Searching journal content for articles similar to Conesa et al. 34 (11): ix.

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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...-to-telomere (T2T) assemblies are revolutionizing our understanding of long-hidden biology “dark matter” such as centromeres, rDNA repeats, inter-haplotype variation, and allele-specific expression (ASE), yet insights into dikaryotic fungi that separate their haploid s into distinct nuclei are limited. Here, we...
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Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
..., are revolutionizing research by providing high-resolution insights into complex and repetitive regions of the human that were previously inaccessible. These advances have been particularly enabling for the comprehensive detection of genomic structural variants (SVs), which is critical for linking genotype...
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Perspective: Realizing the potential of blockchain technologies in genomics
- Halil Ibrahim Ozercan,
- Atalay Mert Ileri,
- Erman Ayday,
- and Can Alkan
Genome Res. September 2018 28: 1255-1263; Published in Advance August 3, 2018, doi:10.1101/gr.207464.116
...calling. Other applications of biological data analysis, such as calculating tertiary structures of RNA and protein molecules, are also computationally infeasible; therefore, they require immense amounts of computation (i.e., NP-complete) (Hart and Istrail 1997; Akutsu 2000).Contemporary genomics research...
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Perspective: Enabling functional genomics with genome engineering
- Isaac B. Hilton and
- Charles A. Gersbach
Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
...and validation methods outside of coding regions will also be extremely useful. Notably, engineering is unique in its ability to perturb regulatory elements in their endogenous genomic context in contrast to other tools, such as RNAi and small molecules that modulate mRNA and protein activity. Large...
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Perspective: The first five years of single-cell cancer genomics and beyond
- Nicholas E. Navin
Genome Res. October 2015 25: 1499-1507; doi:10.1101/gr.191098.115
...study. Single-cell cancer genomics Genome Research 1505 www..org Conclusions and future directions In the first five years since its inception, SCS has already revolutionized our understanding of cancer evolution and diversity. Although initial studies focused mainly on technology development...
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Perspective: Defining cell types and states with single-cell genomics
- Cole Trapnell
Genome Res. October 2015 25: 1491-1498; doi:10.1101/gr.190595.115
...Defining cell types and states with single-cell genomics Cole Trapnell Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA Corresponding author: coletrap@uw.edu Abstract A revolution in cellular measurement...
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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
...immunoprecipitation (ChIP) in 1984 followed by ChIP-qPCR and ChIP-seq, which allowed scientists to probe the full palette of DNA molecules bound by proteins of interest. A ChIP experiment begins by using formaldehyde to chemically cross-link DNA and protein molecules (Das et al. 2004). Nuclei are isolated...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...-of-the-art bioinformatics methods for long-read sequencing.Short-read sequencing revolutionized genomics by providing a fast and cost-effective method for sequencing entire s, establishing it as a cornerstone of modern genomic research (Heather and Chain 2016; Foox et al. 2021). The emergence of long-read sequencing...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge CB10 1SA, United Kingdom Corresponding author: ana.conesa@csic.esAbstractLong-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full...
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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
...years has revolutionized our ability to catalog cancer risk variants and understand the genomic landscape of cancer. Early studies relied on targeted sequencing and microarrays to detect genomic and transcriptomic variations enriched in cancer patients, revealing, for example, the prevalence...
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