Relevant bibliographies by topics / Whole genome sequencing PacBio

Contents

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

Academic literature on the topic 'Whole genome sequencing PacBio'

Author: Grafiati
Published: 2 June 2025
Last updated: 31 July 2025

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Journal articles on the topic "Whole genome sequencing PacBio"

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PARK, Jongsun, Yunho YUN, Hong XI, Woochan KWON, and Janghyuk SON. "Current status of whole-genome sequences of Korean angiosperms." Korean Journal of Plant Taxonomy 53, no. 3 (2023): 181–200. http://dx.doi.org/10.11110/kjpt.2023.53.3.181.

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Owing to the rapid development of sequencing technologies, more than 1,000 plant genomes have been sequenced and released. Among them, 69 Korean plant taxa (85 genome sequences) contain at least one whole-genome sequence despite the fact that some samples were not collected in Korea. The sequencing-by-synthesis method (next-generation sequencing) and the PacBio (third-generation sequencing) method were the most commonly used in studies appearing in 65 publications. Several scaffolding methods, such as the Hi-C and 10x types, have also been used for pseudo-chromosomal assembly. The most abundan
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Kim, Justin, Rebecca L. Lindsey, Lisley Garcia-Toledo, et al. "High-Quality Whole-Genome Sequences for 59 HistoricalShigellaStrains Generated with PacBio Sequencing." Genome Announcements 6, no. 15 (2018): e00282-18. http://dx.doi.org/10.1128/genomea.00282-18.

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ABSTRACTShigellaspp. are enteric pathogens that cause shigellosis. We report here the high-quality whole-genome sequences of 59 historicalShigellastrains that represent the four species and a variety of serotypes.
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Fatima, Nazeefa, Anna Petri, Ulf Gyllensten, Lars Feuk, and Adam Ameur. "Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes." Genes 11, no. 12 (2020): 1444. http://dx.doi.org/10.3390/genes11121444.

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Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× covera
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Sockell, Alexandra, Khi Pin Chua, Christopher Kingsley, et al. "Abstract 6624: Comprehensive, multi-omic detection of somatic variants from the GIAB HG008 matched tumor-normal pair using highly accurate long- and short-read whole-genome sequencing." Cancer Research 85, no. 8_Supplement_1 (2025): 6624. https://doi.org/10.1158/1538-7445.am2025-6624.

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Abstract Disentangling the molecular drivers of cancer progression requires a precise understanding of the somatic alterations that take place at the DNA level during tumor development. These include not only small changes like SNVs and indels, but also structural variants, changes in repetitive elements, differential methylation, as well as the haplotype context in which these changes occur. Existing short-read sequencing methods using sequencing by synthesis (SBS) chemistry lack the read length to characterize large structural variants or to span longer repetitive regions as well as to phase
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Subirana, Juan A., and Xavier Messeguer. "How Long Are Long Tandem Repeats? A Challenge for Current Methods of Whole-Genome Sequence Assembly: The Case of Satellites in Caenorhabditis elegans." Genes 9, no. 10 (2018): 500. http://dx.doi.org/10.3390/genes9100500.

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Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent playground to evaluate different assembly methods. Here, we compare the structure of satellites found in three different assemblies of the Caenorhabditis elegans genome: the original sequence obtained by Sanger sequencing, an assembly based on PacBio technology, and an assembly using Nanopore sequencing reads. In general, satellites were found in equivalent genomic regions,
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Zhang, Pengfei, Dike Jiang, Yin Wang, Xueping Yao, Yan Luo, and Zexiao Yang. "Comparison of De Novo Assembly Strategies for Bacterial Genomes." International Journal of Molecular Sciences 22, no. 14 (2021): 7668. http://dx.doi.org/10.3390/ijms22147668.

