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Journal articles on the topic 'Read'

Author: Grafiati
Published: 4 June 2021
Last updated: 16 June 2025

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1

Miura, Akira, and Janet Ashby. "Read Real Japanese." Modern Language Journal 79, no. 2 (1995): 292. http://dx.doi.org/10.2307/329655.

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2

Kars, Marge, and Mary Doud. "Ready to Read." Reference Librarian 32, no. 67-68 (2000): 85–97. http://dx.doi.org/10.1300/j120v32n67_07.

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3

Jones, Eileen. "Get ready, set, read!" Practical Pre-School 2013, no. 144 (2013): xv—xvi. http://dx.doi.org/10.12968/prps.2013.1.144.xv.

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4

Wick, Ryan R., and Kathryn E. Holt. "Polypolish: Short-read polishing of long-read bacterial genome assemblies." PLOS Computational Biology 18, no. 1 (2022): e1009802. http://dx.doi.org/10.1371/journal.pcbi.1009802.

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Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these errors, but most rely on short-read alignment which is unreliable in repeat regions. Errors in such regions are therefore challenging to fix and often remain after short-read polishing. Here we introduce Polypolish, a new short-read polisher which uses all-per-read alignments to repair errors in repeat sequences that other polishers cannot. Polypolish performed well in benchmarking tests using both simulated and real reads, and it almost never introduced errors during polishing. The best results were achieved by using Polypolish in combination with other short-read polishers.
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5

Schoonover, Judith, and Sally Norton-Darr. "Adapting books: Ready, set, read!" Journal of Occupational Therapy, Schools, & Early Intervention 9, no. 1 (2016): 19–26. http://dx.doi.org/10.1080/19411243.2016.1152831.

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6

Shumate, Alaina, Brandon Wong, Geo Pertea, and Mihaela Pertea. "Improved transcriptome assembly using a hybrid of long and short reads with StringTie." PLOS Computational Biology 18, no. 6 (2022): e1009730. http://dx.doi.org/10.1371/journal.pcbi.1009730.

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Short-read RNA sequencing and long-read RNA sequencing each have their strengths and weaknesses for transcriptome assembly. While short reads are highly accurate, they are rarely able to span multiple exons. Long-read technology can capture full-length transcripts, but its relatively high error rate often leads to mis-identified splice sites. Here we present a new release of StringTie that performs hybrid-read assembly. By taking advantage of the strengths of both long and short reads, hybrid-read assembly with StringTie is more accurate than long-read only or short-read only assembly, and on some datasets it can more than double the number of correctly assembled transcripts, while obtaining substantially higher precision than the long-read data assembly alone. Here we demonstrate the improved accuracy on simulated data and real data from Arabidopsis thaliana, Mus musculus, and human. We also show that hybrid-read assembly is more accurate than correcting long reads prior to assembly while also being substantially faster. StringTie is freely available as open source software at https://github.com/gpertea/stringtie.
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7

Montgomery, Richard Murdoch. "The Real Selfish Gene: Impact of Repetitive Elements on Read Mapping Accuracy, a Simulation Study." Journal of Current Trends in Computer Science Research 3, no. 3 (2024): 01–04. http://dx.doi.org/10.33140/jctcsr.03.03.06.

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Repetitive elements, often referred to as selfish genes, pose significant challenges to genome assembly and read mapping in bioinformatics. These elements can replicate within the genome without providing functional benefits to the host organism, leading to complexities in accurate genome analysis. This study presents a simulation-based approach to illustrate the impact of repetitive elements on read mapping accuracy. By comparing genome sequences with and without repetitive elements, we demonstrate how these selfish genes create ambiguities and errors in read alignment. The findings underscore the importance of developing advanced bioinformatics tools aligned with artificial intelligence to mitigate the effects of repetitive sequences and improve the reliability of genomic analyses.
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8

Bergquist, Greta. "Ready to Read Now and Then." OLA Quarterly 26, no. 2 (2020): 50–53. http://dx.doi.org/10.5399/osu/1093-7374.26.02.11.

