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Bioinformatics tools and databases for analysis of next-generation sequence data

H. C. Lee, K. Lai, M. T. Lorenc, M. Imelfort, C. Duran, D. Edwards
2011 Briefings in Functional Genomics  
Here, we outline some of the tools and databases commonly used for the analysis of next-generation sequence data with comment on their utility.  ...  Genome sequencing has been revolutionized by next-generation technologies, which can rapidly produce vast quantities of data at relatively low cost.  ...  C.D. is a PhD student under the supervision of D.E. and is currently employed as a bioinformatics software developer by Biomatters Ltd.  ... 
doi:10.1093/bfgp/elr037 pmid:22184335 fatcat:7lphlq4uivhcxpsndhzgv5uhpq

Genomic Patterns of Positive Selection at the Origin of Rust Fungi

Diogo N. Silva, Sebastien Duplessis, Pedro Talhinhas, Helena Azinheira, Octávio S. Paulo, Dora Batista, Marc Robinson-Rechavi
2015 PLoS ONE  
Research on the molecular mechanisms responsible for rust fungi evolution has been hampered by their biotrophic life-style until the sequencing of some rust fungi genomes.  ...  Up to 985 genes were screened for positive selection on the phylogenetic branch leading to rusts, revealing a pervasive signal of positive selection throughout the data set with the proportion of positively  ...  Finally, we thank the PIs of Puccinia triticina genome project, Christina Cuomo, John Fellers, Guus Bakkeren, Les Szabo, Xianming Chen and Scot Hulbert, for access to the unpublished sequence data from  ... 
doi:10.1371/journal.pone.0143959 pmid:26632820 pmcid:PMC4669144 fatcat:vntsxthlpfb7ph7zrqe2lhply4

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

Kevin Stoffel, Hans van Leeuwen, Alexander Kozik, David Caldwell, Hamid Ashrafi, Xinping Cui, Xiaoping Tan, Theresa Hill, Sebastian Reyes-Chin-Wo, Maria-Jose Truco, Richard W Michelmore, Allen Van Deynze
2012 BMC Genomics  
However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism  ...  Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up  ...  This project was supported by an award from the University of California UC Discovery Program Bio04-1047 with matching funds from Rijk Zwaan BV, Enza Zaden BV, and Vilmorin Co.  ... 
doi:10.1186/1471-2164-13-185 pmid:22583801 pmcid:PMC3490809 fatcat:xosogukkxfgmbjtxzinhh3iuz4

Implementation of Fog computing for reliable E-health applications

Razvan Craciunescu, Albena Mihovska, Mihail Mihaylov, Sofoklis Kyriazakos, Ramjee Prasad, Simona Halunga
2015 2015 49th Asilomar Conference on Signals, Systems and Computers  
In addition, we will improve on the performance of such Coded ALOHA protocols in terms of the resource efficiency.  ...  The resulting system is highly robust against timing misalignment while attaining high spectral efficiency. Machine-type communications is seen as one of the main drivers of 5G.  ...  While optimal selection of the binary sequence requires combinatorial complexity, we exploit previously proposed convex relaxations that rely on randomized projections to return feasible binary solutions  ... 
doi:10.1109/acssc.2015.7421170 dblp:conf/acssc/CraciunescuMMKP15 fatcat:qm6mki5z6bcvrfimkmqjyrxaxm

Applied Nonparametric Regression

R. L. Eubank
1993 Technometrics  
For complex iterative procedures such as projection pursuit regression (Friedman and Stuetzle 1981) or ACE (Breiman and Friedman 1985) it is vital to have a good choice of smoothing parameter for one-dimensional  ...  Find the projection vector β p+1 that maximizes q p+1 (β) (projection pursuit) and the corresponding smoothĝ p+1 . STEP 4.  ...  We will use an approach which also works in the proof of Theorem 9.3.2. According to theorem 2.1 in de Jong (1987) it suffices  ... 
doi:10.1080/00401706.1993.10485051 fatcat:twvmigjwyjg4tb7c4ujebxdftm

Ping-pong beam training for reciprocal channels with delay spread

Elisabeth de Carvalho, Jorgen Bach Andersen
2015 2015 49th Asilomar Conference on Signals, Systems and Computers  
A major challenge lies in the lack of precise knowledge of the process noise parameters.  ...  For the scenario of targets falling in the same range bin, waveforms with a flat spatial spectrum were shown to be optimal in terms of requirement for good MC performance.  ...  While optimal selection of the binary sequence requires combinatorial complexity, we exploit previously proposed convex relaxations that rely on randomized projections to return feasible binary solutions  ... 
doi:10.1109/acssc.2015.7421451 dblp:conf/acssc/CarvalhoA15 fatcat:mqokuvnh3zg45licnfbgxyvxfu

Applied nonparametric regression

1991 ChoiceReviews  
For complex iterative procedures such as projection pursuit regression (Friedman and Stuetzle 1981) or ACE (Breiman and Friedman 1985) it is vital to have a good choice of smoothing parameter for one-dimensional  ...  Find the projection vector β p+1 that maximizes q p+1 (β) (projection pursuit) and the corresponding smoothĝ p+1 . STEP 4.  ... 
doi:10.5860/choice.29-0364 fatcat:trkgzvpk7jb57ebwdy5pmipvpm

Applied Nonparametric Regression

W. Hardle
1994 Biometrics  
For complex iterative procedures such as projection pursuit regression (Friedman and Stuetzle 1981) or ACE (Breiman and Friedman 1985) it is vital to have a good choice of smoothing parameter for one-dimensional  ...  Find the projection vector β p+1 that maximizes q p+1 (β) (projection pursuit) and the corresponding smoothĝ p+1 . STEP 4.  ... 
doi:10.2307/2533418 fatcat:3hafhlx22bbbbdrugyiwoqcpd4