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(1) Background: Short-read sequencing allows for the rapid and accurate analysis of the whole bacterial genome but does not usually enable complete genome assembly. Long-read sequencing greatly assists with the resolution of complex bacterial genomes, particularly when combined with short-read Illumina data. However, it is not clear how different assembly strategies affect genomic accuracy, completeness, and protein prediction. (2) Methods: we compare different assembly strategies for Haemophilus parasuis, which causes Glässer’s disease, characterized by fibrinous polyserositis and arthritis,
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Gao, Yahui, Li Ma, and George E. Liu. "Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods." Genes 13, no. 5 (2022): 828. http://dx.doi.org/10.3390/genes13050828.

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Structural variations (SVs), as a great source of genetic variation, are widely distributed in the genome. SVs involve longer genomic sequences and potentially have stronger effects than SNPs, but they are not well captured by short-read sequencing owing to their size and relevance to repeats. Improved characterization of SVs can provide more advanced insight into complex traits. With the availability of long-read sequencing, it has become feasible to uncover the full range of SVs. Here, we sequenced one cattle individual using 10× Genomics (10 × G) linked read, Pacific Biosciences (PacBio) co
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An, Dong, Yong Zhou, Changsheng Li, et al. "Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela." Proceedings of the National Academy of Sciences 116, no. 38 (2019): 18893–99. http://dx.doi.org/10.1073/pnas.1910401116.

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Aquatic plants have to adapt to the environments distinct from where land plants grow. A critical aspect of adaptation is the dynamics of sequence repeats, not resolved in older sequencing platforms due to incomplete and fragmented genome assemblies from short reads. Therefore, we used PacBio long-read sequencing of the Spirodela polyrhiza genome, reaching a 44-fold increase of contiguity with an N50 (a median of contig lengths) of 831 kb and filling 95.4% of gaps left from the previous version. Reconstruction of repeat regions indicates that sequentially nested long terminal repeat (LTR) retr
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Lin, Guan, Juntao Gao, Junxian Zou, et al. "Whole-Genome Sequence and Characterization of Ralstonia solanacearum MLY102 Isolated from Infected Tobacco Stalks." Genes 15, no. 11 (2024): 1473. http://dx.doi.org/10.3390/genes15111473.

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Background/Objectives: Bacterial wilt disease is a soil-borne disease caused by Ralstonia solanacearum that causes huge losses to crop economies worldwide. Methods: In this work, strain MLY102 was isolated and further identified as R. solanacearum from a diseased tobacco stalk. The genomic properties of MLY102 were explored by performing biochemical characterization, genome sequencing, compositional analysis, functional annotation and comparative genomic analysis. Results: MLY102 had a pinkish-red color in the center of the colony surrounded by a milky-white liquid with fluidity on TTC medium.
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Jiang, Wansheng, Yunyun Lv, Le Cheng, et al. "Whole-Genome Sequencing of the Giant Devil Catfish, Bagarius yarrelli." Genome Biology and Evolution 11, no. 8 (2019): 2071–77. http://dx.doi.org/10.1093/gbe/evz143.

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AbstractAs one economically important fish in the southeastern Himalayas, the giant devil catfish (Bagarius yarrelli) has been known for its extraordinarily large body size. It can grow up to 2 m, whereas the non-Bagarius sisorids only reach 10–30 cm. Another outstanding characteristic of Bagarius species is the salmonids-like reddish flesh color. Both body size and flesh color are interesting questions in science and also valuable features in aquaculture that worth of deep investigations. Bagarius species therefore are ideal materials for studying body size evolution and color depositions in
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Dissertations / Theses on the topic "Whole genome sequencing PacBio"

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Anson, Eric Lance. "Algorithms for whole genome shotgun sequencing." Diss., The University of Arizona, 2000. http://hdl.handle.net/10150/289091.

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A monumental achievement in the history of science, the sequencing of the entire human genome, will soon be reached. The Human Genome Project (HGP) has been working toward this goal since 1990 using a two-tiered strategy. Recently it was proposed that using a whole-genome shotgun approach to sequence the genome would be faster and less costly. This thesis expands on that proposal by presenting two algorithms that can be used in whole-genome shotgun sequencing. These algorithms were implemented and tested on simulated data. Essential to this approach is the availability of pairs of short, uniqu
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Farmery, James Henry Royston. "Estimating telomere length from whole genome sequencing data." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/275827.

