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Articles published in
Genome Res
    June 2026
  1. VARKI R, Boucher C
    Building genomic data structures from compressed representations using prefix-free parsing.
    Genome Res. 2026;36:1081-1093.
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  2. SHAO J, Chen S, Wang Z, Chen Z, et al
    Balancing Gene Ontology annotation specificity in protein function prediction based on the protein sequence large graph.
    Genome Res. 2026;36:1273-1286.
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  3. QI J, Yang Z, Yu T, Li G, et al
    Enabling efficient and robust analysis of tandem repeats in genomic data using Wavefront-based String Decomposer.
    Genome Res. 2026;36:1265-1272.
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  4. LI J, Liu A, Liu R, Xu Z, et al
    Tissue-specific mRNA m(6)A reprogramming unveils vitamin-driven post-transcriptional regulation in mice.
    Genome Res. 2026;36:1141-1157.
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    May 2026
  5. CHEN K, Li X, Shi Q, Shao M, et al
    Hash functions in nucleotide sequence analysis.
    Genome Res. 2026;36:887-902.
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    April 2026
  6. VADDADI K, Lin MJ, Majidian S, Mun T, et al
    Minimizing reference bias with an imputed personalized reference.
    Genome Res. 2026;36:740-753.
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  7. WEI L, Jiang Z, Fan B, Yan Y, et al
    Automated interpretable artificial intelligence genomic prediction with AIGP.
    Genome Res. 2026;36:814-826.
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  8. RILEY DM, Elsayed R, Walsh MD, Johal S, et al
    Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis.
    Genome Res. 2026;36:695-712.
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  9. LIU T, Huang T, Jin W, Chu T, et al
    spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model.
    Genome Res. 2026;36:754-768.
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  10. NISCHWITZ E, Schoonenberg VAC, Mullner R, Fradera-Sola A, et al
    A systems view on DNA damage response kinetics in Tetrahymena.
    Genome Res. 2026;36:865-874.
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    March 2026
  11. XIE D, Ye P, Ma Y, Zhao Z, et al
    Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility.
    Genome Res. 2026;36:506-521.
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  12. ARRES J, Elavalli S, Behl S, Matias Sanchez D, et al
    Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications.
    Genome Res. 2026;36:460-471.
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  13. SHEMIRANI R, Belbin GM, Cullina S, Caggiano C, et al
    A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis.
    Genome Res. 2026;36:534-546.
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    February 2026
  14. HUANG Z, Zheng R, Jia P, Yan X, et al
    scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment.
    Genome Res. 2026;36:387-396.
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  15. GELETA M, Montserrat DM, Giro-I-Nieto X, Ioannidis AG, et al
    Autoencoders for genomic variation analysis.
    Genome Res. 2026;36:348-360.
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  16. PEEDE D, Banuelos MM, Medina Tretmanis J, Miyagi M, et al
    Recent advances in methods to characterize archaic introgression in modern humans.
    Genome Res. 2026;36:239-256.
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  17. ZHANG W, Liu Y, Li G, Xu J, et al
    Strain-level metagenomic profiling using pangenome graphs with PanTax.
    Genome Res. 2026;36:405-420.
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  18. YE C, Li X, Cheng N, Su Y, et al
    The SynMall resource for characterizing the functional impact of synonymous variation.
    Genome Res. 2026;36:421-431.
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  19. SHIVAKUMAR VS, Langmead B
    Partitioned multi-MUM finding for scalable pangenomics with MumemtoM.
    Genome Res. 2026;36:397-404.
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    January 2026
  20. KOSCH R, Limm K, Staiger AM, Kurz NS, et al
    Integration of high-throughput proteomic data and complementary omics layers with PriOmics.
    Genome Res. 2026;36:197-213.
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  21. THOMAS WR, Baldoni C, Zeng Y, Carlson D, et al
    Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus.
    Genome Res. 2026;36:61-70.
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  22. ZHANG W, Cao L, Gu X, Long Y, et al
    Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN.
    Genome Res. 2026;36:142-158.
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    December 2025
  23. ZHENG H, Sarkar H, Raphael BJ
    Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms.
    Genome Res. 2025;35:2734-2743.
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  24. DOKMAI N, Zhu K, Sahinalp SC, Cho H, et al
    Secure phasing of private genomes in a trusted execution environment with TX-Phase.
    Genome Res. 2025;35:2626-2636.
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  25. AHMED O, Boucher C, Langmead B
    Robust 16S rRNA classification based on a compressed LCA index.
    Genome Res. 2025;35:2650-2660.
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  26. CHANDRA G, Hossen MH, Scholz S, Dilthey AT, et al
    Pangenome-based genome inference using integer programming.
    Genome Res. 2025;35:2661-2670.
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  27. RAEISI DEHKORDI S, Jia Z, Estabrook J, Hauenstein J, et al
    OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities.
    Genome Res. 2025;35:2671-2681.
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    November 2025
  28. PEEL N, Martin S, Heavens D, Yu DW, et al
    Real-time analysis and visualization of nanopore metagenomic samples with MARTi.
    Genome Res. 2025;35:2488-2500.
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  29. RIBEIRO-DOS-SANTOS AM, Maurano MT
    Iterative improvement of deep learning models using synthetic regulatory genomics.
    Genome Res. 2025;35:2539-2549.
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  30. MATTEI G, Baragli M, Gega B, Mingrino A, et al
    PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing.
    Genome Res. 2025;35:2501-2512.
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  31. ZHOU J, Huang Y, Ma H, Chen Y, et al
    Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat.
    Genome Res. 2025;35:2461-2471.
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  32. MARTELOSSI J, Vujovic J, Huang Y, Tatti A, et al
    High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae.
    Genome Res. 2025;35:2601-2616.
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    October 2025
  33. SHU H, Chen J, Xu C, Hu J, et al
    Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA.
    Genome Res. 2025;35:2285-2299.
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    September 2025
  34. 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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  35. 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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  36. 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
  37. 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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  38. 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
  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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
  46. 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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  47. 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
  48. FREEDMAN AH, Sackton TB
    Building better genome annotations across the tree of life.
    Genome Res. 2025;35:1261-1276.
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  49. 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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  50. 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
  51. MONTANO C, Timp W
    Evolution of genome-wide methylation profiling technologies.
    Genome Res. 2025;35:572-582.
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  52. 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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  53. 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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  54. 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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  55. 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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  56. 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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  57. 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
  58. 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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  59. 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
  60. 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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  61. 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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  62. 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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  63. 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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  64. 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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  65. 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
  66. 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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  67. 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
  68. 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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  69. 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
  70. 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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  71. 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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  72. 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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  73. 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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  74. 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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  75. 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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  76. 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
  77. 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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  78. 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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  79. 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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  80. 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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  81. 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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  82. 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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  83. 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
  84. 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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  85. 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
  86. 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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  87. 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
  88. 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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  89. 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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  90. 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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  91. 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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  92. 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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  93. 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
  94. 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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  95. 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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  96. 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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  97. 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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  98. 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.
    >> Share

