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Relevant bibliographies by topics / Whole-transcriptome sequencing

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Journal articles
Dissertations / Theses
Book chapters
Conference papers
Reports

Academic literature on the topic 'Whole-transcriptome sequencing'

Author: Grafiati

Published: 9 March 2023

Last updated: 31 July 2025

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Journal articles on the topic "Whole-transcriptome sequencing"

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Streets, A. M., X. Zhang, C. Cao, et al. "Microfluidic single-cell whole-transcriptome sequencing." Proceedings of the National Academy of Sciences 111, no. 19 (2014): 7048–53. http://dx.doi.org/10.1073/pnas.1402030111.

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Hosokawa, Kohei, Sachiko Kajigaya, Keyvan Keyvanfar, et al. "Whole transcriptome sequencing identifies increasedCXCR2expression in PNH granulocytes." British Journal of Haematology 177, no. 1 (2017): 136–41. http://dx.doi.org/10.1111/bjh.14502.

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Yang, In Seok, and Sangwoo Kim. "Analysis of Whole Transcriptome Sequencing Data: Workflow and Software." Genomics & Informatics 13, no. 4 (2015): 119. http://dx.doi.org/10.5808/gi.2015.13.4.119.

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Petrini, Iacopo, Arun Rajan, Trung Pham, et al. "Whole Genome and Transcriptome Sequencing of a B3 Thymoma." PLoS ONE 8, no. 4 (2013): e60572. http://dx.doi.org/10.1371/journal.pone.0060572.

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Siezen, Roland J., Greer Wilson, and Tilman Todt. "Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays." Microbial Biotechnology 3, no. 2 (2010): 125–30. http://dx.doi.org/10.1111/j.1751-7915.2010.00166.x.

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Ruan, Miaomiao, Jiying Liu, Xueyang Ren, et al. "Whole transcriptome sequencing analyses of DHA treated glioblastoma cells." Journal of the Neurological Sciences 396 (January 2019): 247–53. http://dx.doi.org/10.1016/j.jns.2018.11.027.

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Seliger, Sonja, Verena Geirhos, Torsten Haferlach, et al. "Comprehensive Analysis of MYC Translocations in Multiple Myeloma By Whole Genome Sequencing and Whole Transcriptome Sequencing." Blood 134, Supplement_1 (2019): 1774. http://dx.doi.org/10.1182/blood-2019-124704.

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Background 8q24 translocations leading to overexpression of MYC are an established prognostic marker in multiple myeloma (MM). Currently FISH (fluorescence in situ hybridization) on CD138+ enriched cell population is the standard diagnostic approach to evaluate the presence of 8q24 translocations. Due to the heterogeneity of breakpoints and technical issues the design of FISH probes is challenging and so far no single FISH assay is capable of detecting each translocation. Aims (1) Evaluation of the frequency of 8q24 translocations in MM by whole genome sequencing (WGS). (2) Determination of th

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Mueller, Heiko, Wencke Walter, Manja Meggendorfer, et al. "Can Whole Genome and Whole Transcriptome Sequencing Replace Standard Procedures in CLL Diagnostics?" Blood 142, Supplement 1 (2023): 1912. http://dx.doi.org/10.1182/blood-2023-185732.

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Background: The advantages of genome-wide sequencing approaches over conventional methods in CLL diagnostics are a matter of debate and exact guidelines for the application of next-generation sequencing in a diagnostic context are currently missing. Aim: Compare the accuracy of whole genome sequencing (WGS) and whole transcriptome sequencing (WTS) in determining the presence of point mutations, IGHV mutational status (IGHVms), and chromosomal aberrations to conventional procedures in a clinical setting. Patients and Methods: The cohort comprised 317 CLL patients. Diagnosis was established foll

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Cirulli, Elizabeth T., Abanish Singh, Kevin V. Shianna, et al. "Screening the human exome: a comparison of whole genome and whole transcriptome sequencing." Genome Biology 11, no. 5 (2010): R57. http://dx.doi.org/10.1186/gb-2010-11-5-r57.

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Basu, Gargi D., Kevin Drenner, Audrey Ozols, et al. "Whole exome and transcriptome sequencing of colorectal and pancreatic cancer." Journal of Clinical Oncology 38, no. 15_suppl (2020): e15666-e15666. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e15666.

