Relevant bibliographies by topics / Reduced representation bisulfite sequencing

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

Academic literature on the topic 'Reduced representation bisulfite sequencing'

Author: Grafiati
Published: 3 June 2025
Last updated: 31 July 2025

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Journal articles on the topic "Reduced representation bisulfite sequencing"

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van Gurp, Thomas P., Niels C. A. M. Wagemaker, Björn Wouters, Philippine Vergeer, Joop N. J. Ouborg, and Koen J. F. Verhoeven. "epiGBS: reference-free reduced representation bisulfite sequencing." Nature Methods 13, no. 4 (2016): 322–24. http://dx.doi.org/10.1038/nmeth.3763.

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Tanas, Alexander S., Marina E. Borisova, Ekaterina B. Kuznetsova, et al. "Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing." Epigenomics 9, no. 6 (2017): 833–47. http://dx.doi.org/10.2217/epi-2017-0031.

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Chatterjee, Aniruddha, Euan J. Rodger, Peter A. Stockwell, Robert J. Weeks, and Ian M. Morison. "Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries." Journal of Biomedicine and Biotechnology 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/741542.

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Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform hav
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Chatterjee, Aniruddha, Yuichi Ozaki, Peter A. Stockwell, Julia A. Horsfield, Ian M. Morison, and Shinichi Nakagawa. "Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing." Epigenetics 8, no. 9 (2013): 979–89. http://dx.doi.org/10.4161/epi.25797.

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Chen, Yunshun, Bhupinder Pal, Jane E. Visvader, and Gordon K. Smyth. "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR." F1000Research 6 (November 28, 2017): 2055. http://dx.doi.org/10.12688/f1000research.13196.1.

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Studies in epigenetics have shown that DNA methylation is a key factor in regulating gene expression. Aberrant DNA methylation is often associated with DNA instability, which could lead to development of diseases such as cancer. DNA methylation typically occurs in CpG context. When located in a gene promoter, DNA methylation often acts to repress transcription and gene expression. The most commonly used technology of studying DNA methylation is bisulfite sequencing (BS-seq), which can be used to measure genomewide methylation levels on the single-nucleotide scale. Notably, BS-seq can also be c
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Chen, Yunshun, Bhupinder Pal, Jane E. Visvader, and Gordon K. Smyth. "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR." F1000Research 6 (October 8, 2018): 2055. http://dx.doi.org/10.12688/f1000research.13196.2.

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Cytosine methylation is an important DNA epigenetic modification. In vertebrates, methylation occurs at CpG sites, which are dinucleotides where a cytosine is immediately followed by a guanine in the DNA sequence from 5' to 3'. When located in the promoter region of a gene, DNA methylation is often associated with transcriptional silencing of the gene. Aberrant DNA methylation is associated with the development of various diseases such as cancer. Bisulfite sequencing (BS-seq) is the current "gold-standard" technology for high-resolution profiling of DNA methylation. Reduced representation bisu
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Lee, Yew, Shengnan Jin, Shiwei Duan, et al. "Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples." Biological Procedures Online 16, no. 1 (2014): 1. http://dx.doi.org/10.1186/1480-9222-16-1.

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Meissner, A. "Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis." Nucleic Acids Research 33, no. 18 (2005): 5868–77. http://dx.doi.org/10.1093/nar/gki901.

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Yamane, Junko, Tomoya Mori, Nobuko Taniyama, Kenta Kobayashi, and Wataru Fujibuchi. "Development of Enhanced Reduced Representation Bisulfite Sequencing Method for Single-cell Methylome Analysis." Genomics and Computational Biology 3, no. 2 (2017): 49. http://dx.doi.org/10.18547/gcb.2017.vol3.iss2.e49.

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Single-cell analysis provides molecular signatures to define cell identity. To characterize cell types, DNA methylation patterns are often used as a flag of internal molecular status. There are a few reports of single-cell methylome techniques that involves bisulfite conversion. However, the step often causes DNA fragmentation, which leads to severe PCR substrate reduction. Here we developed a new version of single-cell reduced representation bisulfite sequencing (scRRBS) method to recover more CpG sites to be analysed. Our method succeeded to increase of 4.1 times in sample yield and 1.6 time
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Longtin, Amy, Marina M. Watowich, Baptiste Sadoughi, et al. "Cost-effective solutions for high-throughput enzymatic DNA methylation sequencing." PLOS Genetics 21, no. 5 (2025): e1011667. https://doi.org/10.1371/journal.pgen.1011667.

