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Articles published in Genome Res

Retrieve available abstracts of 73 articles:
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Single Articles


    June 2017
  1. 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


  2. 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


  3. 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
  4. 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


  5. 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


  6. 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


  7. 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


  8. 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


  9. 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


  10. 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


  11. 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


  12. 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


  13. 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


  14. 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


  15. 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


  16. 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


  17. 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


  18. 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


  19. 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
  20. 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


  21. 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


  22. 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
  23. 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


  24. 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


  25. 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


  26. 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


  27. 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
  28. 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


  29. 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
  30. 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


  31. 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
  32. 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
  33. 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


  34. 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
  35. 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


  36. 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


  37. 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


  38. 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


  39. 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


  40. 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
  41. 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
  42. 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


    July 2015
  43. BOSSE M, Megens HJ, Madsen O, Crooijmans RP, et al
    Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations.
    Genome Res. 2015;25:970-81.
    PubMed     Text format     Abstract available


  44. VARSHNEY GK, Pei W, LaFave MC, Idol J, et al
    High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9.
    Genome Res. 2015;25:1030-42.
    PubMed     Text format     Abstract available


  45. PARKS DH, Imelfort M, Skennerton CT, Hugenholtz P, et al
    CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
    Genome Res. 2015;25:1043-55.
    PubMed     Text format     Abstract available


  46. LUBLINER S, Regev I, Lotan-Pompan M, Edelheit S, et al
    Core promoter sequence in yeast is a major determinant of expression level.
    Genome Res. 2015;25:1008-17.
    PubMed     Text format     Abstract available


  47. BARAN Y, Subramaniam M, Biton A, Tukiainen T, et al
    The landscape of genomic imprinting across diverse adult human tissues.
    Genome Res. 2015;25:927-36.
    PubMed     Text format     Abstract available


  48. MARQUEZ Y, Hopfler M, Ayatollahi Z, Barta A, et al
    Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity.
    Genome Res. 2015;25:995-1007.
    PubMed     Text format     Abstract available


  49. AMES SK, Gardner SN, Marti JM, Slezak TR, et al
    Using populations of human and microbial genomes for organism detection in metagenomes.
    Genome Res. 2015;25:1056-67.
    PubMed     Text format     Abstract available


  50. FAIRFIELD H, Srivastava A, Ananda G, Liu R, et al
    Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders.
    Genome Res. 2015;25:948-57.
    PubMed     Text format     Abstract available


  51. WIJCHERS PJ, Geeven G, Eyres M, Bergsma AJ, et al
    Characterization and dynamics of pericentromere-associated domains in mice.
    Genome Res. 2015;25:958-69.
    PubMed     Text format     Abstract available


    June 2015
  52. LIM HW, Uhlenhaut NH, Rauch A, Weiner J, et al
    Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo.
    Genome Res. 2015;25:836-44.
    PubMed     Text format     Abstract available


  53. BUCHNER DA, Nadeau JH
    Contrasting genetic architectures in different mouse reference populations used for studying complex traits.
    Genome Res. 2015;25:775-91.
    PubMed     Text format     Abstract available


  54. KLOOSTERMAN WP, Francioli LC, Hormozdiari F, Marschall T, et al
    Characteristics of de novo structural changes in the human genome.
    Genome Res. 2015;25:792-801.
    PubMed     Text format     Abstract available


  55. JUN G, Wing MK, Abecasis GR, Kang HM, et al
    An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data.
    Genome Res. 2015;25:918-25.
    PubMed     Text format     Abstract available


  56. STARICK SR, Ibn-Salem J, Jurk M, Hernandez C, et al
    ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors.
    Genome Res. 2015;25:825-35.
    PubMed     Text format     Abstract available


    March 2015
  57. SPIERS H, Hannon E, Schalkwyk LC, Smith R, et al
    Methylomic trajectories across human fetal brain development.
    Genome Res. 2015;25:338-52.
    PubMed     Text format     Abstract available


  58. KIM H, Zheng S, Amini SS, Virk SM, et al
    Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution.
    Genome Res. 2015;25:316-27.
    PubMed     Text format     Abstract available


  59. AMENDOLA LM, Dorschner MO, Robertson PD, Salama JS, et al
    Actionable exomic incidental findings in 6503 participants: challenges of variant classification.
    Genome Res. 2015;25:305-15.
    PubMed     Text format     Abstract available


  60. AL ADHAMI H, Evano B, Le Digarcher A, Gueydan C, et al
    A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation.
    Genome Res. 2015;25:353-67.
    PubMed     Text format     Abstract available


  61. RAMACHANDRAN S, Zentner GE, Henikoff S
    Asymmetric nucleosomes flank promoters in the budding yeast genome.
    Genome Res. 2015;25:381-90.
    PubMed     Text format     Abstract available


    February 2015
  62. BHASKAR A, Wang YX, Song YS
    Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data.
    Genome Res. 2015;25:268-79.
    PubMed     Text format     Abstract available


  63. MERCER TR, Clark MB, Andersen SB, Brunck ME, et al
    Genome-wide discovery of human splicing branchpoints.
    Genome Res. 2015;25:290-303.
    PubMed     Text format     Abstract available


  64. LI S, Vandivier LE, Tu B, Gao L, et al
    Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis.
    Genome Res. 2015;25:235-45.
    PubMed     Text format     Abstract available


  65. WANG C, Liu C, Roqueiro D, Grimm D, et al
    Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.
    Genome Res. 2015;25:246-56.
    PubMed     Text format     Abstract available


  66. PARKINSON NJ, Roddis M, Ferneyhough B, Zhang G, et al
    Violation of the 12/23 rule of genomic V(D)J recombination is common in lymphocytes.
    Genome Res. 2015;25:226-34.
    PubMed     Text format     Abstract available


  67. RODRIGUEZ JM, Bercovici S, Huang L, Frostig R, et al
    Parente2: a fast and accurate method for detecting identity by descent.
    Genome Res. 2015;25:280-9.
    PubMed     Text format     Abstract available


    January 2015
  68. LI YI, Sanchez-Pulido L, Haerty W, Ponting CP, et al
    RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts.
    Genome Res. 2015;25:1-13.
    PubMed     Text format     Abstract available


  69. ZHAO HQ, Zhang P, Gao H, He X, et al
    Profiling the RNA editomes of wild-type C. elegans and ADAR mutants.
    Genome Res. 2015;25:66-75.
    PubMed     Text format     Abstract available


  70. MAKSIMENKO O, Bartkuhn M, Stakhov V, Herold M, et al
    Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin.
    Genome Res. 2015;25:89-99.
    PubMed     Text format     Abstract available


  71. SUN Y, Whittle CA, Corcoran P, Johannesson H, et al
    Intron evolution in Neurospora: the role of mutational bias and selection.
    Genome Res. 2015;25:100-10.
    PubMed     Text format     Abstract available


  72. MATEO JL, van den Berg DL, Haeussler M, Drechsel D, et al
    Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.
    Genome Res. 2015;25:41-56.
    PubMed     Text format     Abstract available


  73. NANDI T, Holden MT, Didelot X, Mehershahi K, et al
    Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.
    Genome Res. 2015;25:129-41.
    PubMed     Text format     Abstract available


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