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9

Nguyen, Son Hoang, Minh Duc Cao, and Lachlan J. M. Coin. "Real-time resolution of short-read assembly graph using ONT long reads." PLOS Computational Biology 17, no. 1 (2021): e1008586. http://dx.doi.org/10.1371/journal.pcbi.1008586.

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A streaming assembly pipeline utilising real-time Oxford Nanopore Technology (ONT) sequencing data is important for saving sequencing resources and reducing time-to-result. A previous approach implemented in npScarf provided an efficient streaming algorithm for hybrid assembly but was relatively prone to mis-assemblies compared to other graph-based methods. Here we present npGraph, a streaming hybrid assembly tool using the assembly graph instead of the separated pre-assembly contigs. It is able to produce more complete genome assembly by resolving the path finding problem on the assembly graph using long reads as the traversing guide. Application to synthetic and real data from bacterial isolate genomes show improved accuracy while still maintaining a low computational cost. npGraph also provides a graphical user interface (GUI) which provides a real-time visualisation of the progress of assembly. The tool and source code is available at https://github.com/hsnguyen/assembly.
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10

William Kolbrener. "The "Real Thing": How to Read How to Read the Bible." Jewish Quarterly Review 100, no. 1 (2009): 183–89. http://dx.doi.org/10.1353/jqr.0.0072.

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11

Goodwin, Prue. "Can't read or won't read: Perspectives on reluctance to read." New Review of Children's Literature and Librarianship 5, no. 1 (1999): 29–41. http://dx.doi.org/10.1080/13614549909510613.

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12

Barrios-Collado, César, Diego García-Gómez, Renato Zenobi, Guillermo Vidal-de-Miguel, Alfredo J. Ibáñez, and Pablo Martinez-Lozano Sinues. "Real Time Read-Out of Plant Metabolism." CHIMIA International Journal for Chemistry 70, no. 9 (2016): 660. http://dx.doi.org/10.2533/chimia.2016.660.

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13

Page, Andrew J., and Jacqueline A. Keane. "Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus." PeerJ 6 (July 31, 2018): e5233. http://dx.doi.org/10.7717/peerj.5233.

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Genome sequencing is rapidly being adopted in reference labs and hospitals for bacterial outbreak investigation and diagnostics where time is critical. Seven gene multi-locus sequence typing is a standard tool for broadly classifying samples into sequence types (STs), allowing, in many cases, to rule a sample out of an outbreak, or allowing for general characteristics about a bacterial strain to be inferred. Long-read sequencing technologies, such as from Oxford Nanopore, can produce read data within minutes of an experiment starting, unlike short-read sequencing technologies which require many hours/days. However, the error rates of raw uncorrected long read data are very high. We present Krocus which can predict a ST directly from uncorrected long reads, and which was designed to consume read data as it is produced, providing results in minutes. It is the only tool which can do this from uncorrected long reads. We tested Krocus on over 700 isolates sequenced using long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore. It provides STs for isolates on average within 90 s, with a sensitivity of 94% and specificity of 97% on real sample data, directly from uncorrected raw sequence reads. The software is written in Python and is available under the open source license GNU GPL version 3.
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14

MULLEN, LAURA. "Read." Fairy Tale Review 6, no. 1 (2010): 126–35. http://dx.doi.org/10.1353/fair.2010.a813007.

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15

Read, James. "The Read clinical classification (Read codes)." British Homeopathic Journal 80, no. 01 (1991): 14–20. http://dx.doi.org/10.1016/s0007-0785(05)80418-1.

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16

Raeymaeckers, Karin, Laurence Hauttekeete, and Annelore Deprez. "To Read or Not to Read." European Journal of Communication 22, no. 1 (2007): 89–107. http://dx.doi.org/10.1177/0267323107073749.

