Relevant bibliographies by topics / Chimeric transcripts

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

Academic literature on the topic 'Chimeric transcripts'

Author: Grafiati
Published: 4 June 2021
Last updated: 6 July 2024

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Journal articles on the topic "Chimeric transcripts"

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Lalani, Samir, Sehajroop Gadh, Justin Elfman, Sandeep Singh, and Hui Li. "Abstract 4351: Differential dependency mapping of chimeric RNAs across cancer reveals a new landscape of functional fusion transcripts." Cancer Research 84, no. 6_Supplement (March 22, 2024): 4351. http://dx.doi.org/10.1158/1538-7445.am2024-4351.

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Abstract Chimeric RNAs are RNA transcripts containing sequences originating from multiple distinct genetic loci and can form through a variety of mechanisms such as DNA rearrangement, cis-splicing of adjacent genes, or RNA trans-splicing. Chimeras have long been known to be a hallmark of cancer and due to their unique properties are promising targets for precision medicine. Appropriately, fusion proteins transcribed from chimeras such as BCR-ABL1 and TPM3-NTRK1 have been shown to be effective targets. Due to these past successes, there exists an opportunity to identify new chimeras as therapeu
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Rowsell, Joanna, Renata da Silva Camargo, William B. Langdon, Maria A. Stalteri, and Andrew P. Harrison. "Uncovering the expression patterns of chimeric transcripts using surveys of Affymetrix GeneChips." Journal of Integrative Bioinformatics 7, no. 3 (December 1, 2010): 300–330. http://dx.doi.org/10.1515/jib-2010-137.

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Summary Background: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras.Results: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression
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Amundarain, Ane, Luis Vitores Valcárcel, Raquel Ordoñez, Leire Garate, Estíbaliz Miranda, Xabier Cendoya, Maria Jose Calasanz, et al. "Lncrnas As New Partners of Novel Chimeric Transcripts in Multiple Myeloma." Blood 134, Supplement_1 (November 13, 2019): 4356. http://dx.doi.org/10.1182/blood-2019-122568.

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Deregulation of long non-coding RNAs (lncRNAs) is a common feature of cancer, including Multiple Myeloma (MM). In our previous studies, we detected 11,495 and 40,511 previously non-annotated lncRNAs during normal humoral immune response and MM patient samples, respectively. These results support an important role for the lncRNAs transcriptome in this hematological malignancy. lncRNAs are genes that differ from coding genes in that they do not give rise to a protein. Nevertheless, lncRNA could undergo the same genetic alterations as coding genes. In this study, we hypothesize that lncRNAs can b
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Alterman, R. B., C. Sprecher, R. Graves, W. F. Marzluff, and A. I. Skoultchi. "Regulated expression of a chimeric histone gene introduced into mouse fibroblasts." Molecular and Cellular Biology 5, no. 9 (September 1985): 2316–24. http://dx.doi.org/10.1128/mcb.5.9.2316-2324.1985.

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The regulated expression of a mouse histone gene was studied by DNA-mediated gene transfer. A chimeric H3 histone gene was constructed by fusing the 5' and 3' portions of two different mouse H3 histone genes. Transfection of the chimeric gene into mouse fibroblasts resulted in the production of chimeric mRNA at levels nearly equal to that of the total endogenous H3 histone mRNAs. Most chimeric RNA transcripts had correct 5' and 3' termini, and the chimeric mRNA was translated into an H3.1 protein that accumulated in the nucleus of the transfected cells. Expression of the chimeric gene was stud
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Alterman, R. B., C. Sprecher, R. Graves, W. F. Marzluff, and A. I. Skoultchi. "Regulated expression of a chimeric histone gene introduced into mouse fibroblasts." Molecular and Cellular Biology 5, no. 9 (September 1985): 2316–24. http://dx.doi.org/10.1128/mcb.5.9.2316.

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The regulated expression of a mouse histone gene was studied by DNA-mediated gene transfer. A chimeric H3 histone gene was constructed by fusing the 5' and 3' portions of two different mouse H3 histone genes. Transfection of the chimeric gene into mouse fibroblasts resulted in the production of chimeric mRNA at levels nearly equal to that of the total endogenous H3 histone mRNAs. Most chimeric RNA transcripts had correct 5' and 3' termini, and the chimeric mRNA was translated into an H3.1 protein that accumulated in the nucleus of the transfected cells. Expression of the chimeric gene was stud
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Claxton, DF, P. Liu, HB Hsu, P. Marlton, J. Hester, F. Collins, AB Deisseroth, JD Rowley, and MJ Siciliano. "Detection of fusion transcripts generated by the inversion 16 chromosome in acute myelogenous leukemia." Blood 83, no. 7 (April 1, 1994): 1750–56. http://dx.doi.org/10.1182/blood.v83.7.1750.1750.