Applied Nonparametric Regression

R. L. Eubank, Wolfgang Härdle, Wolfgang Hardle
1993 Technometrics  
For complex iterative procedures such as projection pursuit regression (Friedman and Stuetzle 1981) or ACE (Breiman and Friedman 1985) it is vital to have a good choice of smoothing parameter for one-dimensional  ...  Find the projection vector β p+1 that maximizes q p+1 (β) (projection pursuit) and the corresponding smoothĝ p+1 . STEP 4.  ... 
doi:10.2307/1269674 fatcat:o7l4v2yprnardlsjsrb5ubx6zq

Energy and Flow Effects of Optimal Automated Driving in Mixed Traffic: Vehicle-in-the-Loop Experimental Results [article]

Tyler Ard, Longxiang Guo, Robert Austin Dollar, Alireza Fayazi, Nathan Goulet, Yunyi Jia, Beshah Ayalew, Ardalan Vahidi
2020 arXiv   pre-print
We propose a Vehicle-in-the-Loop (VIL) testing environment in which experimental CAVs driven on a track interact with surrounding virtual traffic in real-time.  ...  A combination of classical feedback control and data-driven nonlinear feedforward control of pedals achieve acceleration tracking at the low level.  ...  Acknowledgment This work was supported by an award from the U.S. Department of Energy Vehicle Technologies Office (Project DE-EE0008469). The authors would like to thank Dr.  ... 
arXiv:2009.07872v1 fatcat:22ouvupsm5cvhjune6yfcfutj4

Methods for Collision-Free Navigation of Multiple Mobile Robots in Unknown Cluttered Environments [article]

Michael Hoy
2014 arXiv   pre-print
The main contributions of this work are as follows; firstly, the integration of the robust model predictive control concept with reactive navigation strategies based on local path planning, which is applied  ...  the obstacle is limited to a discrete ray-based sensor model, for which provably safe, convergent boundary following can be shown; and thirdly the development of novel constraints allowing decentralized  ...  In this case, the optimal path consists of a sequence of no more than three maximal turns or straight segments.  ... 
arXiv:1401.6775v1 fatcat:mkjwxvzynfegpfsxqivwobuuru

Membrane Trafficking Modulation during Entamoeba Encystation

Emily Herman, Maria A. Siegesmund, Michael J. Bottery, Ronny van Aerle, Maulood Mohammed Shather, Elisabet Caler, Joel B. Dacks, Mark van der Giezen
2017 Scientific Reports  
MMS acknowledges support from the Iraqi Ministry of Higher Education and Scientiic Research (MOHESR) and the University of Baghdad. MvdG is grateful for support from the University of  ...  Acknowledgements The authors thank Audrey Farbos, Karen Moore and Konrad Paszkiewicz for facilitating the sequencing experiments. he Exeter Sequencing Facility was funded by a Wellcome Trust Institutional  ...  Raw reads were trimmed, clipped and iltered using the FASTX-Toolkit (http://hannonlab.cshl.edu/ fastx_toolkit/). he irst 12 bp were trimmed of the reads using the fastx_trimmer, and adapter sequences were  ... 
doi:10.1038/s41598-017-12875-6 pmid:28993644 pmcid:PMC5634486 fatcat:z7wmtr3qqzc73ety4eb25ajppa

Applications of next generation sequencing in molecular ecology of non-model organisms

R Ekblom, J Galindo
2010 Heredity  
We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.  ...  The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008  ...  Acknowledgements We wish to thank Roger Butlin, Jon Slate, Gavin Horsburgh, Eleanor Jones and three anonymous reviewers for providing very valuable comments on earlier versions of this paper.  ... 
doi:10.1038/hdy.2010.152 pmid:21139633 pmcid:PMC3186121 fatcat:xuj36erlefgzdndaa7l6h4vcbi

Industrial and Project Presentations [article]

Felipe A. Lozano, Francisco Serón
2003 Eurographics State of the Art Reports  
This volume contains the Industrial and Project Presentations for the 24th annual Conference of the European Association for Computer Graphics, EUROGRAPHICS´03, held in Granada, Spain, between the 1st  ...  and 6th of September 2003.  ...  We thank our project partners Acknowledgements The GAMA project is being supported by grants 1FD97-2158-C04-01 and TIC2002-04166-C03-01 from the European Community and the Spanish Ministry of Science  ... 
doi:10.2312/egid.20031006 fatcat:loh7chebubg2vatd5syfugub24

Large scale changes in the transcriptome of Eisenia fetida during regeneration

Aksheev Bhambri, Neeraj Dhaunta, Surendra Singh Patel, Mitali Hardikar, Abhishek Bhatt, Nagesh Srikakulam, Shruti Shridhar, Shamsudheen Vellarikkal, Rajesh Pandey, Rijith Jayarajan, Ankit Verma, Vikram Kumar (+9 others)
2018 PLoS ONE  
Earthworms belong to the phylum Annelida, in which the genomes of the marine oligochaete Capitella telata and the freshwater leech Helobdella robusta have been sequenced and studied.  ...  We also generated a draft genome sequence of this terrestrial red worm using short reads and mate-pair reads.  ...  Acknowledgments Technical assistance in using DESeq2 for differential expression analysis from Megha Lal, IGIB.  ... 
doi:10.1371/journal.pone.0204234 fatcat:r5kdn2aljbfntnc3vyep2bhfqe
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