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This thesis details the development of two computational tools, Telomerecat and Parabam, as well as their applications to whole genome sequencing (WGS) data. Telomerecat is a tool for estimating telomere length from WGS data. The strength of Telomerecat lies in its applicability. This applicability is due to a number of advantages over previous attempts to estimate telomere length from WGS. Chief amongst these advantages is that it makes no assumption about the underlying chromosome count or size of the genome within input samples. This means that Telomerecat lends itself well to analysing can
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Huang, Jie. "Whole-genome sequencing-based association studies of cardiovascular biomarkers." Thesis, University of Cambridge, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708994.

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Li, Karen Christine. "Supporting decision-making in whole genome/exome sequencing : parents' perspectives." Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/50835.

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Whole genome sequencing/exome sequencing (WGS/ES) technology is becoming more affordable and accessible, and will become more frequently used in various clinical settings, including for diagnosing rare childhood diseases. However, its use means that parents face decisions that could uncover life-altering information, unrelated to their child’s illness that may also have personal and ethical implications for their families. The purpose of this study is to explore and describe parents’ perceptions of their decisional needs when deciding on WGS/ES for their child. The qualitative methodological
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Mattisson, Jonas. "Identifying esophageal atresi associated variants from whole genome sequencing data." Thesis, Uppsala universitet, Institutionen för immunologi, genetik och patologi, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-345329.

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Knowing the underlying cause of a genetic disorder could not only further our understanding of the disease itself, and the otherwise healthy mechanism that is disrupted. It could potentially improve people’s lives. Even if whole genome sequencing has drastically improved the potential of discovering the cause, a comparison of two non-related individual’s genome will find several million sequence variations. While most variants have no significant impact, it is enough for only one to functionally impact a gene, for it to cause a genetic disorder. This project therefore focused on the filtering
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Kolicheski, Ana Leticia. "Discovering Disease Causing Variants in Dogs Through Whole Genome Sequencing." Thesis, University of Missouri - Columbia, 2019. http://pqdtopen.proquest.com/#viewpdf?dispub=13877152.

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<p> This dissertation focuses on the use of whole genome sequencing (WGS) for the identification of disease causing variants in canine genomes. A brief review on the historical milestones of genetics, the creation and popularization of the fast throughput DNA sequencing technologies and their advantages and potential problems and biases, the importance of the study of canine genetics and the current state of the canine genome assembly is presented. Our lab sequenced ~100 dogs in the attempt to discover disease-causing variants. So far 20 such variants have been identified. This dissertation co
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Wong, Tse Hua Nicholas. "Investigation of in-hospital norovirus transmission using whole genome sequencing." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:0c059680-337e-4a70-aab7-5b7d7e483962.

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Norovirus is the commonest cause of viral gastroenteritis, affecting all age groups worldwide. Outbreaks frequently occur in semi-closed communities such as schools, cruise ships, prisons and hospitals. Within the healthcare environment, the economic and logistical burdens and the inconvenience caused by norovirus is significant, since ward closure remains central to infection control. The aim of this study was to investigate norovirus transmission dynamics during hospital outbreaks. The ultimate goal was to provide information that could, in future, lead to the development of novel, less disr
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Colombini, Lorenzo. "Whole genome sequencing and comparative genomics in lactic acid bacteria." Doctoral thesis, Università di Siena, 2022. http://hdl.handle.net/11365/1182475.

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In the present thesis, the genomes of different microbial species, belonging to the lactic acid bacteria and including Lactobacillus crispatus, Streptococcus pneumoniae and Enterococcus faecalis, were obtained and analyzed using comparative genomics tools. In the first part of the thesis was described the genome of the probiotic L. crispatus strain M247, which contains a novel integrative and mobilizable element named Tn7088. Tn7088 carries a biosynthetic gene cluster coding for a class I bacteriocin which is homologous to the listeriolysin S gene cluster of Listeria monocytogenes and may conf
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Clouse, Jared William. "The Amaranth (Amaranthus Hypochondriacus) Genome: Genome, Transcriptome and Physical Map Assembly." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/5916.

