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Assembly of Long Error-Prone Reads Using Repeat Graphs
[article]
2018
bioRxiv
pre-print
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However, most algorithms for assembling long error-prone reads use an alternative overlap-layout-consensus (OLC) approach that does not provide a repeat characterization. ...
Flye iteratively untangle edges and finds maximum weight matchings until no extra repeats can be resolved. ...
The algorithm then proceeds to the next iteration unless no new reads mapping to the original repeat consensus were classified or all of the consensus sequences are identical to those in the previous iteration ...
doi:10.1101/247148
fatcat:qzlfzaakajczhdefxrf6t6xaqi
2018 Index IEEE Transactions on Knowledge and Data Engineering Vol. 30
2019
IEEE Transactions on Knowledge and Data Engineering
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Lian, D., þ, TKDE June 2018 1122-1135
Crowdsourcing
Computing Crowd Consensus with Partial Agreement. ...
Huang, W., þ, TKDE April 2018 772-785
Xu, C., þ, TKDE April 2018 630-644
B
Bayes methods
Computing Crowd Consensus with Partial Agreement. ...
doi:10.1109/tkde.2018.2882359
fatcat:asiids266jagrkx5eac6higrlq
Notes on Theory of Distributed Systems
[article]
2021
arXiv
pre-print
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2020 pre-print arXiv:2001.04235v1 fatcat:pnhkktkxfvgqvmxmgk7vqbtwya
Lattice agreement A lattice is a partial order in which every pair of elements x, y has a least upper bound x ∨ y called the join of x and y and a greatest lower bound x ∧ y called the meet of x and y. ...
BG simulation and consensus BG simulation was originally developed to attack k-set agreement, but (as pointed out by Gafni [Gaf09] ) it gives a particularly simple proof of the impossibility of consensus ...
The Chandra-Toueg protocol [CT96] then solves consensus for us provided f < n/2. 0 from a 0 , computes x = 1, advances a 0 to 2, then re-reads 0 from a 0 , computes x = 2, and returns 0. • When m = 4 ...
arXiv:2001.04235v2
fatcat:viv5nl6qyvdnhjb73vm64gxj5u
Inferring species interaction networks from species abundance data: A comparative evaluation of various statistical and machine learning methods
2010
Ecological Informatics
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Material and Methods Simulation study ...
We first test the success of these methods for recovering the structure of simulated food webs, where the true structure is known precisely. ...
We thank Jonathan Yearsley for providing the initial community simulation model and Marco Grzegorczyk for providing the Bayesian Network code and being available for questions. ...
doi:10.1016/j.ecoinf.2010.06.005
fatcat:bccq4vnfkffvhejli27z546jda
The NMR Solution Structure of Intestinal Fatty Acid-binding Protein Complexed with Palmitate: Application of a Novel Distance Geometry Algorithm
1996
Journal of Molecular Biology
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, was comparable to that of 2.5 Å X-ray crystal structures. ...
The first stage of this procedure relied critically upon an initial structural model based on the consensus 1 H/ 13 C chemical shift-derived secondary structure and a set of symmetry-checked restraints ...
Simulated annealing failed to refine these structures to convergence, generally producing final structures with improper local geometry and poor agreement with the experimental restraints. ...
doi:10.1006/jmbi.1996.0663
pmid:8969307
fatcat:q5b4x5vibjai5g5zslxnpnhlcm
A novel method for analysing consistency and unravelling multiple solutions in sediment fingerprinting
2021
Science of the Total Environment
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solutions X i and its corresponding set of consistent tracers S i which will be used in the fingerprinting models. ...
Triangle backgrounds represent the density of solutions after iterating through all the analysed tracer pairs. ...
doi:10.1016/j.scitotenv.2021.147804
pmid:34049142
fatcat:65774wz52vaavnolhra4clsygu
Engineering strategies for rational polyketide synthase design
2018
Natural product reports (Print)
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Particularly, the rst almost complete X-ray structural model of the iterative Mycobacterium smegmatis mycocerosic acid synthase (MAS)-like PKS gave important insight, 21 but also earlier models on separate ...
This complexity needs to be further untangled in structural and functional studies before programmable engineering becomes possible. ...
doi:10.1039/c8np00030a
pmid:29938731
fatcat:6cdhvbucyre7pjs7osqkbujzem
Novel methods for epistasis detection in genome-wide association studies
2020
PLoS ONE
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EpiGWAS encompasses several methods, which we compare to state-of-the-art techniques for epistasis detection on simulated and real data. ...
For iterative simulations, HAPGEN can be time-consuming, notably for large cohorts consisting of thousands of samples. ...
