Relevant bibliographies by topics / HTS sequencing

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'HTS sequencing'

Author: Grafiati
Published: 9 March 2023
Last updated: 31 July 2025

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Journal articles on the topic "HTS sequencing"

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Vuorio, Kristiina, Anita Mäki, Pauliina Salmi, Sanni Aalto, Marja Tiirola, and Marko Järvinen. "Consistency between high throughput sequencing and microscopy-based morphological characterization of phytoplankton communities." ARPHA Conference Abstracts 4 (March 4, 2021): e64972. https://doi.org/10.3897/aca.4.e64972.

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Thus far, the phytoplankton community composition analyses, used e.g. monitoring and assessment of the ecological status of water bodies, are based on time-consuming and expertise-demanding light microscopy analyses. Currently, DNA-based molecular tools are being developed to replace microscopy-based analyses. Although most of the DNA is expected to be found in living cells, long-lasting DNA in damaged cells or soluble extracellular or relic DNA can make up a large proportion of the total DNA in water samples. DNA-based phytoplankton analysis has been shown to be affected by the huge variation
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Komarova, Natalia, Daria Barkova, and Alexander Kuznetsov. "Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology." International Journal of Molecular Sciences 21, no. 22 (2020): 8774. http://dx.doi.org/10.3390/ijms21228774.

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Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HT
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Pérez-Losada, Marcos, Miguel Arenas, Juan Carlos Galán, et al. "High-throughput sequencing (HTS) for the analysis of viral populations." Infection, Genetics and Evolution 80 (June 2020): 104208. http://dx.doi.org/10.1016/j.meegid.2020.104208.

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He, Xuejun, Ningzhi Zhang, Wenye Cao, Yiqiao Xing, and Ning Yang. "Application Progress of High-Throughput Sequencing in Ocular Diseases." Journal of Clinical Medicine 11, no. 12 (2022): 3485. http://dx.doi.org/10.3390/jcm11123485.

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Ocular diseases affect multiple eye parts and can be caused by pathogenic infections, complications of systemic diseases, genetics, environment, and old age. Understanding the etiology and pathogenesis of eye diseases and improving their diagnosis and treatment are critical for preventing any adverse consequences of these diseases. Recently, the advancement of high-throughput sequencing (HTS) technology has paved wide prospects for identifying the pathogenesis, signaling pathways, and biomarkers involved in eye diseases. Due to the advantages of HTS in nucleic acid sequence recognition, HTS ha
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GIZA, ALEKSANDRA, EWELINA IWAN, ARKADIUSZ BOMBA, and DARIUSZ WASYL. "Basics of high throughput sequencing Summary." Medycyna Weterynaryjna 77, no. 11 (2025): 6589–2025. http://dx.doi.org/10.21521/mw.6594.

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Sequencing can provide genomic characterisation of a specific organism, as well as of a whole environmental or clinical sample. High Throughput Sequencing (HTS) makes it possible to generate an enormous amount of genomic data at gradually decreasing costs and almost in real-time. HTS is used, among others, in medicine, veterinary medicine, microbiology, virology and epidemiology. The paper presents practical aspects of the HTS technology. It describes generations of sequencing, which vary in throughput, read length, accuracy and costs ̶ and thus are used for different applications. The stages
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Aronesty, Erik. "Comparison of Sequencing Utility Programs." Open Bioinformatics Journal 7, no. 1 (2013): 1–8. http://dx.doi.org/10.2174/1875036201307010001.

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High throughput sequencing (HTS) has resulted in extreme growth rates of sequencing data. At our lab, we generate terabytes of data every day. It is usually seen as required for data output to be “cleaned” and processed in various ways prior to use for common tasks such as variant calling, expression quantification and assembly. Two common tasks associated with HTS are adapter trimming and paired-end joining. I have developed two tools at Expression Analysis, Inc. to address these common tasks. The names of these programs are fastq-mcf and fastq-join. I compared the performance of these tools
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Pu, Dan, and Pengfeng Xiao. "A real-time decoding sequencing technology—new possibility for high throughput sequencing." RSC Advances 7, no. 64 (2017): 40141–51. http://dx.doi.org/10.1039/c7ra06202h.