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Amaranthus hypochondriacus is an emerging pseudo-cereal native to the New World which has garnered increased attention in recent years due to its nutritional quality, in particular its seed protein, and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleotetraploid that shows amphidiploid inheritance (2n=32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth A. hypochondriacus. The genome assembly consisted of 377 Mb in 3,518 scaffolds with an N50 of
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Ramos, Alexis. "Cancer Genome Characterization with SNP Array and Whole-Exome Sequencing Analysis." Thesis, Harvard University, 2011. http://dissertations.umi.com/gsas.harvard:10036.

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Cancer, the uncontrolled growth of morphologically and genetically abnormal cells in the body, is a major worldwide public health problem and there is a great need for novel insights into this disease. The majority of tumors arise from the acquisition of somatic alterations leading to changes in gene function and expression. The clinical success of targeted therapeutics in molecularly defined subsets of patients has highlighted the need for comprehensive characterization of the somatic alterations in individual cancer types. Copy number profiling using SNP arrays is a common approach for profi
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Books on the topic "Whole genome sequencing PacBio"

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Issues, United States Presidential Commission for the Study of Bioethical. Privacy and progress in whole genome sequencing. Presidential Commission for the Study of Bioethical Issues, 2012.

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Liu, Zhanjiang. Next generation sequencing and whole genome selection in aquaculture. Wiley-Blackwell, 2011.

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Liu, Zhanjiang John, ed. Next Generation Sequencing and Whole Genome Selection in Aquaculture. Wiley-Blackwell, 2011. http://dx.doi.org/10.1002/9780470958964.

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Minevich, Gregory. Identifying genes required for the formation of neurons from skin cells using forward genetic screens and whole genome sequencing in C. elegans. [publisher not identified], 2015.

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Liu, Zhanjiang (John). Next Generation Sequencing and Whole Genome Selection in Aquaculture. Wiley & Sons, Incorporated, John, 2010.

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Liu, Zhanjiang (John). Next Generation Sequencing and Whole Genome Selection in Aquaculture. Wiley & Sons, Incorporated, John, 2011.

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Liu, J. Next Generation Sequencing and Whole Genome Selection in Aquaculture. Wiley & Sons, Limited, John, 2020.

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Liu, Zhanjiang (John). Next Generation Sequencing and Whole Genome Selection in Aquaculture. Wiley & Sons, Incorporated, John, 2010.

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Next Generation Sequencing and Whole Genome Selection in Aquaculture. Wiley & Sons, Incorporated, John, 2010.

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Schneeberger, Korbinian. Whole genome analysis of Arabidopsis thaliana using next generation sequencing. 2010.

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Book chapters on the topic "Whole genome sequencing PacBio"

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Ng, Pauline C., and Ewen F. Kirkness. "Whole Genome Sequencing." In Methods in Molecular Biology. Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60327-367-1_12.

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Schlundt, Joergen. "Whole Genome Sequencing." In Encyclopedia of Gerontology and Population Aging. Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-319-69892-2_943-1.

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Luiselli, James, Francesca Happé, Hillary Hurst, et al. "Whole-Genome Sequencing." In Encyclopedia of Autism Spectrum Disorders. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-1698-3_101559.

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Schlundt, Joergen. "Whole Genome Sequencing." In Encyclopedia of Gerontology and Population Aging. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-22009-9_943.

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Gabaldón, Toni, and Tyler S. Alioto. "Whole-Genome Sequencing Recommendations." 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_2.

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Rendón-Anaya, Martha, and Alfredo Herrera-Estrella. "Requirement of Whole-Genome Sequencing." In The Common Bean Genome. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-63526-2_5.

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Krepelova, Anna, and Francesco Neri. "Low-Input Whole-Genome Sequencing." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1597-3_20.

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Isobe, Sachiko, Ung-Han Yoon, Qinghe Cao, et al. "Trilateral Research Association of Sweetpotato (TRAS) Ipomoea. trifida and I. batatas Sequencing and Crop Improvement Efforts." In Compendium of Plant Genomes. Springer International Publishing, 2024. http://dx.doi.org/10.1007/978-3-031-65003-1_3.

