Searching journal content for articles similar to Chaisson and Pevzner 18 (2): 000.

Displaying results 1-10 of 625

For checked items

view abstracts
download to citation manager

Select this article
Method: Accurate short-read alignment through r-index-based pangenome indexing
- Rahul Varki,
- Massimiliano Rossi,
- Eddie Ferro,
- Marco Oliva,
- Erik Garrison,
- Ben Langmead,
- and Christina Boucher
Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
...applying the concept of syncmers (Dutta et al. 2022) or strobemers (Sahlin 2021, 2022) to the context of Moni-align. With further refinement, Moni-align has the potential to enhance both short-read and long-read sequencing applications, broadening the scope of genomic research.MethodsThis section provides...
OPEN ACCESS ARTICLE
Select this article
Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...significantly improved bacterial pathogen genomics, diagnostics, and epidemiology. Despite its high accuracy, short-read sequencing struggles with the complete reconstruction and assembly of extrachromosomal elements such as plasmids. Long-read sequencing with Oxford Nanopore Technologies (ONT) presents...
Select this article
Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...of genetic diversity in microbes, viruses, or even genes.With high-throughput sequencing, we can obtain haplotypes by linking reads that share informative alleles, for example, single-nucleotide polymorphisms (SNPs). Unfortunately, standard de novo short-read or long-read assembly approaches can collapse...
Select this article
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
.... These collaborative efforts have yielded invaluable insights into the molecular mechanisms underlying cancer initiation, progression, and metastasis, uncovering recurring patterns of genomic alterations, novel cancer genes, and pathways. Consequently, short-read sequencing for both tumor and germline is routinely...
OPEN ACCESS ARTICLE
Select this article
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...
Select this article
Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...long-reads and surpassing the capabilities of antibody-based short-read approaches. This technological advance will further our understanding of the role of genetics in determining mRNA modifications.Allele-specific expression (ASE) refers to the differences in gene expression from two alleles...
Select this article
Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
- Nathan Hammond,
- Linda Liao,
- Pun Wai Tong,
- Zena Ng,
- Thuy-Mi P. Nguyen,
- Chandler Ho,
- Yao Yang,
- and Stuart A. Scott
Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
...Fi sequencing was performed on DNA from reference materials and clinical specimen types, and accuracy results were compared to short-read sequencing data. HiFi sequencing recall and precision across Genome in a Bottle (GIAB)-defined non-difficult and difficult genomic regions (high confidence) for SNVs are >99...
Select this article
Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...that occur in linkage disequilibrium (LD), they are expensive to produce, are commonly short (<200 bp), and may lack naturally occurring genetic patterns. In turn, studies of epigenetic variation have exclusively focused on DNA from a single European ancestry individual (Lea et al. 2018; Johnston et al. 2024...
OPEN ACCESS ARTICLE
Select this article
Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...and Keightley 2009; Bergeron et al. 2022). This has enabled mutation rates to be estimated in a wide range of taxa (Lynch et al. 2023; Wang and Obbard 2023), including humans and mice (Ohno 2019). However, the most widely available short-read sequencing technologies only allow inference of the rate and spectrum...
OPEN ACCESS ARTICLE
Select this article
Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
- Niccoló Tesi,
- Alex Salazar,
- Yaran Zhang,
- Sven van der Lee,
- Marc Hulsman,
- Lydian Knoop,
- Sanduni Wijesekera,
- Jana Krizova,
- Anne-Fleur Schneider,
- Maartje Pennings,
- Kristel Sleegers,
- Erik-Jan Kamsteeg,
- Marcel Reinders,
- and Henne Holstege
Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
...-PCR) and Southern blot assays, are time-consuming and limited in detecting TRs within PCR-based boundaries. Short-read sequencing approaches offer an alternative, but their limited read lengths often fail to span repetitive regions effectively. Despite heuristic methods and statistical modeling (Gymrek et al. 2012...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Chaisson and Pevzner 18 (2): 000.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: