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Analysis of adaptive walks on NK fitness landscapes with different interaction schemes

Stefan Nowak, Joachim Krug
2015 Journal of Statistical Mechanics: Theory and Experiment  
Our main tool for the analysis are adaptive walks, an idealized dynamics by which the population moves uphill in fitness and terminates at a local fitness maximum.  ...  The focus is on how this scheme influences the overall shape of the landscape.  ...  Acknowledgments We thank Cristian Giardina for pointing us to the literature on reluctant adaptive walks. This work was supported by DFG within SPP 1590 Probabilistic structures in evolution.  ... 
doi:10.1088/1742-5468/2015/06/p06014 fatcat:i67paqqq6fe6dls6gndjxhanmm

Correction: Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation

2014 PLoS ONE  
The pairs of populations representing the contrast between fragmented versus continuous landscapes are shown by gray shading. doi:10.1371/journal.pone.0101467.g003 PLOS ONE | July  ...  of populations with statistically significant (FDR,0.05) allele frequencies (c; Fisher's exact test) and for the number of statistically significant (FDR,0.05) differentially expressed genes (d; edgeR analysis  ... 
doi:10.1371/journal.pone.0104668 fatcat:nk7cwt3ncndn7hj32hgapioare

Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation

Panu Somervuo, Jouni Kvist, Suvi Ikonen, Petri Auvinen, Lars Paulin, Patrik Koskinen, Liisa Holm, Minna Taipale, Anne Duplouy, Annukka Ruokolainen, Suvi Saarnio, Jukka Sirén (+6 others)
2014 PLoS ONE  
Citation: Somervuo P, Kvist J, Ikonen S, Auvinen P, Paulin L, et al. (2014) Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation. PLoS ONE 9(7): e101467.  ...  We conclude that differences in gene expression between the landscape types reflect genomic adaptations to landscape fragmentation.  ...  To supplement the results on the contrast between the landscape types, we bring into the analysis two types of additional information.  ... 
doi:10.1371/journal.pone.0101467 pmid:24988207 pmcid:PMC4079591 fatcat:ictpwzs24fgsnfzk4fjgfcs5oe

Mixed integer programming and adaptive problem solver learned by landscape analysis for clinical laboratory scheduling [article]

Keyao Wang, Bo Liu
2022 arXiv   pre-print
Preliminary landscape analysis sustains that these clinics-orientated scheduling instances are difficult to solve.  ...  This paper attempts to derive a mathematical formulation for real-practice clinical laboratory scheduling, and to present an adaptive problem solver by leveraging landscape structures.  ...  An adaptive problem solver taking advantage of landscape analysis is highly needed.  ... 
arXiv:2204.08320v1 fatcat:d3bisu2sgjgnbovrmisooysvu4

Weighted force analysis method for derivation of multidimensional free energy landscapes from adaptively-biased replica simulations [article]

Fabrizio Marinelli, José D. Faraldo-Gómez
2021 bioRxiv   pre-print
AbstractA methodology is proposed for calculating multidimensional free-energy landscapes of molecular systems, based on post-hoc analysis of multiple molecular dynamics trajectories wherein adaptive biases  ...  facilitates calculating accurate multidimensional free-energy landscapes from different trajectories and time-dependent biases, outperforming other post-hoc unbiasing methods.  ...  For similar reasons, it has been not straightforward so far to apply dynamic histogram [31, 32] or transitionbased reweighting analysis [33, 34] in the context of adaptive biases.  ... 
doi:10.1101/2021.02.17.431654 fatcat:hbiagkdrwrcwdbbtaezbzos6ku

Electronic Supplementary Material from Analysis of statistical correlations between properties of adaptive walks in fitness landscapes

Sandro M. Reia, Paulo R. A. Campos
2020 Figshare  
This electronic supplementary material provides additional figures of the mutational pathways for the Gb1 and NK fitness landscapes, as well as additional correlation tables.  ...  FIG. 2 . 2 The set of the monotonic mutational pathways to the two local maxima of a single instance of the NK fitness landscape, with K = 1. Upper panels: random adaptive walks.  ...  Upper panels: random adaptive walks (first two rows).Lower panels: probabilistic adaptive walks (last two rows).  ... 
doi:10.6084/m9.figshare.11665668 fatcat:5aosljptqfb3vet5yiu4h5m2tm

Analysis of statistical correlations between properties of adaptive walks in fitness landscapes

Sandro M. Reia, Paulo R. A. Campos
2020 Royal Society Open Science  
The fitness landscape metaphor has been central in our way of thinking about adaptation.  ...  Here, we exhaustively analyse the statistical properties of adaptive walks for two empirical fitness landscapes and theoretical NK landscapes.  ...  The authors also acknowledge Claudia Bank for providing the data of the Hsp90 fitness landscape.  ... 
doi:10.1098/rsos.192118 pmid:32218986 pmcid:PMC7029893 fatcat:faimch3z5jha7lbiqbgjcejt3q

Sequence-Based Analysis of Protein Energy Landscapes Reveals Nonuniform Thermal Adaptation within the Proteome

J. Gu, V. J. Hilser
2009 Molecular biology and evolution  
Unexpectedly, however, the analysis shows that protein thermostability is modified to different extents across the proteome and depends on the functional role for which the protein is involved.  ...  According to the current paradigm, the adaptation of an organism for survival at higher or lower temperatures is facilitated by the adaptation of the component proteins.  ...  This score was used as a measure for comparative analysis to identify nonuniform thermostability modulation within the proteomes for thermal adaptation.  ... 
doi:10.1093/molbev/msp140 pmid:19592668 pmcid:PMC2912464 fatcat:kazu7r5wyngsherbjndzc2shaa

