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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...regulation resulting from pathogenic large genomic rearrangements or structural variants (SVs), including deletions, insertions, inversions, and duplications (Shanta et al. 2020). These genomic rearrangements can disturb the normal 3D structure of the and lead to aberrant interactions between chromatin...
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Research: Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
- Kevin Vanneste,
- Guy Baele,
- Steven Maere,
- and Yves Van de Peer
Genome Res. August 2014 24: 1334-1347; Published in Advance May 16, 2014, doi:10.1101/gr.168997.113
...had a higher chance of establishment in the short term.Most explanations for the success of recently formed polyploids focus on their unstable genomic background which, despite most often leading to negative phenotypic effects through chromosomal abnormalities, also can infer the necessary plasticity...
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Perspective: The path to routine use of genomic biomarkers in the cancer clinic
- Paul C. Boutros
Genome Res. October 2015 25: 1508-1513; doi:10.1101/gr.191114.115
...ploidy changes or local chromosomal abnormalities that alter as much as 50% of the (Zack et al. 2013). They can have dozens of genomic rearrangements of various types (Yang et al. 2013). Large-scale sequencing projects like the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...processes of selection on somatic mutations, driving tumor growth through aberrant regulation of the cell cycle. Somatic mutations caused by multiple endogenous and exogenous factors are mostly neutral passengers, with only a few drivers of clonal expansion under strong positive selection. Cancer genomic...
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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
...-Y with the CHM13 reference, along with population variation, clinical variants, and functional genomics data, has created a comprehensive reference for all 24 human chromosomes. The use of the T2T-CHM13 as a reference broadly improves our ability to detect variation in human s. Specifically, T2T-CHM13 improves...
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Research: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123
...TF activity through enhancers to transcriptional activation of specific gene responses. We further investigate mutational and copy number (CN) alterations as genomic aberrations underlying the dysregulation of these key TFs. Finally, we relate GC cell line subtypes to other tissues using models...
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RESOURCE: A Whole-Genome Mouse BAC Microarray With 1-Mb Resolution for Analysis of DNA Copy Number Changes by Array Comparative Genomic Hybridization
- Yeun-Jun Chung,
- Jos Jonkers,
- Hannah Kitson,
- Heike Fiegler,
- Sean Humphray,
- Carol Scott,
- Sarah Hunt,
- Yuejin Yu,
- Ichiko Nishijima,
- Arno Velds,
- Henne Holstege,
- Nigel Carter,
- and Allan Bradley
Genome Res. January 2004 14: 188-196; doi:10.1101/gr.1878804
...and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA Abstract Microarray-basedcomparative genomic hybridization (CGH) has become a powerful methodfor the genome-wide detection of chromosomal imbalances. Although BAC microarrays have been usedfor mouse CGH studies...
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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...in higher eukaryotes, and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets...
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Research: Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors
- J. Keith Killian,
- Lambert C.J. Dorssers,
- Britton Trabert,
- Ad J.M. Gillis,
- Michael B. Cook,
- Yonghong Wang,
- Joshua J. Waterfall,
- Holly Stevenson,
- William I. Smith, Jr.,
- Natalia Noyes,
- Parvathy Retnakumar,
- J. Hans Stoop,
- J. Wolter Oosterhuis,
- Paul S. Meltzer,
- Katherine A. McGlynn,
- and Leendert H.J. Looijenga
Genome Res. November 2016 26: 1490-1504; Published in Advance October 20, 2016, doi:10.1101/gr.201293.115
...aberration (SCNA) analysis for presence of anticipated anomalies (see Methods), typified by tumor-specific gain of the short arm of Chromosome 12, which is independent of subtype histology (Atkin and Baker 1982; Gibas et al. 1986; van Echten et al. 1995). Based on these data, 108 of the 130 assayed tumors...
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Resource: Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes
- Andrea Halaburkova,
- Vincent Cahais,
- Alexei Novoloaca,
- Mariana Gomes da Silva Araujo,
- Rita Khoueiry,
- Akram Ghantous,
- and Zdenko Herceg
Genome Res. October 2020 30: 1517-1532; Published in Advance September 22, 2020, doi:10.1101/gr.268292.120
....05) negatively or positively with expression across tumor samples and chromosomes, so the correlation was not unidirectional (Fig. 3A,C). ERG-specific analysis revealed some ERGs with noticeably high expression aberrations within tumor samples (Fig. 3A). Among them, several ERGs were repeatedly up- or down...
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