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Assembly of Long Error-Prone Reads Using Repeat Graphs [article]

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel Pevzner
2018 bioRxiv   pre-print
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  
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]

James Aspnes
2021 arXiv   pre-print
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

Ali Faisal, Frank Dondelinger, Dirk Husmeier, Colin M. Beale
2010 Ecological Informatics  
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

Michael E. Hodsdon, Jay W. Ponder, David P. Cistola
1996 Journal of Molecular Biology  
, 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

Borja Latorre, Ivan Lizaga, Leticia Gaspar, Ana Navas
2021 Science of the Total Environment  
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

Maja Klaus, Martin Grininger
2018 Natural product reports (Print)  
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

Lotfi Slim, Clément Chatelain, Chloé-Agathe Azencott, Jean-Philippe Vert, Jiang Gui
2020 PLoS ONE  
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

José Manuel Muñoz-Redondo, Belén Puertas, Gema Pereira-Caro, José Luis Ordóñez-Díaz, María José Ruiz-Moreno, Emma Cantos-Villar, José Manuel Moreno-Rojas
2021 Fermentation  
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

Santos Alonso, John A.L. Armour
1998 Genome Research  
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

Yuqing Tang, Christian Lebiere, Katia Sycara, Don Morrison, Michael Lewis, Paul Smart
2016 2016 49th Hawaii International Conference on System Sciences (HICSS)  
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

Lisa V. Alexander, Julie M. Arblaster
2009 International Journal of Climatology  
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

Johannes Dröge, Alice C. McHardy
2017 Zenodo  
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

Yen-Kung Hsieh, Wei-Sheng Chen, Jinning Zhu, Yi-Jing Wu, Qianli Huang
2018 Aerosol and Air Quality Research  
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

Björn 't Hart, Marijn E. Struiksma, Anton van Boxtel, Jos J. A. van Berkum
2018 Frontiers in Psychology  
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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