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Abstract Pericentric inversion of chromosome 16 [inv(16)(p13q22)] and the related t(16;16)(p13;q22) are seen in a subset of acute myelogenous leukemia (AML) phenotypically and prognostically differing from other cases. We have recently shown that inv(16) results in fusion of CBFB/PEBP2B, a gene encoded at 16q22 to MYH11, a smooth muscle myosin heavy chain gene encoded at 16p13. Chimeric transcripts consisting of upstream CBFB fused to downstream MYH11 coding sequences result from this fusion. In this study we have examined a series of 37 of these cases using reverse transcriptase-polymerase ch
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Claxton, DF, P. Liu, HB Hsu, P. Marlton, J. Hester, F. Collins, AB Deisseroth, JD Rowley, and MJ Siciliano. "Detection of fusion transcripts generated by the inversion 16 chromosome in acute myelogenous leukemia." Blood 83, no. 7 (April 1, 1994): 1750–56. http://dx.doi.org/10.1182/blood.v83.7.1750.bloodjournal8371750.

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Pericentric inversion of chromosome 16 [inv(16)(p13q22)] and the related t(16;16)(p13;q22) are seen in a subset of acute myelogenous leukemia (AML) phenotypically and prognostically differing from other cases. We have recently shown that inv(16) results in fusion of CBFB/PEBP2B, a gene encoded at 16q22 to MYH11, a smooth muscle myosin heavy chain gene encoded at 16p13. Chimeric transcripts consisting of upstream CBFB fused to downstream MYH11 coding sequences result from this fusion. In this study we have examined a series of 37 of these cases using reverse transcriptase-polymerase chain react
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Fujieda, S., Y. Q. Lin, A. Saxon, and K. Zhang. "Multiple types of chimeric germ-line Ig heavy chain transcripts in human B cells: evidence for trans-splicing of human Ig RNA." Journal of Immunology 157, no. 8 (October 15, 1996): 3450–59. http://dx.doi.org/10.4049/jimmunol.157.8.3450.

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Abstract Germ-line transcripts from Ig heavy chain loci precede the occurrence of isotype switching and are thought to play an important though still controversial role in Ig class switching. In this study, we employed a reverse transcriptase-PCR approach to detect human chimeric Ig germ-line mRNA transcripts. Multiple types of chimeric Ig germ-line transcripts (Imu-Cepsilon, Iepsilon-Cmu, Imu-Cgamma4, Igamma-Cmu, Igamma-Cepsilon, Iepsilon-Cgamma, and Igamma4-Calpha1 transcripts) were readily detected in human B cells stimulated with IL-4 alone. Sequence analysis revealed that all of these chi
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Zoubek, A., B. Dockhorn-Dworniczak, O. Delattre, H. Christiansen, F. Niggli, I. Gatterer-Menz, T. L. Smith, H. Jürgens, H. Gadner, and H. Kovar. "Does expression of different EWS chimeric transcripts define clinically distinct risk groups of Ewing tumor patients?" Journal of Clinical Oncology 14, no. 4 (April 1996): 1245–51. http://dx.doi.org/10.1200/jco.1996.14.4.1245.

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PURPOSE Because of the high heterogeneity of EWS gene fusions with FLI1 and ERG genes due to variable chromosomal breakpoint locations in Ewing tumors (ET) (14 different chimeric transcripts identified so far), we evaluated the clinical impact of the expression of diverse fusion transcripts in ET patients. PATIENTS AND METHODS In a European multicenter study, 147 ET were analyzed by reverse-transcriptase polymerase chain reaction (RT-PCR) and the molecular data statistically compared with all clinical data available. RESULTS Most tumors expressed chimeric transcripts with fusion of EWS exon 7
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Katsuya, Hiroo, Paola Miyazato, Saiful Islam, Benjy Jek Yang Tan, Yuki Inada, Misaki Matsuo, Takaharu Ueno, et al. "The Presence and Possible Role of Virus-Host Chimeric Transcripts in Adult T-Cell Leukemia-Lymphoma." Blood 134, Supplement_1 (November 13, 2019): 2779. http://dx.doi.org/10.1182/blood-2019-124361.