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17

Wescott Dodd, Anne. "Learning To Read, Teaching To Read." NASSP Bulletin 70, no. 488 (1986): 110–11. http://dx.doi.org/10.1177/019263658607048824.

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18

McWilliams, Alan, Christian Glide, and Fiona Henderson. "To read or not to read." Journal of Block and Intensive Learning and Teaching 1, no. 2 (2023): 59–70. http://dx.doi.org/10.15209/jbilt.1303.

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Reading continues to be a critical skill for success in university studies. However, students have competing interests and activities which make academic reading less of a priority. The aim of the study is to explore the reasons why students do or do not engage with set reading tasks using an extant survey instrument. The literature highlights several factors, including a lack of interest in the academic subject, family duties and work obligations, which contribute to this behaviour and indicates how it might possibly be addressed. The theoretical foundations of this work stem from areas such as strategic learning, reading non-compliance, curriculum structure, and student engagement. The aim of the study is to explore the reasons why students do or do not engage with set reading tasks using an extant survey instrument. Building on the literature which discusses why students do not read, the pilot study presented in this paper examines the reading behaviours amongst a group of first year business students studying in block mode at Victoria University (Australia). The paper explores the implications for teaching practice and the potential for further research.
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19

Andersdotter, Karolina. "Right to Read Without Being Read." Privacy Studies Journal 4 (February 18, 2025): 1–24. https://doi.org/10.7146/psj.v4i.150182.

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The impact of digitalization on privacy is obvious in many parts of society, including the collection of behavioural data of readers who access literature through digital means (e-books, audiobooks). This data can provide a lot of personal information about the reader (e.g. reading speed, time spent reading, opinions and interests linked to one’s book selection) and in combination with other collected data creates a very detailed picture of a person's lifestyle and movement patterns. In this position paper, I discuss ethical implications related to the use of large commercial data sets consisting of sensitive personal data in humanities and social sciences research. The ethical implications are explored through the lens of two case studies on digital reading behaviour. By raising ethical questions related to the study of reading, user consent, and legal certainty in the fast-developing information society, I present issues that there is an urgent need for the academic community to discuss to make sure good research practices are in place even when using new types of data and digital methods. I highlight current privacy and power asymmetry issues between the stakeholders in the research process, especially the users-turned-research subjects, and argue that the research community must assume a larger ethical responsibility when applying novel data-driven methods.
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20

Nederbragt, Alexander J., Trine Ballestad Rounge, Kyrre L. Kausrud, and Kjetill S. Jakobsen. "Identification and Quantification of Genomic Repeats and Sample Contamination in Assemblies of 454 Pyrosequencing Reads." Sequencing 2010 (January 5, 2010): 1–12. http://dx.doi.org/10.1155/2010/782465.

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Contigs assembled from 454 reads from bacterial genomes demonstrate a range of read depths, with a number of contigs having a depth that is far higher than can be expected. For reference genome sequence datasets, there exists a high correlation between the contig specific read depth and the number of copies present in the genome. We developed a sequence of applied statistical analyses, which suggest that the number of copies present can be reliably estimated based on the read depth distribution in de novo genome assemblies. Read depths of contigs of de novo cyanobacterial genome assemblies were determined, and several high read depth contigs were identified. These contigs were shown to mainly contain genes that are known to be present in multiple copies in bacterial genomes. For these assemblies, a correlation between read depth and copy number was experimentally demonstrated using real-time PCR. Copy number estimates, obtained using the statistical analysis developed in this work, are presented. Per-contig read depth analysis of assemblies based on 454 reads therefore enables de novo detection of genomic repeats and estimation of the copy number of these repeats. Additionally, our analysis efficiently identified contigs stemming from sample contamination, allowing for their removal from the assembly.
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21

Wang, Ziye, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, and Shanfeng Zhu. "Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences." Briefings in Bioinformatics 21, no. 3 (2019): 777–90. http://dx.doi.org/10.1093/bib/bbz025.

