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Articles published in
Genome Res
    September 2025
  1. LITTLE JH, Meyer GH, Grover A, Francette AM, et al
    ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies.
    Genome Res. 2025;35:2041-2051.
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  2. BIAGINI SA, Becelaere S, Aerden M, Jatsenko T, et al
    Genotype imputation from low-coverage data for medical and population genetic analyses.
    Genome Res. 2025;35:1929-1941.
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  3. WU HL, Kaufman ID, Hsu PY
    The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data.
    Genome Res. 2025;35:2130-2142.
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    August 2025
  4. ICHIKAWA K, Shoura MJ, Artiles KL, Jeong DE, et al
    CGC1, a new reference genome for Caenorhabditis elegans.
    Genome Res. 2025;35:1902-1918.
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  5. KALLEBERG J, Rissman J, Schnabel RD
    Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain.
    Genome Res. 2025;35:1859-1874.
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    July 2025
  6. VARKI R, Rossi M, Ferro E, Oliva M, et al
    Accurate short-read alignment through r-index-based pangenome indexing.
    Genome Res. 2025;35:1609-1620.
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  7. ZEKRI Y, Gregoricchio S, Yapici E, Huang CF, et al
    Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts.
    Genome Res. 2025;35:1530-1543.
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  8. YAO J, Yu J, Caffo B, Page SC, et al
    Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies.
    Genome Res. 2025;35:1621-1632.
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  9. MASTORAS M, Asri M, Brambrink L, Hebbar P, et al
    Highly accurate assembly polishing with DeepPolisher.
    Genome Res. 2025;35:1595-1608.
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  10. ANTIPOV D, Rautiainen M, Nurk S, Walenz BP, et al
    Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding.
    Genome Res. 2025;35:1583-1594.
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  11. JAYASOORIYA K, Jenner SP, Marasinghe P, Senanayake U, et al
    A new compression strategy to reduce the size of nanopore sequencing data.
    Genome Res. 2025;35:1574-1582.
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  12. MENDOZA-FERRI MG, Lozachmeur G, Duvina M, Perret L, et al
    Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase.
    Genome Res. 2025;35:1633-1645.
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    June 2025
  13. TAM R, Moller M, Luo R, Luo Z, et al
    Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus.
    Genome Res. 2025;35:1364-1376.
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  14. HAMMOND N, Liao L, Tong PW, Ng Z, et al
    Analytical validation of germline small variant detection using long-read HiFi genome sequencing.
    Genome Res. 2025;35:1391-1399.
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    May 2025
  15. FREEDMAN AH, Sackton TB
    Building better genome annotations across the tree of life.
    Genome Res. 2025;35:1261-1276.
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  16. SMITH BJ, Zhao C, Dubinkina V, Jin X, et al
    Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.
    Genome Res. 2025;35:1247-1260.
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  17. LEE DI, Roy S
    Examining the dynamics of three-dimensional genome organization with multitask matrix factorization.
    Genome Res. 2025;35:1179-1193.
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    April 2025
  18. MONTANO C, Timp W
    Evolution of genome-wide methylation profiling technologies.
    Genome Res. 2025;35:572-582.
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  19. RAUSCH T, Marschall T, Korbel JO
    The impact of long-read sequencing on human population-scale genomics.
    Genome Res. 2025;35:593-598.
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  20. MAHMOUD M, Agustinho DP, Sedlazeck FJ
    A Hitchhiker's Guide to long-read genomic analysis.
    Genome Res. 2025;35:545-558.
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  21. JENSEN TD, Ni B, Reuter CM, Gorzynski JE, et al
    Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.
    Genome Res. 2025;35:914-928.
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  22. LI Q, Keskus AG, Wagner J, Izydorczyk MB, et al
    Unraveling the hidden complexity of cancer through long-read sequencing.
    Genome Res. 2025;35:599-620.
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  23. MONZO C, Frankish A, Conesa A
    Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation.
    Genome Res. 2025;35:583-592.
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  24. VRCEK L, Bresson X, Laurent T, Schmitz M, et al
    Geometric deep learning framework for de novo genome assembly.
    Genome Res. 2025;35:839-849.
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    March 2025
  25. MA J, Bechsgaard J, Aagaard A, Villesen P, et al
    The genomic consequences and persistence of sociality in spiders.
    Genome Res. 2025;35:499-511.
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  26. LI Y, Zhang J
    Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved.
    Genome Res. 2025;35:512-521.
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    February 2025
  27. JENIKE KM, Campos-Dominguez L, Bodde M, Cerca J, et al
    k-mer approaches for biodiversity genomics.
    Genome Res. 2025;35:219-230.
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  28. MIAO Z, Yue JX
    Interactive visualization and interpretation of pangenome graphs by linear reference-based coordinate projection and annotation integration.
    Genome Res. 2025;35:296-310.
