeted  ...  Robert Clay Rivers for his critical reading of this review.  ... 
doi:10.1186/1559-0275-11-22 pmid:24994965 pmcid:PMC4067069 fatcat:6so4o3yqzbg6rau4z53xnneu4q

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis

Daniel Spies, Constance Ciaudo
2015 Computational and Structural Biotechnology Journal  
Computational methods developed originally for microarrays analysis can now be optimized and applied to genome-wide studies in order to have access to a better comprehension of the whole transcriptome.  ...  Furthermore, possible improvements in analysis, data integration as well as future applications of differential expression analysis are discussed.  ...  Beyer and Jian Yu for discussion and helpful comments on the manuscript. This work was supported by a core grant from ETH-Z (PP12/BIOL.160) (supported by Roche).  ... 
doi:10.1016/j.csbj.2015.08.004 pmid:26430493 pmcid:PMC4564389 fatcat:r5j35ddvazcd7jr5trpz6el3ou

Integrative Systems Biology Resources and Approaches in Disease Analytics [chapter]

Marco Fernandes, Holger Husi
2019 Systems Biology [Working Title]  
Currently, our analytical competences are struggling to keep-up the pace of in-deep analysis of all generated large-scale data resultant of high-throughput omics platforms.  ...  Here, we will describe several database resources, standalone and web-based tools applied in disease analytics workflows based in data-driven integration of outputs of multi-omic detection platforms.  ...  The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.5772/intechopen.84834 fatcat:szdavjmg2jbwpnjl2irao6ehty

GeneTrail: A Framework for the Analysis of High-Throughput Profiles

Nico Gerstner, Tim Kehl, Kerstin Lenhof, Lea Eckhart, Lara Schneider, Daniel Stöckel, Christina Backes, Eckart Meese, Andreas Keller, Hans-Peter Lenhof
2021 Frontiers in Molecular Biosciences  
In general, these platforms generate high-dimensional and noisy data sets.  ...  We highlight the capabilities of our web service with an analysis of a single-cell COVID-19 data set that demonstrates its potential for uncovering complex molecular mechanisms.GeneTrail can be accessed  ...  The resulting data sets are usually high-dimensional and noisy, making a manual inspection impossible.  ... 
doi:10.3389/fmolb.2021.716544 pmid:34604304 pmcid:PMC8481803 fatcat:6h7j4qzyzzax7nvwljt6pgakcu
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