Searching journal content for articles similar to Frohman 4 (1): S40.

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  1. Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
    • Ezequiel Calvo-Roitberg,
    • Rachel F. Daniels,
    • and Athma A. Pai
    Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
    ...RNA or cDNA, pass through the pore. In ONT sequencing, the motor protein that facilitates molecular translation is positioned 10–15 nt away from the terminal end, resulting in the final nucleotides being pulled through the pore rapidly as they are released by the enzyme (Fig. 2B). This rapid movement...
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  2. Methods: Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
    • Philipp Kapranov,
    • Jorg Drenkow,
    • Jill Cheng,
    • Jeffrey Long,
    • Gregg Helt,
    • Sujit Dike,
    • and Thomas R. Gingeras
    Genome Res. July 2005 15: 987-997; doi:10.1101/gr.3455305
    ...% of the human and elucidated the structures of several hundred novel transcripts. In this report, we describe a novel combination of techniques including the rapid amplification of cDNA ends (RACE) and tiling array technologies that was used to further characterize transcripts in the human transcriptome...
  3. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...reason for the absence of cirrhosis has been identified, race and family history of HCC are the main risk factors for HCC in the absence of cirrhosis in patients with CHB (Chayanupatkul et al. 2017). Among the patients included in our study, the three male patients without cirrhosis had a family history...
  4. ARTICLE: Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
    • France Denoeud,
    • Philipp Kapranov,
    • Catherine Ucla,
    • Adam Frankish,
    • Robert Castelo,
    • Jorg Drenkow,
    • Julien Lagarde,
    • Tyler Alioto,
    • Caroline Manzano,
    • Jacqueline Chrast,
    • Sujit Dike,
    • Carine Wyss,
    • Charlotte N. Henrichsen,
    • Nancy Holroyd,
    • Mark C. Dickson,
    • Ruth Taylor,
    • Zahra Hance,
    • Sylvain Foissac,
    • Richard M. Myers,
    • Jane Rogers,
    • Tim Hubbard,
    • Jennifer Harrow,
    • Roderic Guigó,
    • Thomas R. Gingeras,
    • Stylianos E. Antonarakis,
    • and Alexandre Reymond
    Genome Res. June 2007 17: 746-759; doi:10.1101/gr.5660607
    ...presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5′ rapid amplification of cDNA ends (RACE) and high-density resolution tiling...
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  5. ARTICLE: Generation of a transcriptional map for a 700-kb region surrounding the polycystic kidney disease type 1 (PKD1) and tuberous sclerosis type 2 (TSC2) disease genes on human chromosome 16p3.3.
    • T C Burn,
    • T D Connors,
    • T J Van Raay,
    • W R Dackowski,
    • J M Millholland,
    • K W Klinger,
    • and G M Landes
    Genome Res. June 1996 6: 525-537; doi:10.1101/gr.6.6.525
    ...and tumors. Genomics 25 : 256 – 263 . Frohman, M.A. Frohman, M.A. 1994 . On beyond classic RACE (rapid amplification of cDNA ends). PCR Methods Applic. 4 : S40 – S58 . Germino, G.G., , Weinstat-Saslow, D. , Himmelbauer, H. , Gillespie, G.A. , Somlo, S. , Wirth, B. , Barton, N. , Harris, K.L. , Frischauf, A...
  6. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...were widely used to quantify transcript levels across the by hybridizing fluorescently labeled cDNA to thousands of predefined DNA probes immobilized on a solid surface. Each probe was designed to be complementary to a specific transcript, allowing its abundance in a sample to be inferred from...
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  7. Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
    • Terence Gall-Duncan,
    • Nozomu Sato,
    • Ryan K.C. Yuen,
    • and Christopher E. Pearson
    Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
    ...expansion in the C9orf72 gene associated with familial amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) (Renton et al. 2011). Massive parallel paired-end sequencing by HiSeq 2000 permitted rapid data collection, but the expanded repeat was identified through manual inspection and realignment...
  8. LETTER: On the origin of new genes in Drosophila
    • Qi Zhou,
    • Guojie Zhang,
    • Yue Zhang,
    • Shiyu Xu,
    • Ruoping Zhao,
    • Zubing Zhan,
    • Xin Li,
    • Yun Ding,
    • Shuang Yang,
    • and Wen Wang
    Genome Res. September 2008 18: 1446-1455; Published in Advance June 11, 2008, doi:10.1101/gr.076588.108
    ...than 8×) sequences of high quality and a relatively short divergence time. We inferred the paralog number in D. melanogaster and D. yakuba after aligning 12,017 D. melanogaster cDNAs to their sequences. Taking both species as reciprocal outgoups, focal genes with extra copies in certain species were...
  9. Letter: 5′-Transducing SVA retrotransposon groups spread efficiently throughout the human genome
    • Annette Damert,
    • Julija Raiz,
    • Axel V. Horn,
    • Johannes Löwer,
    • Hui Wang,
    • Jinchuan Xing,
    • Mark A. Batzer,
    • Roswitha Löwer,
    • and Gerald G. Schumann
    Genome Res. November 2009 19: 1992-2008; Published in Advance August 3, 2009, doi:10.1101/gr.093435.109
    ...culture. More recently a disease-linked L1-mediated 59 transduction event has been reported in mice (Chen et al. 2006). The fact that more than 8% of human SVA elements carry 59 transductions, together with our RT-PCR results and 59-RACE experiments performed in the Kazazian laboratory (Hancks et al. 2009...
  10. PERSPECTIVE: What is a gene, post-ENCODE? History and updated definition
    • Mark B. Gerstein,
    • Can Bruce,
    • Joel S. Rozowsky,
    • Deyou Zheng,
    • Jiang Du,
    • Jan O. Korbel,
    • Olof Emanuelsson,
    • Zhengdong D. Zhang,
    • Sherman Weissman,
    • and Michael Snyder
    Genome Res. June 2007 17: 669-681; doi:10.1101/gr.6339607
    ...genes have alternative TSSs that are sometimes >100 kb upstream of the annotated transcription start site. In particular, Denoeud et al. (2007) performed 5′ rapid amplification of cDNA ends (RACE) on all 399 well-characterized protein-coding loci contained in the ENCODE regions. The RACE primer...
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