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AbCD: arbitrary coverage design for sequencing-based genetic studies

J. Kang, K.-C. Huang, Z. Xu, Y. Wang, G. R. Abecasis, Y. Li
2013 Bioinformatics  
Here, we present AbCD (arbitrary coverage design) to aid the design of sequencingbased studies.  ...  Recent advances in sequencing technologies have revolutionized genetic studies.  ...  ACKNOWLEDGEMENT The authors thank Dr Mingyao Li and Dr Wei Chen for reviewing early versions of this manuscript.  ... 
doi:10.1093/bioinformatics/btt041 pmid:23357921 pmcid:PMC3597143 fatcat:44qaambdqberbe4ny3zhzbkije

A semantically integrated, user-friendly data model for species observation data

L.E. Veen, G.B.A. van Reenen, F.P. Sluiter, E.E. van Loon, W. Bouten
2012 Ecological Informatics  
Information Facility, the Knowledge Network for Biocomplexity, BioCASE and the British National Biodiversity Network (NBN).  ...  In this paper, we evaluate this approach and the NDFF data model, by comparison with Darwin Core, Access to Biological Collections Data (ABCD) and the Recorder 2000 model used by the NBN.  ...  Organisaties for sharing their protocol manuals and observation forms.  ... 
doi:10.1016/j.ecoinf.2011.11.002 fatcat:lz2uzjttz5galfouxxpb6dzcpq

The impact of OTU sequence similarity threshold on diatom-based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

Kálmán Tapolczai, Valentin Vasselon, Agnès Bouchez, Csilla Stenger-Kovács, Judit Padisák, Frédéric Rimet
2018 Ecology and Evolution  
The high-throughput sequencing (HTS) and meta-barcoding methods now used for bioassessment traditionally employ an arbitrary sequence similarity threshold (SST) around 95% or 97% to cluster sequences into  ...  HTS sequencing was performed on the biofilms using the rbcL region as the genetic marker and diatom-specific primers.  ...  , and KT devised the concept and designed the study.  ... 
doi:10.1002/ece3.4701 pmid:30680104 pmcid:PMC6342121 fatcat:pqpwtfeo5jcp3deumaxkfth74y

Brain Network Mechanisms of General Intelligence [article]

Chandra Sripada, Mike Angstadt, Saige Rutherford, Aman Taxali
2019 bioRxiv   pre-print
adults in the Human Connectome Project dataset, we demonstrate that these network separation patterns across hard and easy task conditions are strongly associated with general intelligence, accounting for  ...  ABCD consortium investigators designed and implemented the study and/or provided data but did not necessarily participate in analysis or writing of this report.  ...  This is a multisite, longitudinal study designed to recruit more than 10,000 children age 9-10 and follow them over 10 years into early adulthood.  ... 
doi:10.1101/657205 fatcat:ddgwrd7cafembf5tfvjoi7ycji

Symbolic search-based testing

Arthur Baars, Mark Harman, Youssef Hassoun, Kiran Lakhotia, Phil McMinn, Paolo Tonella, Tanja Vos
2011 2011 26th IEEE/ACM International Conference on Automated Software Engineering (ASE 2011)  
We present an algorithm for constructing fitness functions that improve the efficiency of search-based testing when trying to generate branch adequate test data.  ...  The test for significance was done using a onesided, paired Wilcoxon signed rank test.  ...  Rather than make an arbitrary choice of algorithms to study, we choose to empirically study a local search (the widely used Alternating Variable Method (AVM) of Korel [3] ) and a global search (the Genetic  ... 
doi:10.1109/ase.2011.6100119 dblp:conf/kbse/BaarsHHLMTV11 fatcat:paymetsglbcllezsfhkndszjme

Semiotic Structure Labeling Of Music Pieces: Concepts, Methods And Annotation Conventions

Frédéric Bimbot, Emmanuel Deruty, Gabriel Sargent, Emmanuel Vincent
2012 Zenodo  
The functional structure which is based on usual designations of the different parts in terms of their role in the music piece, for instance : intro -versechorus -bridge -etc… (cf. [6], for instance),  ...  Inferring a semiotic code : an intuitive example 2.3 Let's consider the following sequence : A careful study of this sequence reveals that : -Almost all items are directional.  ...  The sequence [A][B<A] could be described as a single morphological system at the immediately upper timescale.  ... 
doi:10.5281/zenodo.1416411 fatcat:kcfl7rltmjdfbgm5xos7q6tnuu

Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data

Matthew S. Ackerman, Parul Johri, Ken Spitze, Sen Xu, Thomas G. Doak, Kimberly Young, Michael Lynch
2017 Genetics  
There are nine pairwise relatedness coefficients in the most general model, and we show that these can be reduced to seven coefficients for biallelic loci.  ...  Simulations show that the procedure is nearly unbiased, even at 3× coverage, and errors in five of the seven coefficients are statistically uncorrelated.  ...  Kelley Thomas and the Hubbard Center for Genome Studies for their continued help with the sequencing; The Center for Genomics and Bioinformatics and especially James Ford for the preparation of libraries  ... 
doi:10.1534/genetics.116.190660 pmid:28341647 pmcid:PMC5419463 fatcat:jxhyjmtnljhvnaijthhk3u24na

Estimating seven coefficients of pairwise relatedness using population genomic data [article]

