Searching journal content for articles similar to Mahmoud et al. 35 (4): 545.

Displaying results 1-10 of 13

For checked items

view abstracts
download to citation manager

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
Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
....41 0.66 (SR) short-read assembly; (LR) long-read assembly; (OM) optical mapping. aThe SR +OM and LR +OM assemblies were generated via OM-assisted hybrid scaffolding. bOM_cc is an OM assembly of a carrion crow. Weissensteiner et al. 698 Genome Research www..org We further generated single...
Select this article
Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
...level of isoform diversity that creates new analytical challenges (Monzó et al. 2025). Finally, a Hitchhiker's Guide to long-read genomic analysis reviews the development of novel bioinformatic tools tailored to LRS data analysis (Mahmoud et al. 2025).The growing maturity and applicability of LRS...
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
...using long-read Hi-C technology (Garg 2023) or statistical approaches (Brunette et al. 2024) to alleviate this issue. Nevertheless, a significant gap remains in the availability of computational pipelines tailored for comprehensive downstream analysis of reordered cancer data relative...
Select this article
Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
...sequencing is a viable alternative to HiFi sequencing for de novo assembly, and provides a multirun single-instrument solution for the reconstruction of complete s.Recently, long-read sequencing has revolutionized assembly, and the combination of long and accurate circular consensus sequencing (Wenger et al...
Select this article
Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...of the softshell turtles R. swinhoei (Ren et al. 2022) and P. cantorii (Liu et al. 2023), also produced by long-read sequencing (Supplemental Fig. S1B). Likewise, GC-rich microchromosomic regions were underrepresented in the Staurotypus and Apalone assemblies, which include portions of the sex chromosomes...
OPEN ACCESS ARTICLE
Select this article
Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
..., the structural diversity of MHC genomic organization in macaques remains poorly understood owing to a lack of adequate genomic reference sequences. We used ultralong Oxford Nanopore and high-accuracy Pacific Biosciences (PacBio) HiFi sequences to fully assemble the ∼5.2-Mb M3 haplotype of an MHC...
Select this article
Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
...-molecule real-time (SMRT) long-read sequencing or linked-reads (Zimin et al. 2017). WRC is one of only two conifers outside of the Pinaceae whose sequence has been published. Recently, Scott et al. (2020) reported the first sequence in Cupressaceae, giant sequoia, with a near-chromosome-scale assembly of 8...
OPEN ACCESS ARTICLE
Select this article
Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
- Seung Cho Lee,
- Evan Ernst,
- Benjamin Berube,
- Filipe Borges,
- Jean-Sebastien Parent,
- Paul Ledon,
- Andrea Schorn,
- and Robert A. Martienssen
Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
...RNA (easiRNA) that depend on RNA DEPENDENT RNA POLYMERASE 6 (RDR6). We purified virus-like particles (VLPs) from ddm1 and ddm1rdr6 mutants in which genomic RNA is reverse transcribed into complementary DNA. High-throughput short-read and long-read sequencing of VLP DNA (VLP DNA-seq) revealed a comprehensive...
Select this article
Method: A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
- Marta Tomaszkiewicz,
- Samarth Rangavittal,
- Monika Cechova,
- Rebeca Campos Sanchez,
- Howard W. Fescemyer,
- Robert Harris,
- Danling Ye,
- Patricia C.M. O'Brien,
- Rayan Chikhi,
- Oliver A. Ryder,
- Malcolm A. Ferguson-Smith,
- Paul Medvedev,
- and Kateryna D. Makova
Genome Res. April 2016 26: 530-540; Published in Advance March 2, 2016, doi:10.1101/gr.199448.115
...and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Mahmoud et al. 35 (4): 545.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: