Searching journal content for articles similar to Helman et al. 24 (7): 1053.

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  1. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...Consortium (ICGC) (Zhang et al. 2019), and the Pan-Cancer Analysis of Whole Genomes (PCAWG) project (The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020) to characterize thousands of cancers across dozens of cancer types. Building on these population-scale efforts, the Catalogue Of Somatic...
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  2. Research: Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types
    • Akihiro Fujimoto,
    • Masashi Fujita,
    • Takanori Hasegawa,
    • Jing Hao Wong,
    • Kazuhiro Maejima,
    • Aya Oku-Sasaki,
    • Kaoru Nakano,
    • Yuichi Shiraishi,
    • Satoru Miyano,
    • Go Yamamoto,
    • Kiwamu Akagi,
    • Seiya Imoto,
    • and Hidewaki Nakagawa
    Genome Res. March 2020 30: 334-346; Published in Advance March 24, 2020, doi:10.1101/gr.255026.119
    ...Genomes Consortium 2020) with our method and compared them against somatic and germline variants detected by the Pan-Cancer Analysis of Whole Genomes (PCAWG) project (The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020). To compare our results with somatic consensus indels from the four...
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  3. Research: Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
    • Pedro G. Ferreira,
    • Pedro Jares,
    • Daniel Rico,
    • Gonzalo Gómez-López,
    • Alejandra Martínez-Trillos,
    • Neus Villamor,
    • Simone Ecker,
    • Abel González-Pérez,
    • David G. Knowles,
    • Jean Monlong,
    • Rory Johnson,
    • Victor Quesada,
    • Sarah Djebali,
    • Panagiotis Papasaikas,
    • Mónica López-Guerra,
    • Dolors Colomer,
    • Cristina Royo,
    • Maite Cazorla,
    • Magda Pinyol,
    • Guillem Clot,
    • Marta Aymerich,
    • Maria Rozman,
    • Marta Kulis,
    • David Tamborero,
    • Anaïs Gouin,
    • Julie Blanc,
    • Marta Gut,
    • Ivo Gut,
    • Xose S. Puente,
    • David G. Pisano,
    • José Ignacio Martin-Subero,
    • Nuria López-Bigas,
    • Armando López-Guillermo,
    • Alfonso Valencia,
    • Carlos López-Otín,
    • Elías Campo,
    • and Roderic Guigó
    Genome Res. February 2014 24: 212-226; Published in Advance November 21, 2013, doi:10.1101/gr.152132.112
    ...behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from...
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  4. Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
    • Yohan An,
    • Ji-Hyun Lee,
    • Joonoh Lim,
    • Jeonghwan Youk,
    • Seongyeol Park,
    • Ji-Hyung Park,
    • Kijong Yi,
    • Taewoo Kim,
    • Chang Hyun Nam,
    • Won Hee Lee,
    • Soo A Oh,
    • Yoo Jin Bae,
    • Thomas M. Klompstra,
    • Haeun Lee,
    • Jinju Han,
    • Junehwak Lee,
    • Jung Woo Park,
    • Jie-Hyun Kim,
    • Hyunki Kim,
    • Hugo Snippert,
    • Bon-Kyoung Koo,
    • and Young Seok Ju
    Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
    ...-associated mutationsIn cancer s, APOBEC-induced localized hypermutation events are frequently observed (Nik-Zainal et al. 2012a; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020). Across the mutations detected in our hGOiA3A and TP53KO-hGOiA3A lines, ∼5% of the 29,650 acquired base substitutions were...
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  5. Research: Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability
    • Keiko Akagi,
    • Jingfeng Li,
    • Tatevik R. Broutian,
    • Hesed Padilla-Nash,
    • Weihong Xiao,
    • Bo Jiang,
    • James W. Rocco,
    • Theodoros N. Teknos,
    • Bhavna Kumar,
    • Danny Wangsa,
    • Dandan He,
    • Thomas Ried,
    • David E. Symer,
    • and Maura L. Gillison
    Genome Res. February 2014 24: 185-199; Published in Advance November 7, 2013, doi:10.1101/gr.164806.113
    ...genomic structural variation in human cancer cell lines and primary tumors. Whole-genome sequencing revealed HPV integrants flanking and bridging extensive host genomic amplifications and rearrangements, including deletions, inversions, and chromosomal translocations. We present a model of “looping...
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