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  29. ZHI D, Jiang X, Harmanci A
    Proxy panels enable privacy-aware outsourcing of genotype imputation.
    Genome Res. 2025;35:326-339.
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  30. LIU Y, Botelho J, Iranzo J
    Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer.
    Genome Res. 2025;35:268-278.
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  31. MOURATIDIS I, Konnaris MA, Chantzi N, Chan CSY, et al
    Identification of the shortest species-specific oligonucleotide sequences.
    Genome Res. 2025;35:279-295.
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  32. YAN M, Andersen TO, Pope PB, Yu Z, et al
    Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.
    Genome Res. 2025;35:368-378.
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    January 2025
  33. LEWIN TD, Liao IJ, Chen ME, Bishop JDD, et al
    Fusion, fission, and scrambling of the bilaterian genome in Bryozoa.
    Genome Res. 2025;35:78-92.
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  34. WOMERSLEY HJ, Muliaditan D, DasGupta R, Cheow LF, et al
    Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression.
    Genome Res. 2025;35:162-177.
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    December 2024
  35. OROZCO-ARIAS S, Sierra P, Durbin R, Gonzalez J, et al
    MCHelper automatically curates transposable element libraries across eukaryotic species.
    Genome Res. 2024;34:2256-2268.
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  36. BURGER KE, Klepper S, von Luxburg U, Baumdicker F, et al
    Inferring ancestry with the hierarchical soft clustering approach tangleGen.
    Genome Res. 2024;34:2244-2255.
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    November 2024
  37. IYER SV, Goodwin S, McCombie WR
    Leveraging the power of long reads for targeted sequencing.
    Genome Res. 2024;34:1701-1718.
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  38. BYERLY PA, von Thaden A, Leushkin E, Hilgers L, et al
    Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe.
    Genome Res. 2024;34:2094-2107.
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  39. LI K, Smith ML, Blazier JC, Kochan KJ, et al
    Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding.
    Genome Res. 2024;34:2081-2093.
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  40. SLIZOVSKIY IB, Bonin N, Bravo JE, Ferm PM, et al
    Factors impacting target-enriched long-read sequencing of resistomes and mobilomes.
    Genome Res. 2024;34:2048-2060.
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  41. GOMEZ-SIMMONDS A, Annavajhala MK, Seeram D, Hokunson TW, et al
    Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla (KPC).
    Genome Res. 2024;34:1895-1907.
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  42. GUSTAFSON JA, Gibson SB, Damaraju N, Zalusky MPG, et al
    High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation.
    Genome Res. 2024;34:2061-2073.
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  43. JHA A, Bohaczuk SC, Mao Y, Ranchalis J, et al
    DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools.
    Genome Res. 2024;34:1976-1986.
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    October 2024
  44. DERELLE R, von Wachsmann J, Maklin T, Hellewell J, et al
    Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis.
    Genome Res. 2024;34:1661-1673.
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  45. VALENTIN-ALVARADO LE, Shi LD, Appler KE, Crits-Christoph A, et al
    Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements.
    Genome Res. 2024;34:1595-1609.
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  46. SCHROD S, Luck N, Lohmayer R, Solbrig S, et al
    Spatial Cellular Networks from omics data with SpaCeNet.
    Genome Res. 2024;34:1371-1383.
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  47. SAPCI AOB, Mirarab S
    Memory-bound k-mer selection for large and evolutionarily diverse reference libraries.
    Genome Res. 2024;34:1455-1467.
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  48. HONG MM, Froelicher D, Magner R, Popic V, et al
    Secure discovery of genetic relatives across large-scale and distributed genomic data sets.
    Genome Res. 2024;34:1312-1323.
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  49. AZIZPOUR A, Balaji A, Treangen TJ, Segarra S, et al
    Graph-based self-supervised learning for repeat detection in metagenomic assembly.
    Genome Res. 2024;34:1468-1476.
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  50. CHANDRA G, Gibney D, Jain C
    Haplotype-aware sequence alignment to pangenome graphs.
    Genome Res. 2024;34:1265-1275.
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    September 2024
  51. TIBBS-CORTES LE, Guo T, Andorf CM, Li X, et al
    Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize.
    Genome Res. 2024;34:1253-1263.
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  52. CHEN S, Wang J, Jung I, Qiu Z, et al
    A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data.
    Genome Res. 2024;34:1174-1184.
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    August 2024
  53. KURONEN J, Horsfield ST, Pontinen AK, Mallawaarachchi S, et al
    Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs.
    Genome Res. 2024;34:1081-1088.
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  54. XIANG G, He X, Giardine BM, Isaac KJ, et al
    Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.
    Genome Res. 2024;34:1089-1105.
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    July 2024
  55. LEE S, Portlock T, Le Chatelier E, Garcia-Guevara F, et al
    Global compositional and functional states of the human gut microbiome in health and disease.
    Genome Res. 2024;34:967-978.
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  56. HIRTH A, Fatti E, Netz E, Acebron SP, et al