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Abstract In metagenomic studies of microbial communities, the short reads come from mixtures of genomes. Read assembly is usually an essential first step for the follow-up studies in metagenomic research. Understanding the power and limitations of various read assembly programs in practice is important for researchers to choose which programs to use in their investigations. Many studies evaluating different assembly programs used either simulated metagenomes or real metagenomes with unknown genome compositions. However, the simulated datasets may not reflect the real complexities of metagenomic samples and the estimated assembly accuracy could be misleading due to the unknown genomes in real metagenomes. Therefore, hybrid strategies are required to evaluate the various read assemblers for metagenomic studies. In this paper, we benchmark the metagenomic read assemblers by mixing reads from real metagenomic datasets with reads from known genomes and evaluating the integrity, contiguity and accuracy of the assembly using the reads from the known genomes. We selected four advanced metagenome assemblers, MEGAHIT, MetaSPAdes, IDBA-UD and Faucet, for evaluation. We showed the strengths and weaknesses of these assemblers in terms of integrity, contiguity and accuracy for different variables, including the genetic difference of the real genomes with the genome sequences in the real metagenomic datasets and the sequencing depth of the simulated datasets. Overall, MetaSPAdes performs best in terms of integrity and continuity at the species-level, followed by MEGAHIT. Faucet performs best in terms of accuracy at the cost of worst integrity and continuity, especially at low sequencing depth. MEGAHIT has the highest genome fractions at the strain-level and MetaSPAdes has the overall best performance at the strain-level. MEGAHIT is the most efficient in our experiments. Availability: The source code is available at https://github.com/ziyewang/MetaAssemblyEval.
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22

Li, Kexue, Yakang Lu, Li Deng, Lili Wang, Lizhen Shi, and Zhong Wang. "Deconvolute individual genomes from metagenome sequences through short read clustering." PeerJ 8 (April 8, 2020): e8966. http://dx.doi.org/10.7717/peerj.8966.

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Metagenome assembly from short next-generation sequencing data is a challenging process due to its large scale and computational complexity. Clustering short reads by species before assembly offers a unique opportunity for parallel downstream assembly of genomes with individualized optimization. However, current read clustering methods suffer either false negative (under-clustering) or false positive (over-clustering) problems. Here we extended our previous read clustering software, SpaRC, by exploiting statistics derived from multiple samples in a dataset to reduce the under-clustering problem. Using synthetic and real-world datasets we demonstrated that this method has the potential to cluster almost all of the short reads from genomes with sufficient sequencing coverage. The improved read clustering in turn leads to improved downstream genome assembly quality.
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23

Zerbino, Daniel R., and Ewan Birney. "Velvet: Algorithms for de novo short read assembly using de Bruijn graphs." Genome Research 18, no. 5 (2008): 821–29. https://doi.org/10.5281/zenodo.13451474.

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(Uploaded by Plazi for the Bat Literature Project) We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words ( k -mers) that is ideal for high coverage, very short read (25–50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of ∼8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.
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24

Zerbino, Daniel R., and Ewan Birney. "Velvet: Algorithms for de novo short read assembly using de Bruijn graphs." Genome Research 18, no. 5 (2008): 821–29. https://doi.org/10.5281/zenodo.13451474.

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(Uploaded by Plazi for the Bat Literature Project) We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words ( k -mers) that is ideal for high coverage, very short read (25–50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of ∼8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.
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25

An, Mijin, Soojun Im, Dawoon Jung, and Sang-Won Lee. "Your read is our priority in flash storage." Proceedings of the VLDB Endowment 15, no. 9 (2022): 1911–23. http://dx.doi.org/10.14778/3538598.3538612.

