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Articles published in Genome Res

Retrieve available abstracts of 85 articles:
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Single Articles

    October 2019
  1. VITALI V, Hagen R, Catania F
    Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia.
    Genome Res. 2019;29:1693-1704.
    PubMed     Abstract available

  2. MADANI TONEKABONI SA, Mazrooei P, Kofia V, Haibe-Kains B, et al
    Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks.
    Genome Res. 2019;29:1733-1743.
    PubMed     Abstract available

  3. VAINBERG SLUTSKIN I, Weinberger A, Segal E
    Sequence determinants of polyadenylation-mediated regulation.
    Genome Res. 2019;29:1635-1647.
    PubMed     Abstract available

    September 2019
  4. FESENKO I, Kirov I, Kniazev A, Khazigaleeva R, et al
    Distinct types of short open reading frames are translated in plant cells.
    Genome Res. 2019;29:1464-1477.
    PubMed     Abstract available

  5. REFOYO-MARTINEZ A, da Fonseca RR, Halldorsdottir K, Arnason E, et al
    Identifying loci under positive selection in complex population histories.
    Genome Res. 2019;29:1506-1520.
    PubMed     Abstract available

    August 2019
  6. HUNT LC, Jiao J, Wang YD, Finkelstein D, et al
    Circadian gene variants and the skeletal muscle circadian clock contribute to the evolutionary divergence in longevity across Drosophila populations.
    Genome Res. 2019;29:1262-1276.
    PubMed     Abstract available

  7. JOHNSTON MJ, Nikolic A, Ninkovic N, Guilhamon P, et al
    High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma.
    Genome Res. 2019;29:1211-1222.
    PubMed     Abstract available

  8. HUANG YF, Siepel A
    Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.
    Genome Res. 2019;29:1310-1321.
    PubMed     Abstract available

  9. MELESHKO D, Mohimani H, Tracanna V, Hajirasouliha I, et al
    BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs.
    Genome Res. 2019;29:1352-1362.
    PubMed     Abstract available

    June 2019
  10. SIDOLI S, Kori Y, Lopes M, Yuan ZF, et al
    One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry.
    Genome Res. 2019;29:978-987.
    PubMed     Abstract available

  11. KIM C, Kim J, Kim S, Cook DE, et al
    Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans.
    Genome Res. 2019;29:1023-1035.
    PubMed     Abstract available

  12. YOSHIMURA J, Ichikawa K, Shoura MJ, Artiles KL, et al
    Recompleting the Caenorhabditis elegans genome.
    Genome Res. 2019;29:1009-1022.
    PubMed     Abstract available

  13. BREITWIESER FP, Pertea M, Zimin AV, Salzberg SL, et al
    Human contamination in bacterial genomes has created thousands of spurious proteins.
    Genome Res. 2019;29:954-960.
    PubMed     Abstract available

  14. ANTIPOV D, Raiko M, Lapidus A, Pevzner PA, et al
    Plasmid detection and assembly in genomic and metagenomic data sets.
    Genome Res. 2019;29:961-968.
    PubMed     Abstract available

    May 2019
  15. MILLER S, Naccache SN, Samayoa E, Messacar K, et al
    Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.
    Genome Res. 2019;29:831-842.
    PubMed     Abstract available

  16. FUENTES RR, Chebotarov D, Duitama J, Smith S, et al
    Structural variants in 3000 rice genomes.
    Genome Res. 2019;29:870-880.
    PubMed     Abstract available

  17. WANG O, Chin R, Cheng X, Wu MKY, et al
    Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly.
    Genome Res. 2019;29:798-808.
    PubMed     Abstract available

  18. SINNAMON JR, Torkenczy KA, Linhoff MW, Vitak SA, et al
    The accessible chromatin landscape of the murine hippocampus at single-cell resolution.
    Genome Res. 2019;29:857-869.
    PubMed     Abstract available

  19. PUCKETT EE, Munshi-South J
    Brown rat demography reveals pre-commensal structure in eastern Asia before expansion into Southeast Asia.
    Genome Res. 2019;29:762-770.
    PubMed     Abstract available

    February 2019
  20. LEES JA, Harris SR, Tonkin-Hill G, Gladstone RA, et al
    Fast and flexible bacterial genomic epidemiology with PopPUNK.
    Genome Res. 2019;29:304-316.
    PubMed     Abstract available