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Malapi-Wight, Martha, Bishwo Adhikari, Jing Zhou, et al. "HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection." Viruses 13, no. 8 (2021): 1627. http://dx.doi.org/10.3390/v13081627.

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Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnosti
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Ma, Hailun, Trent J. Bosma, and Arifa S. Khan. "Long-Read High-Throughput Sequencing (HTS) Revealed That the Sf-Rhabdovirus X+ Genome Contains a 3.7 kb Internal Duplication." Viruses 15, no. 10 (2023): 1998. http://dx.doi.org/10.3390/v15101998.

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We previously reported a novel rhabdovirus produced from the Spodoptera frugiperda Sf9 cell line, designated as Sf-rhabdovirus X+ since it contained a unique accessory gene X. The Sf-rhabdovirus X+ genome sequence was generated using Sanger sequencing and short-read high-throughput sequencing (HTS). In this study, we have used long-read HTS technologies, PacBio’s single-molecule real-time sequencing and Oxford’s Nanopore RNA direct sequencing, to analyze the parent Sf9 cell line transcriptome and the virus RNA produced from an X+ cell clone, respectively. A unique 3.7 kb duplication was identi
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Bester, Rachelle, Chanel Steyn, Johannes H. J. Breytenbach, Rochelle de Bruyn, Glynnis Cook, and Hans J. Maree. "Reproducibility and Sensitivity of High-Throughput Sequencing (HTS)-Based Detection of Citrus Tristeza Virus and Three Citrus Viroids." Plants 11, no. 15 (2022): 1939. http://dx.doi.org/10.3390/plants11151939.

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The credibility of a pathogen detection assay is measured using specific parameters including repeatability, specificity, sensitivity, and reproducibility. The use of high-throughput sequencing (HTS) as a routine detection assay for viruses and viroids in citrus was previously evaluated and, in this study, the reproducibility and sensitivity of the HTS assay were assessed. To evaluate the reproducibility of HTS, the same plants assayed in a previous study were sampled again, one year later, and assessed in triplicate using the same analyses to construct the virome profile. The sensitivity of t
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Dissertations / Theses on the topic "HTS sequencing"

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Solayman, Md. "High-Throughput Sequencing Based Probing of Protein/RNA Structures and Functions." Thesis, Griffith University, 2022. http://hdl.handle.net/10072/416290.

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The rapid advancement in sequencing chemistry, sequencing technologies, and bioinformatics has significantly increased the sequencing automation and lowered the cost. The applications of high-throughput sequencing (HTS) technologies are expanding from research laboratories to diagnostic clinics on a regular basis. Moreover, diverse methods used in epigenetics, proteomics, structure probing of macromolecules (DNA, RNA, and proteins) have been developed based on the HTS technology. This thesis describes the development of two novel techniques, high-throughput split-protein profiling (HiTS) and R
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AGOSTINETTO, GIULIA. "Data-driven approaches for biodiversity exploration via DNA metabarcoding data analysis." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2022. http://hdl.handle.net/10281/365346.

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Gli approcci metagenomici hanno cambiato il modo di studiare la biologia e la biodiversità in diversi campi. In particolare, il progresso tecnologico ci consente di determinare la composizione tassonomica dei campioni e di studiare la biodiversità in ambienti molto diversi. Al giorno d'oggi, il DNA metabarcoding è una procedura standard, applicata in un'ampia gamma di settori, dalla salute umana all'ecologia, alle applicazioni industriali. Negli ultimi anni, il DNA metabarcoding applicato al 16S rRNA è stato ampiamente utilizzato per studiare la comunità batterica, portando ad analisi di routi
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Snyder, Matthew Robert. "Environmental DNA Detection and Population Genetic Patterns of Native and Invasive Great Lakes Fishes." University of Toledo / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1564680483342507.

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Horton, Dean J. "Using molecular techniques to investigate soil invertebrate communities in temperate forests." Kent State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=kent1448799316.

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Eschlimann, Marine. "Influence de la variabilité des protéines d’enveloppe du virus de l’hépatite B sur l’évolution de l’infection évaluée par la persistance de l’antigène HBs." Thesis, Université de Lorraine, 2017. http://www.theses.fr/2017LORR0133/document.

