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RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment
2014
Cancer Informatics
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Sample size and power calculation is required for applications for National Institutes of Health (NIH) funding. ...
Recent developments in high-throughput sequencing technology have allowed RNAseq to replace microarray as the technology of choice for high-throughput gene expression profiling. ...
Acknowledgement The authors thank Margot Bjoring for her editorial support. ...
doi:10.4137/cin.s17688
pmid:25374457
pmcid:PMC4213196
fatcat:iatllwtct5c5jb6qcgvnpmzqvm
Targeted DNA Methylation Analysis by High Throughput Sequencing in Porcine Peri-attachment Embryos
2013
Journal of reproduction and development
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The purpose of this experiment was to implement and evaluate the effectiveness of a next-generation sequencing-based method for DNA methylation analysis in porcine embryonic samples. ...
Resulting PCR products were subjected to high-throughput sequencing using the Illumina Genome Analyzer IIx platform. The average depth of sequencing coverage was 14,611 for IVV and 17,068 for PA. ...
We also recognize Bill Spollen at the Informatics Research Core Facility (University of Missouri) and Jon Huppi of the Center for High Performance Computing (Utah State University) for their contributions ...
doi:10.1262/jrd.2012-144
pmid:23428632
pmcid:PMC3934139
fatcat:me4dgkgj4nb3bne2x7hco7i7mi
Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers
2018
Biomolecular Detection and Quantification
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However, nowadays the falling costs and high specificity of small RNA sequencing make NGS a more attractive tool for high-throughput screening. ...
Independent of the method used for high throughput screening, this can lead erroneous study results of the experiment: the so-called small sample size error. ...
doi:10.1016/j.bdq.2017.11.002
pmid:29276692
pmcid:PMC5737945
fatcat:x7rmiujmfjfllkpyba53s5bwpq
A note on statistical repeatability and study design for high-throughput assays
2016
Statistics in Medicine
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Characterizing the technical precision of measurements is a necessary stage in the planning of experiments and in the formal sample size calculation for optimal design. ...
We present an alternative framework for assessing the precision of high-throughput assays and planning biomedical experiments. ...
Acknowledgements The authors would like to thank Rory Bowden, Tristan Gray-Davies, Davis McCarthy, Matti Pirinen, Chris Spencer, Aimee Taylor, James Watson and Quin Wills for helpful comments on the paper ...
doi:10.1002/sim.7175
pmid:27882571
pmcid:PMC5299465
fatcat:svprk7xxuvgtrckb3timh3a7ya
COPAR: A ChIP-Seq Optimal Peak Analyzer
2017
BioMed Research International
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It provides a versatile perspective for biologists to perform quality-check for high-throughput experiments and optimize their experiment design. ...
The package COPAR can process mapped ChIP-seq read file in BED format and output statistically sound results for multiple high-throughput experiments. ...
and statistically compare multiple ChIP-seq samples for NGS high-throughput experiments. ...
doi:10.1155/2017/5346793
pmid:28357402
pmcid:PMC5357551
fatcat:ahw7d6ogdbg47dopyagdtuhxhi
Fragmentation of pooled PCR products for highly multiplexed TILLING
[article]
2018
biorxiv/medrxiv
pre-print
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Evaluation of read coverage and base quality across amplicons suggests this approach is suitable for high-throughput TILLING and other applications employing highly pooled complex sampling schemes. ...
Using PCR to target and sequence chosen genomic regions provides an attractive alternative as the vast reduction in interrogated bases means that sample size can be dramatically increased through amplicon ...
ACKNOWLEDGMENTS We thank Keji Dada of the Cocoa Research Institute of Nigeria for assistance in coffee primer design and testing. Professor Margit Laimer of BOKU provided Coffea arabica genomic DNA. ...
doi:10.1101/451567
fatcat:jmnookhlrvf2jninh7q6kmjjla
A Measurement Study for Predicting Throughput from LQI and RSSI
[chapter]
2012
Lecture Notes in Computer Science
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Results include variability of throughput, RSSI and LQI observed for different transmission powers, transmission ranges, and number of transmitting nodes. we present the tested system and configuration ...
settings used in the experiments, and system validation results. ...
For such system we believe a cognitive and distributed scheduler to be a key component, making the system stable and predictable for communicating sensed data. ...
doi:10.1007/978-3-642-34976-8_10
fatcat:6x4fl7pqcnf6pdlewh4ajt3hxi
High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae
2020
PeerJ
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These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. ...
The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements. ...
Botero and Justin C. Fay labs, specifically Angela M. Chira, Trevor S. Fristoe, Emery Longan, and Dilys M. Vela Diaz for ongoing feedback and helpful advice. ...
doi:10.7717/peerj.10118
pmid:33088623
pmcid:PMC7571412
fatcat:256xzzhph5eonllgirzp2c2nvu
Fragmentation of Pooled PCR Products for Highly Multiplexed TILLING
2019
G3: Genes, Genomes, Genetics
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Evaluation of read coverage and base quality across amplicons suggests this approach is suitable for high-throughput TILLING and other applications employing highly pooled complex sampling schemes. ...
