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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
..., identification of conserved CRMs is often confounded by rearrangement and substitution of TFBSs, leading to similar functional capabilities without deep sequence conservation (for reviews, see Nelson and Wardle 2013; Long et al. 2016; Jindal and Farley 2021). Despite this, comparative genomic analyses indicate...
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Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
- Shingo Kato,
- Sachiko Masuda,
- Arisa Shibata,
- Takashi Itoh,
- Mitsuo Sakamoto,
- Ken Shirasu,
- and Moriya Ohkuma
Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
...305-0074, Japan; 2Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Corresponding authors: skato@riken.jp, mohkuma@riken.jpAbstractGenome sequences provide fundamental information for both basic and applied life sciences. Whole...
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Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
...available s displays a wonderful diversity in size, composition, and structure and is quickly expanding thanks to several global biodiversity genomics initiatives. However, sequencing of s, even with the latest technologies, can still be challenging for both technical (e.g., small physical size...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...) significantly improved variant allele frequency estimates, stressing the need for high-quality, diverse ancestry population reference such as the ongoing LR-GS sequencing of the 1000 Genome Consortium or All of Us (Gustafson et al. 2024; Mahmoud et al. 2024). In addition, we also examined variation at TR loci...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...: In this window In a new window Figure 1. Overview of the experimental setup and bioinformatic pipeline. (A) Schematics of DNA sample preparation and sequencing. High-molecular-weight gDNA was extracted from peripheral blood mononuclear cells (PBMCs), isolated monocytes, or the HG002 Epstein–Barr virus...
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Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
- Nathan Hammond,
- Linda Liao,
- Pun Wai Tong,
- Zena Ng,
- Thuy-Mi P. Nguyen,
- Chandler Ho,
- Yao Yang,
- and Stuart A. Scott
Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
...Fi sequencing and short-read sequencing: (A) single nucleotide variants (SNVs); (B) insertions/deletion variants (indels); and (C) SNVs and indels combined.Long-read HiFi sequencing concordance and reproducibilityHiFi sequencing library preparation included both manual and automated workflows, and minor updates...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...; barcoding, library preparation, and PCR amplification with Illumina TruSeq amplification primers; size selection for 300–500 bp with the BluePippin system; and sequencing on an Illumina NextSeq 500/550. Sequences were then demultiplexed in house by LGC Genomics using proprietary software. Further details...
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Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
- Artem Mikelov,
- George Nefediev,
- Alexander Tashkeev,
- Oscar L. Rodriguez,
- Diego Aguilar Ortmans,
- Valeriia Skatova,
- Mark Izraelson,
- Alexey N. Davydov,
- Stanislav Poslavsky,
- Souad Rahmouni,
- Corey T. Watson,
- Dmitriy Chudakov,
- Scott D. Boyd,
- and Dmitry Bolotin
Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
...sets. The developed algorithm is a part of the MiXCR software. We demonstrate the accuracy of this approach using AIRR-seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) AIRR-seq data from...
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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
...long reads. Variations of this approach have been used by other groups to target large ROIs using a partially automated version of CATCH on the SageHLS (HMW Library System) instrument (Sage Science) for sequencing with the 10x Genomics Chromium platform (Shin et al. 2019) and the PacBio Sequel I...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge CB10 1SA, United Kingdom Corresponding author: ana.conesa@csic.esAbstractLong-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full...
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