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L’hépatite B chronique touche environ 257 millions de personnes dans le monde. La perte de l’antigène HBs (AgHBs), marqueur de guérison fonctionnelle, n’est que très rarement observée, même sous traitement antiviral (3-16 %). Les protéines d’enveloppe du virus de l’hépatite B (VHB), formant l’AgHBs, sont très variables et cruciales pour le pouvoir infectieux du virus de l’hépatite B (VHB) et la physiopathologie. Nous avons émis l’hypothèse que cette variabilité pourrait expliquer, au moins partiellement, l’évolution de l’infection par le VHB, évaluée par la clairance de l’AgHBs, chez des patie
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Young, Jennifer M. "Application of DNA metabarcoding and high-throughput sequencing for enhanced forensic soil DNA analysis." Thesis, 2014. http://hdl.handle.net/2440/91437.

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The complex and variable soil matrix can support a wide range of biota that can provide information about local vegetation, soil conditions (e.g. soil acidity) and habitat type. As the combination of microbes, plants and animals within a soil is often specific to a given site, identification of the soil biota can narrow the likely source of a soil sample. DNA fingerprinting analysis of soil microbes has been used as forensic evidence in court to establish a link between a suspect and a site, victim or object. However, previous genetic analyses have relied on patterns of fragment length variati
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Lin, Wei-Chih, and 林威志. "Development of Pilot-Scale Chemical-Biological H2S Elimination Systems and Characterization of Genome and Transcriptome of Acidithiobacillus ferrooxidans Mutant W3 by Next Generation Sequencing." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/33913990273447439232.

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博士<br>國立交通大學<br>生物科技系所<br>102<br>The acidophilic and autotrophic Acidithiobacillus ferrooxidans oxidizes ferrous iron into ferric iron to obtain the electrons and reducing power. The ferric iron was used to be an oxidant for H2S elimination and A. ferrooxidans was immobilized in the bioreactor for the ferric iron regeneration. This combined and renewable system was applied for the biogas purification in this study. The former “carrier-based” reactors are unadvisable as H2S elimination system because they are prone to sulfur blockage problems under heavy loading operations. Therefore, the “scru
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Books on the topic "HTS sequencing"

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Newman, Abraham L. Sequencing, Layering, and Feedbacks in Global Regulation. Edited by Orfeo Fioretos, Tulia G. Falleti, and Adam Sheingate. Oxford University Press, 2016. http://dx.doi.org/10.1093/oxfordhb/9780199662814.013.38.

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From banking standards to data privacy, regulation has entered the lexicon of international affairs. Unlike trade or currencies, however, there are few formal treaty-based international organizations resolving disputes or setting the rules for the world. Instead, global regulation is frequently shaped by informal networks of regulators or at times by the extraterritorial extension of domestic law by large markets. Drawing on work from historical institutionalism, this chapter argues that the global politics of regulation is in important respects the product of domestic and international instit
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Bantekas, Ilias. Sequencing Peace and Justice in Post-Conflict Africa. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198810568.003.0005.

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This chapter discusses the extent to which there is any conflict or harm in the ICC Prosecutor’s involvement in cases undergoing mediation by the international community, most of which are currently in Africa. The ICC Prosecutor’s discretion, as per the Court’s Statute, to hold a prosecution in abeyance in anticipation of the outcomes of mediating efforts which aim at ending a conflict is at best ambivalent. Recent practice suggests that stakeholders engaged in ending long-running African conflicts prefer the Prosecutor to decline to exercise jurisdiction in order to encourage the parties to r
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Sadleir, Lynette G., Jozef Gecz, and Ingrid E. Scheffer. Epilepsies That Occur Predominantly in Girls. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0041.

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Availability of DNA sequencing has led to an increase in the number of children being identified with mutations in specific genes in specific epilepsy phenotypes. The presence of mutations that cause epilepsy only in females is one of the discoveries revealed in the sequencing era. Mutations in PCDH19 and CDKL5 are distinctive and identifiable forms of female-only epilepsy, and clinicians should consider PCDH19 in normal girls presenting with clusters of afebrile or febrile seizures in the first 3 years of life, and CDKL5 in girls or boys presenting with severe developmental delay within the f
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Walsh, Richard A. Siblings with Instability. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780190607555.003.0015.

