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Systems approaches in understanding evolution and evolvability

Sumeet Agarwal
2013 Progress in Biophysics and Molecular Biology  
of time and resources.  ...  Systems and network-based approaches are becoming increasingly popular in cellular biology.  ...  within the class can be evolved in polynomial time and resources.  ... 
doi:10.1016/j.pbiomolbio.2013.09.004 pmid:24120732 fatcat:iaa262aj6bg5veduasz7cqd52m

Growth signals determine the topology of evolving networks [article]

Ana Vranić, Marija Mitrović Dankulov
2020 arXiv   pre-print
We show that networks with power-law degree distributions, which are obtained with time-varying growth signals, are correlated and clustered, while networks obtained with a constant growth signal are not  ...  Indeed, the properties of the growth signal significantly determine the topology of the obtained networks and thus ought to be considered prominently in models of complex systems.  ...  The work of M.M.D. was, in part, supported by the Ito Foundation fellowship.  ... 
arXiv:2009.00444v1 fatcat:vljtij5etjd5pamvm76jud5vbq


Akila V., Govindasay V.
2018 Indian Journal of Computer Science and Engineering  
This will in turn assist in understanding the informal research groups evolution in an institution. It should also taken to consideration that Co-authorship networks usually evolve over time.  ...  The formation of groups is unavoidable in this setting. The identification of these groups in this setting may help in harnessing the social dynamics that exist in the institution.  ...  It introduces a time component to concept lattices allowing concepts to evolve with time . The evolution of concepts in a dynamic network can assist in understanding the dynamics of the network.  ... 
doi:10.21817/indjcse/2018/v9i2/180902028 fatcat:fhi5ciqstvcctkf7b222ay35sy

Understanding Modularity in Molecular Networks Requires Dynamics

R. P. Alexander, P. M. Kim, T. Emonet, M. B. Gerstein
2009 Science Signaling  
sigtrans;2/81/pe44#otherarticles This article cites 32 articles, 14 of which can be accessed for free: Glossary Look up definitions for abbreviations and terms found in  ...  Network motifs can be recognized from network structure alone by finding groups of molecules connected in the network more often than would be expected at random.  ...  A clear understanding of dynamic modularity emerges only when the time-dependent activity of molecular networks is monitored.  ... 
doi:10.1126/scisignal.281pe44 pmid:19638611 pmcid:PMC4243459 fatcat:hfehd27adnfwxftgsrkw5qoxem

Challenges on Probabilistic Modeling for Evolving Networks [article]

Jianguo Ding, Pascal Bouvry
2013 arXiv   pre-print
areas of network performance, network management and network security for evolving networks.  ...  This paper presents a survey on probabilistic modeling for evolving networks and identifies the new challenges which emerge on the probabilistic models and optimization strategies in the potential application  ...  It is a time related function during the evolution. Two types of dynamics are required in order to fully understand how networks evolve over time.  ... 
arXiv:1304.7820v2 fatcat:qvtskgtvpvh2npqbyjlghyu774

KELLER: estimating time-varying interactions between genes

L. Song, M. Kolar, E. P. Xing
2009 Bioinformatics  
These methods will be an enabling first step for studying the driving forces underlying the dynamic gene regulation circuitry and predicting the future network structures in response to internal and external  ...  Our results offer the first glimpse into the temporal evolution of gene networks in a living organism during its full developmental course.  ...  Recall that we assume that the time-evolving network varies smoothly across time.  ... 
doi:10.1093/bioinformatics/btp192 pmid:19477978 pmcid:PMC2687946 fatcat:d6jwn657bvaivck6yg2uzrj3hm

New Insights about Enzyme Evolution from Large Scale Studies of Sequence and Structure Relationships

Shoshana D. Brown, Patricia C. Babbitt
2014 Journal of Biological Chemistry  
Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms.  ...  Comparison among all of the sequences and/or structures in a superfamily can then be used to deduce how evolution has varied these features to produce new enzyme functions from the ancestral structural  ...  Two other important themes complicate our understanding and at the same time offer new clues about the ways that new reactions may evolve.  ... 
doi:10.1074/jbc.r114.569350 pmid:25210038 pmcid:PMC4215206 fatcat:biiui2rljngshklchfp6465hom

Temporal Multivariate Networks [chapter]

