Searching journal content for articles similar to Yoshihama et al. 12 (3): 379.

Displaying results 1-10 of 1356
For checked items
  1. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...RNA-seq) is a specific technique to sequence small RNAs, mostly microRNAs (miRNAs) (Grimson et al. 2007; Ruby et al. 2007). To perform sRNA-seq, a size selection step is introduced, in which cDNA sequences are selected to be in a particular size range. Some sRNA-seq experiments are also coupled with ribosomal RNA (r...
  2. 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
    ...represent the replicates (circle for replicate 1, triangle for replicate 2) The y-axis displays the allele bias ratio obtained from long-read (left), short-read (middle) sequencing, and ribosome profiling (right). The x-axis shows the difference in m6A modification ratios between the two alleles (CAST–B6...
  3. Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
    • Wouter Steyaert,
    • Lydia Sagath,
    • German Demidov,
    • Vicente A. Yépez,
    • Anna Esteve-Codina,
    • Julien Gagneur,
    • Kornelia Ellwanger,
    • Ronny Derks,
    • Marjan Weiss,
    • Amber den Ouden,
    • Simone van den Heuvel,
    • Hilde Swinkels,
    • Nick Zomer,
    • Marloes Steehouwer,
    • Luke O'Gorman,
    • Galuh Astuti,
    • Kornelia Neveling,
    • Rebecca Schüle,
    • Jishu Xu,
    • Matthis Synofzik,
    • Danique Beijer,
    • Holger Hengel,
    • Ludger Schöls,
    • Kristl G. Claeys,
    • Jonathan Baets,
    • Liedewei Van de Vondel,
    • Alessandra Ferlini,
    • Rita Selvatici,
    • Heba Morsy,
    • Marwa Saeed Abd Elmaksoud,
    • Volker Straub,
    • Juliane Müller,
    • Veronica Pini,
    • Luke Perry,
    • Anna Sarkozy,
    • Irina Zaharieva,
    • Francesco Muntoni,
    • Enrico Bugiardini,
    • Kiran Polavarapu,
    • Rita Horvath,
    • Evan Reid,
    • Hanns Lochmüller,
    • Marco Spinazzi,
    • Marco Savarese,
    • Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
    • Leslie Matalonga,
    • Steven Laurie,
    • Han G. Brunner,
    • Holm Graessner,
    • Sergi Beltran,
    • Stephan Ossowski,
    • Lisenka E.L.M. Vissers,
    • Christian Gilissen,
    • Alexander Hoischen,
    • and on behalf of the Solve-RD consortium
    Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
    ...*164035, NM_005381.3), among other genes. RNA-seq confirmed upregulation NCL within the duplicated sequence.Nucleolin is a ubiquitously expressed, major nucleolar protein in growing eukaryotic cells, and plays a role in the regulation of ribosomal RNA transcription, ribosome maturation and assembly...
    OPEN ACCESS ARTICLE
  4. Method: Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
    • Leszek P. Pryszcz,
    • Gregor Diensthuber,
    • Laia Llovera,
    • Rebeca Medina,
    • Anna Delgado-Tejedor,
    • Luca Cozzuto,
    • Julia Ponomarenko,
    • and Eva Maria Novoa
    Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
    ...Fabra (UPF), Barcelona 08003, Spain; 3ICREA, Barcelona 08010, Espana ↵4 These authors contributed equally to this work. Corresponding authors: leszek.pryszcz@crg.eu, eva.novoa@crg.euAbstractNanopore direct RNA sequencing (DRS) enables direct measurement of RNA molecules, including their native RNA...
    OPEN ACCESS ARTICLE
  5. Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
    • Hongke Peng,
    • Jafar S. Jabbari,
    • Luyi Tian,
    • Changqing Wang,
    • Yupei You,
    • Chong Chyn Chua,
    • Natasha S. Anstee,
    • Noorul Amin,
    • Andrew H. Wei,
    • Nadia M. Davidson,
    • Andrew W. Roberts,
    • David C.S. Huang,
    • Matthew E. Ritchie,
    • and Rachel Thijssen
    Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
    ...Laboratory, Guangdong 510005, China Corresponding author: r.thijssen@amsterdamumc.nlAbstractSingle-cell long-read sequencing has transformed our understanding of isoform usage and the mutation heterogeneity between cells. Despite unbiased in-depth analysis, the low sequencing throughput often results...
    OPEN ACCESS ARTICLE
  6. 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
    ...for Evolutionary Biology, 24306 Plön, Germany Corresponding author: elcortegano@protonmail.comAbstractAll forms of genetic variation originate from new mutations, making it crucial to understand their rates and mechanisms. Here, we use long-read sequencing from Pacific Biosciences (PacBio) to investigate de novo...
    OPEN ACCESS ARTICLE
  7. Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
    • Gage S. Black,
    • Xiaomeng Huang,
    • Yi Qiao,
    • Philip Moos,
    • Deepa Sampath,
    • Deborah M. Stephens,
    • Jennifer A. Woyach,
    • and Gabor T. Marth
    Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
    ...-mutated subclones exhibit distinct transcriptomic behavior when compared to other cancer subclones. To achieve these goals, we use scBayes, which integrates bulk DNA sequencing and single-cell RNA sequencing (scRNA-seq) data to genotype individual cells for subclone-defining mutations. Although the most common...
  8. Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
    • Alexander J. Ritter,
    • Jolene M. Draper,
    • Christopher Vollmers,
    • and Jeremy R. Sanford
    Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
    ...localization, stability, and translational efficiency. To rigorously investigate mRNA isoform-specific ribosome association, we generated subcellular fractionation and sequencing (Frac-seq) libraries using both conventional short reads and long reads from human embryonic stem cells (ESCs) and neural progenitor...
    OPEN ACCESS ARTICLE
  9. Method: Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
    • Haotian Teng,
    • Marcus Stoiber,
    • Ziv Bar-Joseph,
    • and Carl Kingsford
    Genome Res. November 2024 34: 1987-1999; Published in Advance October 15, 2024, doi:10.1101/gr.278960.124
    ...@cs.cmu.eduAbstractDirect nanopore-based RNA sequencing can be used to detect posttranscriptional base modifications, such as N6-methyladenosine (m6A) methylation, based on the electric current signals produced by the distinct chemical structures of modified bases. A key challenge is the scarcity of adequate training data...
    OPEN ACCESS ARTICLE
  10. 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
    ..., Haikou, Hainan 571101, China Corresponding authors: sergey.koren@nih.gov, adam.phillippy@nih.govAbstractThe combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human...
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research