    DEAD box RNA helicases are pervasive protein kinase interactors and activators.
    Genome Res. 2024;34:952-966.
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  57. MORRISSEY A, Shi J, James DQ, Mahony S, et al
    Accurate allocation of multimapped reads enables regulatory element analysis at repeats.
    Genome Res. 2024;34:937-951.
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  58. BELLINZONA G, Nardi T, Castelli M, Batisti Biffignandi G, et al
    Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States.
    Genome Res. 2024;34:877-887.
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  59. BUCKLEY RM, Ostrander EA
    Large-scale genomic analysis of the domestic dog informs biological discovery.
    Genome Res. 2024;34:811-821.
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  60. ULRICH JU, Renard BY
    Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters.
    Genome Res. 2024;34:914-924.
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    June 2024
  61. GABRIEL L, Bruna T, Hoff KJ, Ebel M, et al
    BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA.
    Genome Res. 2024;34:769-777.
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  62. BRUNA T, Lomsadze A, Borodovsky M
    GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.
    Genome Res. 2024;34:757-768.
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  63. WON S, Yu J, Kim H
    Identifying genes within pathways in unannotated genomes with PaGeSearch.
    Genome Res. 2024;34:784-795.
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  64. MURPHY WJ, Harris AJ
    Toward telomere-to-telomere cat genomes for precision medicine and conservation biology.
    Genome Res. 2024;34:655-664.
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  65. KOENIG Z, Yohannes MT, Nkambule LL, Zhao X, et al
    A harmonized public resource of deeply sequenced diverse human genomes.
    Genome Res. 2024;34:796-809.
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  66. GAMAARACHCHI H, Ferguson JM, Samarakoon H, Liyanage K, et al
    Simulation of nanopore sequencing signal data with tunable parameters.
    Genome Res. 2024;34:778-783.
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    May 2024
  67. CAI Q, Fu Y, Lyu C, Wang Z, et al
    A new framework for exploratory network mediator analysis in omics data.
    Genome Res. 2024;34:642-654.
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  68. JI S, Zhu T, Sethia A, Wang W, et al
    Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples.
    Genome Res. 2024;34:633-641.
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    April 2024
  69. LORIG-ROACH R, Meredith M, Monlong J, Jain M, et al
    Phased nanopore assembly with Shasta and modular graph phasing with GFAse.
    Genome Res. 2024;34:454-468.
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  70. FOROOZANDEH SHAHRAKI M, Farahbod M, Libbrecht MW
    Robust chromatin state annotation.
    Genome Res. 2024;34:469-483.
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    March 2024
  71. YU W, Luo H, Yang J, Zhang S, et al
    Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes.
    Genome Res. 2024;34:326-340.
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  72. CHE H, Jiang P, Choy LYL, Cheng SH, et al
    Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma.
    Genome Res. 2024;34:189-200.
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    February 2024
  73. LEBARON VON BAEYER S, Crocker R, Rakotoarivony R, Ranaivoarisoa JF, et al
    Why community consultation matters in genomic research benefit-sharing models.
    Genome Res. 2024;34:1-6.
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    December 2023
  74. HARVEY WT, Ebert P, Ebler J, Audano PA, et al
    Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall.
    Genome Res. 2023;33:2029-2040.
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  75. EMANI PS, Geradi MN, Gursoy G, Grasty MR, et al
    Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases.
    Genome Res. 2023;33:2156-2173.
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  76. METZGER DCH, Porter I, Mobley B, Sandkam BA, et al
    Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation.
    Genome Res. 2023;33:1917-1931.
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    October 2023
  77. CHRISMAN B, He C, Jung JY, Stockham N, et al
    Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity.
    Genome Res. 2023;33:1734-1746.
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  78. BARIL T, Pym A, Bass C, Hayward A, et al
    Transposon accumulation at xenobiotic gene family loci in aphids.
    Genome Res. 2023;33:1718-1733.
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  79. SPROUL JS, Hotaling S, Heckenhauer J, Powell A, et al
    Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges.
    Genome Res. 2023;33:1708-1717.
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    September 2023
  80. LI Z, Meisner J, Albrechtsen A
    Fast and accurate out-of-core PCA framework for large scale biobank data.
    Genome Res. 2023;33:1599-1608.
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  81. PAREY E, Fernandez-Aroca D, Frost S, Uribarren A, et al
    Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits.
    Genome Res. 2023;33:1513-1526.
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    August 2023
  82. DE TRIBOLET-HARDY J, Thorball CW, Forey R, Planet E, et al
    Genetic features and genomic targets of human KRAB-zinc finger proteins.
    Genome Res. 2023;33:1409-1423.
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  83. DAI X, Bian P, Hu D, Luo F, et al
    A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species.
    Genome Res. 2023;33:1284-1298.
    >> Share