Daniel Archambault, James Abello, Jessie Kennedy, Stephen Kobourov, Kwan-Liu Ma, Silvia Miksch, Chris Muelder, Alexandru C. Telea
2014 Lecture Notes in Computer Science  
In a multivariate scenario, however, attributes play an important role and can also evolve over time.  ...  Networks that evolve over time, or dynamic graphs, have been of interest to the areas of information visualization and graph drawing for many years.  ...  In a time varying scenario, both the graph structure and attribute values can evolve over time.  ... 
doi:10.1007/978-3-319-06793-3_8 fatcat:fdvjfwg4jvathcj2mxchrotv6y


2010 Advances in Complex Systems  
Such competition is likely to have an impact on the way in which social structure and group affiliation co-evolve.  ...  How can we understand the interaction between the social network topology of a population and the patterns of group affiliation in that population?  ...  Acknowledgements We thank two anonymous reviewers for their helpful comments-and specifically for suggesting the example domain described in Section 7-and acknowledge financial support from the EPSRC (  ... 
doi:10.1142/s0219525910002712 fatcat:7o6dycyfwvcezbz4ij3i5ckzae

On the evolution of user interaction in Facebook

Bimal Viswanath, Alan Mislove, Meeyoung Cha, Krishna P. Gummadi
2009 Proceedings of the 2nd ACM workshop on Online social networks - WOSN '09  
We find that links in the activity network tend to come and go rapidly over time, and the strength of ties exhibit a general decreasing trend of activity as the social network link ages.  ...  In this paper, we take a first look at the evolution of activity between users in the Facebook social network.  ...  In this section, we focus on understanding how the global structure of the activity network changes over time.  ... 
doi:10.1145/1592665.1592675 dblp:conf/sigcomm/ViswanathMCG09 fatcat:yim5ltktwvguvbqqhzrkr4gxk4


2012 International Journal of Bifurcation and Chaos in Applied Sciences and Engineering  
In addition, the values of important topological properties of a network that is evolving in time were studied; more recently, it was revealed that the complex organization of networks results in a wide  ...  Gomez-Gar denes et al. develop this concept in adaptive networks: here, the process (spreading of a disease) is driven by the topology, while at the same time the network evolves as a consequence of the  ... 
doi:10.1142/s0218127412020063 fatcat:xfzfwzhpffcmlagybfdqemnjvi

Analysis and Visualization of Dynamic Networks [chapter]

Faraz Zaidi, Chris Muelder, Arnaud Sallaberry
2017 Encyclopedia of Social Network Analysis and Mining  
This holistic approach helps in understanding the complex behaviour of real world systems and allow us to predict and forecast how these networks evolve over time.  ...  That is, each time-varying cluster V C i is a cluster whose membership can evolve over time, where vc t i represents the set of nodes in the cluster i at time t.  ... 
doi:10.1007/978-1-4614-7163-9_382-1 fatcat:wcnq6a5ncffh7baxftl43vs6eq

Analysis and Visualization of Dynamic Networks [chapter]

Faraz Zaidi, Chris Muelder, Arnaud Sallaberry
2014 Encyclopedia of Social Network Analysis and Mining  
This holistic approach helps in understanding the complex behaviour of real world systems and allow us to predict and forecast how these networks evolve over time.  ...  That is, each time-varying cluster V C i is a cluster whose membership can evolve over time, where vc t i represents the set of nodes in the cluster i at time t.  ... 
doi:10.1007/978-1-4614-6170-8_382 fatcat:ccsnmkpgjnbgjofm3dtcedjgjm

Detecting change points in the large-scale structure of evolving networks

Leto Peel, Aaron Clauset
2014 arXiv   pre-print
An important task in analyzing such evolving networks is change-point detection, in which we both identify the times at which the large-scale pattern of interactions changes fundamentally and quantify  ...  Interactions among people or objects are often dynamic in nature and can be represented as a sequence of networks, each providing a snapshot of the interactions over a brief period of time.  ...  DISCUSSION When analyzing a sequence of time evolving networks, a central goal is to understand how the network's structure has changed over time, and how it might change in the future.  ... 
arXiv:1403.0989v2 fatcat:xodjl7vqvvde7dpesx7s2pbx7e

Evolutionary Network Analysis

Charu Aggarwal, Karthik Subbian
2014 ACM Computing Surveys  
Furthermore, the specific kinds of changes to the structure of the network, such as the impact on community structure or the impact on network structural parameters, such as node degrees, also needs to  ...  When a network evolves, the results of data mining algorithms such as community detection need to be correspondingly updated.  ...  The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Laboratory  ... 
doi:10.1145/2601412 fatcat:hvm37apdbzgnzkgilt2te6gfba
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