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The retrovirus human T-cell leukemia virus type 1 (HTLV-1) integrates into the host genome and persists for the lifetime of the host. There are tens of thousands of different infected clones in a HTLV-1 carrier and each clone can be identified by its unique viral integration site. Only about 5% of infected people develop the hematological malignancy, adult T-cell leukemia-lymphoma (ATL). However, it is unclear how a certain infected clone, among various different ones, is selected as a malignant clone. It has been reported that viral integration alters transcripts of the cellular host genes ad
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Dissertations / Theses on the topic "Chimeric transcripts"

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Xu, Hang. "Investigating the activity of L1 chimeric transcripts in human cancer." Thesis, University of Nottingham, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.718854.

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Transposable elements (TEs) are repetitive sequences that occupy 45% to 65% of the human genome. TEs can transfer themselves to different locations in a host genome and they have had a considerable impact on the structural and functional evolution of genomes and transcriptomes. TE mobilisation ac­tivity can have deleterious consequences and de novo insertions have been implicated in genetic disorders, and acquired diseases such as cancer. A vari­ety of mechanisms have evolved to prevent TE mobilisation in somatic cells spanning from epigenetic mechanisms that prevent transcription from TE pro­
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Thomson, Gabrielle Anne Biotechnology &amp Biomolecular Sciences Faculty of Science UNSW. "Retroelements as controlling elements in mammals." Awarded by:University of New South Wales. Biotechnology and Biomolecular Sciences, 2006. http://handle.unsw.edu.au/1959.4/26203.

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Retroelements are genomic parasites which make up ~42% of the human genome and 38% of the mouse genome. Most are degenerate, but a large number have relatively intact promoter elements, suggesting that they are capable of transcription. Transcriptionally active retroelements can perturb normal transcription units in their vicinity through a variety of mechanisms, leading to phenotypic effects and in some cases disease. This phenomenon of transcriptional interference has been observed in organisms as diverse as maize, Drosophila, and the mouse. We analysed the extent of retroelement transcr
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Herai, Roberto Hirochi. "Metodologias de bioinformatica para detecção e estudo de sequencias repetitivas em loci genicos de transcritos quimericos." [s.n.], 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/317152.

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Orientador: Michel Eduardo Beleza Yamagishi<br>Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia<br>Made available in DSpace on 2018-08-15T17:21:19Z (GMT). No. of bitstreams: 1 Herai_RobertoHirochi_D.pdf: 3625854 bytes, checksum: 3f19d10a9b0bb7f77091197cd302f66e (MD5) Previous issue date: 2010<br>Resumo: A grande quantidade de dados biológicos gerados recentemente permitiu verificar que os genomas são repletos de seqüências repetitivas (SR), como microsatélites e elementos genéticos móveis, altamente improváveis de ocorrer estatisticamente se os genomas fossem gerad
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Pinson, Marie-Elisa. "Etude de l'impact de la dérégulation transcriptionnelle liée à des transcrits chimères initiés à partir d'éléments répétés de type LINE-1 dans la tumorigenèse gliale." Thesis, Université Clermont Auvergne‎ (2017-2020), 2017. http://www.theses.fr/2017CLFAS006/document.

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Les éléments LINE-1 (L1) sont une classe abondante de rétrotransposons représentant 17% du génome humain. La région 5’UTR des sous-familles les plus récentes (L1PA1 à 6) contient un promoteur bidirectionnel contenant non seulement un promoteur sens interne mais aussi un promoteur antisens, nommé ASP. Dans les cellules normales, l’un des mécanismes impliqués dans la régulation du promoteur de L1 est la méthylation ADN. Dans les tumeurs, une hypométhylation globale affectant notamment les L1 est observée. Il a été mis en évidence que cette hypométhylation pouvait induire la transcription, à part
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Mir, Ashfaq Ali. "Variations structurales du génome et du transcriptome humains induites par les rétrotransposons LINE-1." Thesis, Nice, 2015. http://www.theses.fr/2015NICE4106.

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Les rétrotransposons sont des éléments génétiques mobiles qui constituent presque la moitié de notre génome. Seule la sous-famille L1HS appartenant à la classe des Long Interspersed Element-1(LINE-1 ou L1) a gardé une capacité de mobilité autonome chez l’Homme. Leur mobilisation dans la lignée germinale, mais Aussi dans certains tissus somatiques, contribue à la diversité du génome humain ainsi qu’à certaines maladies comme le cancer. Ainsi, de nouvelles copies de L1 peuvent directement s'intégrer dans des séquences codantes ou régulatrices, et altérer leur fonction. De plus, les séquences L1
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Mir, Ashfaq Ali. "Variations structurales du génome et du transcriptome humains induites par les rétrotransposons LINE-1." Electronic Thesis or Diss., Nice, 2015. http://theses.unice.fr/2015NICE4106.