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When replacing a dirty victim page upon page miss, the conventional buffer managers flush the dirty victim first to the storage before reading the missing page. This read-after-write (RAW) protocol, unfortunately, causes the read stall problem on flash storage; because of the asymmetric I/O speed and parallelism in flash storage, the clean frames are quickly consumed, so the read for the missing page often has to wait for the slow write to complete and for the frame to be clean due to the resource conflict for the same buffer frame. RAW will thus make the performance-critical synchronous reads often blocked by writes, severely worsening transaction throughput and latency. In addition, its strict I/O ordering will make flash storage with abundant parallelism under-utilized. To avoid read stalls in the DBMS buffer, we propose RW ( fused read and write ) as a new storage interface. Using RW on read stall, the buffer manager can issue both read and write requests at once to the storage. Then, once the dirty page is copied to the storage buffer, it can immediately serve the read. In addition, to resolve read stalls in the flash storage buffer, we propose R-Buf, where the read buffer is separated from the write buffer so that reads can proceed at no stall. RW and R-Buf, working at different layers, complement each other when used together. We prototype RW and R-Buf on a real Cosmos+ OpenSSD board. Evaluation results show that RW alone improves TPC-C throughput over RAW by 3.2x and, combined with R-Buf, does by 3.9x. In addition, we demonstrate that R-Buf effectively mitigates the I/O interference in multi-tenancy.
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26

Piskorska-Dobrzeniecka, Izabela. "Norwid read and teaching how to read." Studia Norwidiana 36 English Version (2018): 305–16. http://dx.doi.org/10.18290/sn.2018.36-15en.

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27

Linden, Greg. "People Who Read This Article Also Read..." IEEE Spectrum 45, no. 3 (2008): 46–60. http://dx.doi.org/10.1109/mspec.2008.4457854.

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28

McDonough, Paul G., Jacques E. Rossouw, Loretta P. Finnegan, and William R. Harlan. ""Don't Read My Lips—Read the Exclusions"." Fertility and Sterility 64, no. 4 (1995): 872–73. http://dx.doi.org/10.1016/s0015-0282(16)57872-8.

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29

Cummins, Jim. "Right to Read Implies Opportunity to Read." Journal of Teaching and Learning 17, no. 1 (2023): 129–44. http://dx.doi.org/10.22329/jtl.v17i1.7950.

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This paper extends discussion of the Ontario Human Rights Commission (OHRC) (2022a, 2022b) report entitled Right to Read, which recommended significant changes to both reading instruction and special education programs aimed at providing equitable opportunities for all children to develop strong reading skills. In a critique of the OHRC report (Cummins, 2022), I endorsed the report’s call for the establishment of an identification and intervention infrastructure to support students who are struggling to develop reading skills. However, I also critiqued the report’s misrepresentation of the strong reading achievements of Ontario students and the scapegoating of “balanced literacy.” Klein (2022) disputed this characterization of the OHRC report, highlighting the important contributions of the report to special education policies. In continuing this dialogue, I argue that the OHRC report has omitted consideration of significant dimensions of literacy acquisition and development that are directly relevant to preventing reading difficulties among Ontario children. Specifically, I argue that beyond the systematic teaching of phonics and other foundational literacy skills, which the OHRC report emphasizes almost exclusively, literacy policies should ensure that all children experience extensive opportunities for literacy socialization, which must involve active engagement with print, in both the preschool and early elementary years.
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30

Melvyn New. ""Read, read, read, read, my unlearned reader!": Five Twenty-First-Century Studies of Laurence Sterne and His Works." Eighteenth-Century Studies 43, no. 1 (2009): 122–35. http://dx.doi.org/10.1353/ecs.0.0096.

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31

Phillips, Beth M., Christopher J. Lonigan, and Marcy A. Wyatt. "Predictive Validity of theGet Ready to Read!Screener." Journal of Learning Disabilities 42, no. 2 (2008): 133–47. http://dx.doi.org/10.1177/0022219408326209.

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32

Mills, J. Elizabeth, Ivette Bayo Urban, Kathleen Campana, and Judy T. Nelson. "Every Child Ready to Read: Hooray for Research." Children and Libraries 12, no. 4 (2015): 32. http://dx.doi.org/10.5860/cal.12n4.32.