Using PCR to target and sequence chosen genomic regions provides an attractive alternative as the vast reduction in interrogated bases means that sample size can be dramatically increased through amplicon ...
ACKNOWLEDGMENTS We thank Keji Dada of the Cocoa Research Institute of Nigeria for assistance in coffee primer design and testing. Professor Margit Laimer of BOKU provided Coffea arabica genomic DNA. ...
doi:10.1534/g3.119.400301
pmid:31213514
pmcid:PMC6686939
fatcat:b7qxoarl5zeftnicwnb3355gjm
High-Throughput Massively Parallel Sequencing for Fetal Aneuploidy Detection from Maternal Plasma
2013
PLoS ONE
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Numerous research and clinical studies have described the analysis of ccf DNA using next generation sequencing for the detection of fetal aneuploidies with high sensitivity and specificity. ...
Classification was based upon a standard normal transformed cutoff value of z = 3 for chromosome 21 and z = 3.95 for chromosomes 18 and 13. ...
Author Contributions Conceived and designed the experiments: PO CD DvdB ME GEP JAC. Performed the experiments: TJJ TZ RCT JT. Analyzed the data: TJJ ZD SKK ARM ZZ TL CD ME. ...
doi:10.1371/journal.pone.0057381
pmid:23483908
pmcid:PMC3590217
fatcat:s4kcwqa3p5fiblnn2i3gkleq6a
PROPER: comprehensive power evaluation for differential expression using RNA-seq
2014
Computer applications in the biosciences : CABIOS
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The complexity and flexibility of RNA-seq experiments, the high-throughput nature of transcriptome-wide expression measurements and the unique characteristics of RNA-seq data make the power assessment ...
Results: We propose prospective power assessment instead of a direct sample size calculation by making assumptions on all of these factors. ...
Power reassessment One challenge in the sample size determination in high-throughput experiment is the choice of type I error control. ...
doi:10.1093/bioinformatics/btu640
pmid:25273110
pmcid:PMC4287952
fatcat:5goycrvg45ezpon6e7ztlv2ohq
Improved Performance of SRAM-Based True Random Number Generator by Leveraging Irradiation Exposure
2020
Sensors
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., randomness and throughput) improvement method of SRAM-based TRNG is proposed, and its implementation can be divided into two phases: irradiation exposure and hardware postprocessing. ...
Additionally, while the data remanence effect hampers obtaining random bitstreams with high speed, the ionization irradiation can also weaken this impact and improve the throughput of TRNG. ...
The min-entropy of every bit (bit i ) in the SRAM power-on sequence can be calculated by Equations (1) and (2) . ...
doi:10.3390/s20216132
pmid:33126596
fatcat:mgom2r46n5aibdg2nyhoxfmabu
An experimental study on performance comparison of rate adaptation and fixed rate in IEEE 802.11g
2011
2011 Australasian Telecommunication Networks and Applications Conference (ATNAC)
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Qiang Fu for the continuous help and support of my master study and research, for his patience, motivation, enthusiasm, and immense knowledge. ...
In the last few years, we have seen that the demand for high-bandwidth wireless local area networks increases rapidly, due to the proliferation of mobile devices such as laptops, smart phones and tablet ...
Retransmission counter and throughput for each data rate is calculated based on an ideal transmission time for each rate. ...
doi:10.1109/atnac.2011.6096661
dblp:conf/itnac/XiaF11
fatcat:hz6qgkma7nexflayoedb7zboja
A Highly-Accurate and Low-Overhead Prediction Model for Transfer Throughput Optimization
2012
2012 SC Companion: High Performance Computing, Networking Storage and Analysis
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To alleviate this bottleneck, we propose an application-layer throughput optimization model based on parallel stream number prediction. ...
We test and compare these four models on emulated testbeds as well as on production environments using a wide variety of data set sizes, RTT, and bandwidth combinations. ...
ACKNOWLEDGMENT This project is partially supported by NSF under award numbers CNS-1131889 (CAREER), OCI-0926701 (STCI-Stork), and CCF-1115805 (CiC-Stork). ...
doi:10.1109/sc.companion.2012.109
dblp:conf/sc/KimYK12
fatcat:vvtj6rjuljdkfnnyfgvfaofrm4
Analysis of Pel Decimation and Technology Choices to Reduce Energy on SAD Calculation
2014
Journal of Integrated Circuits and Systems
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The architectures were synthesized for 90nm, 65nm and 45nm standard cell libraries assuming both nominal and Low-Vdd/High-Vt (LH) cases for maximum and for a given target throughput. ...
The impacts of both subsampling and LH on delay, power and energy efficiency are analyzed. ...
ACKNOWLEDGEMENTS This work was partially supported by the Brazilian Federal Agency for the Support and Evaluation of Graduate Education (CAPES) and by the Brazilian Council for Scientific and Technological ...
doi:10.29292/jics.v9i1.388
fatcat:jrbittlvwbed5l7xe2z657fv6a
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