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Over the past 5 years, there has been a shift in the approach to searching for a genetic diagnosis in familial ataxic syndromes. Whereas in the past, a limited but expensive search through a selection of commercially available genes using Sanger sequencing was performed, there is now widespread availability of gene panels utilizing next-generation sequencing techniques. This is an efficient and powerful approach that may achieve a diagnosis in more than 30% of patients with a familial ataxia that remain undiagnosed. However, accurate phenotyping remains critical to allow interpretation of sequ
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Purcell, Shaun M. Genetic Methodologies and Applications. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0001.

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Mental illness is highly heritable, yet it has been difficult historically to identify the specific genes that comprise that risk. This difficulty resides in the fact that the genetic risk for all common mental disorders is polygenic, with perhaps hundreds of genetic variations, each of small effect, contributing to the overall risk. Despite these challenges, the field has made dramatic advances over the past decade in beginning to understand the genetic basis of mental illness. This chapter provides an overview of the experimental approaches used, beginning with epidemiology and population ge
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Maher, Christopher J., and Elaine R. Mardis. Genomic Landscape of Cancer. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0004.

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The study of cancer genomics has advanced rapidly during the last decade due to the development of next generation or massively parallel technology for DNA sequencing. The resulting knowledge is transforming the understanding of both inherited (germline) genetic susceptibility and the somatic changes in tumor tissue that drive abnormal growth and progression. The somatic alterations in tumor tissue vary depending on the type of cancer and its characteristic “genomic landscape.” New technologies have increased the speed and lowered the cost of DNA sequencing and have enabled high-volume charact
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Munro, Carol A., and Duncan Wilson. Fungal genomics and transcriptomics. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0006.

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The advent of whole-genome sequencing has resulted in a range of platforms for large-scale analysis of the DNA (genomics), RNA (transcriptomics), protein (proteomics), and metabolite (metabolomics) content of cells. These inclusive ‘omics’ approaches have allowed for unparalleled insights into fungal biology. In this chapter we will discuss how genomics and transcriptomics have been used to broaden our understanding of the biology of human pathogenic fungi and their interactions with their hosts.
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Ingles, Jodie, Charlotte Burns, and Laura Yeates. Genetic counselling. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0145.

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Cardiac genetic counselling is an emerging but important subspecialty. The qualifications of cardiac genetic counsellors depend on the country of practice, but at a minimum they are Master’s-level trained health professionals with expertise in genetics, and are integral members of the multidisciplinary inherited cardiovascular disease clinic. Though the framework is diverse in different countries, key roles include investigation and confirmation of family history details, discussion of inheritance risks and facilitation of cardiac genetic testing, communication with at-risk relatives, and incr
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Kirchman, David L. Genomes and meta-omics for microbes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0005.

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The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacte
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Halliday, Catriona L., and Sarah E. Kidd. Cryptococcus species. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0012.

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Cryptococcus neoformans and Cryptococcus gattii are the principal pathogenic species within the genus Cryptococcus and the causative agents of cryptococcosis. Although rare, the incidence of infection due to other Cryptococcus species previously regarded as saprophytes, has increased over the last 40 years. Irrespective of the infecting species, infections are acquired following inhalation from the environment, causing localised or disseminated disease. The severity of disease is dependent on the organism’s virulence factors and the host’s immune response, and the clinical manifestations are i
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Book chapters on the topic "HTS sequencing"

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Quadros, Ayane F. F., and Francisco Murilo Zerbini. "High-throughput Sequencing (HTS)-Based Diagnosis of Geminiviruses." In Methods in Molecular Biology. Springer US, 2025. https://doi.org/10.1007/978-1-0716-4454-6_15.

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Lavín Trueba, José Luis, and Ana M. Aransay. "The High-Throughput Sequencing Technologies Triple-W Discussion: Why Use HTS, What Is the Optimal HTS Method to Use, and Which Data Analysis Workflow to Follow." In Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31350-4_1.