  99. 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
  100. 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.
    >> Share

  101. 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
  102. 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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  103. FOROOZANDEH SHAHRAKI M, Farahbod M, Libbrecht MW
    Robust chromatin state annotation.
    Genome Res. 2024;34:469-483.
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    March 2024
  104. 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.
    >> Share

  105. 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
  106. 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.
    >> Share

    December 2023
  107. 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.
    >> Share

  108. 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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  109. 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
  110. 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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  111. 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.
    >> Share

  112. 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
  113. 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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  114. 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
  115. 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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  116. 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

  117. 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
  118. SCHWEIGER R, Durbin R
    Ultrafast genome-wide inference of pairwise coalescence times.
    Genome Res. 2023;33:1023-1031.
    >> Share

  119. BAKER DN, Langmead B
    Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2.
    Genome Res. 2023;33:1218-1227.
    >> Share

  120. RAHMAN HERA M, Pierce-Ward NT, Koslicki D
    Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash.
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  121. CRACCO A, Tomescu AI
    Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT.
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  122. VENKATESARAMANI R, Wan Z, Malin BA, Vorobeychik Y, et al
    Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics.
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    June 2023
  123. 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.
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  124. 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.
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  125. ATKINSON EG, Artomov M, Loboda AA, Rehm HL, et al
    Discordant calls across genotype discovery approaches elucidate variants with systematic errors.
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    May 2023
  126. 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.
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  127. 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.
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  128. JIAO Y, Li M, He X, Wang Y, et al
    Targeted, programmable, and precise tandem duplication in the mammalian genome.
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  129. MUMM C, Drexel ML, McDonald TL, Diehl AG, et al
    Multiplexed long-read plasmid validation and analysis using OnRamp.
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  130. ZHUO X, Hsu S, Purushotham D, Kuntala PK, et al
    Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser.
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  131. 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.
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  132. GERSHMAN A, Hauck Q, Dick M, Jamison JM, et al
    Genomic insights into metabolic flux in hummingbirds.
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    April 2023
  133. BARROSO GV, Lohmueller KE
    Inferring the mode and strength of ongoing selection.
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  134. SUN Y, Cheng Z, Li X, Yang Q, et al
    Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing.
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    March 2023
  135. 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.
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  136. LIU J, Dawe RK
    Large haplotypes highlight a complex age structure within the maize pan-genome.
    Genome Res. 2023;33:359-370.
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  137. DEBO BM, Mallory BJ, Stergachis AB
    Evaluation of N (6)-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes.
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    February 2023
  138. TIAN T, Zhong C, Lin X, Wei Z, et al
    Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning.
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  139. O'CONNELL BL, Nichols RV, Pokholok D, Thomas J, et al
    Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing.
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