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e15666 Background: Integration of Whole Exome Sequencing (WES) into clinical cancer therapeutics has revolutionized medicine in recent years. DNA sequencing alone may miss clinically actionable variants or identify aberrations that are not being transcribed. In this study we investigated the utility of integrating DNA and RNA sequencing in clinical samples. Methods: A cohort of 32 patient samples were analyzed by WES and RNA sequencing. Differential expression analysis was performed using a cohort of controls. Pathway analysis was performed using Ingenuity Pathway Analysis. WES and RNA analysi

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Dissertations / Theses on the topic "Whole-transcriptome sequencing"

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Khan, Hamza. "De novo annotation of non-model organisms using whole genome and transcriptome shotgun sequencing." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/60152.

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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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Raykova, Doroteya. "Genetics of Two Mendelian Traits and Validation of Induced Pluripotent Stem Cell (iPSC) Technology for Disease Modeling." Doctoral thesis, Uppsala universitet, Medicinsk genetik och genomik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-246228.

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Novel technologies for genome analysis have provided almost unlimited opportunities to uncover structural gene variants behind human disorders. Whole exome sequencing (WES) is especially useful for understanding rare Mendelian conditions, because it reduces the requirements for a priori clinical data, and can be applied on a small number of patients. However, supporting functional data on the effect of specific gene variants are often required to power these findings. A variety of methods and biological model systems exists for this purpose. Among those, induced pluripotent stem cells (iPSCs),

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BARZAGO, CLAUDIA. "Identification of a new molecular signature in peripheral blood mononuclear cells from patients affected by myasthenia gravis." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2016. http://hdl.handle.net/10281/105298.

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La miastenia grave è una malattia autoimmune T-dipendente mediata da autoanticorpi diretti contro proteine della giunzione neuromuscolare. È caratterizzata da un danno alla trasmissione neuromuscolare che causa affaticamento e debolezza muscolare. In circa l’80% dei pazienti, la malattia è associata alla produzione di autoanticorpi diretti contro il recettore dell’acetilcolina (AChR) localizzato a livello della membrana post-sinaptica della giunzione neuromuscolare. Numerose evidenze sperimentali suggeriscono che il processo autoimmune si sviluppi nel timo; tuttavia, i meccanismi molecolari so

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Burkert, Christian Martin. "Cis-regulation and genetic control of gene expression in neuroblastoma." Doctoral thesis, Humboldt-Universität zu Berlin, 2021. http://dx.doi.org/10.18452/23008.

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Genregulation beeinflusst Phänotypen im Kontext von Gesundheit und Krankheit. In Krebszellen regulieren genetische und epigenetische Faktoren die Genexpression in cis. Das Neuroblastom ist eine Krebserkrankung, die häufig im Kindesalter auftritt. Es ist gekennzeichnet durch eine geringe Anzahl exonischer Mutationen und durch häufige Veränderungen der somatischen Kopienzahl, einschließlich Genamplifikationen auf extrachromosomaler zirkulärer DNA. Bisher ist wenig darüber bekannt, wie lokale genetische und epigenetische Faktoren Gene im Neuroblastom regulieren. In dieser Arbeit kombiniere ich di

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Tan, Yuxiang. "Computational approaches for whole-transcriptome cancer analysis based on RNA sequencing data." Thesis, 2016. https://hdl.handle.net/2144/14502.

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RNA-Seq (Whole Transcriptome Shotgun Sequencing) provides an ideal platform to study the complete set of transcripts for a specific developmental stage or physiological condition. It reveals not only expression-level changes, but also structural changes in the coding sequences, including gene rearrangements. In this dissertation, I present my contributions to the development of computational tools for the robust and efficient analysis of RNA-seq data to support cancer research. To automate the laborious and computationally intensive procedure of RNA-seq data management, I worked on the dev

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Lin, Kuan-Ting, and 林冠廷. "Identification of latent biomarkers in hepatocellular carcinoma by ultra-deep whole-transcriptome sequencing." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/97773695842537346649.

