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Genetics

Free Subscription Articles published in Genome Res Retrieve available abstracts of 98 articles: HTML format

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May 2024
1. 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
   
   
   
2. 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
3. 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
   
   
   
4. FOROOZANDEH SHAHRAKI M, Farahbod M, Libbrecht MW
   Robust chromatin state annotation.
   Genome Res. 2024;34:469-483.
   PubMed     Abstract available
   
   
   March 2024
5. 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
   
   
   
6. 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
7. 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
8. 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
   
   
   October 2023
9. 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
   
   
   
10. 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
    
    
    
11. 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
12. 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
    
    
    
13. 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
14. 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
    
    
    
15. 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
    
    
    
16. 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
17. SCHWEIGER R, Durbin R
    Ultrafast genome-wide inference of pairwise coalescence times.
    Genome Res. 2023;33:1023-1031.
    PubMed     Abstract available
    
    
    
18. BAKER DN, Langmead B
    Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2.
    Genome Res. 2023;33:1218-1227.
    PubMed     Abstract available
    
    
    
19. 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
    
    
    
20. 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
    
    
    
21. 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
22. 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
    
    
    
23. 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
    
    
    
24. 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
25. 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
    
    
    
26. 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
    
    
    
27. 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
    
    
    
28. 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
    
    
    
29. 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
    
    
    
30. 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
    
    
    
31. 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
32. BARROSO GV, Lohmueller KE
    Inferring the mode and strength of ongoing selection.
    Genome Res. 2023;33:632-643.
    PubMed     Abstract available
    
    
    
33. 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
34. 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
    
    
    
35. 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
    
    
    
36. 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
37. 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
    
    
    
38. 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
    
    
    January 2023
39. HARI A, Zhou Q, Gonzaludo N, Harting J, et al
    An efficient genotyper and star-allele caller for pharmacogenomics.
    Genome Res. 2023;33:61-70.
    PubMed     Abstract available
    
    
    
40. MAROILLEY T, Flibotte S, Jean F, Rodrigues Alves Barbosa V, et al
    Genome sequencing of C. elegans balancer strains reveals previously unappreciated complex genomic rearrangements.
    Genome Res. 2023;33:154-167.
    PubMed     Abstract available
    
    
    
41. MULHAIR PO, Crowley L, Boyes DH, Harper A, et al
    Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera.
    Genome Res. 2023;33:32-44.
    PubMed     Abstract available
    
    
    November 2022
42. FEDARKO MW, Kolmogorov M, Pevzner PA
    Analyzing rare mutations in metagenomes assembled using long and accurate reads.
    Genome Res. 2022;32.
    PubMed     Abstract available
    
    
    October 2022
43. GENG K, Merino LG, Wedemann L, Martens A, et al
    Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells.
    Genome Res. 2022;32:1876-1891.
    PubMed     Abstract available
    
    
    
44. RUGGIERI AA, Livraghi L, Lewis JJ, Evans E, et al
    A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility.
    Genome Res. 2022;32:1862-1875.
    PubMed     Abstract available
    
    
    
45. YU H, Ness S, Li CI, Bai Y, et al
    Surveying mutation density patterns around specific genomic features.
    Genome Res. 2022;32:1930-1940.
    PubMed     Abstract available
    
    
    July 2022
46. XU B, Gao X, Li X, Jia Y, et al
    Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells.
    Genome Res. 2022;32:1285-1297.
    PubMed     Abstract available
    
    
    
47. SIAHPIRANI AF, Knaack S, Chasman D, Seirup M, et al
    Dynamic regulatory module networks for inference of cell type-specific transcriptional networks.
    Genome Res. 2022;32:1367-1384.
    PubMed     Abstract available
    
    
    
48. LEE HJ, Hou Y, Maeng JH, Shah NM, et al
    Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish.
    Genome Res. 2022;32:1424-1436.
    PubMed     Abstract available
    
    
    
49. CHANG NC, Rovira Q, Wells J, Feschotte C, et al
    Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression.
    Genome Res. 2022;32:1408-1423.
    PubMed     Abstract available
    
    
    
50. MIKULASOVA A, Kent D, Trevisan-Herraz M, Karataraki N, et al
    Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers.
    Genome Res. 2022;32:1343-1354.
    PubMed     Abstract available
    
    
    June 2022
51. CHEN DW, Garud NR
    Rapid evolution and strain turnover in the infant gut microbiome.
    Genome Res. 2022;32:1124-1136.
    PubMed     Abstract available
    
    
    May 2022
52. SHALON N, Relman DA, Yaffe E
    Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors.
    Genome Res. 2022;32:986-1003.
    PubMed     Abstract available
    
    
    
53. ZHANG F, Xue H, Dong X, Li M, et al
    Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes.
    Genome Res. 2022;32:853-863.
    PubMed     Abstract available
    