  21. WANG Z, Chu T, Choate LA, Danko CG, et al
    Identification of regulatory elements from nascent transcription using dREG.
    Genome Res. 2019;29:293-303.
    PubMed     Abstract available

    January 2019
  22. DANKO DC, Meleshko D, Bezdan D, Mason C, et al
    Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics.
    Genome Res. 2019;29:116-124.
    PubMed     Abstract available

    December 2018
  23. YE CJ, Chen J, Villani AC, Gate RE, et al
    Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection.
    Genome Res. 2018;28:1812-1825.
    PubMed     Abstract available

  24. GUIBLET WM, Cremona MA, Cechova M, Harris RS, et al
    Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate.
    Genome Res. 2018;28:1767-1778.
    PubMed     Abstract available

    October 2018
  25. GOLTSMAN DSA, Sun CL, Proctor DM, DiGiulio DB, et al
    Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome.
    Genome Res. 2018;28:1467-1480.
    PubMed     Abstract available

  26. JAVASKY E, Shamir I, Gandhi S, Egri S, et al
    Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns.
    Genome Res. 2018;28:1455-1466.
    PubMed     Abstract available

  27. LEE D, Kapoor A, Safi A, Song L, et al
    Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants.
    Genome Res. 2018;28:1577-1588.
    PubMed     Abstract available

    September 2018
  28. OZERCAN HI, Ileri AM, Ayday E, Alkan C, et al
    Realizing the potential of blockchain technologies in genomics.
    Genome Res. 2018;28:1255-1263.
    PubMed     Abstract available

    July 2018
  29. LAZAR NH, Nevonen KA, O'Connell B, McCann C, et al
    Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.
    Genome Res. 2018;28:983-997.
    PubMed     Abstract available

  30. MAGALHAES WCS, Araujo NM, Leal TP, Araujo GS, et al
    EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow.
    Genome Res. 2018;28:1090-1095.
    PubMed     Abstract available

  31. LIU G, Wang W, Hu S, Wang X, et al
    Inherited DNA methylation primes the establishment of accessible chromatin during genome activation.
    Genome Res. 2018;28:998-1007.
    PubMed     Abstract available

  32. LOMSADZE A, Gemayel K, Tang S, Borodovsky M, et al
    Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.
    Genome Res. 2018;28:1079-1089.
    PubMed     Abstract available

    June 2018
  33. GOMEZ-CARBALLA A, Pardo-Seco J, Brandini S, Achilli A, et al
    The peopling of South America and the trans-Andean gene flow of the first settlers.
    Genome Res. 2018;28:767-779.
    PubMed     Abstract available

  34. KOFLER R, Senti KA, Nolte V, Tobler R, et al
    Molecular dissection of a natural transposable element invasion.
    Genome Res. 2018;28:824-835.
    PubMed     Abstract available

  35. O'FLAHERTY BM, Li Y, Tao Y, Paden CR, et al
    Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing.
    Genome Res. 2018;28:869-877.
    PubMed     Abstract available

    May 2018
  36. PIDSLEY R, Lawrence MG, Zotenko E, Niranjan B, et al
    Enduring epigenetic landmarks define the cancer microenvironment.
    Genome Res. 2018;28:625-638.
    PubMed     Abstract available

  37. BRUNET MA, Levesque SA, Hunting DJ, Cohen AA, et al
    Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship.
    Genome Res. 2018;28:609-624.
    PubMed     Abstract available

  38. LI C, Lenhard B, Luscombe NM
    Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome.
    Genome Res. 2018;28:676-688.
    PubMed     Abstract available

  39. MCGURK MP, Barbash DA
    Double insertion of transposable elements provides a substrate for the evolution of satellite DNA.
    Genome Res. 2018;28:714-725.
    PubMed     Abstract available

  40. KELLEY DR, Reshef YA, Bileschi M, Belanger D, et al
    Sequential regulatory activity prediction across chromosomes with convolutional neural networks.
    Genome Res. 2018;28:739-750.
    PubMed     Abstract available

  41. CORVELO A, Clarke WE, Robine N, Zody MC, et al
    taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.
    Genome Res. 2018;28:751-758.
    PubMed     Abstract available

    April 2018
  42. WALA JA, Bandopadhayay P, Greenwald NF, O'Rourke R, et al
    SvABA: genome-wide detection of structural variants and indels by local assembly.
    Genome Res. 2018;28:581-591.
    PubMed     Abstract available