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AbstractEast Asia is an important region of sweetpotato production and consumption. To promote exchange among scientists studying sweetpotato in East Asia, the Trilateral Research Association of Sweetpotato (TRAS) was established in 2004 by sweetpotato scientists from China, South Korea, and Japan. The TRASgenome sequencing consortium was formally launched in 2014 and established a haploid-resolved and chromosome-scale de novo assembly of autohexaploid sweetpotato genome sequences. Before constructing the genome, we created chromosome-scale genome sequences in Ipomoea trifida using a highly ho
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Bottacini, Francesca, and Douwe van Sinderen. "Bifidobacterium Genome Assembly and Methylome Analysis Using Pacbio SMRT Sequencing." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1274-3_18.

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Hongoh, Yuichi, and Atsushi Toyoda. "Whole-Genome Sequencing of Unculturable Bacterium Using Whole-Genome Amplification." In Methods in Molecular Biology. Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-089-8_2.

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Conference papers on the topic "Whole genome sequencing PacBio"

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Anson, Eric, and Gene Myers. "Algorithms for whole genome shotgun sequencing." In the third annual international conference. ACM Press, 1999. http://dx.doi.org/10.1145/299432.299442.

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Yi-Xue Li. "Whole genome sequencing of disease animal models." In 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2016. http://dx.doi.org/10.1109/bibm.2016.7822475.

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Dymova, Maya, Olga Alkhovik, Lubov Evdokimova, Andrey Cherednichenko, Tatjana Petrenko, and Yana Batyrshina. "Whole genome-sequencing of non-tuberculous mycobacteria." In ERS International Congress 2016 abstracts. European Respiratory Society, 2016. http://dx.doi.org/10.1183/13993003.congress-2016.pa891.

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Janevski, Angel, Vinay Varadan, Sitharthan Kamalakaran, Nilanjana Banerjee, and Nevenka Dimitrova. "Comparative copy number variation from whole genome sequencing." In 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). IEEE, 2011. http://dx.doi.org/10.1109/gensips.2011.6169460.

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Sutton, R., M. Roth, R. Grubs, et al. "Whole Genome Sequencing of Patients with Pulmonary Fibrosis." In American Thoracic Society 2019 International Conference, May 17-22, 2019 - Dallas, TX. American Thoracic Society, 2019. http://dx.doi.org/10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5264.

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MacBeth, Alyssa, Tera Bowers, Betty Woolf, Maegan Harden, Niall Lennon, and Stacey Gabriel. "Abstract 3543: Clinical whole genome sequencing at scale." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-3543.

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MacBeth, Alyssa, Tera Bowers, Betty Woolf, Maegan Harden, Niall Lennon, and Stacey Gabriel. "Abstract 3543: Clinical whole genome sequencing at scale." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-3543.

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Ren, Li, Jia Fei, W. K. Zhang, Z. G. Fang, Z. Y. Hu, and Z. W. Wei. "A Microfluidic Chip for CTC Whole Genome Sequencing." In 2019 IEEE 32nd International Conference on Micro Electro Mechanical Systems (MEMS). IEEE, 2019. http://dx.doi.org/10.1109/memsys.2019.8870769.

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Atkinson, Neil, Blanche Griffin, Robert Robinson, and Jane Runnacles. "16 5 whole metres of heart-sinking genome sequencing." In Royal College of Paediatrics and Child Health, Abstracts of the RCPCH Conference, Glasgow, 23–25 May 2023. BMJ Publishing Group Ltd and Royal College of Paediatrics and Child Health, 2023. http://dx.doi.org/10.1136/archdischild-2023-rcpch.607.

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Vazquez, Vinicius L., Adriane Evangelista, Henrique C. Silveira, et al. "Abstract 3386: Brazilian melanoma genome project: mutational landscape based on whole-genome sequencing." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-3386.