Landscape genomics and pathway analysis to understand genetic adaptation of South African indigenous goat populations

K. Mdladla, E. F. Dzomba, F. C. Muchadeyi
2018 Heredity  
Landscape genomic approaches of spatial analysis method (SAM) identified a total of 843 (1.75%) SNPs, while latent factor mixed models (LFMM) identified 714 (1.48%) SNPs significantly associated with environmental  ...  The first axis (Model I) of the RDA analysis revealed 329 outlier SNPs.  ...  Gugger for helpful discussions and manual on the redundancy analysis, Dr Fritchot for helping with data input and LFMM scripts.  ... 
doi:10.1038/s41437-017-0044-z pmid:29422506 fatcat:l522rhnopzcjvjyf7deh7j4abm

Cross-species analysis traces adaptation of Rubisco toward optimality in a low-dimensional landscape

Yonatan Savir, Elad Noor, Ron Milo, Tsvi Tlusty
2010 Proceedings of the National Academy of Sciences of the United States of America  
The analysis presented here suggests that the evolution of Rubisco is confined to an effectively one-dimensional landscape, which is manifested in simple power law correlations between its kinetic parameters  ...  Our analysis indicates that the specificity of Rubisco is not the main determinant of its efficiency but rather the tradeoff between the carboxylation velocity and CO2 affinity.  ...  Adaptation of Rubisco in the 1D landscape is nearly optimal A longstanding question is the optimality of Rubisco to its environment.  ... 
doi:10.1073/pnas.0911663107 pmid:20142476 pmcid:PMC2840432 fatcat:2fozv4onnbfnvhvnxhummnjcye


G. O. Abisheva, PhD, Kokshetau University named after Abay Myrzakhmetov. Head of the Department ", L. Zh. Taukenova, D. T. Ismailova, D. K. Sunakbayeva, N. B. Shamuratova, Petr Hajek, Tourism NVP FCS", , Kokshetau, Kazakhstan,,, Senior Lecturer, Doctor of profile Kazakh University "Turan-Astana", NurSultan, Kazakhstan;; (+4 others)
2020 REPORTS  
Thus we carried out an ecological and economic analysis of the adaptive-landscape system which consists of natural natural and historical characteristics.  ...  Landscaping measures landscape features. Landscaping measures are a never-ending process.  ... 
doi:10.32014/2020.2518-1483.61 fatcat:twmy3txvlzal7gtf2aqwuysp2a

An adaptive landscape for training in the essentials of next gen sequencing data acquisition and bioinformatic analysis

Mark Farman, Patrick Calie, Jerzy Jaromczyk, Jolanta Jaromczyk, Neil Moore, Daniel Harris, Chris Schardl
2014 BMC Bioinformatics  
P O S T E R P R E S E N T A T I O N Open Access An adaptive landscape for training in the essentials of next gen sequencing data acquisition and bioinformatic analysis Mark Farman 1,2 , Patrick Calie 3  ...  In this, our third year, we continue to modify and adapt the Workshop curriculum to address the evolving needs of our clients, based upon our experiences with real time data from our Advanced Genetic Technologies  ... 
doi:10.1186/1471-2105-15-s10-p25 pmcid:PMC4196053 fatcat:r5do5f5mrnhijaqfywzydjk7rm

Applying Partial Order and SWOT analysis in water and land use planning to prioritize the adaptation strategies under changing climate

Hamidreza Solaymani
2018 Journal of Urban and Landscape Planning  
The priority of the differnt operations were achieved based on questionnaire, SWOT (Strengths, Weaknesses, Opportunities and Threats), and Partial Order Analysis (POA) at this research work.  ...  The ranked adaptation operations under the changing climate were exposed at the end.  ...  The research work is focused on formulation of the adaptation strategy to water and land-use planning based on SWOT and POA analysis.  ... 
doaj:469d88c1c64a4fc18e3ee16162e1a3d9 fatcat:omrgtel45jhmrf2sopywjo6fga

Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata

Victoria L. Sork, Kevin Squire, Paul F. Gugger, Stephanie E. Steele, Eric D. Levy, Andrew J. Eckert
2016 American Journal of Botany  
Th is eff ect within the context of landscape genomics, however, needs to be quantifi ed with simulations.  ...  Geography vs. climate -Th e redundancy analysis results in Limitations and future directions -Th is study conveys promising fi ndings of the ability to detect the geographic patterns of putatively adaptive  ... 
doi:10.3732/ajb.1500162 pmid:26744482 fatcat:jy4qag6v7nfqzcj5uby2pewelq

Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis)

Norah P. Saarman, Kord M. Kober, W. Brian Simison, Grant H. Pogson
2017 Genome Biology and Evolution  
Nonetheless, our finding of more stabilizing amino acid changes in the warm adapted lineage is important because it suggests that adaption for thermal stability has contributed to M. galloprovincialis'  ...  Abstract Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions.  ...  Nobua-Behrmann for her help with statistical analysis.  ... 
doi:10.1093/gbe/evx190 pmid:28985307 pmcid:PMC5647807 fatcat:guvj3e2v6nh2xiedwdcwdwrbm4
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