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Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

Marc N Offman, Alexander L Tournier, Paul A Bates
2008 BMC Structural Biology  
Conclusion: This approach improves the overall performance of the GA by allowing models to overcome local energy barriers.  ...  AEP enabled the selection of the best models in 40% of all targets; compared to 25% for a normal GA.  ...  Acknowledgements We thank all the members of the Biomolecular Modelling Laboratory for many useful discussions and insights.  ... 
doi:10.1186/1472-6807-8-34 pmid:18673557 pmcid:PMC2527322 fatcat:ey6rva7povcwhhz4qazqtcfvju

Evolutionary and Principled Search Strategies for Sensornet Protocol Optimization

J. Tate, B. Woolford-Lim, I. Bate, Xin Yao
2012 IEEE Transactions on Systems Man and Cybernetics Part B (Cybernetics)  
Second, we apply the Strength Pareto Evolutionary Algorithm 2 and Two-Archive evolutionary algorithms to explore the problem space, with each iteration potentially yielding solutions of higher quality  ...  First, we apply factorial design and statistical model fitting methods to reject insignificant factors and locate regions of the problem space containing near-optimal solutions by principled search.  ...  are performed with a simulation model of the system, or some combination of the two.  ... 
doi:10.1109/tsmcb.2011.2161466 pmid:21859628 fatcat:lfkegiqkpbhfxlnmmddy5l6uo4

Polygenicity And Epistasis Underlie Fitness-Proximal Traits In TheCaenorhabditis elegansMultiparental Experimental Evolution (CeMEE) Panel [article]

Luke M Noble, Ivo Chelo, Thiago Guzella, Bruno Afonso, David D Riccardi, Patrick Ammerman, Adel Dayarian, Sara Carvalho, Anna Crist, Ania Pino-Querido, Boris Shraiman, Matthew V Rockman (+1 others)
2017 bioRxiv   pre-print
We apply it to study the genetic basis of two fitness components, fertility and hermaphrodite body size at time of reproduction, with high broad sense heritability in the CeMEE.  ...  Understanding the genetic basis of complex traits remains a major challenge in biology.  ...  Notably 1202 for fertility, which is expected to be well aligned with fitness 1203 under the experimental evolution scheme, strong interactions 1204 among four pairs of alleles with weak marginal main  ... 
doi:10.1101/120865 fatcat:5bxi2jutxbh27fwiodxuwy6npy

OUP accepted manuscript

2017 Genome Biology and Evolution  
A theoretical model presented herein suggests that failing to control for the effects of GC-biased gene conversion (gBGC) is potentially a contributor to the overestimation of a, and that this effect cannot  ...  Population genetic theory predicts that selection should be more effective when the effective population size (N e ) is larger, and that the efficacy of selection should correlate positively with recombination  ...  Acknowledgments We thank the three anonymous reviewers for their constructive comments. P.C. and the sequencing were funded by a NERC grant awarded to K.Z. (NE/L005328/1).  ... 
doi:10.1093/gbe/evx213 pmid:29045655 pmcid:PMC5714183 fatcat:qlloyuytknajvb7kcgnnzv73hu

Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist's perspective

Debashish Chowdhury
2013 Physics reports  
We also describe several of those motor-driven intracellular stochastic processes for which quantitative models are yet to be developed.  ...  We review mostly the quantitative models for the kinetics of these motors.  ...  K(t − t ′ ) in the GLE.  ... 
doi:10.1016/j.physrep.2013.03.005 fatcat:2ioahi2wsrdp7f6dyj2gfkxl6q

Learning Capacity in Simulated Virtual Neurological Procedures

Mattia Samuel Mancosu, Silvester Czanner, Martin Punter
2020 Journal of WSCG  
ACKNOWLEDGEMENTS The authors would like to thank Oana Rotaru-Orhei for her comments and the three anonymous reviewers for their insightful suggestions.  ...  ACKNOWLEDGMENTS The authors acknowledge the support of the NSERC/Creaform Industrial Research Chair on 3-D Scanning for conducting the work presented in this paper.  ...  We have evaluated different pipeline combinations with a representative set of models.  ... 
doi:10.24132/csrn.2020.3001.13 fatcat:uytlm7nytrhmnk553ellfhl54a

Selection of Rye (Secale cereale L.) for Powdery Mildew and Leaf Rust Resistance Through Phenotyping, Target Sequencing, and Association Genetics

N.M. Vendelbo, Mogens Hovmøller, Annemarie Fejer Justesen, Ahmed Jahoor, Jihad Orabi
2021 Zenodo  
The 600K SNP genotyping was performed by Eurofins Genomics (Skejby, Denmark). Conflicts of Interest: The authors declare no conflict of interest.  ...  The plant material included in this study was provided by Nordic Seed Germany GmbH (Nienstädt, Germany). The 20K SNP genotyping was performed by Trait Genetics (Gatersleben, Germany).  ...  GWAS using a mixed linear model (MLM) was performed to identify discrete haplotype blocks associated with powdery mildew resistance.  ... 
doi:10.5281/zenodo.5820211 fatcat:mg5v7skd5jggpe7bhephu2c2nq

