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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., Stanford University School of Engineering, Stanford, California 94305, USA Corresponding author: geleta@berkeley.eduAbstractModern biobanks are providing numerous high-resolution genomic sequences of diverse populations. In order to account for diverse and admixed populations, new algorithmic tools...
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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
...).View this table: In this window In a new window Table 3. Single nucleotide and small insertion or deletion variant findingsRE identification with long-read adaptive sequencingTargeted sequencing is an effective tool that provides many advantages for genomic medicine, prioritizing relevant candidate genes...
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Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
- Taishan Hu,
- Timothy L. Mosbruger,
- Nikolaos G. Tairis,
- Amalia Dinou,
- Pushkala Jayaraman,
- Mahdi Sarmady,
- Kingham Brewster,
- Yang Li,
- Tristan J. Hayeck,
- Jamie L. Duke,
- and Dimitri S. Monos
Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
...to design a set of oligos to target and capture this region with RSE. The genomic fragments captured from RSE are then subjected to whole amplification (WGA) and sequenced on either the PacBio Sequel or Sequel II platform.Read selection and editingDepending on the number of reads obtained for the different...
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Method: Automated interpretable artificial intelligence genomic prediction with AlGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
..., China; 3College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; 4National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, China Predicting phenotypes from genomic mutations remains...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...-instrument targeted sampling approaches (Table 1).View this table: In this window In a new window Table 1. Summary of currently available targeted long-read sequencing approachesPCR sequencingBefore “next-generation” sequencing methods revolutionized science, Sanger sequencing of individually amplified targets...
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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
...1, Raony Cardenas1, Thyago Cardoso1, Luis F. Paulin2, Philippe Sanio2, Joseph Mafofo1, Haiguo Wu1, Val Zvereff1, Albarah El-Khani1, Fahed Al Marzooqi1, Tiago R. Magalhães1, Fritz J. Sedlazeck2,3,4 and Javier Quilez1 1M42, Abu Dhabi, United Arab Emirates; 2Human Genome Sequencing Center, Baylor...
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Method: Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing
- Brigid M. O'Flaherty,
- Yan Li,
- Ying Tao,
- Clinton R. Paden,
- Krista Queen,
- Jing Zhang,
- Darrell L. Dinwiddie,
- Stephen M. Gross,
- Gary P. Schroth,
- and Suxiang Tong
Genome Res. June 2018 28: 869-877; Published in Advance April 27, 2018, doi:10.1101/gr.226316.117
...equally to this work. Corresponding author: sot1@cdc.govAbstractNext generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation...
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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...RNA in a single construct, simplifying experimental workflows and enhancing targeting efficiency. Using nanopore direct RNA sequencing, we identify high-confident m6A sites in HeLa cells, which serve as targets for Dem6A-Vec. We validate the targeted demethylation of m6A sites in the EEF2 and RRAGA...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...for gluing the SMRTbell adaptor to the target DNA (https://www.pacb.com/wp-content/uploads/2015/09/Guide-Pacific-Biosciences-Template-Preparation-and-Sequencing.pdf), whereas ONT uses a 1 bp T/A overhang ligation (SQK-LSK114; https://nanoporetech.com/document/genomic-dna-by-ligation-sqk-lsk114). Bauer et al...
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Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
- Wei-Hao Lee,
- Lechuan Li,
- Ruth Dannenfelser,
- and Vicky Yao
Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
...; 4Rice Synthetic Biology Institute, Rice University, Houston, Texas 77005, USA ↵5 These authors contributed equally to this work. Corresponding author: vy@rice.eduAbstractAs sequencing techniques advance in precision, affordability, and diversity, an abundance of heterogeneous sequencing data has...

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