  84. MARMOL-SANCHEZ E, Fromm B, Oskolkov N, Pochon Z, et al
    Historical RNA expression profiles from the extinct Tasmanian tiger.
    Genome Res. 2023;33:1299-1316.
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    July 2023
  85. SCHWEIGER R, Durbin R
    Ultrafast genome-wide inference of pairwise coalescence times.
    Genome Res. 2023;33:1023-1031.
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  86. BAKER DN, Langmead B
    Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2.
    Genome Res. 2023;33:1218-1227.
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  87. RAHMAN HERA M, Pierce-Ward NT, Koslicki D
    Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash.
    Genome Res. 2023;33:1061-1068.
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  88. CRACCO A, Tomescu AI
    Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT.
    Genome Res. 2023;33:1198-1207.
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  89. VENKATESARAMANI R, Wan Z, Malin BA, Vorobeychik Y, et al
    Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics.
    Genome Res. 2023;33:1113-1123.
    >> Share

    June 2023
  90. GRANDCHAMP A, Kuhl L, Lebherz M, Bruggemann K, et al
    Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster.
    Genome Res. 2023;33:872-890.
    >> Share

  91. JOURDAIN J, Barasc H, Faraut T, Calgaro A, et al
    Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets.
    Genome Res. 2023;33:957-971.
    >> Share

  92. ATKINSON EG, Artomov M, Loboda AA, Rehm HL, et al
    Discordant calls across genotype discovery approaches elucidate variants with systematic errors.
    Genome Res. 2023;33:999-1005.
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    May 2023
  93. PALAHI I TORRES A, Hook L, Nasvall K, Shipilina D, et al
    The fine-scale recombination rate variation and associations with genomic features in a butterfly.
    Genome Res. 2023;33:810-823.
    >> Share

  94. MORIN A, Chu EC, Sharma A, Adrian-Hamazaki A, et al
    Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets.
    Genome Res. 2023;33:763-778.
    >> Share

  95. JIAO Y, Li M, He X, Wang Y, et al
    Targeted, programmable, and precise tandem duplication in the mammalian genome.
    Genome Res. 2023;33:779-786.
    >> Share

  96. MUMM C, Drexel ML, McDonald TL, Diehl AG, et al
    Multiplexed long-read plasmid validation and analysis using OnRamp.
    Genome Res. 2023;33:741-749.
    >> Share

  97. ZHUO X, Hsu S, Purushotham D, Kuntala PK, et al
    Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser.
    Genome Res. 2023;33:824-835.
    >> Share

  98. BAFNA A, Banks G, Hastings MH, Nolan PM, et al
    Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock.
    Genome Res. 2023;33:673-688.
    >> Share

  99. GERSHMAN A, Hauck Q, Dick M, Jamison JM, et al
    Genomic insights into metabolic flux in hummingbirds.
    Genome Res. 2023;33:703-714.
    >> Share

    April 2023
  100. BARROSO GV, Lohmueller KE
    Inferring the mode and strength of ongoing selection.
    Genome Res. 2023;33:632-643.
    >> Share

  101. SUN Y, Cheng Z, Li X, Yang Q, et al
    Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing.
    Genome Res. 2023;33:612-621.
    >> Share

    March 2023
  102. ZHU FY, Chen X, Song YC, Lam LPY, et al
    SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress.
    Genome Res. 2023;33:371-385.
    >> Share

  103. LIU J, Dawe RK
    Large haplotypes highlight a complex age structure within the maize pan-genome.
    Genome Res. 2023;33:359-370.
    >> Share

  104. DEBO BM, Mallory BJ, Stergachis AB
    Evaluation of N (6)-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes.
    Genome Res. 2023;33:427-434.
    >> Share

    February 2023
  105. TIAN T, Zhong C, Lin X, Wei Z, et al
    Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning.
    Genome Res. 2023;33:232-246.
    >> Share

  106. O'CONNELL BL, Nichols RV, Pokholok D, Thomas J, et al
    Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing.
    Genome Res. 2023;33:208-217.
    >> Share


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