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O’Sullivan, Christopher, and Jonathan Trow. "Submitting Data to a Public Repository, the Final Step of a Successful HTS Experiment." In Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31350-4_16.

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Bester, Rachelle, and Hans J. Maree. "Validation of High-Throughput Sequencing (HTS) for Routine Detection of Citrus Viruses and Viroids." In Methods in Molecular Biology. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3515-5_14.

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Arumugam, Ramitha, Prithivan Ravichandran, Swee Keong Yeap, et al. "Application of High-Throughput Sequencing (HTS) to Enhance the Well-Being of an Endangered Species (Malayan Tapir): Characterization of Gut Microbiome Using MG-RAST." In Metagenomic Data Analysis. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3072-3_8.

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Sterflinger, Katja, and Guadalupe Piñar. "Molecular-Based Techniques for the Study of Microbial Communities in Artworks." In Microorganisms in the Deterioration and Preservation of Cultural Heritage. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-69411-1_3.

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AbstractThanks to the revolutionary invention of the polymerase chain reaction and the sequencing of DNA and RNA by means of “Sanger sequencing” in the 1970th and 1980th, it became possible to detect microorganisms in art and cultural assets that do not grow on culture media or that are non-viable. The following generation of sequencing systems (next generation sequencing, NGS) already allowed the detection of microbial communities on objects without the intermediate step of cloning, but still most of the NGS technologies used for the study of microbial communities in objects of art rely on “t
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Zhao, Yuanzhe, Jie Zhang, Zepeng Sun, Zheqi Cao, Liqun Xu, and Jian Li. "Scheme Design and Challenges of DNA Sequencing Terminal Equipment Based on Solid-State Nanopore Sequencing." In Lecture Notes in Mechanical Engineering. Springer Nature Singapore, 2025. https://doi.org/10.1007/978-981-97-7887-4_13.

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Abstract Nanopore sequencing has become the primary technology for modern DNA sequencing. Solid nanopores are favored for their cost-effectiveness, stability, and scalability, particularly for portable applications. This paper presents a new design for a portable solid-state nanopore sequencing device based on the Linux platform. It employs a cutting-edge biological sequencing chip with a nanopore channel to capture through-hole data. Electrical signals from the chip are processed to create DNA sequence data files. The Linux-based Raspbian OS serves as the control terminal, facilitating seamle
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Garg, Vanika, and Rajeev K. Varshney. "Analysis of Small RNA Sequencing Data in Plants." In Plant Bioinformatics. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2067-0_26.

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AbstractOver the past decades, next-generation sequencing (NGS) has been employed extensively for investigating the regulatory mechanisms of small RNAs. Several bioinformatics tools are available for aiding biologists to extract meaningful information from enormous amounts of data generated by NGS platforms. This chapter describes a detailed methodology for analyzing small RNA sequencing data using different open source tools. We elaborate on various steps involved in analysis, from processing the raw sequencing reads to identifying miRNAs, their targets, and differential expression studies.
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Lau, Dawn Yan Lam, Jose Roberto Aguirre Sánchez, Craig Baker-Austin, and Jaime Martinez-Urtaza. "What Whole Genome Sequencing Has Told Us About Pathogenic Vibrios." In Advances in Experimental Medicine and Biology. Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-22997-8_16.

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Clear, Rachel, Eric Dumonteil, and Claudia Herrera. "Decoding Chagas Disease: What Next-Generation Sequencing Has Taught Us." In Recent Advances in Parasitomics. Springer Nature Switzerland, 2025. https://doi.org/10.1007/978-3-031-70591-5_3.

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Conference papers on the topic "HTS sequencing"

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Shi, Wei, Paul Evans, Gabrielle Scheffer, and Casey Hubert. "Novel Application of Nitrate as H2S Control Strategy in Permian Basin Produced Water Storage Ponds." In CONFERENCE 2023. AMPP, 2023. https://doi.org/10.5006/c2023-18968.