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Characterizing DNA methylation patterns is important for addressing key questions in evolutionary biology, development, geroscience, and medical genomics. While costs are decreasing, whole-genome DNA methylation profiling remains prohibitively expensive for most population-scale studies, creating a need for cost-effective, reduced representation approaches (i.e., assays that rely on microarrays, enzyme digests, or sequence capture to target a subset of the genome). Most common whole genome and reduced representation techniques rely on bisulfite conversion, which can damage DNA resulting in DNA
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Dissertations / Theses on the topic "Reduced representation bisulfite sequencing"

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Pankin, Artem [Verfasser], and George [Gutachter] Coupland. "Reduced representation sequencing in barley (Hordeum vulgare L.): domestication genomics and rapid gene identification / Artem Pankin ; Gutachter: George Coupland." Köln : Universitäts- und Stadtbibliothek Köln, 2016. http://d-nb.info/1124132430/34.

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SANTO, DEBORA. "The application of reduced-representation sequencing techniques for studying the structure of plant populations: A case study in common bean (Phaseolus vulgaris L.)." Doctoral thesis, Università Politecnica delle Marche, 2018. http://hdl.handle.net/11566/256205.

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The dissertation is comprised of two chapters. The first chapter is a literature review on the application of the two of the most frequently used reduced-representation sequencing techniques: RADseq (RAD sequencing; Restriction-site Associated DNA-sequencing) and GBS (Genotyping-by-Sequencing). Both techniques are based on the use of restriction enzymes and were developed primarily for genome-wide discovery of single-nucleotide polymorphism (SNP) markers. These methods have already been used in hundreds of studies to investigate the genetic diversity of large numbers of individuals under lower
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Cariou, Marie. "Développement et utilisation de marqueurs RADseq pour l'étude de l'impact de Wolbachia sur l'évolution des génomes mitochondriaux chez les Arthropodes." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10092/document.

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La propagation de bactéries intracellulaires invasives peut entrainer celle des génomes mitochondriaux qui leur sont liés génétiquement au sein du cytoplasme. Cette sélection par autostop peut conduire à une réduction de la taille efficace (Ne) pour le génome mitochondrial. Elle peut également favoriser l'introgression d'une mitochondrie introduite dans une espèce suite à une hybridation. Le principal objectif de ma thèse est de quantifier ces différents effets, de manière globale, au moyen d'un large échantillonnage d'Arthropodes de Polynésie française. Les événements d'introgressions mitocho
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Yang, Le. "A Medicago Sativa Draft Genome using Next Generation Sequencing Reads from Reduced Representation Libraries." Thesis, 2012. http://hdl.handle.net/1807/32291.

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Medicago sativa (Alfalfa) is an important agricultural plant for animal forage and nitrogen fixation, and has potential value in ligno-cellulosic energy production. In the quest to understand the plant, I generated a draft genome sequence of M. sativa via two reduced representation sequencing approaches: methylation-dependent filtration, and high CoT filtration. Libraries created from each approach were sequenced on an Illumina next-generation sequencing platform yielding approximately 2.5Gb of raw data. A combination of reference-based genome assembly approaches using the closely related spec
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Young, Carla Jo Logan. "Comparative Genomics of Gossypium spp. through GBS and Candidate Genes – Delving into the Controlling Factors behind Photoperiodic Flowering." Thesis, 2013. http://hdl.handle.net/1969.1/151335.

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Cotton has been a world-wide economic staple in textiles and oil production. There has been a concerted effort for cotton improvement to increase yield and quality to compete with non-natural man-made fibers. Unfortunately, cultivated cotton has limited genetic diversity; therefore finding new marketable traits within cultivated cotton has reached a plateau. To alleviate this problem, traditional breeding programs have been attempting to incorporate practical traits from wild relatives into cultivated lines. This incorporation has presented a new problem: uncultivated cotton hampered by photop
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Book chapters on the topic "Reduced representation bisulfite sequencing"

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Nakabayashi, Kazuhiko, Michihiro Yamamura, Keita Haseagawa, and Kenichiro Hata. "Reduced Representation Bisulfite Sequencing (RRBS)." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2724-2_3.

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Iralu, Nulevino, Dasari Meghanath, Sumiah Wani, Sahar Saleem, and Aflaq Hamid. "Reduced Representation Bisulfite Sequencing (RRBS) for Plant Viruses." In Springer Protocols Handbooks. Springer US, 2025. https://doi.org/10.1007/978-1-0716-4390-7_34.

