Searching journal content for articles similar to Dedhia and McCombie 8 (3): 313.

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  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
    ...), and the development of microarrays first (Schena et al. 1995) and high-throughput sequencing later (Margulies et al. 2005) boosted our capacity to analyze transcriptomes. Nowadays, the most common technique to analyze gene expression is RNA sequencing (RNA-seq). This technique consists of first isolating RNA from...
  2. Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
    • Robin Kosch,
    • Katharina Limm,
    • Annette M. Staiger,
    • Nadine S. Kurz,
    • Nicole Seifert,
    • Bence Oláh,
    • Stefan Solbrig,
    • Viola Poeschel,
    • Gerhard Held,
    • Marita Ziepert,
    • Norbert Schmitz,
    • Emil Chteinberg,
    • Reiner Siebert,
    • Rainer Spang,
    • Helena U. Zacharias,
    • German Ott,
    • Peter J. Oefner,
    • and Michael Altenbuchinger
    Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
    ..., Germany; 12Department of Statistical Bioinformatics, University of Regensburg, 93053 Regensburg, Germany ↵13 These authors contributed equally to this work. Corresponding author: robin.kosch@protonmail.comAbstractHigh-throughput bottom-up proteomic data cover thousands of proteins and related co- and post...
  3. Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
    • Haloom Rafehi,
    • Liam G. Fearnley,
    • Justin Read,
    • Penny Snell,
    • Kayli C. Davies,
    • Liam Scott,
    • Greta Gillies,
    • Genevieve C. Thompson,
    • Tess A. Field,
    • Aleena Eldo,
    • Simon Bodek,
    • Ernest Butler,
    • Luke Chen,
    • John Drago,
    • Himanshu Goel,
    • Anna Hackett,
    • G. Michael Halmagyi,
    • Andrew Hannaford,
    • Katya Kotschet,
    • Kishore R. Kumar,
    • Smitha Kumble,
    • Matthew Lee-Archer,
    • Abhishek Malhotra,
    • Mark Paine,
    • Michael Poon,
    • Kate Pope,
    • Katrina Reardon,
    • Steven Ring,
    • Anne Ronan,
    • Matthew Silsby,
    • Renee Smyth,
    • Chloe Stutterd,
    • Mathew Wallis,
    • John Waterston,
    • Thomas Wellings,
    • Kirsty West,
    • Christine Wools,
    • Kathy H.C. Wu,
    • David J. Szmulewicz,
    • Martin B. Delatycki,
    • Melanie Bahlo,
    • and Paul J. Lockhart
    Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
    ...of ∼250–1000 bp. Therefore, larger RE may not be represented in this process. In addition, the capture probes used may be disrupted by the RE and not efficiently hybridize to the expanded allele. Moreover, like other high-throughput diagnostic technologies such as multiplex amplicon sequencing...
  4. 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
    ...), which reflects the known lower throughput of R10 flow cells (Ni et al. 2023) evident in our data (median yield: 103 Gb for R10 vs. 141 Gb for R9). Although ONT achieved higher mean coverage (∼40×) than SRS (∼35×), the proportion of bases with >10× coverage was slightly lower (92.0–94.0% for ONT vs. 95...
  5. Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
    • Li-Ting Chen,
    • Myrthe Jager,
    • Dàmi Rebergen,
    • Geertruid J. Brink,
    • Tom van den Ende,
    • Willem Vanderlinden,
    • Pauline Kolbeck,
    • Marc Pagès-Gallego,
    • Ymke van der Pol,
    • Nicolle Besselink,
    • Norbert Moldovan,
    • Nizar Hami,
    • Wigard P. Kloosterman,
    • Hanneke van Laarhoven,
    • Florent Mouliere,
    • Ronald Zweemer,
    • Jan Lipfert,
    • Sarah Derks,
    • Alessio Marcozzi,
    • and Jeroen de Ridder
    Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
    ...BX, United Kingdom Corresponding authors: alessio.marcozzi@gmail.com, j.deridder-4@umcutrecht.nlAbstractShallow -wide cell-free DNA sequencing holds great promise for noninvasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single...
    OPEN ACCESS ARTICLE
  6. Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
    • Meilin Zhang,
    • Heng Du,
    • Yu Zhang,
    • Yue Zhuo,
    • Zhen Liu,
    • Yahui Xue,
    • Lei Zhou,
    • Sixuan Zhou,
    • Wanying Li,
    • and Jian-Feng Liu
    Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
    ...structure analyses, genetic diversity evaluation, and ancestry estimation (Kennedy et al. 2003; Zimmerman et al. 2020). Simultaneously, the latest advances in SNP high-throughput arrays and WGS facilitate the SNPs applied in the usual genetic analyses. However, compared with WGS, SNP arrays were primarily...
    OPEN ACCESS ARTICLE
  7. Method: A new compression strategy to reduce the size of nanopore sequencing data
    • Kavindu Jayasooriya,
    • Sasha P. Jenner,
    • Pasindu Marasinghe,
    • Udith Senanayake,
    • Hassaan Saadat,
    • David Taubman,
    • Roshan Ragel,
    • Hasindu Gamaarachchi,
    • and Ira W. Deveson
    Genome Res. July 2025 35: 1574-1582; Published in Advance May 15, 2025, doi:10.1101/gr.280090.124
    ....Nanopore sequencing enables high-throughput sequencing of native DNA or RNA molecules of any length. Platform updates from Oxford Nanopore Technologies (ONT) have enabled increasingly cost-effective and scalable sequencing in recent years (Wang et al. 2021; Marx 2023). As the technology continues to improve...
    OPEN ACCESS ARTICLE
  8. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...of Pharmaceutical Biotechnology and Department of Medicine, the University of Hong Kong, Hong Kong SAR, China ↵9 These authors contributed equally to this work. Corresponding authors: su@chemie.uni-siegen.de, zhouxm@scnu.edu.cn, qz.lian@siat.ac.cnAbstractRNA sequencing (RNA-seq) is a pivotal tool for transcriptomic...
  9. 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
  10. 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
    ...OfPores NextFlow workflow. The availability of an efficient and simple multiplexing strategy improves the cost-effectiveness of this technology and facilitates the analysis of low-input biological samples.Nanopore sequencing technologies have revolutionized our ability to study the transcriptome, by enabling...
    OPEN ACCESS ARTICLE
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