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33

Mikheenko, Alla, Andrey D. Prjibelski, Anoushka Joglekar, and Hagen U. Tilgner. "Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns." Genome Research 32, no. 4 (2022): 726–37. http://dx.doi.org/10.1101/gr.276405.121.

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Long-read transcriptomics require understanding error sources inherent to technologies. Current approaches cannot compare methods for an individual RNA molecule. Here, we present a novel platform-comparison method that combines barcoding strategies and long-read sequencing to sequence cDNA copies representing an individual RNA molecule on both Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). We compare these long-read pairs in terms of sequence content and isoform patterns. Although individual read pairs show high similarity, we find differences in (1) aligned length, (2) transcription start site (TSS), (3) polyadenylation site (poly(A)-site) assignment, and (4) exon–intron structures. Overall, 25% of read pairs disagree on either TSS, poly(A)-site, or splice site. Intron-chain disagreement typically arises from alignment errors of microexons and complicated splice sites. Our single-molecule technology comparison reveals that inconsistencies are often caused by sequencing error–induced inaccurate ONT alignments, especially to downstream GUNNGU donor motifs. However, annotation-disagreeing upstream shifts in NAGNAG acceptors in ONT are often confirmed by PacBio and are thus likely real. In both barcoded and nonbarcoded ONT reads, we find that intron number and proximity of GU/AGs better predict inconsistencies with the annotation than read quality alone. We summarize these findings in an annotation-based algorithm for spliced alignment correction that improves subsequent transcript construction with ONT reads.
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34

Kloetgen, Andreas, Arndt Borkhardt, Jessica I. Hoell, and Alice C. McHardy. "The PARA-suite: PAR-CLIP specific sequence read simulation and processing." PeerJ 4 (October 27, 2016): e2619. http://dx.doi.org/10.7717/peerj.2619.

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BackgroundNext-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein–RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth.MethodsWe here compared PAR-CLIP sequencing reads to regular transcriptome sequencing reads (RNA-Seq) to identify distinctive properties that are relevant for reference-based read alignment of PAR-CLIP datasets. We developed a set of freely available tools for PAR-CLIP data analysis, called the PAR-CLIP analyzer suite (PARA-suite). The PARA-suite includes error model inference, PAR-CLIP read simulation based on PAR-CLIP specific properties, a full read alignment pipeline with a modified Burrows–Wheeler Aligner algorithm and CLIP read clustering for binding site detection.ResultsWe show that differences in the error profiles of PAR-CLIP reads relative to regular transcriptome sequencing reads (RNA-Seq) make a distinct processing advantageous. We examine the alignment accuracy of commonly applied read aligners on 10 simulated PAR-CLIP datasets using different parameter settings and identified the most accurate setup among those read aligners. We demonstrate the performance of the PARA-suite in conjunction with different binding site detection algorithms on several real PAR-CLIP and HITS-CLIP datasets. Our processing pipeline allowed the improvement of both alignment and binding site detection accuracy.AvailabilityThe PARA-suite toolkit and the PARA-suite aligner are available athttps://github.com/akloetgen/PARA-suiteandhttps://github.com/akloetgen/PARA-suite_aligner, respectively, under the GNU GPLv3 license.
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35

Prodanov, Timofey, and Vikas Bansal. "Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications." Nucleic Acids Research 48, no. 19 (2020): e114-e114. http://dx.doi.org/10.1093/nar/gkaa829.