Abstracts from the virtual 46th American Society of Andrology Annual Meeting

2021 Andrology  
mental models of genetic- or diet-induced obesity.  ...  Thus, the aim of this study is to evaluate the nation evaluations.  ... 
doi:10.1111/andr.13044 fatcat:r3cgjac7uzawbewb7vreye2mpe

The 2019 Motile Active Matter Roadmap [article]

Gerhard Gompper, Roland G. Winkler, Thomas Speck, Alexandre Solon, Cesare Nardini, Fernando Peruani, Hartmut Loewen, Ramin Golestanian, U. Benjamin Kaupp, Luis Alvarez, Thomas Kioerboe, Eric Lauga, Wilson Poon, Antonio De Simone (+21 others)
2019 arXiv   pre-print
Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external  ...  The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people.  ...  Acknowledgements The theoretical work on molecular swimming and nonequilibrium activity of enzymes has been performed jointly with Tunrayo Adeleke-Larodo, Jaime Agudo-Canalejo, Armand Ajdari, Pierre  ... 
arXiv:1912.06710v1 fatcat:7hv3b5l2vbedveybk2hkj67y4q

Introduction [chapter]

2016 Music Data Analysis  
The interface between the computer and statistical sciences is increasing, as each discipline seeks to harness the power and resources of the other.  ...  This series aims to foster the integration between the computer sciences and statistical, numerical, and probabilistic methods by publishing a broad range of reference works, textbooks, and handbooks.  ...  In [12] , Measures beyond Classification Performance The evaluation of music classification models is typically done with respect to clas sification performance.  ... 
doi:10.1201/9781315370996-5 fatcat:avooqogcpnbjngqmzuonil3exq

The comparative psychology of uncertainty monitoring and metacognition

J. David Smith, Wendy E. Shields, David A. Washburn
2003 Behavioral and Brain Sciences  
We provide a unifying formal description of animals' performances and examine the optimality of their decisional strategies.  ...  This exploration could extend the study of animal self-awareness and establish the relationship of self-awareness to other-awareness.  ...  ACKNOWLEDGMENT Support for the writing of this commentary was provided by National Institutes of Health Grant HD-38051.  ... 
doi:10.1017/s0140525x03000086 fatcat:6u3d5kjs7fa5naqpgcz6xjzxsi

Jahrestagung der Deutschen, Österreichischen und Schweizerischen Gesellschaften für Hämatologie und Onkologie. Wien, 18.-22. Oktober 2013: Abstracts

2013 Onkologie (Basel)  
We aim to gain deeper insights into this topic by combining physician and patient data from the WIN ON-study and analyzing the data in multivariate regression models.  ...  Systemic chemotherapy in metastatic lung cancer depends on tumor histology, performance status and age of patients, organ functions, side effects and other parameters.  ...  Posterdiskussion Sonstige Onkologie P834 Expression of GLI-1 in tumor surrounding stroma in patients with skin cancer P842 Bone metastasis in solid tumors in German outpatient centers -data from  ... 
doi:10.1159/000356365 pmid:24157728 fatcat:mc6krvlgcjhdrd7rhmvjoeqspq

Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes

Hannah L Klein, Kenny K.H. Ang, Michelle R. Arkin, Emily C. Beckwitt, Yi-Hsuan Chang, Jun Fan, Youngho Kwon, Michael J. Morten, Sucheta Mukherjee, Oliver J. Pambos, Hafez el Sayyed, Elizabeth S. Thrall (+14 others)
2019 Microbial Cell  
Each type of assay is a powerful tool but each comes with its particular advantages and limitations.  ...  Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis.  ...  TRS would like to acknowledge grants RepOne and PrTxConf (French ANR), NanoRep (Université PSL) as well as the "Equipe Labelisée" program of the French League Against Cancer.  ... 
doi:10.15698/mic2019.01.665 pmid:30652106 pmcid:PMC6334232 fatcat:j6dtywwil5df7ipmfgglppizoi

Fast Evolution of Custom Machine Representations

L. Huelsbergen
2005 IEEE Congress on Evolutionary Computation  
require an additional small amount of work to rewrite the forward address once it  ...  Described are new approaches for evaluating computer program representations for use in automated search methodologies such as the evolutionary design of software.  ...  This paper's work on fast evaluation of custom instruction sets is part of the & (AMP-automatic machine programming) project currently being designed and implemented to experiment with modular evolution  ... 
doi:10.1109/cec.2005.1554672 dblp:conf/cec/Huelsbergen05 fatcat:mxsqvoe3lvfetfdu6nkj2rjrdq

Evolution of cooperation in artificial ants

Markus Waibel
to confirm the robustness of our results with respect to two important model parameters.  ...  A complete theory of kin selection needs to account for genetic similarity in a social group with respect to the genetic similarity to competitors.  ... 
doi:10.5075/epfl-thesis-3943 fatcat:tuphxuqkhfh3zc6plkzex7j33m
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