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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
...important to this day due to their predictable performance and low costs.More recently, short-read sequencing has gained widespread adoption for cancer research as it enables the -wide identification of alterations, including single-nucleotide variants (SNVs), small insertions and deletions (indels), copy...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...of RT and transcriptomes from independent batches of samples, which obscures the complex coregulation between the epi and transcriptome. Here, we present PARTAGE, a multiomics approach that enables joint profiling of copy number variation (CNV), RT, and gene expression from the same sample, providing...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...to resolve pathogenic alleles within homologous regions, SVs, or STRs. In many cases, the reported SNV is merely in linkage disequilibrium with a more complex causative variant—such as a copy number variant (CNV) or small insertion or deletion (indel) in a paralogous gene or deep intronic rearrangement...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
..., Germany Corresponding authors: pnavarro@pasteur.fr, job.dekker@umassmed.eduAbstractMitotic chromosomes are considered to be universally folded as loop arrays across species and cell types. However, some studies suggest that features of mitotic chromosomes might be cell type– or species-specific. We...
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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
...An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human s Chong Li1,2, Marc Jan Bonder3,4, Sabriya Syed5, Matthew Jensen6,7, Human Genome Structural Variation Consortium (HGSVC), HGSVC Functional Analysis Working Group, Mark B...
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Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
...(Wagner et al. 2022), highlighting the complexity of accurate determination of KIR gene copy numbers (Béziat et al. 2013).The biological and clinical significance of KIR genes is rooted in their involvement in immune-mediated diseases, hematopoietic stem cell and organ transplantation (Boudreau et al...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...) (Supplemental Table S8). As our sequencing and analysis pipeline cannot differentiate between recurrent insertion events and PCR duplicates, we quantified the number of unique insertion sites per gene, unless otherwise noted (Supplemental Tables S9, S10). The nine libraries showed variation in the number...
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Method: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
- Fei Qin,
- Guoshuai Cai,
- Christopher I. Amos,
- and Feifei Xiao
Genome Res. January 2024 34: 85-93; Published in Advance January 30, 2024, doi:10.1101/gr.278098.123
...Markov model to detect copy number variations, was designed for data from array comparative genomic hybridization (aCGH) and high-throughput sequencing (Shah et al. 2006; Ha et al. 2012), although it has been extensively applied in SCS data (https://rdrr.io/bioc/HMMcopy/; Laks et al. 2019). A single...
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Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
- Joshua Lee,
- Elizabeth A. Snell,
- Joanne Brown,
- Charlotte E. Booth,
- Rosamonde E. Banks,
- Daniel J. Turner,
- Naveen S. Vasudev,
- and Dimitris Lagos
Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
...(see Methods and Supplemental Table S1). For each clinical specimen, the same RNA sample was used for DRS and PCS analysis. No significant differences in RNA quality (based on RNA integrity numbers [RINs]) were observed between recurrent and nonrecurrent controls (Supplemental Fig. S1A). An overview...
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Research: Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis
- Brooke Weckselblatt,
- Karen E. Hermetz,
- and M. Katharine Rudd
Genome Res. July 2015 25: 937-947; Published in Advance June 12, 2015, doi:10.1101/gr.191247.115
...and EGL321. Though the copy number changes were relatively minor in these individuals, chromosome banding revealed multiple translocations, so we were not surprised to find additional breakpoints besides those detected by array CGH. On the other hand, WGS does not always reveal additional complexity...

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