  43. WEST PT, Probst AJ, Grigoriev IV, Thomas BC, et al
    Genome-reconstruction for eukaryotes from complex natural microbial communities.
    Genome Res. 2018;28:569-580.
    PubMed     Abstract available

    June 2017
  44. TRANCHEVENT LC, Aube F, Dulaurier L, Benoit-Pilven C, et al
    Identification of protein features encoded by alternative exons using Exon Ontology.
    Genome Res. 2017;27:1087-1097.
    PubMed     Abstract available

  45. DUBOIS-CHEVALIER J, Dubois V, Dehondt H, Mazrooei P, et al
    The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions.
    Genome Res. 2017;27:985-996.
    PubMed     Abstract available

  46. COOK-DEEGAN R, McGuire AL
    Moving beyond Bermuda: sharing data to build a medical information commons.
    Genome Res. 2017;27:897-901.
    PubMed     Abstract available

    May 2017
  47. BAAIJENS JA, Aabidine AZE, Rivals E, Schonhuth A, et al
    De novo assembly of viral quasispecies using overlap graphs.
    Genome Res. 2017;27:835-848.
    PubMed     Abstract available

  48. SCHNEIDER VA, Graves-Lindsay T, Howe K, Bouk N, et al
    Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
    Genome Res. 2017;27:849-864.
    PubMed     Abstract available

  49. PATEN B, Novak AM, Eizenga JM, Garrison E, et al
    Genome graphs and the evolution of genome inference.
    Genome Res. 2017;27:665-676.
    PubMed     Abstract available

  50. NORMAN PJ, Norberg SJ, Guethlein LA, Nemat-Gorgani N, et al
    Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II.
    Genome Res. 2017;27:813-823.
    PubMed     Abstract available

  51. KAMATH GM, Shomorony I, Xia F, Courtade TA, et al
    HINGE: long-read assembly achieves optimal repeat resolution.
    Genome Res. 2017;27:747-756.
    PubMed     Abstract available

  52. KOREN S, Walenz BP, Berlin K, Miller JR, et al
    Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
    Genome Res. 2017;27:722-736.
    PubMed     Abstract available

  53. NURK S, Meleshko D, Korobeynikov A, Pevzner PA, et al
    metaSPAdes: a new versatile metagenomic assembler.
    Genome Res. 2017;27:824-834.
    PubMed     Abstract available

  54. JACKMAN SD, Vandervalk BP, Mohamadi H, Chu J, et al
    ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.
    Genome Res. 2017;27:768-777.
    PubMed     Abstract available

  55. JIAO WB, Accinelli GG, Hartwig B, Kiefer C, et al
    Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data.
    Genome Res. 2017;27:778-786.
    PubMed     Abstract available

  56. ZIMIN AV, Puiu D, Luo MC, Zhu T, et al
    Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.
    Genome Res. 2017;27:787-792.
    PubMed     Abstract available

  57. FAN X, Chaisson M, Nakhleh L, Chen K, et al
    HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies.
    Genome Res. 2017;27:793-800.
    PubMed     Abstract available

  58. VASER R, Sovic I, Nagarajan N, Sikic M, et al
    Fast and accurate de novo genome assembly from long uncorrected reads.
    Genome Res. 2017;27:737-746.
    PubMed     Abstract available

  59. EDGE P, Bafna V, Bansal V
    HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies.
    Genome Res. 2017;27:801-812.
    PubMed     Abstract available

  60. DAMAS J, O'Connor R, Farre M, Lenis VPE, et al
    Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.
    Genome Res. 2017;27:875-884.
    PubMed     Abstract available

  61. HUDDLESTON J, Chaisson MJP, Steinberg KM, Warren W, et al
    Discovery and genotyping of structural variation from long-read haploid genome sequence data.
    Genome Res. 2017;27:677-685.
    PubMed     Abstract available

  62. LI M, Chen L, Tian S, Lin Y, et al
    Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies.
    Genome Res. 2017;27:865-874.
    PubMed     Abstract available

    February 2017
  63. DOLLE DD, Liu Z, Cotten M, Simpson JT, et al
    Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.
    Genome Res. 2017;27:300-309.
    PubMed     Abstract available