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Abstract Produced water (PW) ponds are important facilities for supporting hydraulic fracturing in the Permian Basin. The control of H2S in these facilities is critical to safe and reliable frac and production operations. Effective microbial control strategies are required to mitigate sulfate-reducing bacteria (SRB) activity and fouling of production facilities with iron sulfide. Next generation sequencing (NGS) DNA analyses of Delaware Basin produced water (PW) samples highlighted a bacterial consortium dominated by putative halophilic fermentative and sulfate-reducing bacteria such as Halana
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Farschon, Christopher, Michael Hewins, and Charles Moran. "Repainting Bridges During Rehabilitation Projects: Sequencing Options." In Paint and Coatings Expo (PACE) 2006. SSPC, 2006. https://doi.org/10.5006/s2006-00025.

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Abstract Major bridge rehabilitation projects may include painting of the steel superstructure in addition to deck replacement, expansion joint improvements, bearing replacement, etc. This paper will review the scheduling of the coatings work during a bridge rehabilitation project and how the order of coatings work affects the project schedule, cost, and quality. Constructing and then painting a complex steel structure is no easy task. Designers and constructors face numerous challenges throughout the process, not the least of these is how to protect the steel from corrosion during the life of
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Manna, Kathleen, Joseph Moore, Kenneth Wunch, et al. "Relative Performance of Various 16S iTag Amplicon Sequencing Primer Pairs in Profiling Microbial Communities Relevant to Oil & Gas Operations." In CORROSION 2019. NACE International, 2019. https://doi.org/10.5006/c2019-13442.

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Abstract The oil and gas industry's efforts to characterize microbial communities in oilfield process fluids has shed increasing light on the influence of bacteria and archaea on hydrocarbon production. Notably, topside or downhole water contamination by microorganisms such as sulfate-reducing bacteria, acid-producing bacteria, and/or other halophiles can negatively impact asset integrity and reduce the quality and quantity of produced hydrocarbons. Molecular microbiology methods have contributed to our understanding of these complex processes by providing unprecedented resolution of resident
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Almahamedh, Hussain H., Charles Williamson, John R. Spear, Brajendra Mishra, and David L. Olson. "Identification of Microorganisms and Their Effects on Corrosion of Carbon Steels Pipelines." In CORROSION 2011. NACE International, 2011. https://doi.org/10.5006/c2011-11231.

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Abstract Microbial influenced corrosion on different grades of carbon steel coupons used in pipelines were investigated in this study. Microbes were isolated and cultivated from oil well produced water samples, and immersion tests were conducted with these waters, microbes and coupons. Bacteria were identified with 16S rRNA gene sequencing. Sequencing analyses revealed the existence of different kinds of bacteria including iron, manganese, and sulfate-reducing bacteria. Corrosion products were characterized by X-ray diffraction (XRD), and scanning electron microscopy (SEM) coupled with energy
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Wallrath, Roderich, Edwin Zondervan, and Meik B. Franke. "Integration of MILP and Discrete-Event Simulation for Flowshop Scheduling Using Benders Decomposition." In The 35th European Symposium on Computer Aided Process Engineering. PSE Press, 2025. https://doi.org/10.69997/sct.180841.

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Real-world flowshop problems which are very common in the chemical industry are often difficult to solve in a reasonable time with allocation, sequencing, and lot-sizing decisions. Although great progress has been made in the last 20 years regarding MILP model formulations and solution algorithms, realistically-sized flowshop problems with resource and buffer constraints are still difficult to solve. On the other hand, discrete-event simulation (DES) allows for very detailed modelling of process plants, but lacking of optimization capabilities. Simulation Optimization (SO) combines the high-de
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Geissler, Brett, Carrie Keller-Schultz, and Vic Keasler. "Don’t Just Blame the SRBs and APBs for MIC." In CORROSION 2015. NACE International, 2015. https://doi.org/10.5006/c2015-06083.

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Abstract Microbiologically influenced corrosion has historically been attributed to the activity of sulfate reducing and acid producing bacteria. Recent advances in DNA isolation and sequencing have led to the realization that these two classes of bacteria often represent only a small portion of the corrosive microbial population present in the oil and gas environment. Numerous different genera from multiple other classes of bacteria and archaea have been found to be associated with failures and are now recognized as contributors to the MIC process. The presence of these microbes, while not fr
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Demeter, Marc, Shawna Johnston, Kim Dockens, and Raymond J. Turner. "Molecular MIC Diagnoses from ATP Field Test: Streamlined Workflow from Field to 16S rRNA Gene Metagenomics Results." In CORROSION 2017. NACE International, 2017. https://doi.org/10.5006/c2017-09420.

