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Genetics

Free Subscription Articles published in Genome Res Retrieve available abstracts of 92 articles: HTML format

Single Articles

May 2025
1. FREEDMAN AH, Sackton TB
   Building better genome annotations across the tree of life.
   Genome Res. 2025;35:1261-1276.
   PubMed     Abstract available
   
   
   
2. 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.
   PubMed     Abstract available
   
   
   
3. LEE DI, Roy S
   Examining the dynamics of three-dimensional genome organization with multitask matrix factorization.
   Genome Res. 2025;35:1179-1193.
   PubMed     Abstract available
   
   
   April 2025
4. MONTANO C, Timp W
   Evolution of genome-wide methylation profiling technologies.
   Genome Res. 2025;35:572-582.
   PubMed     Abstract available
   
   
   
5. RAUSCH T, Marschall T, Korbel JO
   The impact of long-read sequencing on human population-scale genomics.
   Genome Res. 2025;35:593-598.
   PubMed     Abstract available
   
   
   
6. MAHMOUD M, Agustinho DP, Sedlazeck FJ
   A Hitchhiker's Guide to long-read genomic analysis.
   Genome Res. 2025;35:545-558.
   PubMed     Abstract available
   
   
   
7. 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.
   PubMed     Abstract available
   
   
   
8. 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.
   PubMed     Abstract available
   
   
   
9. 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.
   PubMed     Abstract available
   
   
   
10. 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.
    PubMed     Abstract available
    
    
    March 2025
11. 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.
    PubMed     Abstract available
    
    
    
12. LI Y, Zhang J
    Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved.
    Genome Res. 2025;35:512-521.
    PubMed     Abstract available
    
    
    February 2025
13. JENIKE KM, Campos-Dominguez L, Bodde M, Cerca J, et al
    k-mer approaches for biodiversity genomics.
    Genome Res. 2025;35:219-230.
    PubMed     Abstract available
    
    
    
14. 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.
    PubMed     Abstract available
    
    
    
15. ZHI D, Jiang X, Harmanci A
    Proxy panels enable privacy-aware outsourcing of genotype imputation.
    Genome Res. 2025;35:326-339.
    PubMed     Abstract available
    
    
    
16. 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.
    PubMed     Abstract available
    
    
    
17. MOURATIDIS I, Konnaris MA, Chantzi N, Chan CSY, et al
    Identification of the shortest species-specific oligonucleotide sequences.
    Genome Res. 2025;35:279-295.
    PubMed     Abstract available
    
    
    
18. 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.
    PubMed     Abstract available
    
    
    January 2025
19. 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.
    PubMed     Abstract available
    
    
    
20. 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.
    PubMed     Abstract available
    
    
    December 2024
21. 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.
    PubMed     Abstract available
    
    
    
22. 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.
    PubMed     Abstract available
    
    
    November 2024
23. IYER SV, Goodwin S, McCombie WR
    Leveraging the power of long reads for targeted sequencing.
    Genome Res. 2024;34:1701-1718.
    PubMed     Abstract available
    
    
    
24. 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.
    PubMed     Abstract available
    
    
    
25. 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.
    PubMed     Abstract available
    
    
    
26. 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.
    PubMed     Abstract available
    
    
    
27. 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.
    PubMed     Abstract available
    
    
    
28. 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.
    PubMed     Abstract available
    
    
    
29. 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.
    PubMed     Abstract available
    
    
    October 2024
30. 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.
    PubMed     Abstract available
    
    
    
31. 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.
    PubMed     Abstract available
    
    
    
32. SCHROD S, Luck N, Lohmayer R, Solbrig S, et al
    Spatial Cellular Networks from omics data with SpaCeNet.
    Genome Res. 2024;34:1371-1383.
    PubMed     Abstract available
    
    
    
33. SAPCI AOB, Mirarab S
    Memory-bound k-mer selection for large and evolutionarily diverse reference libraries.
    Genome Res. 2024;34:1455-1467.
    PubMed     Abstract available
    
    
    
34. 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.
    PubMed     Abstract available
    
    
    
35. 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.
    PubMed     Abstract available
    
    
    
36. CHANDRA G, Gibney D, Jain C
    Haplotype-aware sequence alignment to pangenome graphs.
    Genome Res. 2024;34:1265-1275.
    PubMed     Abstract available
    
    
    September 2024
37. 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.
    PubMed     Abstract available
    
    
    
38. 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.
    PubMed     Abstract available
    
    
    August 2024
39. 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.
    PubMed     Abstract available
    
    
    
40. 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.
    PubMed     Abstract available
    
    
    July 2024
41. 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.
    PubMed     Abstract available
    
    
    
42. 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.
    PubMed     Abstract available
    
    
    
