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  1. Mini-Review: Evolution of genome-wide methylation profiling technologies
    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    ..., Bruhm DC, Jensen SØ, Medina JE, Hruban C, White JR, et al. 2019. Genome-wide cell-free DNA fragmentation in patients with cancer. Nature 570: 385–389. doi:10.1038/s41586-019-1272-6 ↵De Coster W, Weissensteiner MH, Sedlazeck FJ. 2021. Towards population-scale long-read sequencing. Nat Rev Genet 22: 572...
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  2. Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
    • Samuel H. Kim,
    • Georgi K. Marinov,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
    ...of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet 46: 1311–1320. doi:10.1038/ng.3142 ↵Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, et al. 2006. Genome-wide mapping of DNase...
  3. Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
    • Kavitha Uthanumallian,
    • Andrea Del Cortona,
    • Susana M. Coelho,
    • Olivier De Clerck,
    • Sebastian Duchene,
    • and Heroen Verbruggen
    Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
    ...Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage Kavitha Uthanumallian1, Andrea Del Cortona2, Susana M. Coelho3, Olivier De Clerck2, Sebastian Duchene4,5 and Heroen Verbruggen1,6 1Melbourne Integrative Genomics, School of Bio...
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  4. 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
    ..., Isogai T, Suzuki Y, Akimitsu N. 2012. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res 22: 947–956. doi:10.1101/gr.130559.111 ↵Thomson DW, Bracken CP, Goodall GJ. 2011. Experimental strategies for microRNA target identification...
  5. Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
    • Uditi Bhatt,
    • Anne Cucchiarini,
    • Yu Luo,
    • Cameron W. Evans,
    • Jean-Louis Mergny,
    • K. Swaminathan Iyer,
    • and Nicole M. Smith
    Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
    ...regions and the stability of the Z-RNA sequences identified in this study will provide better understanding of Z-RNA formation in the noncoding transcriptome.In summary, we provide a comprehensive data set of predicted noncanonical secondary structures throughout the long noncoding transcriptome...
  6. Research: Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation
    • Joanna Delimata-Raczek,
    • Natalia Koralewska,
    • Bart Krist,
    • Magdalena Rakoczy,
    • Marek Figlerowicz,
    • and Ireneusz Stolarek
    Genome Res. April 3, 2026 ; Published in Advance April 3, 2026, doi:10.1101/gr.281150.125
    ..., and long noncoding RNA (lncRNA) transcripts (P<0.01). To experimentally validate the computationally identified isoform switches, we used RT-qPCR to measure the relative abundance of specific transcript variants for three representative genes (ATP2A2, TPM2, and GCNT2) at D4 and D30. For ATP2A2 and TPM2...
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  7. Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
    ..., revolutionizing the field of human genetics (Tam et al. 2019). Despite these successes, the interpretation of GWAS signals represents a challenging task as they are often located within noncoding regions of the and manifest as complex linkage disequilibrium (LD) blocks where identification of the causal variant...
  8. Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
    • Ishwarya Venkata Narayanan,
    • Karan Bedi,
    • Brian Magnuson,
    • Ariel McShane,
    • Mario Ashaka,
    • Michelle Paulsen,
    • Thomas E Wilson,
    • and Mats Ljungman
    Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
    .... 97 2020). 98 A recent study using the same Bru-seq and BruChase-seq datasets analyzed 99 here reported that allele-specific genetic variants can affect RNA stability by altering 100 conserved binding sequences of miRNAs and RNA-binding proteins (Huang et al. 101 2025). Many of the genes that have...
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  9. Research: Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • Yongbin Li,
    • Xiao Liu,
    • Peter Sarkies,
    • and Zhongying Zhao
    Genome Res. November/December 2022 32: 2015-2027; Published in Advance November 9, 2022, doi:10.1101/gr.277205.122
    .... Misregulation of transposable elements, coding genes, and small regulatory RNAs was more widespread in the bB2 compared with the nB2 hybrids, which is a plausible explanation for the differential phenotypes between the two hybrids. Our results show that regulation of the C. briggsae is strongly affected...
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  10. Research: Genome-wide promoter assembly in E. coli measured at single-base resolution
    • Jordan John,
    • Javaid Jabbar,
    • Nitika Badjatia,
    • Matthew J. Rossi,
    • William K.M. Lai,
    • and B. Franklin Pugh
    Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121
    ...are enriched with YR nucleotides (IUPAC nomenclature), this determination was based on only 88 promoters (Hawley and McClure 1983). Genome-wide studies based on mapping RNA 5′ ends have found the YR motif to be enriched, with 79% of the +1 nucleotide being an R (Kim et al. 2012), whereas another study had R...
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