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Abstract Microbiologically influenced corrosion (MIC) describes the negative impacts of microbial growth within various industries. While culture based growth tests are the traditional means of assessing MIC, they are not accurate. New culture-independent assays have been developed; one of which is the adenosine triphosphate (ATP) assay. This field assay allows for indirect enumeration of microorganisms; however, it does not divulge which microorganisms are present. Molecular methods such as 16S metagenomics (16S rRNA gene sequencing and data interpretation) are often used for characterizing t
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De Paula, Renato, Cruz St Peter, Ian Alex Richardson, et al. "DNA Sequencing of Oilfield Samples: Impact of Protocol Choices on the Microbiological Conclusions." In CORROSION 2018. NACE International, 2018. https://doi.org/10.5006/c2018-11662.

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Abstract In the last decade, molecular microbiology techniques have significantly expanded the understanding of the resident microflora in hydrocarbon reservoirs and production systems. These methods have been steadily accepted by the industry and are widely viewed as accurate, comprehensive and highly valuable tools that augment or may eventually replace conventional methods. The resulting information has helped operators and service companies to develop better monitoring programs, assess risks and tailor mitigation strategies to control undesired microbial activities in wells, flowlines and
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Geissler, Brett, Alicia M. Jones, and Vic Keasler. "Prevalence and Distribution of Sulfide Generating Microbes in the Oil and Gas Industry." In CORROSION 2016. NACE International, 2016. https://doi.org/10.5006/c2016-07569.

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Abstract Hydrogen sulfide generation is one of the key detriments linked to microbial activity in the oil and gas industry and is the most likely cause of most microbiologically influenced corrosion. H2S is extremely corrosive to most metals and can significantly devalue produced fluids and gases as well as raise HS&amp;E concerns for production facilities. Microbial sulfidogenesis has historically been linked to only a few types of sulfate reducing bacteria that are capable of growth in Modified Postgate’s B medium, but recent advances in microbial identification techniques have shown that th
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Le Borgne, S., J. Jan, J. M. Romero, and M. Amaya. "Impact of Molecular Biology Techniques on the Detection and Characterization of Microorganisms and Biofilms Involved in MIC." In CORROSION 2002. NACE International, 2002. https://doi.org/10.5006/c2002-02461.

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Abstract Recently, the application of molecular techniques has greatly improved our knowledge of microbial diversity and distribution in environmental samples. In this paper, we have reviewed the molecular biology techniques that can be used to study microorganisms and biofilms involved in the MIC phenomenon. These techniques include 16S ribosomal DNA (16S rDNA) gene based techniques. In particular, 16S rDNA sequencing, the construction of 16S rDNAs libraries, Fluorescence In Situ Hybridization (FISH), Denaturing Gradient Gel Electrophoresis (DGGE) and Random Amplification of Polymorphic DNA (
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Reports on the topic "HTS sequencing"

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Lora, Eduardo. What Makes Reforms Likely?: Timing and Sequencing of Structural Reforms in Latin America. Inter-American Development Bank, 2000. http://dx.doi.org/10.18235/0011559.

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The wave of structural reforms in Latin America and elsewhere has stimulated the development of a wide body of theoretical literature on the political economy of reform, i.e., the study of the political constraints that condition the timing, speed and sequencing of reforms. This paper tests some of the hypotheses associated with these theoretical models, using a set of structural reform indicators for approximately twenty Latin American countries for the period 1985-1995. Although there is strong support for some hypotheses, recent reforms in Latin America cannot be adequately explained withou
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Seroussi, Eyal, and George Liu. Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle. United States Department of Agriculture, 2010. http://dx.doi.org/10.32747/2010.7593397.bard.

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Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association w
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Rajarajan, Kunasekaran, Alka Bharati, Hirdayesh Anuragi, et al. Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts. World Agroforestry, 2020. http://dx.doi.org/10.5716/wp20050.pdf.