All elements are positive which indicates a relative agreement between the methods. ...
doi:10.1371/journal.pone.0242927
pmid:33253293
fatcat:rbiafaowrjb2jh2hpnpuyof63a
A Statistical Workflow to Evaluate the Modulation of Wine Metabolome and Its Contribution to the Sensory Attributes
2021
Fermentation
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Each set of volatile and non-volatile metabolites selected was then related to the sensory attributes of the wines by means of partial least squares regression (PLSR). ...
Wine volatile and non-volatile metabolites modulation was independently evaluated by means of partial least squares discriminant analysis (PLS-DA), obtaining potential markers of the fermentation strategies ...
The drift correction was performed as followed (Equation (1) ): X corrected (i) = X original (i) + mean(X QC ) − f drift (i) (1) where i is the injection order of each sample, X corrected is the corrected ...
doi:10.3390/fermentation7020072
fatcat:risi4lwduvacjo6mgyouurk55a
MS205 Minisatellite Diversity in Basques: Evidence for a Pre-Neolithic Component
1998
Genome Research
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Subsequently, an averaged interpopulation diversity value between populations x and y, K inter.xy = ͚ i=1 nx ͚ j=1 ny d ij ր ͑ n x n y͒ was calculated by comparing all alleles in population x to all alleles ...
In addition, Neolithic culture in the Basque Country seems to be a late and partial process (Cava 1990 ). ...
doi:10.1101/gr.8.12.1289
pmid:9872983
pmcid:PMC310805
fatcat:xzd7sk243ra65m3x6iansjfwc4
Information Sharing for Collective Sensemaking
2016
2016 49th Hawaii International Conference on System Sciences (HICSS)
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Ministry of Defense and was accomplished under Agreement Number W911NF-06-3-0001. ...
guess
−2.8053
2.0008
−1.402
0.16089
robot x question
−1.6171
0.9668
−1.673
0.09439
robot x guess x
question
2.9267
1.4176
2.064
0.03897 ...
EXPERIMENTAL TASK The task used simulates, using textual information, an artificial world region with political unrest. ...
doi:10.1109/hicss.2016.53
dblp:conf/hicss/TangLSM0S16
fatcat:kzvvkronpraxjpkmes72ocvhhy
Assessing trends in observed and modelled climate extremes over Australia in relation to future projections
2009
International Journal of Climatology
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Multiple simulations from nine globally coupled climate models were assessed for their ability to reproduce observed trends in a set of indices representing temperature and precipitation extremes over ...
When averaged across Australia, the magnitude of trends and interannual variability of temperature extremes were well simulated by most models, particularly for the index for warm nights. ...
Acknowledgements We acknowledge the modelling groups for making their simulations available for analysis, the PCMDI for collecting and archiving the CMIP3 model output, and the WCRP's Working Group on ...
doi:10.1002/joc.1730
fatcat:omgx6k52l5hthltlwrpoiu5sym
Computational Methods For Taxonomic Annotation And Genome Reconstruction In Metagenomics
2017
Zenodo
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In agreement with the results for the simulated metagenome datasets, the taxatortk results were the most consistent among all tested methods, regardless of the alignment type ( Supplementary Fig. 22 ) ...
Different programs can be run for each process and iteration. ...
In recent studies, the joint analysis of assembly information and sequence composition allowed the reconstruction of several partial genomes by taxonomic binning (Hess et al., 2011; Iverson et al., 2012 ...
doi:10.5281/zenodo.1263098
fatcat:eribyymx3zatpbsrxphmc3ugje
Health Risk Assessment and Correlation Analysis on PCDD/Fs in the Fly Ash from a Municipal Solid Waste Incineration Plant
2018
Aerosol and Air Quality Research
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0.939); Meanwhile, the results of the cluster analysis unveiled the specific features of several congeners (such as 1,2,3,7,8,9-HxCDF, OCDD and OCDF). (4) Through assessing health risk with a Monte Carlo simulation ...
The capital letters A-Q on x-axis denote 17 PCDD/F congeners. ...
Despite the numerous studies on PCDD/Fs, a unified consensus regarding the formation mechanisms of PCDD/Fs has not yet been reached. ...
doi:10.4209/aaqr.2017.12.0587
fatcat:elrs7y5hrvcqbh6keujrmcpakm
Emotion in Stories: Facial EMG Evidence for Both Mental Simulation and Moral Evaluation
2018
Frontiers in Psychology
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Here, the corrugator response did not track the valence of the event, but reflected both simulation and moral evaluation. ...
To examine what happens in such cases, we independently manipulated simulation valence and moral evaluative valence in short narratives. ...
led to a relative consensus on its existence. ...
doi:10.3389/fpsyg.2018.00613
pmid:29760671
pmcid:PMC5937160
fatcat:cxrxq53gu5ante3u3z3y2e5qyy
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