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Showing 1–21 of 21 results
Advanced filters: Author: Jacob O. Kitzman Clear advanced filters

  • Interaction between transcription factors and chromatin is fundamental for genome organization and regulation. Here, the authors use information theory to measure signatures of organized chromatin resulting from transcription factor-chromatin interactions, termed chromatin information enrichment, and find that variations in the information encoded in chromatin architecture reflects functional biological variation.

    • Ricardo D’Oliveira Albanus
    • Yasuhiro Kyono
    • Stephen C. J. Parker
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-12

  • Sequencing a human genome using next-generation methods does not distinguish between the two copies of each chromosome. Kitzman et al. determine a haplotype-resolved genome sequence by efficiently constructing and sequencing long-insert clones that cover the diploid genome with a low likelihood of overlap.

    • Jacob O Kitzman
    • Alexandra P MacKenzie
    • Jay Shendure
    Research
    Nature Biotechnology
    Volume: 29, P: 59-63

  • Using data from a single time point, passenger-approximated clonal expansion rate (PACER) estimates the fitness of common driver mutations that lead to clonal haematopoiesis and identifies TCL1A activation as a mediator of clonal expansion.

    • Joshua S. Weinstock
    • Jayakrishnan Gopakumar
    • Siddhartha Jaiswal
    Research
    Nature
    Volume: 616, P: 755-763

  • Analysis of 97,691 high-coverage human blood DNA-derived whole-genome sequences enabled simultaneous identification of germline and somatic mutations that predispose individuals to clonal expansion of haematopoietic stem cells, indicating that both inherited and acquired mutations are linked to age-related cancers and coronary heart disease.

    • Alexander G. Bick
    • Joshua S. Weinstock
    • Pradeep Natarajan
    Research
    Nature
    Volume: 586, P: 763-768

  • High-throughput DNA sequencing technologies are providing an ever-expanding wealth of genome sequence data, including detailed information on human genetic variation. However, such data typically lack haplotype information (that is, thecis-connectivity of variants along individual chromosomes). This Review describes diverse recent experimental methods by which genetic variants can be resolved into haplotypes, accompanying computational methods and important applications of these methods in genomics and biomedical science.

    • Matthew W. Snyder
    • Andrew Adey
    • Jay Shendure
    Reviews
    Nature Reviews Genetics
    Volume: 16, P: 344-358

  • Lysosomal biogenesis errors often result in diseases including mucolipidosis. Here Zhang and Yang et al. identify TMEM251/GCAF as a mannose-6-phosphate modification regulator that is necessary for correct lysosomal targeting, and classify Mucolipidosis Type V as resulting from GCAF mutations.

    • Weichao Zhang
    • Xi Yang
    • Ming Li
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-17

  • Short-read sequencing provides haplotype information when long DNA fragments are barcoded in microfluidic droplets.

    • Jacob O Kitzman
    News & Views
    Nature Biotechnology
    Volume: 34, P: 296-298

  • The two homoeologous subgenomes in the allotetraploid frog Xenopus laevis evolved asymmetrically; one often retained the ancestral state, whereas the other experienced gene loss, deletion, rearrangement and reduced gene expression.

    • Adam M. Session
    • Yoshinobu Uno
    • Daniel S. Rokhsar
    ResearchOpen Access
    Nature
    Volume: 538, P: 336-343

  • Bicuspid aortic valve (BAV) is the most common human congenital cardiovascular malformation. Here, the authors perform a genome-wide association study for BAV and identify risk variants in the gene region of cardiac-specific transcription factor GATA4 and implicate GATA4 in heart valve development.

    • Bo Yang
    • Wei Zhou
    • Cristen J. Willer
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-10

  • A comprehensive allelic series for a protein of interest with a single mutation per cDNA template can be generated using a combination of microarray-based DNA synthesis and overlap-extension mutagenesis.

    • Jacob O Kitzman
    • Lea M Starita
    • Jay Shendure
    Research
    Nature Methods
    Volume: 12, P: 203-206

  • A complete genome sequence is presented of a female Neanderthal from Siberia, providing information about interbreeding between close relatives and uncovering gene flow events among Neanderthals, Denisovans and early modern humans, as well as establishing substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

    • Kay Prüfer
    • Fernando Racimo
    • Svante Pääbo
    Research
    Nature
    Volume: 505, P: 43-49

  • Haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain shows that HeLa is relatively stable in terms of point variation; integration of several data sets reveals strong, haplotype-specific activation of the proto-oncogene MYC by the human papilloma virus type 18 genome, and enables the relationship between gene dosage and expression to be examined.

    • Andrew Adey
    • Joshua N. Burton
    • Jay Shendure
    Research
    Nature
    Volume: 500, P: 207-211

  • Large-scale association analyses identify 142 independent risk variants for atrial fibrillation. Pathway and functional enrichment analyses suggest that many of the putative risk genes act via cardiac structural remodeling.

    • Jonas B. Nielsen
    • Rosa B. Thorolfsdottir
    • Cristen J. Willer
    Research
    Nature Genetics
    Volume: 50, P: 1234-1239