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博士<br>國立陽明大學<br>生物醫學資訊研究所<br>102<br>There is an urgent need to identify biomarkers for hepatocellular carcinoma due to limited treatment options and the poor prognosis of this common lethal disease. Whole-transcriptome shotgun sequencing (RNA-Seq) provides new possibilities for biomarker identification. We sequenced ∼250 million pair-end reads from a pair of adjacent normal and tumor liver samples. With the aid of bioinformatics tools, we determined the transcriptome landscape and sought novel biomarkers by further empirical validations in 55 pairs of adjacent normal and tumor liver samples wi

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Radovich, Milan. "DECODING THE TRANSCRIPTIONAL LANDSCAPE OF TRIPLE-NEGATIVE BREAST CANCER USING NEXT GENERATION WHOLE TRANSCRIPTOME SEQUENCING." Thesis, 2012. http://hdl.handle.net/1805/2745.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>Triple-negative breast cancers (TNBCs) are negative for the expression of estrogen (ER), progesterone (PR), and HER-2 receptors. TNBC accounts for 15% of all breast cancers and results in disproportionally higher mortality compared to ER & HER2-positive tumours. Moreover, there is a paucity of therapies for this subtype of breast cancer resulting primarily from an inadequate understanding of the transcriptional differences that differentiate TNBC from normal breast. To this end, we embarked on a comprehensive examination of the trans

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Lin, Fang-Yu, and 林芳瑜. "Whole Genome Sequencing, Transcriptome Analysis of Acid Response, and Urease Gene Cluster Characterization of Klebsiella pneumoniae CG43." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/72275031070553698724.

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碩士<br>國立清華大學<br>分子醫學研究所<br>101<br>Klebsiella pneumoniae is an important opportunistic pathogen that causes various human diseases such as pneumonia, urinary tract infection, meningitis, bacteremia and septicemia. In Taiwan, K. pneumoniae is the predominant pathogen responsible for pyogenic liver abscess in diabetic patients and K1 and K2 serotypes account for the majority of the isolates. K. pneumoniae CG43 was originally isolated from a patient with pyogenic liver abscess in Taiwan. It is a highly virulent K2 serotype strain. In this study, the whole genome sequence of K. pneumoniae CG43 was

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Chow, Anthony. "Whole Transcriptome Analysis Reveals Established and Novel Associations with TMPRSS2:ERG Fusion in Prostate Cancer." Thesis, 2012. http://hdl.handle.net/1807/33381.

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Shortcomings of current methods of prostate cancer detection draw attention to a need for improved biomarkers. The TMPRSS2:ERG gene fusion leads to the overexpression of ERG, an ETS family transcription factor, and is the most prevalent genetic lesion in prostate cancer, but its clinical utility remains to be defined. Two radical prostatectomy samples were analysed by next-generation whole transcriptome sequencing. The chosen samples differed in fusion gene status, as previously determined by RT-PCR. The involvement of novel and previously reported prostate cancer-related transcripts, Wnt sign

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Book chapters on the topic "Whole-transcriptome sequencing"

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Benjak, Andrej, Claudia Sala, and Ruben C. Hartkoorn. "Whole-Transcriptome Sequencing for High-Resolution Transcriptomic Analysis in Mycobacterium tuberculosis." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2450-9_2.

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Alexander, Thomas B., and Jeremy R. Wang. "Nanopore Whole Transcriptome Sequencing Offers the Potential for Accessible Classification of Pediatric Cancers." In Cancer Detection and Diagnosis. CRC Press, 2025. https://doi.org/10.1201/9781003449942-36.

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Sinjab, Ansam, Reem Daouk, Wassim Abou-Kheir, and Humam Kadara. "Whole Transcriptome Sequencing Analysis of Cancer Stem/Progenitor Cells Obtained from Mouse Lung Adenocarcinomas." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1278-1_15.

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Küçük, Can. "Genomik Ve Uygulamaları." In Moleküler Biyoloji ve Genetik. Türkiye Bilimler Akademisi, 2023. http://dx.doi.org/10.53478/tuba.978-625-8352-48-1.ch09.

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With the proliferation of genomic technology and analysis methods in recent years, groundbreaking developments have occured in topics such as differential diagnosis, prediction of prognosis, or disease follow-up. Genomic methods leading to rapid and simultaneous detection of hereditary and somatic mutations in patient genomes have resulted in faster discovery of novel therapeutic targets. Whole genome sequencing, whole exome sequencing, targeted sequencing as well as whole-transcriptome sequencing take place among the genome analyses methods that are based on next-generation sequencing technol

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M. Alhattab, Dana, Salwa Alshehri, and Fatima Jamali. "Clinical Relevance of Mesenchymal Stromal Cells from Various Sources: Insights into Transcriptome Analysis for Identifying Inherent Potential." In Recent Update on Mesenchymal Stem Cells [Working Title]. IntechOpen, 2023. http://dx.doi.org/10.5772/intechopen.1004004.