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Reports on the topic "Whole genome sequencing PacBio"

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Walsh, Tom, and Mary-Claire King. Whole Genome Sequencing of High-Risk Families to Identify New Mutational Mechanisms of Breast Cancer Predisposition. Defense Technical Information Center, 2014. http://dx.doi.org/10.21236/ada613072.

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Sun, Jielin. Identification of Novel Inherited Genetic Markers for Aggressive PCa in European and African Americans Using Whole Genome Sequencing. Defense Technical Information Center, 2014. http://dx.doi.org/10.21236/ada612747.

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Sun, Jielin, and Siqun L. Zheng. Identification of Novel, Inherited Genetic Markers for Aggressive PCa in European and African Americans Using Whole Genome Sequencing. Defense Technical Information Center, 2013. http://dx.doi.org/10.21236/ada612827.

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Sun, Jielin. Identification of Novel, Inherited Genetic Markers for Aggressive PCa in European and African Americans Using Whole Genome Sequencing. Defense Technical Information Center, 2012. http://dx.doi.org/10.21236/ada574325.

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McCarthy, Noel, Eileen Taylor, Martin Maiden, et al. Enhanced molecular-based (MLST/whole genome) surveillance and source attribution of Campylobacter infections in the UK. Food Standards Agency, 2021. http://dx.doi.org/10.46756/sci.fsa.ksj135.

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This human campylobacteriosis sentinel surveillance project was based at two sites in Oxfordshire and North East England chosen (i) to be representative of the English population on the Office for National Statistics urban-rural classification and (ii) to provide continuity with genetic surveillance started in Oxfordshire in October 2003. Between October 2015 and September 2018 epidemiological questionnaires and genome sequencing of isolates from human cases was accompanied by sampling and genome sequencing of isolates from possible food animal sources. The principal aim was to estimate the co
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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule se
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Mishra, Shivangi, Steve Crookes, and Srijak Bhatnagar. Muskoxen and Genomics in the Community (MAGIC) Workshop: A Detailed Report. Arctic Institute of North America, 2025. https://doi.org/10.33174/aina2025tr04magicreport.

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This report provides an overview and summary of the Muskoxen and Genomics in the Community (MAGIC) Workshop held in Cambridge Bay, Nunavut in January 2024. The workshop brought together Inuit Knowledge Holders, hunters, and decision makers, scientists from a variety of disciplines and international participants. Together the group considered Inuit knowledge of and priorities for muskoxen, scientific knowledge and gaps, and the potential for genomic and DNA-based tools to help secure a viable future for muskoxen in the face of multiple climate-related stressors. Indigenous Knowledge combined wi
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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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Shpigel, Nahum Y., Ynte Schukken, and Ilan Rosenshine. Identification of genes involved in virulence of Escherichia coli mastitis by signature tagged mutagenesis. United States Department of Agriculture, 2014. http://dx.doi.org/10.32747/2014.7699853.bard.

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Mastitis, an inflammatory response of the mammary tissue to invading pathogenic bacteria, is the largest health problem in the dairy industry and is responsible for multibillion dollar economic losses. E. coli are a leading cause of acute mastitis in dairy animals worldwide and certainly in Israel and North America. The species E. coli comprises a highly heterogeneous group of pathogens, some of which are commensal residents of the gut, infecting the mammary gland after contamination of the teat skin from the environment. As compared to other gut microflora, mammary pathogenic E. coli (MPEC) m
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Savaldi-Goldstein, Sigal, and Todd C. Mockler. Precise Mapping of Growth Hormone Effects by Cell-Specific Gene Activation Response. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7699849.bard.

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Plant yield largely depends on a complex interplay and feedback mechanisms of distinct hormonal pathways. Over the past decade great progress has been made in elucidating the global molecular mechanisms by which each hormone is produced and perceived. However, our knowledge of how interactions between hormonal pathways are spatially and temporally regulated remains rudimentary. For example, we have demonstrated that although the BR receptor BRI1 is widely expressed, the perception of BRs in epidermal cells is sufficient to control whole-organ growth. Supported by additional recent works, it is
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