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Les rétrotransposons sont des éléments génétiques mobiles qui constituent presque la moitié de notre génome. Seule la sous-famille L1HS appartenant à la classe des Long Interspersed Element-1(LINE-1 ou L1) a gardé une capacité de mobilité autonome chez l’Homme. Leur mobilisation dans la lignée germinale, mais Aussi dans certains tissus somatiques, contribue à la diversité du génome humain ainsi qu’à certaines maladies comme le cancer. Ainsi, de nouvelles copies de L1 peuvent directement s'intégrer dans des séquences codantes ou régulatrices, et altérer leur fonction. De plus, les séquences L1
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Mittal, Vinay K. "Detection and characterization of gene-fusions in breast and ovarian cancer using high-throughput sequencing." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/54014.

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Gene-fusions are a prevalent class of genetic variants that are often employed as cancer biomarkers and therapeutic targets. In recent years, high-throughput sequencing of the cellular genome and transcriptome have emerged as a promising approach for the investigation of gene-fusions at the DNA and RNA level. Although, large volumes of sequencing data and complexity of gene-fusion structures presents unique computational challenges. This dissertation describes research that first addresses the bioinformatics challenges associated with the analysis of the massive volumes of sequencing data by d
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Book chapters on the topic "Chimeric transcripts"

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Chu, Hsueh-Ting. "Transcriptome Sequencing for the Detection of Chimeric Transcripts." In Methods in Molecular Biology, 239–53. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3204-7_14.

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MacDiarmid, Robin M. "Chimeric, Infectious, and Stable Virus Transcripts to Study RNA Silencing in “Dark Green” Islands." In Methods in Molecular Biology, 299–308. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-882-5_20.

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Huppi, K. "The Generation of Pvt-1/Ck Chimeric Transcripts as an Assay for Chromosomal Translocations in Mouse Plasmacytomas." In Current Topics in Microbiology and Immunology, 399–404. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-642-79275-5_46.

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Koller, Barbara, Etienne Roux, Paul-Etienne Montandon, and Erhard Stutz. "A Chimeric Transcript Containing a 16S rRNA and a Potential mRNA in Chloro-Plasts of Euglena Gracilis." In Plant Molecular Biology, 652. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4615-7598-6_86.

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"Chimeric Transcripts." In Encyclopedia of Cancer, 814. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-16483-5_1097.

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Panovska-Stavridis, Irina. "Molecular Monitoring in Acute Myeloid Leukemia Patients Undergoing Matched Unrelated Donor: Hematopoietic Stem Cell Transplantation." In Acute Leukemias [Working Title]. IntechOpen, 2020. http://dx.doi.org/10.5772/intechopen.94830.

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Minimal residual disease (MRD) in acute myeloid leukemia (AML) is a complex, multi-modality assessment and much as its clinical implications at different points are extensively studied, it remains even now a challenging area. It is the disease biology that governs the modality of MRD assessment; in patients harboring specific molecular targets, high sensitivity techniques can be applied. In AML patients undergoing allogenic hematopoietic stem cell transplantation (alloHSCT), relapse in considered as leading cause for treatment failure. In post-transplant setting, regular MRD status assessment enables to identify patients at risk of impending relapse when early therapeutic intervention may be beneficent. We analyzed data of AML patients who underwent matched unrelated donor (MUD) HSCT since the introduction of this procedure in the Republic of North Macedonia. Chimeric fusion transcripts were identified in three patients; two of them positive for RUNX-RUNX1T1 transcript and one for CBFB-MYH11. One patient harbored mutation in the transcription factor CCAAT/enhancer binding protein α (CEBPA). Post-transplant MRD kinetics was measured by quantitative polymerase chain or multiplex fluorescent-PCR every three months after the transplantation during the first two years after the transplant. MRD negativity was achieved in three patients by the sixth month of HSCT, who were pre-transplant MRD positive. They sustained hematological and molecular remission for 19, 9 and 7 months, respectively. The forth patient died due to transplant-related complication. Our experience suggests, when molecularly-defined AML patients undergo HSCT, regular MRD monitoring helps predict impending relapse and direct future treatment strategies.
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Oflaz, Ofcan. "Mechanism of HIV-1 Reverse Transcriptase Inhibitors." In Current Researches in Health Sciences-IV. Özgür Yayınları, 2023. http://dx.doi.org/10.58830/ozgur.pub387.c1596.

