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COVID-19: Daily Top 10 Papers


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Articles published in Genome Res

Retrieve available abstracts of 97 articles:
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    October 2020
  1. 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
  2. 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

  3. 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

  4. 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
  5. 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

  6. 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

  7. 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
  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

    October 2019
  13. 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

  14. 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

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

    September 2019
  16. 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

  17. 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
  18. 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

  19. 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

  20. 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

  21. 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
  22. 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

  23. 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

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

  25. 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

  26. 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
  27. 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

  28. 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

  29. 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

  30. 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

  31. 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
  32. 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

  33. 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
  34. 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
  35. 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

  36. 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
  37. 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

  38. 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

  39. 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
  40. 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
  41. 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

  42. 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

  43. 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

  44. 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
  45. 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

  46. 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

  47. 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
  48. 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

  49. 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

  50. 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

  51. 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

  52. 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

  53. 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
  54. 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

  55. 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
  56. 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

  57. 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

  58. 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
  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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

  73. 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

  74. 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
  75. 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

  76. 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

  77. 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
  78. 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

  79. 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

  80. 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

  81. 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

  82. 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
  83. 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

  84. 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
  85. 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

  86. 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
  87. 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
  88. 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

  89. 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
  90. 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

  91. 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

  92. 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

  93. 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

  94. 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

  95. 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
  96. 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
  97. 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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