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Showing 1–27 of 27 results
Advanced filters: Author: Howard C. Nusbaum Clear advanced filters

  • Semiconductor-based, non-optical DNA sequencing technologies such as Ion Torrent sequencing offer speed and cost advantages compared with alternative techniques. Cheng et al. demonstrate a protocol allowing the use of Ion Torrent technology to sequence DNA from chromatin immunoprecipitation experiments.

    • Christine S. Cheng
    • Kunal Rai
    • Ido Amit
    Research
    Nature Communications
    Volume: 4, P: 1-7

  • The FET family proteins FUS, EWSR1 and TAF15 are RNA-binding proteins with diverse nuclear functions. PAR-CLIP analyses now reveal the genome-wide RNA targets of all three human FET proteins and of two FUS mutants that cause amyotrophic lateral sclerosis. Although the RNA-binding properties of the mutants remain unchanged, the spectrum of RNA targets is altered because of the changed subcellular localization of the mutants.

    • Jessica I Hoell
    • Erik Larsson
    • Thomas Tuschl
    Research
    Nature Structural & Molecular Biology
    Volume: 18, P: 1428-1431

  • The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources.

    • Barbara A. Methé
    • Karen E. Nelson
    • Owen White
    ResearchOpen Access
    Nature
    Volume: 486, P: 215-221

  • An improved, fully re-annotated Aedes aegypti genome assembly (AaegL5) provides insights into the sex-determining M locus, chemosensory systems that help mosquitoes to hunt humans and loci involved in insecticide resistance and will help to generate intervention strategies to fight this deadly disease vector.

    • Benjamin J. Matthews
    • Olga Dudchenko
    • Leslie B. Vosshall
    ResearchOpen Access
    Nature
    Volume: 563, P: 501-507

  • Sleep is important for memory consolidation but its role in reconsolidation is not known. Here, the authors show in starlings that an auditory memory consolidated by sleep can be destabilized by retrieval and impaired by subsequent interference, but the memory recovers and stabilizes after a night of sleep-dependent reconsolidation.

    • Timothy P. Brawn
    • Howard C. Nusbaum
    • Daniel Margoliash
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-11

  • High-throughput sequencing of total cellular RNA by RNA-Seq promises rapid reconstruction of spliced transcripts in a cell population. Guttman et al. accomplish this using only paired-end RNA-seq data and an unannotated genome sequence, and apply the method to better define many new, conserved long intergenic noncoding RNAs (lincRNAs).

    • Mitchell Guttman
    • Manuel Garber
    • Aviv Regev
    Research
    Nature Biotechnology
    Volume: 28, P: 503-510

  • RNA-recognition elements are identified for the fragile-X-syndrome-associated RNA-binding protein FMRP, in addition to its target messenger RNAs; although many of FMRP gene targets discovered are involved in brain function and autism spectrum disorder, a proportion are also dysregulated in mouse ovaries, suggesting cross-regulation of signalling pathways in different tissues.

    • Manuel Ascano
    • Neelanjan Mukherjee
    • Thomas Tuschl
    Research
    Nature
    Volume: 492, P: 382-386

  • Reconstructing full-length transcripts from high-throughput RNA sequencing data is difficult without a reference genome sequence. Grabherr et al. describe Trinity, an algorithm for assembling full-length transcripts from short reads without first mapping the reads to a genome sequence.

    • Manfred G Grabherr
    • Brian J Haas
    • Aviv Regev
    Research
    Nature Biotechnology
    Volume: 29, P: 644-652

  • The relative contributions of RNA production, processing and degradation rates to cellular RNA levels are not well understood. Using pulsed metabolic RNA labeling of stimulated dendritic cells in conjunction with nCounter RNA quantification, RNA sequencing and computer modeling, Regev and colleagues unravel principles that determine RNA expression levels.

    • Michal Rabani
    • Joshua Z Levin
    • Aviv Regev
    Research
    Nature Biotechnology
    Volume: 29, P: 436-442

  • The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

    • Curtis Huttenhower
    • Dirk Gevers
    • Owen White
    ResearchOpen Access
    Nature
    Volume: 486, P: 207-214

  • The authors compare quality metrics of libraries from seven strand-specific RNA-seq methods in terms of complexity, strand specificity, evenness and continuity of coverage, and expression profiling. They provide a computational pipeline to compare these metrics from any RNA-seq protocol.

    • Joshua Z Levin
    • Moran Yassour
    • Aviv Regev
    Research
    Nature Methods
    Volume: 7, P: 709-715

  • The physical and social environment that surrounds us has a profound impact on our brains and behaviour. This impact is so fundamental that a complete understanding of neural mechanisms cannot be developed without taking into account the extensive interactions between neurobiology, psychology, behaviour and the environment.

    • Marc G. Berman
    • Omid Kardan
    • Sarah E. London
    Comments & Opinion
    Nature Human Behaviour
    Volume: 3, P: 414-417

  • Phytophthora infestans is a fungus-like eukaryote and the most destructive pathogen of potato, with current annual worldwide potato crop losses due to late blight estimated at $6.7 billion. Here, the sequence of the P. infestans genome is reported. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of certain secreted disease effector proteins, probably explaining the rapid adaptability of the pathogen to host plants.

    • Brian J. Haas
    • Sophien Kamoun
    • Chad Nusbaum
    ResearchOpen Access
    Nature
    Volume: 461, P: 393-398

  • This Registered Report finds that an implicit measure of subjective agency – intentional binding, where the perceived time of an action is biased toward that of its consequence – is altered when the consequence is masked from conscious awareness.

    • John P. Veillette
    • Yimeng Cheng
    • Howard C. Nusbaum
    ResearchOpen Access
    Communications Psychology
    Volume: 3, P: 1-11