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  1. Editorial: Scope note Genome Res. May 2011 21: xi
    ...genome;21/5/xi 1088-9051 Scope note Editorial Scope note The broader goal of Genome Research is to publish research findings that offer novel insights into the structure, function, and biology of s and the biology of diseases. Specific areas of interest include proteomics, systems biology, single...
  2. Method: Multisample motif discovery and visualization for tandem repeats
    • Yaran Zhang,
    • Marc Hulsman,
    • Alex Salazar,
    • Niccolò Tesi,
    • Lydian Knoop,
    • Sven van der Lee,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Erik-Jan Kamsteeg,
    • and Henne Holstege
    Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
    ...for haplotype 1 and (GACAG)1420(GACAA)114GAAG(AAAAG)15 with 20 indels for haplotype 2. Note that the results of MotifScope also represent the indels through additional motifs (total of six motifs), resulting in a fully accurate representation of the actual repeat sequences (edit distance = 0.0). In contrast, u...
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  3. Research: Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay
    • Jessica A. Hurt,
    • Alex D. Robertson,
    • and Christopher B. Burge
    Genome Res. October 2013 23: 1636-1650; Published in Advance June 13, 2013, doi:10.1101/gr.157354.113
    ...Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay Jessica A. Hurt , Alex D. Robertson and Christopher B. Burge 1 Department of Biology, Massachusetts Institute of Technology, Cambridge...
  4. Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
    • Paras Verma,
    • Deeksha Thakur,
    • Deepanshi Awasthi,
    • and Shashi Bhushan Pandit
    Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
    ...in isoforms (Fig. 1A). Some exons can be noncoding in some transcripts while coding in others, and these are classified with global scope value “D,” noting dual (“D”) exons (Fig. 1A, top). Other global scope descriptors are described in the Methods section. Briefly, these include “M” and “R,” where “M...
  5. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...adenocarcinomas, including some metabolic enzymes with the potential to be neofunctional. The postduplication diversification of driver genes and functions may indicate selection for somatic copy number changes in lung tumors and an increased scope for tumor adaptations.Cancers result from the evolutionary...
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  6. Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ..., antisense transcripts (NATs) results in a perfect RNA duplex, which may be targeted by ADARs. To explore the scope of ADAR editing of NAT-derived dsRNA, we examined editing levels at locations where both strands are transcribed. Our findings indicate that editing is rare in regions for which both strands co...
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  7. Method: Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
    • Vikram S. Shivakumar and
    • Ben Langmead
    Genome Res. February 2026 36: 397-404; Published in Advance November 7, 2025, doi:10.1101/gr.280940.125
    ...over 2.7 TB of memory. However, we note that the primary bottleneck in this case is the size of the parse rather than the dictionary, which recursive extensions to PFP aim to address (Ferro et al. 2024).With CHM13 as the common coordinate system for merging, we divided the HPRC data set into nine...
  8. 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
    ...evaluation of performance. Of note, HiFi sequencing F1-scores for SNVs and indels surpass 99% at ∼15× and ∼25×, respectively. In addition, high confidence small variant concordance across all HiFi sequencing reproducibility assessments (two specimens, three independent sequencing data sets) are >99...
  9. Method: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
    • Fei Qin,
    • Guoshuai Cai,
    • Christopher I. Amos,
    • and Feifei Xiao
    Genome Res. January 2024 34: 85-93; Published in Advance January 30, 2024, doi:10.1101/gr.278098.123
    ...and CNA detection performance of FLCNA, benchmarking it against existing copy number estimation methods (SCOPE, HMMcopy) in combination with commonly used clustering methods. Application of FLCNA to a scDNA-seq data set of breast cancer revealed different genomic variation patterns in neoadjuvant...
  10. Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
    • Michael K.B. Ford,
    • Ananth Hari,
    • Meredith Yeager,
    • Lisa Mirabello,
    • Stephen Chanock,
    • Ibrahim Numanagić,
    • COVNET Consortium,
    • and S. Cenk Sahinalp
    Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
    ...challenging.View larger version: In this window In a new window Figure 1. Distribution of Mendelian concordance rates for functional variable gene rates across immune loci. Box plots show the median, quartiles, and outliers for each locus type. Note the distinct clustering of trio concordance in TRGV...
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