43. 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.
    PubMed     Abstract available
    
    
    
44. 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.
    PubMed     Abstract available
    
    
    
45. BUCKLEY RM, Ostrander EA
    Large-scale genomic analysis of the domestic dog informs biological discovery.
    Genome Res. 2024;34:811-821.
    PubMed     Abstract available
    
    
    
46. ULRICH JU, Renard BY
    Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters.
    Genome Res. 2024;34:914-924.
    PubMed     Abstract available
    
    
    June 2024
47. 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.
    PubMed     Abstract available
    
    
    
48. 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.
    PubMed     Abstract available
    
    
    
49. WON S, Yu J, Kim H
    Identifying genes within pathways in unannotated genomes with PaGeSearch.
    Genome Res. 2024;34:784-795.
    PubMed     Abstract available
    
    
    
50. MURPHY WJ, Harris AJ
    Toward telomere-to-telomere cat genomes for precision medicine and conservation biology.
    Genome Res. 2024;34:655-664.
    PubMed     Abstract available
    
    
    
51. 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.
    PubMed     Abstract available
    
    
    
52. 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.
    PubMed     Abstract available
    
    
    May 2024
53. 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.
    PubMed     Abstract available
    
    
    
54. 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.
    PubMed     Abstract available
    
    
    April 2024
55. 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.
    PubMed     Abstract available
    
    
    
56. FOROOZANDEH SHAHRAKI M, Farahbod M, Libbrecht MW
    Robust chromatin state annotation.
    Genome Res. 2024;34:469-483.
    PubMed     Abstract available
    
    
    March 2024
57. 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.
    PubMed     Abstract available
    
    
    
58. 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.
    PubMed     Abstract available
    
    
    February 2024
59. 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.
    PubMed    
    
    
    December 2023
60. 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.
    PubMed     Abstract available
    
    
    
61. 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.
    PubMed     Abstract available
    
    
    
62. 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.
    PubMed     Abstract available
    
    
    October 2023
63. 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.
    PubMed     Abstract available
    
    
    
64. 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.
    PubMed     Abstract available
    
    
    
65. 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.
    PubMed     Abstract available
    
    
    September 2023
66. 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.
    PubMed     Abstract available
    
    
    
67. 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.
    PubMed     Abstract available
    
    
    August 2023
68. 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.
    PubMed     Abstract available
    
    
    
69. 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.
    PubMed     Abstract available
    
    
    
70. 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.
    PubMed     Abstract available
    
    
    July 2023
71. SCHWEIGER R, Durbin R
    Ultrafast genome-wide inference of pairwise coalescence times.
    Genome Res. 2023;33:1023-1031.
    PubMed     Abstract available
    
    
    
72. BAKER DN, Langmead B
    Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2.
    Genome Res. 2023;33:1218-1227.
    PubMed     Abstract available
    
    
    
73. 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.
    PubMed     Abstract available
    
    
    
74. CRACCO A, Tomescu AI
    Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT.
    Genome Res. 2023;33:1198-1207.
    PubMed     Abstract available
    
    
    
75. 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.
    PubMed     Abstract available
    
    
    June 2023
76. 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.
    PubMed     Abstract available
    
    
    
77. 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.
    PubMed     Abstract available
    
    
    
78. 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.
    PubMed     Abstract available
    
    
    May 2023
79. 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.
    PubMed     Abstract available
    
    
    
80. 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.
    PubMed     Abstract available
    
    
    
81. 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.
    PubMed     Abstract available
    
    
    
82. 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.
    PubMed     Abstract available
    
    
    
83. 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.
    PubMed     Abstract available
    
    
    
84. 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.
    PubMed     Abstract available
    
    
    
85. GERSHMAN A, Hauck Q, Dick M, Jamison JM, et al
    Genomic insights into metabolic flux in hummingbirds.
    Genome Res. 2023;33:703-714.
    PubMed     Abstract available
    
    
    April 2023
86. BARROSO GV, Lohmueller KE
    Inferring the mode and strength of ongoing selection.
    Genome Res. 2023;33:632-643.
    PubMed     Abstract available
    
    
    
87. 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.
    PubMed     Abstract available
    
    
    March 2023
88. 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.
    PubMed     Abstract available
    
    
    
89. LIU J, Dawe RK
    Large haplotypes highlight a complex age structure within the maize pan-genome.
    Genome Res. 2023;33:359-370.
    PubMed     Abstract available
    
    
    
90. DEBO BM, Mallory BJ, Stergachis AB
    Evaluation of N (6)-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes.
    Genome Res. 2023;33:427-434.
    PubMed     Abstract available
    
    
    February 2023
91. 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.
    PubMed     Abstract available
    
    
    
92. 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.
    PubMed     Abstract available
    
    

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