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Articles published in Genome Res

Retrieve available abstracts of 64 articles:
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Single Articles


    January 2019
  1. 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     Text format     Abstract available


    December 2018
  2. 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     Text format     Abstract available


  3. 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     Text format     Abstract available


    October 2018
  4. 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     Text format     Abstract available


  5. 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     Text format     Abstract available


  6. 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     Text format     Abstract available


    September 2018
  7. 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     Text format     Abstract available


    July 2018
  8. 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     Text format     Abstract available


  9. 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     Text format     Abstract available


  10. 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     Text format     Abstract available


  11. 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     Text format     Abstract available


    June 2018
  12. 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     Text format     Abstract available


  13. 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     Text format     Abstract available


  14. 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     Text format     Abstract available


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


  16. 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     Text format     Abstract available


  17. 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     Text format     Abstract available


  18. 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     Text format     Abstract available


  19. 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     Text format     Abstract available


  20. 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     Text format     Abstract available


    April 2018
  21. 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     Text format     Abstract available


  22. 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     Text format     Abstract available


    June 2017
  23. 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     Text format     Abstract available


  24. 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     Text format     Abstract available


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


    May 2017
  26. 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     Text format     Abstract available


  27. 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     Text format     Abstract available


  28. 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     Text format     Abstract available


  29. 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     Text format     Abstract available


  30. 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     Text format     Abstract available


  31. 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     Text format     Abstract available


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


  33. 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     Text format     Abstract available


  34. 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     Text format     Abstract available


  35. 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     Text format     Abstract available


  36. 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     Text format     Abstract available


  37. 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     Text format     Abstract available


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


  39. 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     Text format     Abstract available


  40. 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     Text format     Abstract available


  41. 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     Text format     Abstract available


    February 2017
  42. 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     Text format     Abstract available


  43. 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     Text format     Abstract available


  44. 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     Text format     Abstract available


    January 2017
  45. 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     Text format     Abstract available


  46. 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     Text format     Abstract available


  47. 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     Text format     Abstract available


  48. 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     Text format     Abstract available


  49. 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     Text format     Abstract available


    August 2016
  50. 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     Text format     Abstract available


  51. 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     Text format     Abstract available


    July 2016
  52. 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     Text format     Abstract available


  53. 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     Text format     Abstract available


    May 2016
  54. 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     Text format     Abstract available


    April 2016
  55. 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     Text format     Abstract available


  56. 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     Text format     Abstract available


    March 2016
  57. 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     Text format     Abstract available


  58. 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     Text format     Abstract available


  59. 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     Text format     Abstract available


  60. 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     Text format     Abstract available


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


  62. 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     Text format     Abstract available


    February 2016
  63. 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     Text format     Abstract available


    January 2016
  64. 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     Text format     Abstract available


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