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Abstract The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies can potentially overcome this limitation, long segmental duplications with high sequence identity pose challenges for long-read mapping. We describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping in segmental duplications. It analyzes reads mapped to segmental duplications using existing long-read aligners and leverages paralogous sequence variants (PSVs)—sequence differences between paralogous sequences—to distinguish between multiple alignment locations. On simulated datasets, DuploMap increased the percentage of correctly mapped reads with high confidence for multiple long-read aligners including Minimap2 (74.3–90.6%) and BLASR (82.9–90.7%) while maintaining high precision. Across multiple whole-genome long-read datasets, DuploMap aligned an additional 8–21% of the reads in segmental duplications with high confidence relative to Minimap2. Using DuploMap-aligned PacBio circular consensus sequencing reads, an additional 8.9 Mb of DNA sequence was mappable, variant calling achieved a higher F1 score and 14 713 additional variants supported by linked-read data were identified. Finally, we demonstrate that a significant fraction of PSVs in segmental duplications overlaps with variants and adversely impacts short-read variant calling.
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36

HORIUCHI, Miho. "ReaD^|^amp;Researchmap Symposium 2013." Journal of Information Processing and Management 56, no. 11 (2014): 801–3. http://dx.doi.org/10.1241/johokanri.56.801.

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37

Zagni, Frances. "Ernest Read." Musical Times 128, no. 1737 (1987): 614. http://dx.doi.org/10.2307/965518.

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38

Hassler, Frank, Thomas F. Norton, and James W. Anderson III. "Weed Read." Science News 163, no. 21 (2003): 335. http://dx.doi.org/10.2307/4014572.

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39

Dusenbery, Alayna. "Read Me." Rocky Mountain Review of Language and Literature 50, no. 1 (1996): 50. http://dx.doi.org/10.2307/1348337.

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Bonner, John. "READ dogs." BSAVA Companion 2011, no. 11 (2011): 4–7. http://dx.doi.org/10.22233/20412495.1111.4.

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Ainley, Alison. "Well read." Philosophers' Magazine, no. 33 (2006): 89. http://dx.doi.org/10.5840/tpm200633125.

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Кулибина, Н. В. "Read Dostoevsky…" Russkii iazyk za rubezhom, no. 6(289) (January 14, 2022): 98–101. http://dx.doi.org/10.37632/pi.2021.289.6.015.

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Abstract:
В статье описаны основные положения авторской методики обу-чения чтению художественной литературы, а также представлен новый проект Института Пушкина – мультимедийный комплекс по обучению чтению художественной литературы «Достоевский на интерактивном уроке чтения», создаваемый при финансовой поддержке фонда «Русский мир». The article describes the main provisions of the author's methodology for teaching reading fiction, and also presents a new project of the Pushkin Institute Multimedia complex for teaching reading fiction «Dostoevsky in an interactive reading lesson», created with the financial support of the Russian World Foundation.
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43

Cavan, Kay. "Read This." English Journal 88, no. 6 (1999): 111. http://dx.doi.org/10.2307/822201.

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Robinson, T. N., and T. D. Killen. "Adolescents Read?" Nurse Practitioner 22, no. 6 (1997): 164. http://dx.doi.org/10.1097/00006205-199706000-00024.

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Bachtold, Louis M., and Keith Barton. "Please read!" Contemporary Psychology: A Journal of Reviews 30, no. 7 (1985): 585. http://dx.doi.org/10.1037/023968.

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Mims, Forrest M. "Compulsory read?" Nature 366, no. 6451 (1993): 104. http://dx.doi.org/10.1038/366104d0.

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Frank, Morgan Day. "Don't Read." New Literary History 51, no. 1 (2020): 45–66. http://dx.doi.org/10.1353/nlh.2020.0002.

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Philippe, Nicolas, Mikael Salson, Thierry Lecroq, Martine Leonard, Therese Commes, and Eric Rivals. "Read indexing." EMBnet.journal 17, B (2012): 45. http://dx.doi.org/10.14806/ej.17.b.289.

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Prickett, Stephen. "Take, Read." Theology 100, no. 798 (1997): 449–50. http://dx.doi.org/10.1177/0040571x9710000617.

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Teagarden, J. Russell. "“Well Read”." Hospital Pharmacy 40, no. 1 (2005): 94–96. http://dx.doi.org/10.1177/001857870504000113.

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