  64. PEREZ-RICO YA, Boeva V, Mallory AC, Bitetti A, et al
    Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes.
    Genome Res. 2017;27:259-268.
    PubMed     Abstract available

  65. QIAN M, Zhang H, Kham SK, Liu S, et al
    Whole-transcriptome sequencing identifies a distinct subtype of acute lymphoblastic leukemia with predominant genomic abnormalities of EP300 and CREBBP.
    Genome Res. 2017;27:185-195.
    PubMed     Abstract available

    January 2017
  66. PRASAD TS, Mohanty AK, Kumar M, Sreenivasamurthy SK, et al
    Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.
    Genome Res. 2017;27:133-144.
    PubMed     Abstract available

  67. JORDA M, Diez-Villanueva A, Mallona I, Martin B, et al
    The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells.
    Genome Res. 2017;27:118-132.
    PubMed     Abstract available

  68. DZAMBA M, Ramani AK, Buczkowicz P, Jiang Y, et al
    Identification of complex genomic rearrangements in cancers using CouGaR.
    Genome Res. 2017;27:107-117.
    PubMed     Abstract available

  69. WONG EH, Khrunin A, Nichols L, Pushkarev D, et al
    Reconstructing genetic history of Siberian and Northeastern European populations.
    Genome Res. 2017;27:1-14.
    PubMed     Abstract available

  70. EBERLE MA, Fritzilas E, Krusche P, Kallberg M, et al
    A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.
    Genome Res. 2017;27:157-164.
    PubMed     Abstract available

    August 2016
  71. FAINO L, Seidl MF, Shi-Kunne X, Pauper M, et al
    Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen.
    Genome Res. 2016;26:1091-100.
    PubMed     Abstract available

  72. SHARMIN M, Bravo HC, Hannenhalli S
    Heterogeneity of transcription factor binding specificity models within and across cell lines.
    Genome Res. 2016;26:1110-23.
    PubMed     Abstract available

    July 2016
  73. BRONNER IF, Otto TD, Zhang M, Udenze K, et al
    Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants.
    Genome Res. 2016;26:980-9.
    PubMed     Abstract available

  74. URICCHIO LH, Zaitlen NA, Ye CJ, Witte JS, et al
    Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants.
    Genome Res. 2016;26:863-73.
    PubMed     Abstract available

    May 2016
  75. ZHAO L, Chen Y, Bajaj AO, Eblimit A, et al
    Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes.
    Genome Res. 2016;26:660-9.
    PubMed     Abstract available

    April 2016
  76. TOMASZKIEWICZ M, Rangavittal S, Cechova M, Campos Sanchez R, et al
    A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.
    Genome Res. 2016;26:530-40.
    PubMed     Abstract available

  77. HALLAST P, Maisano Delser P, Batini C, Zadik D, et al
    Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal.
    Genome Res. 2016;26:427-39.
    PubMed     Abstract available

    March 2016
  78. HSIEH P, Woerner AE, Wall JD, Lachance J, et al
    Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.
    Genome Res. 2016;26:291-300.
    PubMed     Abstract available

  79. HSIEH P, Veeramah KR, Lachance J, Tishkoff SA, et al
    Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection.
    Genome Res. 2016;26:279-90.
    PubMed     Abstract available

  80. PUTNAM NH, O'Connell BL, Stites JC, Rice BJ, et al
    Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.
    Genome Res. 2016;26:342-50.
    PubMed     Abstract available

  81. KIM D, Kim S, Kim S, Park J, et al
    Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq.
    Genome Res. 2016;26:406-15.
    PubMed     Abstract available

  82. ZHONG J, Luo K, Winter PS, Crawford GE, et al
    Mapping nucleosome positions using DNase-seq.
    Genome Res. 2016;26:351-64.
    PubMed     Abstract available

  83. KNOUSE KA, Wu J, Amon A
    Assessment of megabase-scale somatic copy number variation using single-cell sequencing.
    Genome Res. 2016;26:376-84.
    PubMed     Abstract available

    February 2016
  84. MULDER NJ, Adebiyi E, Alami R, Benkahla A, et al
    H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa.
    Genome Res. 2016;26:271-7.
    PubMed     Abstract available

    January 2016
  85. ZHANG J, White NM, Schmidt HK, Fulton RS, et al
    INTEGRATE: gene fusion discovery using whole genome and transcriptome data.
    Genome Res. 2016;26:108-18.
    PubMed     Abstract available

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