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Nagarajan, Arvindhan, Christine Roden, and Narendra Wajapeyee. "Reduced Representation Bisulfite Sequencing to Identify Global Alteration of DNA Methylation." In Methods in Molecular Biology. Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0992-6_3.

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Accomando, William P., and Karin B. Michels. "Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size Selection." In Methods in Molecular Biology. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7481-8_8.

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Chatterjee, Aniruddha, Euan J. Rodger, Peter A. Stockwell, Gwenn Le Mée, and Ian M. Morison. "Generating Multiple Base-Resolution DNA Methylomes Using Reduced Representation Bisulfite Sequencing." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6685-1_16.

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Liu, Yong, Alison J. Kriegel, and Mingyu Liang. "Library Preparation for Multiplexed Reduced Representation Bisulfite Sequencing with a Universal Adapter." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9581-3_8.

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Choudhury, Samrat Roy, and Brian A. Walker. "A Rapid and Robust Protocol for Reduced Representation Bisulfite Sequencing in Multiple Myeloma." In Methods in Molecular Biology. Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7865-6_13.

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Ross, Samuel E., and Ozren Bogdanovic. "Generation and Molecular Characterization of Transient tet1/2/3 Knockouts." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1294-1_17.

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Abstract5-methylcytosine (5mC) is a gene-regulatory mark associated with transcriptional repression. 5mC can be erased through the catalytic action of Ten-eleven translocation (TET) methylcytosine dioxygenases (TET1, TET2, TET3), which oxidize 5mC resulting in its removal from the genome. In vertebrates, TET enzymes facilitate DNA demethylation of regulatory regions linked to genes involved in developmental processes. Consequently, TET ablation leads to severe morphological defects and developmental arrest. Here we describe a system that can facilitate the study of relationships between TET en
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Smallwood, Sébastien A., and Gavin Kelsey. "Genome-Wide Analysis of DNA Methylation in Low Cell Numbers by Reduced Representation Bisulfite Sequencing." In Methods in Molecular Biology. Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-011-3_12.

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Perrier, Jean-Philippe, Aurélie Chaulot-Talmon, Francesca Ali, Laurent Schibler, Hélène Jammes, and Hélène Kiefer. "Reduced Representation Bisulfite Sequencing Library Preparation for Sperm DNA Methylation Analyses: Manual and Automated Methods." In Methods in Molecular Biology. Springer US, 2025. https://doi.org/10.1007/978-1-0716-4406-5_36.

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Conference papers on the topic "Reduced representation bisulfite sequencing"

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Fecteau, Ryan E., Helen Moinova, Joseph E. Willis, Omar De la Cruz, Thomas LaFramboise, and Sanford D. Markowitz. "Abstract 3830: Employing reduced representation bisulfite sequencing for biomarker discovery in colorectal cancer." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-3830.

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Van Paemel, Ruben, Andries De Koker, Charlotte Vandeputte, et al. "Abstract B48: Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA." In Abstracts: AACR Special Conference on Advances in Liquid Biopsies; January 13-16, 2020; Miami, FL. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1557-3265.liqbiop20-b48.

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Ashktorab, Hassan, Mohammad Daremipouran, Hamed Rahi, et al. "Abstract 4247: Identification of new hypermethylated candidate genes in colorectal cancer using reduced representation bisulfite next generation sequencing." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-4247.

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Capra, E., B. Lazzari, M. Milanesi, et al. "172. Bos taurus and Bos indicus reduced representation bisulfite sequencing comparison showed high epigenetic variability in Bos subspecies." In World Congress on Genetics Applied to Livestock Production. Wageningen Academic Publishers, 2022. http://dx.doi.org/10.3920/978-90-8686-940-4_172.

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Reports on the topic "Reduced representation bisulfite sequencing"

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Cohen, Yuval, Christopher A. Cullis, and Uri Lavi. Molecular Analyses of Soma-clonal Variation in Date Palm and Banana for Early Identification and Control of Off-types Generation. United States Department of Agriculture, 2010. http://dx.doi.org/10.32747/2010.7592124.bard.

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Date palm (Phoenix dactylifera L.) is the major fruit tree grown in arid areas in the Middle East and North Africa. In the last century, dates were introduced to new regions including the USA. Date palms are traditionally propagated through offshoots. Expansion of modern date palm groves led to the development of Tissue Culture propagation methods that generate a large number of homogenous plants, have no seasonal effect on plant source and provide tools to fight the expansion of date pests and diseases. The disadvantage of this procedure is the occurrence of off-type trees which differ from t
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