Searching journal content for articles similar to Simpson and Durbin 22 (3): 549.

Displaying results 1-10 of 79

For checked items

view abstracts
download to citation manager

Select this article
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
...models of variation, which will require large-scale LRS efforts now underway in several consortia. ONT's ability to efficiently capture these complex variants at scale, as demonstrated by our pipeline, highlights its value in comprehensive genomic studies.Despite these advancements, ONT sequencing still...
Select this article
Method: Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
- Vikram S. Shivakumar and
- Ben Langmead
Genome Res. February 2026 36: 397-404; Published in Advance November 7, 2025, doi:10.1101/gr.280940.125
...:10.1093/bioinformatics/btaf104 ↵Shivakumar VS, Langmead B. 2025. Mumemto: Efficient maximal matching across pans. Genome Biol 26: 169. doi:10.1186/s13059-025-03644-0 ↵Taylor DJ, Eizenga JM, Li Q, Das A, Jenike KM, Kenny EE, Miga KH, Monlong J, McCoy RC, Paten B, et al. 2024. Beyond the human project...
Select this article
Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...carrying a particular mutation in a known risk gene often demonstrate variable phenotypes, suggesting the presence of genetic modifiers. To explore oligogenic causes of CHD without assessing billions of variant combinations, we develop an efficient, simulation-based method to detect gene sets that carry co...
OPEN ACCESS ARTICLE
Select this article
Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...” as a microbial with sufficient genomic variation to be distinguished from other s within the same species. This definition aligns with previous studies (Vicedomini et al. 2021; Liao et al. 2023b), although we acknowledge that the term “strain” may be interpreted differently in traditional taxonomy and other...
OPEN ACCESS ARTICLE
Select this article
Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...is accompanied by the formation of de novo enhancer contacts and activation of MYC, illustrating how structural genomic variants can alter the 3D during oncogenesis. In summary, our findings provide evidence for the loss of organization at multiple scales during breast cancer progression, revealing novel...
Select this article
Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere assembly, phasing, and scaffolding Dmitry Antipov1,4, Mikko Rautiainen2,4, Sergey Nurk3, Brian P. Walenz1, Steven J. Solar1, Adam M. Phillippy1 and Sergey Koren1 1Genome Informatics Section...
OPEN ACCESS ARTICLE
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
...then leverage the length of long reads by finding walks along the PDBG through unitig construction and read-to-graph alignment. We find that devider efficiently resolves haplotypes in a variety of synthetic and real data sets and show its versatility to reveal genomic heterogeneity.MethodsAt a high level...
Select this article
Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
- Jenna Kalleberg,
- Jacob Rissman,
- and Robert D. Schnabel
Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
...impacts when used with non-human species. Here, we use bovine s to assess the limits of using human –trained variant callers, including the allele frequency channel (DV-AF) and joint-caller DeepTrio (DT). Our novel approach, TrioTrain, automates extending DV for diploid species lacking Genome...
OPEN ACCESS ARTICLE
Select this article
Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...-throughput technique known as Hi-C, have greatly advanced the development of 3D genomics (Dekker et al. 2002; Dostie et al. 2006; Lieberman-Aiden et al. 2009). For instance, studies by Dixon et al. (2012) demonstrated that chromosomes encompass numerous chromatin domains spanning tens to hundreds of kilobases. Within...
Select this article
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
...progress, challenges remain in scaling long-read technologies to large populations due to cost, computational complexity, and the lack of tools to facilitate the efficient interpretation of SVs in graphs. This perspective provides a succinct review on the current state of long-read sequencing in genomics...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Simpson and Durbin 22 (3): 549.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: