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Method: Robust 16S rRNA classification based on a compressed LCA index
- Omar Ahmed,
- Christina Boucher,
- and Ben Langmead
Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
...of distinct s. The linear dependence on d is limiting, because real taxonomies can easily contain 10,000s of leaves or more. We propose a method called cliff compression that reduces this size by a large factor, >250× when indexing the SILVA 16S rRNA gene database. This method uses words of space...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
..., spotting, and depigmentation patterns. The assumed autosomal dominant inherited genetic variants underlying the characteristic white head of Fleckvieh, Simmental, and Hereford cattle have not been identified yet, although the contribution of structural variation upstream of the KIT gene has been proposed...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...in the annotation gene set, as the assembly was substantiated with concordant alignments. There were five genes that could not be investigated because no Iso-Seq alignments were present. Of the four remaining genes, one was not located in the assembly, two appear to reflect gaps in the assembly, and the final one...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
...and cDNA sequencing, based on patient-derived DNA and RNA, to systematically evaluate deep intronic variation. We identified all variants across the full genomic loci of targeted genes, applied the in silico tools SpliceAI and Pangolin to predict variants of functional consequence, and then carried out...
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Method: Accurate short-read alignment through r-index-based pangenome indexing
- Rahul Varki,
- Massimiliano Rossi,
- Eddie Ferro,
- Marco Oliva,
- Erik Garrison,
- Ben Langmead,
- and Christina Boucher
Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
...and memory values reported were obtained from the Snakemake benchmark files.Evaluation of the index construction scalabilityFigure 5A compares the indexing CPU time and peak memory usage of Moni-align with the other aligners. GraphAligner was not included in our evaluation owing to its lack of an in...
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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
...genomics. Early works in molecular biology on gene expression were limited, because purified RNA is unstable and difficult to work with. However, the discovery (and use in the laboratory) of reverse transcriptase, permitting the controlled synthesis of RNAs into cDNAs (Maniatis et al. 1976...
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Resource: Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
- Alexander S. Leonard,
- Xena M. Mapel,
- and Hubert Pausch
Genome Res. February 2024 34: 300-309; Published in Advance February 14, 2024, doi:10.1101/gr.278267.123
.... All eGenes found uniquely with the short-read data set were just missed by the significance threshold in the PanGenie+ data set, suggesting they are of marginal importance (Fig. 3C). On the other hand, there were 26 eGenes found only with the PanGenie+ data set, including four for which the top e...
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Method: Memory-bound k-mer selection for large and evolutionarily diverse reference libraries
- Ali Osman Berk Şapcı and
- Siavash Mirarab
Genome Res. September 2024 34: 1455-1467; Published in Advance August 29, 2024, doi:10.1101/gr.279339.124
...ultra-large genomic reference sets (e.g., Parks et al. 2018; McDonald et al. 2024), often used with marker genes (Asnicar et al. 2020; Balaban et al. 2024). Using these data sets with k-mers-based methods, however, runs into a mundane but key limitation—the memory needed to use these s as reference...
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Method: MCHelper automatically curates transposable element libraries across eukaryotic species
- Simon Orozco-Arias,
- Pío Sierra,
- Richard Durbin,
- and Josefa González
Genome Res. December 2024 34: 2256-2268; Published in Advance December 9, 2024, doi:10.1101/gr.278821.123
...for terminal inverted repeat (TIR) elements in the raw libraries produced by 2/3 of the programs tested (2/2 in H. sapiens). In the case of Helitrons, MCHelper generated longer consensus sequences in the raw libraries produced by 1/3 of the programs tested in four species (C. cornix, D. rerio, Z. mays, and H...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...were widely used to quantify transcript levels across the by hybridizing fluorescently labeled cDNA to thousands of predefined DNA probes immobilized on a solid surface. Each probe was designed to be complementary to a specific transcript, allowing its abundance in a sample to be inferred from...
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