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The HIV life cycle involves a series of intricate steps: viral entry, reverse transcription, integration into the host genome, transcription and translation, assembly, budding, maturation, and release. The reverse transcriptase (RT) enzyme, a pivotal player in this cycle, facilitates the conversion of viral RNA into double-stranded DNA during reverse transcription. Comprising polymerase and RNase H domains, RT's structure is crucial for its multifunctional role. The polymerase domain synthesizes a complementary DNA strand, while the RNase H domain degrades the RNA template. This enzymatic process results in the formation of a provirus integrated into the host cell's genome. Inhibitors targeting RT, classified into non-nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTIs), disrupt this critical step in the HIV life cycle. NNRTIs act allosterically to inhibit RT's activity, while NRTIs function as chain terminators during DNA synthesis, collectively impeding the virus's replication and offering crucial therapeutic interventions in managing HIV infections. Our book chapter covers the fundamental life cycle of HIV, the working mechanism of the RT enzyme, and the effects of inhibitors on this mechanism. The enzyme structure has been visualized using the UCSF Chimera program.&#x0D;
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Conference papers on the topic "Chimeric transcripts"

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Jian-lei Gu, Yao Lu, Shi-yi Liu, Cong Liu, and Hui Lu. "A novel scoring estimator to screening for oncogenic chimeric transcripts in cancer transcriptome sequencing." In 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2016. http://dx.doi.org/10.1109/bibm.2016.7822792.

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Haines, Katherine, Angshumoy Roy, Linghua Wang, Pavel Sumazin, Kyle R. Covington, Donna M. Muzny, Vijetha Kumar, et al. "Abstract A33: Discovery of chimeric transcripts involving APC and TERT in pediatric HCC by RNA sequencing." In Abstracts: AACR Special Conference: Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; November 9-12, 2015; Fort Lauderdale, Florida. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.pedca15-a33.

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Sarver, Nava, and George A. Ricca. "SUSTAINED EXPRESSION OF FULL LENGTH AND VARIANT RECOMBINANT FACTOR VIII IN GENETICALLY ENGINEERED CELLS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643875.

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A major effort is presently underway to provide factor VIII (FVIII) in a form free of viral pathogens via a recombinant DNA approach. We have constructed two chimeric FVIII cDNA vectors based on the bovine papillomavirus mammalian expression system. The first vector (FVIII) contained a full length FVIII cDNA; the second vector (AFVIII) contained a cDNA insert with an extensive deletion, corresponding to amino acid residues 747 to 1560 in the region encoding the "B" domain. This internal region is removed during activation of the parental FVIII molecule and is believed not to be required for co
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Гордеев, Александр Андреевич, Елена Владимировна Четверина, Марина Витальевна Фалалеева, and Александр Борисович Четверин. "OVERCOMING FALSE POSITIVES OF REVERSE TRANSCRIPTION AT THE DETECTION OF CHIMERIC RNAS." In Высокие технологии и инновации в науке: сборник избранных статей Международной научной конференции (Санкт-Петербург, Январь 2021). Crossref, 2021. http://dx.doi.org/10.37539/vt189.2021.69.97.008.

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Работа посвящена исследованию формирования ложных химерных кДНК в результате смены матриц обратной транскриптазой. Показано, что, изменяя ряд параметров реакции обратной транскрипции, можно существенно уменьшить частоту ложноположительных результатов при выявлении истинных химерных РНК. Полученные результаты позволяют улучшить качество анализа транскриптомов и диагностики заболеваний, ассоциированных с образованием химерных РНК. This work is aimed at the study of formation of false chimeric cDNA as a result of template switch by reverse transcriptase. It is shown that by manipulating a number
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Abate, F., A. Acquaviva, E. Ficarra, G. Paciello, E. Macii, A. Ferrarini, M. Delledonne, S. Soverini, and G. Martinelli. "A novel framework for chimeric transcript detection based on accurate gene fusion model." In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). IEEE, 2011. http://dx.doi.org/10.1109/bibmw.2011.6112352.

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Azmi, Muhammad Bilal. "In Silico Basis to Understand the Molecular Interaction of Human NNATGene With Therapeutic Compounds of Anorexia Nervosa." In INTERNATIONAL CONFERENCE ON BIOLOGICAL RESEARCH AND APPLIED SCIENCE. Jinnah University for Women, Karachi,Pakistan, 2022. http://dx.doi.org/10.37962/ibras/2022/1-2.

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Introduction: Anorexia nervosa (AN)– a perplexing heritable, psychiatric eating disorder condition characterized by low body weight. The prevalence of AN is found to be high in younger age adults with a raised mortality rate. Genetic studies have been insufficient in identifying the role of specific genes that predispose an individual to AN. Objectives: The objective was to explore the role of NNAT (neuronatin) gene variants and its structure based molecular interactions with therapeutic compounds of AN. To investigate the role of structural missense pathogenic variants (SNPs: single nucleotid
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