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This book chapter provides an in-depth overview of the clinical relevance of mesenchymal stem cells (MSCs) derived from various sources, highlighting the importance of whole transcriptome analysis in revealing their inherent potential. The chapter delves into different sources of MSCs, such as bone marrow, adipose tissue, umbilical cord, and placenta, and compares their respective properties and capabilities. Additionally, it explores the latest advancements in whole transcriptome analysis, including RNA sequencing and microarray analysis, and their applications in MSC research. The aim is to

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Machlowska, Julita, and Ryszard Maciejewski. "Gastric Cancer in the Next-Generation Sequencing Era: Diagnostic and Therapeutic Strategies." In Molecular Diagnostics of Cancer [Working Title]. IntechOpen, 2023. http://dx.doi.org/10.5772/intechopen.1002517.

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Gastric cancer (GC) is one of the most common malignancies and the fourth major cause of cancer-related deaths worldwide. There is growing interest in the role of genetic and epigenetic changes in the development of the disease. Next-generation sequencing (NGS) studies have identified candidate cancer-driving genes in the GC. Whole transcriptome sequencing and whole-genome sequencing analysis is also important methodology in discovering novel changes in GC. Importantly, cancer epigenetics has opened the way to reveal cancer-related genes in epigenetic machinery, including DNA methylation, nucl

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Niranjan, Vidya, Lavanya Chandramouli, Pooja SureshKumar, and Jitendra Kumar. "Recent Advancement on In-Silico Tools for Whole Transcriptome Analysis." In Population Genetics - From DNA to Evolutionary Biology [Working Title]. IntechOpen, 2024. http://dx.doi.org/10.5772/intechopen.114077.

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Delving into the intricate world of transcriptome analysis, this chapter unfolds the story of gene expression in organisms. The classic DNA microarray and RNA-seq methods have long been the pillars, with RNA-seq taking the spotlight for its superior resolution in understanding dynamic aspects. Yet, tools like Hisat2 and DESeq2, while effective, come with the drawback of being time-consuming and reliant on powerful GPUs. The need for quicker, less resource-intensive techniques has sparked a shift toward simpler R and Python-based tools that not only sidestep GPU dependence but also offer enhanc

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Detera-Wadleigh, Sevilla D., Nirmala Akula, and Liping Hou. "Basic Molecular Genetics Concepts and Tools." In Psychiatric Genetics. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780190221973.003.0003.

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Progress in genetics in the last decades has been spurred largely by the Human Genome Project. Successful sequencing of the human genome and genomes of organisms across the evolutionary scale has been achieved. Scientific discoveries and innovations steered the refinement and annotation of sequences, cataloging of variation including SNPs and CNVs, development of fast, precise, high throughput methods and improved bioinformatics and statistical tools. These advances boosted GWAS on large samples identifying multiple susceptibility loci in diverse complex diseases and traits. Exome, whole genom

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Ghosh, Sanatan, Arnab Purohit, Sweta Mahanta, Rituparna Kundu Chaudhuri, and Dipankar Chakraborti. "Molecular Perspectives of Host-Pathogen Interaction in Fusarium-Wilt in Pigeonpea." In Plant-Microbe Interactions: A Comprehensive Review. BENTHAM SCIENCE PUBLISHERS, 2025. https://doi.org/10.2174/9789815324150125010009.

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Pigeonpea (Cajanus cajan (L.) Millspaugh) is the seventh most economically important legume crop in the world, cultivated on 6.09 million hectares of land across the world with 5.01 million tonnes of global productivity. Fusarium udum Butler is responsible for vascular wilt, the most devastating pigeon pea disease throughout the world. Management of Fusarium-wilt through cultural practices is not effective enough, and chemical control methods cause the killing of non-target beneficial soil microorganisms. Biological practices using various antagonistic fungi or microorganisms are found to be m

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Pandya, Nishi, Parth Pandya, and Pragna Parikh. "THE GENOMIC ERA OF INSECT TAXONOMY: BIOTECHNOLOGICAL ADVANCEMENTS." In Futuristic Trends in Biotechnology Volume 3 Book 3. Iterative International Publisher, Selfypage Developers Pvt Ltd, 2024. http://dx.doi.org/10.58532/v3bfbt3p2ch2.