Matthew Ackerman, Parul Johri, Ken Spitze, Thomas Doak, Kimberly Young, Michael Lynch, Sen Xu
2016 bioRxiv   pre-print
There are nine pair-wise relatedness coefficients in the most general model, and we show that these can be reduced to seven coefficients for biallelic loci.  ...  Simulations show that the procedure is nearly unbiased, even at 3× coverage, and errors in five of the seven coefficients are statistically uncorrelated.  ...  Kelley Thomas and the Hubbard Center for Genome Studies for their continued help with the sequencing; The Center for Genomics and Bioinformatics and especially James Ford for the preparation of libraries  ... 
doi:10.1101/049411 fatcat:5m7gnu644nd37ndq5f5yud6r2e

Mapping genes governing flower architecture and pollen development in a double mutant population of carrot

Holger Budahn, Rafał Barański, Dariusz Grzebelus, Agnieszka Kiełkowska, Petra Straka, Kai Metge, Bettina Linke, Thomas Nothnagel
2014 Frontiers in Plant Science  
A linkage map of carrot (Daucus carota L.) was developed in order to study reproductive traits.  ...  The genetic map has a total length of 781 cM and included 285 loci. The length of the nine linkage groups (LGs) ranged between 65 and 145 cM. All LGs have been anchored to the reference map.  ...  FIGURE 2 | 2 Genetic map of carrot (Daucus carota L.) based on the F 2 population DM19.  ... 
doi:10.3389/fpls.2014.00504 pmid:25339960 pmcid:PMC4189388 fatcat:qnic2bkgjrf7zfk6tqbugumhz4

De Novo Transcriptome Assembly from Inflorescence of Orchis italica: Analysis of Coding and Non-Coding Transcripts

Sofia De Paolo, Marco Salvemini, Luciano Gaudio, Serena Aceto, Szabolcs Semsey
2014 PLoS ONE  
and statistically significant positive correlation with the RNA-seq based expression data.  ...  The differential expression pattern observed for the selected putative long non-coding RNAs suggests their possible functional role in different floral tissues.  ...  Rosaria Terracciano for their technical support and to Prof. Salvatore Cozzolino for plant material. Special thanks to Dr.  ... 
doi:10.1371/journal.pone.0102155 pmid:25025767 pmcid:PMC4099010 fatcat:d25sv7vpbnczrchsuosbxelmkm

TandemMapper and TandemQUAST: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats [article]

Alla Mikheenko, Andrey V Bzikadze, Alexey Gurevich, Karen H Miga, Pavel A Pevzner
2019 bioRxiv   pre-print
To address these problems, we developed the tandemMapper tool for mapping reads to ETRs and the tandemQUAST tool for polishing ETR assemblies and their quality assessment.  ...  Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there is no standard tool for their quality assessment.  ...  ., 2018a. studies of tandem repeats revealed their role in various cellular processes and demonstrated that mutations in tandem repeats may lead to genetic disorders (McFarland et al., 2015; Giunta and  ... 
doi:10.1101/2019.12.23.887158 fatcat:ja7qqkej7jfz3a2lfktusg4un4

Static, Dynamic, and Adaptive Heterogeneity in Distributed Smart Camera Networks

Peter R. Lewis, Lukas Esterle, Arjun Chandra, Bernhard Rinner, Jim Torresen, Xin Yao
2015 ACM Transactions on Autonomous and Adaptive Systems  
However, if camera 1 deviates from the strategy sequence in Table II, then the strategy sequence for camera 2 in Table II may no longer be optimal.  ...  In Section 3 we for- mally introduce the problem studied and detail relevant aspects of the smart camera case study.  ... 
doi:10.1145/2764460 fatcat:5dw37j7525eurjxf2ik42tdjvy

Physiological diversity enhanced by recurrent divergence and secondary gene flow within a grass species [article]

Matheus Bianconi, Luke T Dunning, Emma V Curran, Oriane Hidalgo, Robyn Powell, Sahr Mian, Ilia Leitch, Marjorie Lundgren, Sophie Manzi, Maria Vorontsova, Guillaume Besnard, Colin P Osborne (+2 others)
2020 bioRxiv   pre-print
We further establish the genetic origins of polyploids in this species.  ...  Overall, our study suggests that local adaptation followed by recurrent secondary gene flow promoted physiological diversification in this grass species.  ...  We thank Pauline Raimondeau for lab support. 491 492 Author contributions 493 MEB, LTD, JKO, CPO and PAC designed the study. MEB did the phylogenetic analyses. LTD did 494 the allele analyses.  ... 
doi:10.1101/2020.04.23.053280 fatcat:q4ji47ypujc7liglqlbsc7agdq

Developing an algorithm to minimize boolean functions for the visual-matrix form of the analytical method

Mykhailo Solomko
2021 Eastern-European Journal of Enterprise Technologies  
The experimental study has confirmed that the visual-matrix form of the analytical method, whose special feature is the use of 2-(n, b)-design and 2-(n, x/b)-design systems in the first matrix, improves  ...  Also, by optimally combining the sequence of logical operations of super-gluing the variables and simply gluing the variables, based on the selection, according to the established criteria, of the stack  ...  The aim and objectives of the study The purpose of this study is to establish an updated procedure for alternating the protocols of equivalent transformations for the first and second matrices of the assigned  ... 
doi:10.15587/1729-4061.2021.225325 fatcat:kscjnjb4qnadpdefyxx2rx2ota

A Study on the Impact of Compiler Optimizations on High-Level Synthesis [chapter]

Jason Cong, Bin Liu, Raghu Prabhakar, Peng Zhang
2013 Lecture Notes in Computer Science  
We also study the phase-ordering problem for IR-level optimizations from a HLS perspective.  ...  In this design flow, the quality of the generated RTL is greatly influenced by high-level description of the language.  ...  for design in 3.2.  ... 
doi:10.1007/978-3-642-37658-0_10 fatcat:n4dsqcsbvnbvjnbjmnkl6crswy
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