    
    April 2022
54. ANTONARAKIS SE
    Short arms of human acrocentric chromosomes and the completion of the human genome sequence.
    Genome Res. 2022;32:599-607.
    PubMed     Abstract available
    
    
    
55. TALBERT PB, Henikoff S
    The genetics and epigenetics of satellite centromeres.
    Genome Res. 2022;32:608-615.
    PubMed     Abstract available
    
    
    
56. 
    Implications of the first complete human genome assembly.
    Genome Res. 2022;32:595-598.
    PubMed    
    
    
    
57. KAMINOW B, Ballouz S, Gillis J, Dobin A, et al
    Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses.
    Genome Res. 2022;32:738-749.
    PubMed     Abstract available
    
    
    March 2022
58. VILUMA A, Flagstad O, Akesson M, Wikenros C, et al
    Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.
    Genome Res. 2022;32:449-458.
    PubMed     Abstract available
    
    
    
59. RIBEIRO-DOS-SANTOS AM, Hogan MS, Luther RD, Brosh R, et al
    Genomic context sensitivity of insulator function.
    Genome Res. 2022;32:425-436.
    PubMed     Abstract available
    
    
    
60. JOSEPH TA, Chlenski P, Litman A, Korem T, et al
    Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.
    Genome Res. 2022;32:558-568.
    PubMed     Abstract available
    
    
    January 2022
61. GALL-DUNCAN T, Sato N, Yuen RKC, Pearson CE, et al
    Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences.
    Genome Res. 2022;32:1-27.
    PubMed     Abstract available
    
    
    
62. LIU L, Chen H, Sun C, Zhang J, et al
    Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling.
    Genome Res. 2022;32:44-54.
    PubMed     Abstract available
    
    
    
63. CHEN S, Liu Y, Zhang Y, Wierbowski SD, et al
    A full-proteome, interaction-specific characterization of mutational hotspots across human cancers.
    Genome Res. 2022;32:135-149.
    PubMed     Abstract available
    
    
    
64. HONG CKY, Cohen BA
    Genomic environments scale the activities of diverse core promoters.
    Genome Res. 2022;32:85-96.
    PubMed     Abstract available
    
    
    November 2021
65. CAHILL JA, Armstrong J, Deran A, Khoury CJ, et al
    Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans.
    Genome Res. 2021;31:2035-2049.
    PubMed     Abstract available
    
    
    
66. LIU X, Ogilvie HA, Nakhleh L
    Variational inference using approximate likelihood under the coalescent with recombination.
    Genome Res. 2021;31:2107-2119.
    PubMed     Abstract available
    
    
    
67. STANEVA DP, Carloni R, Auchynnikava T, Tong P, et al
    A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination.
    Genome Res. 2021;31:2138-2154.
    PubMed     Abstract available
    
    
    October 2021
68. AUERBACH BJ, Hu J, Reilly MP, Li M, et al
    Applications of single-cell genomics and computational strategies to study common disease and population-level variation.
    Genome Res. 2021;31:1728-1741.
    PubMed     Abstract available
    
    
    
69. ADEY AC
    Tagmentation-based single-cell genomics.
    Genome Res. 2021;31:1693-1705.
    PubMed     Abstract available
    
    
    
70. OHNUKI H, Venzon DJ, Lobanov A, Tosato G, et al
    Iterative epigenomic analyses in the same single cell.
    Genome Res. 2021;31:1819-1830.
    PubMed     Abstract available
    
    
    September 2021
71. SAUTERAUD R, Stahl JM, James J, Englebright M, et al
    Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases.
    Genome Res. 2021;31:1629-1637.
    PubMed     Abstract available
    
    
    August 2021
72. ROODGAR M, Good BH, Garud NR, Martis S, et al
    Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment.
    Genome Res. 2021;31:1433-1446.
    PubMed     Abstract available
    
    
    
73. BRASHEAR WA, Bredemeyer KR, Murphy WJ
    Genomic architecture constrained placental mammal X Chromosome evolution.
    Genome Res. 2021;31:1353-1365.
    PubMed     Abstract available
    
    
    
74. HERPIN A, Schartl M, Depince A, Guiguen Y, et al
    Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish.
    Genome Res. 2021;31:1366-1380.
    PubMed     Abstract available
    
    
    
75. RIDDIFORD N, Siudeja K, van den Beek M, Boumard B, et al
    Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells.
    Genome Res. 2021;31:1419-1432.
    PubMed     Abstract available
    
    
    June 2021
76. SHIRAI K, Sato MP, Nishi R, Seki M, et al
    Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants.
    Genome Res. 2021;31:1060-1068.
    PubMed     Abstract available
    
    
    
77. BOHM KA, Hodges AJ, Czaja W, Selvam K, et al
    Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repair.
    Genome Res. 2021;31:1047-1059.
    PubMed     Abstract available
    
