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Analysis of adaptive walks on NK fitness landscapes with different interaction schemes
2015
Journal of Statistical Mechanics: Theory and Experiment
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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
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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 | www.plosone.org
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
2014
PLoS ONE
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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]
2022
arXiv
pre-print
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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]
2021
bioRxiv
pre-print
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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
2020
Figshare
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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
2020
Royal Society Open Science
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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
2009
Molecular biology and evolution
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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
2018
Heredity
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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
2010
Proceedings of the National Academy of Sciences of the United States of America
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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
ECOLOGICAL AND ECONOMIC ANALYSIS OF ADAPTIVE LANDSCAPE SYSTEMS UNDER CONDITIONS OF SUSTAINABLE DEVELOPMENT
2020
REPORTS
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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
2014
BMC Bioinformatics
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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
2018
Journal of Urban and Landscape Planning
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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
2016
American Journal of Botany
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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)
2017
Genome Biology and Evolution
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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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