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Insects, characterized by their high diversity and adaptability, play a pivotal role in insect biotechnology, addressing challenges such as identification and pest control. The integration of DNA barcoding, specifically targeting the COI gene, expedites biodiversity documentation and overcomes traditional taxonomy challenges. Biotechnological methods, including PCR and DNA sequencing, revolutionize molecular systematics, allowing for comprehensive gene analysis and a deeper understanding of insect phylogeny. Moreover, Next-generation sequencing (NGS) has transformed molecular taxonomy by enabl

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Conference papers on the topic "Whole-transcriptome sequencing"

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Darabi, Sourat, Andrew Elliott, David R. Braxton, et al. "Abstract 2221: Whole transcriptome sequencing reveals oncogenic fusions in melanoma." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-2221.

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Radovich, Milan, Bradley A. Hancock, Nawal Kassem, et al. "Abstract 4858: Next-generation whole transcriptome sequencing of thymic malignancies." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-4858.

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Mak, Cathy Ka-Yan, Grace Tin-Yan Chung, Kevin Yuk-Lap Yip, et al. "Abstract 3425: Whole-transcriptome analyses of EBV-associated nasopharyngeal carcinoma using next-generation transcriptome sequencing." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-3425.

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Tang, Wei, and Ludmila Prokunina-Olsson. "Abstract 2128: Whole transcriptome sequencing in normal and cancer prostate tissue." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-2128.

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Kwon, Nak-Jung, Woo Chung Lee, Jiwoong Kim, et al. "Abstract 3574: Analysis of whole genome and transcriptome sequencing in single cell." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-3574.

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Kohno, Takashi, Hitoshi Ichikawa, Yasushi Totoki, et al. "Abstract B93: Gene fusions detected by whole transcriptome sequencing of lung adenocarcinoma." In Abstracts: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics--Nov 12-16, 2011; San Francisco, CA. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1535-7163.targ-11-b93.

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Song, Seulki, Hyejoo Park, Daeyoon Kim, et al. "Abstract 145: Comparison of whole transcriptome sequencing immune repertoire sequencing using RNA for tumor milieu analysis." 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.sabcs18-145.

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Song, Seulki, Hyejoo Park, Daeyoon Kim, et al. "Abstract 145: Comparison of whole transcriptome sequencing immune repertoire sequencing using RNA for tumor milieu analysis." 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.am2019-145.

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Duitama, Jorge, Pramod K. Srivastava, and Ion I. Mandoiu. "Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data." In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2011. http://dx.doi.org/10.1109/iccabs.2011.5729949.

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Shen, Yaoqing, Martin R. Jones, Erin Pleasance, et al. "Abstract A184: Clinical application of whole genome and transcriptome sequencing in cancer care." In Abstracts: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; October 26-30, 2017; Philadelphia, PA. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1535-7163.targ-17-a184.

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Reports on the topic "Whole-transcriptome sequencing"

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Ghanim, Murad, Joe Cicero, Judith K. Brown, and Henryk Czosnek. Dissection of Whitefly-geminivirus Interactions at the Transcriptomic, Proteomic and Cellular Levels. United States Department of Agriculture, 2010. http://dx.doi.org/10.32747/2010.7592654.bard.

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Our project focuses on gene expression and proteomics of the whitefly Bemisia tabaci (Gennadius) species complex in relation to the internal anatomy and localization of expressed genes and virions in the whitefly vector, which poses a major constraint to vegetable and fiber production in Israel and the USA. While many biological parameters are known for begomovirus transmission, nothing is known about vector proteins involved in the specific interactions between begomoviruses and their whitefly vectors. Identifying such proteins is expected to lead to the design of novel control methods that i

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Hovav, Ran, Peggy Ozias-Akins, and Scott A. Jackson. The genetics of pod-filling in peanut under water-limiting conditions. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7597923.bard.

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Pod-filling, an important yield-determining stage is strongly influenced by water stress. This is particularly true for peanut (Arachishypogaea), wherein pods are developed underground and are directly affected by the water condition. Pod-filling in peanut has a significant genetic component as well, since genotypes are considerably varied in their pod-fill (PF) and seed-fill (SF) potential. The goals of this research were to: Examine the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Detect global changes in mRNA and metabolites levels that accompany PF and SF. Explo

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