    
    
78. RADKE DW, Sul JH, Balick DJ, Akle S, et al
    Purifying selection on noncoding deletions of human regulatory loci detected using their cellular pleiotropy.
    Genome Res. 2021;31:935-946.
    PubMed     Abstract available
    
    
    May 2021
79. CHEN M, Wei R, Wei G, Xu M, et al
    Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes.
    Genome Res. 2021;31:890-899.
    PubMed     Abstract available
    
    
    
80. SERRES-ARMERO A, Davis BW, Povolotskaya IS, Morcillo-Suarez C, et al
    Copy number variation underlies complex phenotypes in domestic dog breeds and other canids.
    Genome Res. 2021;31:762-774.
    PubMed     Abstract available
    
    
    
81. RANALLO-BENAVIDEZ TR, Lemmon Z, Soyk S, Aganezov S, et al
    Optimized sample selection for cost-efficient long-read population sequencing.
    Genome Res. 2021;31:910-918.
    PubMed     Abstract available
    
    
    April 2021
82. LI Y, Cao K, Li N, Zhu G, et al
    Genomic analyses provide insights into peach local adaptation and responses to climate change.
    Genome Res. 2021;31:592-606.
    PubMed     Abstract available
    
    
    March 2021
83. MA Q, Srivastav SP, Gamez S, Dayama G, et al
    A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons.
    Genome Res. 2021;31:512-528.
    PubMed     Abstract available
    
    
    
84. LIAO Y, Zhang X, Chakraborty M, Emerson JJ, et al
    Topologically associating domains and their role in the evolution of genome structure and function in Drosophila.
    Genome Res. 2021;31:397-410.
    PubMed     Abstract available
    
    
    January 2021
85. BAKER JL, Morton JT, Dinis M, Alvarez R, et al
    Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules.
    Genome Res. 2021;31:64-74.
    PubMed     Abstract available
    
    
    
86. UZUN Y, Wu H, Tan K
    Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data.
    Genome Res. 2021;31:101-109.
    PubMed     Abstract available
    
    
    October 2020
87. GOMEZ-CARBALLA A, Bello X, Pardo-Seco J, Martinon-Torres F, et al
    Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders.
    Genome Res. 2020;30:1434-1448.
    PubMed     Abstract available
    
    
    March 2020
88. CHEN LX, Anantharaman K, Shaiber A, Eren AM, et al
    Accurate and complete genomes from metagenomes.
    Genome Res. 2020;30:315-333.
    PubMed     Abstract available
    
    
    
89. FREEMAN TM, Wang D, Harris J
    Genomic loci susceptible to systematic sequencing bias in clinical whole genomes.
    Genome Res. 2020;30:415-426.
    PubMed     Abstract available
    
    
    
90. BEAULAURIER J, Luo E, Eppley JM, Uyl PD, et al
    Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities.
    Genome Res. 2020;30:437-446.
    PubMed     Abstract available
    
    
    February 2020
91. MILLS RH, Wozniak JM, Vrbanac A, Campeau A, et al
    Organ-level protein networks as a reference for the host effects of the microbiome.
    Genome Res. 2020;30:276-286.
    PubMed     Abstract available
    
    
    
92. ZHANG F, Flickinger M, Taliun SAG, Abecasis GR, et al
    Ancestry-agnostic estimation of DNA sample contamination from sequence reads.
    Genome Res. 2020;30:185-194.
    PubMed     Abstract available
    
    
    
93. BLAKE LE, Roux J, Hernando-Herraez I, Banovich NE, et al
    A comparison of gene expression and DNA methylation patterns across tissues and species.
    Genome Res. 2020;30:250-262.
    PubMed     Abstract available
    
    
    January 2020
94. THORNLOW BP, Armstrong J, Holmes AD, Howard JM, et al
    Predicting transfer RNA gene activity from sequence and genome context.
    Genome Res. 2020;30:85-94.
    PubMed     Abstract available
    
    
    
95. ROTHSTEIN M, Simoes-Costa M
    Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification.
    Genome Res. 2020;30:35-48.
    PubMed     Abstract available
    
    
    
96. BARRIO-HERNANDEZ I, Jafari A, Rigbolt KTG, Hallenborg P, et al
    Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow-derived stromal stem cells.
    Genome Res. 2020;30:127-137.
    PubMed     Abstract available
    
    
    
97. ZHOU Z, Alikhan NF, Mohamed K, Fan Y, et al
    The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity.
    Genome Res. 2020;30:138-152.
    PubMed     Abstract available
    
    
    
98. BELOKOPYTOVA PS, Nuriddinov MA, Mozheiko EA, Fishman D, et al
    Quantitative prediction of enhancer-promoter interactions.
    Genome Res. 2020;30:72-84.
    PubMed     Abstract available
    
    

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