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Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, researc
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Steffenson, B. J., I. Mayrose, Gary J. Muehlbauer, and A. Sharon. ing and comparative sequence analysis of powdery mildew and leaf rust resistance gene complements in wild barley. United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134173.bard.

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Our overall, long-term goal is to exploit the genetic diversity present in cereal wild relatives for the development of cultivars with durable disease resistance. Our specific objectives for this proposal were to: 1) Utilize Association Genetics Resistance Gene Enrichment Sequencing (AgRenSeq) to identify and clone powdery mildew and leaf rust resistance gene complements in wild barley and 2) Conduct comparative sequence analyses of the cloned resistance genes to elucidate the basis of their specificity and evolution. The deployment of resistant cultivars is the most effective, economically ef
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Holland, Jeremy. Oxfam Bangladesh Economic Justice and Resilience Pillar: Integrated impact evaluation report. Oxfam GB, 2022. http://dx.doi.org/10.21201/2022.9813.

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The Economic Justice and Resilience Pillar of the Oxfam Bangladesh Country Strategy 2016–19 was an ambitious and far-reaching portfolio of initiatives conducted across widely varying contexts and with a large cast of partners. This integrated evaluation report is the result of a rich study process that captured this ambitious complexity through a careful sequencing of mixed-method data collection and multi-stakeholder sense making and analysis. Despite the ambitious scope and challenging context, this report confirms that the Pillar has been highly successful and effective across several of it
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Gelb, Jr., Jack, Yoram Weisman, Brian Ladman, and Rosie Meir. Identification of Avian Infectious Brochitis Virus Variant Serotypes and Subtypes by PCR Product Cycle Sequencing for the Rational Selection of Effective Vaccines. United States Department of Agriculture, 2003. http://dx.doi.org/10.32747/2003.7586470.bard.

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Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically imp
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Fridman, Eyal, Jianming Yu, and Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7597925.bard.

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Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a gene
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Hicks, Julie, Laurin Yates, and Jackie Pettway. Mat Sinking Unit supply study : Mississippi River revetment. Engineer Research and Development Center (U.S.), 2021. http://dx.doi.org/10.21079/11681/41867.

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The Mississippi Valley Division (MVD) has maintained the Mississippi River banks for over 80 years. The Mat Sinking Unit (MSU), built in 1946, was considered state-of-the-art at the time. This system is still in operation today and has placed over 1,000 miles of Articulated Concrete Mats along the Mississippi River from Head of Passes, LA, to Cairo, IL. A new MSU has been designed and is expected to be fully mission capable and operational by the 2023 season, which is expected to increase the productivity from 2,000 squares/day up to 8,000 squares/day with double shifts and optimal conditions.
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Rodriguez Muxica, Natalia. Open configuration options Bioinformatics for Researchers in Life Sciences: Tools and Learning Resources. Inter-American Development Bank, 2022. http://dx.doi.org/10.18235/0003982.

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The COVID-19 pandemic has shown that bioinformatics--a multidisciplinary field that combines biological knowledge with computer programming concerned with the acquisition, storage, analysis, and dissemination of biological data--has a fundamental role in scientific research strategies in all disciplines involved in fighting the virus and its variants. It aids in sequencing and annotating genomes and their observed mutations; analyzing gene and protein expression; simulation and modeling of DNA, RNA, proteins and biomolecular interactions; and mining of biological literature, among many other c
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Minz-Dub, A., G. J. Muehlbauer, E. Millet, and A. Sharon. ing and characterization of a novel leaf rust and stripe rust resistance gene from Sharon goatgrass. United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134171.bard.

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Each year, significant global wheat yield loss occurs due to diseases that affect yield quantity or quality. Breeding for resistance has been the best economic and environmentally safe approach to control wheat diseases, however many disease resistance (R) genes succumbed to the pathogens and are no longer effective. Hence, new sources of resistance are necessary to boost the wheat gene pool. The main source for such genes are species of wheat wild relatives in the secondary gene pool that contain an unexploited reservoir of novel R genes. Sharon goatgrass (Aegilops sharonensis Eig) is a wild
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