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Showing 1–50 of 67 results
Advanced filters: Author: Josh Allen Clear advanced filters
    • Josh Burnell
    • Lydia Ng
    • Angela Guillozet-Bongaarts
    ResearchOpen Access
    Nature Precedings
    P: 1
    • Josh Burnell
    • Lydia Ng
    • Angela Guillozet-Bongaarts
    ResearchOpen Access
    Nature Precedings
    P: 1
  • A comprehensive single-cell RNA sequencing study delineates cell-type-specific transcriptomic changes in the brain associated with normal ageing that will inform the investigation into functional changes and the interaction of ageing and disease.

    • Kelly Jin
    • Zizhen Yao
    • Hongkui Zeng
    ResearchOpen Access
    Nature
    Volume: 638, P: 182-196
  • Multi-modal analysis is used to generate a 3D atlas of the upper limb area of the mouse primary motor cortex, providing a framework for future studies of motor control circuitry.

    • Rodrigo Muñoz-Castañeda
    • Brian Zingg
    • Hong-Wei Dong
    ResearchOpen Access
    Nature
    Volume: 598, P: 159-166
  • The activity of somatostatin-expressing inhibitory neurons (SOMs) in the superficial layers of the mouse visual cortex increases with stimulation of the receptive-field surround, thereby contributing to the surround suppression of pyramidal cells.

    • Hillel Adesnik
    • William Bruns
    • Massimo Scanziani
    Research
    Nature
    Volume: 490, P: 226-231
  • The BRAIN Initiative Cell Census Network has constructed a multimodal cell census and atlas of the mammalian primary motor cortex in a landmark effort towards understanding brain cell-type diversity, neural circuit organization and brain function.

    • Edward M. Callaway
    • Hong-Wei Dong
    • Susan Sunkin
    ResearchOpen Access
    Nature
    Volume: 598, P: 86-102
  • Sparse labelling and whole-brain imaging are used to reconstruct and classify brain-wide complete morphologies of 1,741 individual neurons in the mouse brain, revealing a dependence on both brain region and transcriptomic profile.

    • Hanchuan Peng
    • Peng Xie
    • Hongkui Zeng
    ResearchOpen Access
    Nature
    Volume: 598, P: 174-181
  • A combination of genetic strategies and tools is used to define and fate-map different subtypes of glutamatergic pyramidal neurons according to their developmental and molecular programs, providing insight into the assembly of cortical processing networks.

    • Katherine S. Matho
    • Dhananjay Huilgol
    • Z. Josh Huang
    ResearchOpen Access
    Nature
    Volume: 598, P: 182-187
  • RNA sensing-mediated payload expression provides a specific, versatile, simple and generalizable means of detecting and manipulating animal cells with broad potential applications.

    • Yongjun Qian
    • Jiayun Li
    • Z. Josh Huang
    Research
    Nature
    Volume: 610, P: 713-721
  • Timothy Frayling, Joel Hirschhorn, Peter Visscher and colleagues report a meta-analysis of genome-wide association studies for adult height in 253,288 individuals. They identify 697 variants in 423 loci significantly associated with adult height and find that these variants cluster in pathways involved in growth and together explain one-fifth of the heritability for this trait.

    • Andrew R Wood
    • Tonu Esko
    • Timothy M Frayling
    Research
    Nature Genetics
    Volume: 46, P: 1173-1186
  • FlyWire presents a neuronal wiring diagram of the whole fly brain with annotations for cell types, classes, nerves, hemilineages and predicted neurotransmitters, with data products and an open ecosystem to facilitate exploration and browsing.

    • Sven Dorkenwald
    • Arie Matsliah
    • Meet Zandawala
    ResearchOpen Access
    Nature
    Volume: 634, P: 124-138
  • Zhang et al. report that the BLA contains ‘hardwired’ positive-valence and negative-valence neurons, which each express Fezf2 but have distinct connectivity. These neurons separately drive learning and expression of avoidance or approach behavior.

    • Xian Zhang
    • Wuqiang Guan
    • Bo Li
    Research
    Nature Neuroscience
    Volume: 24, P: 1586-1600
  • Nebulin-based nemaline myopathy is a heterogenous disease with unclear pathological mechanisms. Here, the authors generate a mouse model that mimics the most common genetic cause of the disease and demonstrate that muscle weakness in this model is associated with twisted actin filaments and altered tropomyosin and troponin behaviour.

    • Johan Lindqvist
    • Weikang Ma
    • Henk Granzier
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-17
  • Pancreatic surgery is challenging for both surgeon and patient. With the advent of minimally invasive surgical techniques, patient morbidity could be reduced. In this article, Josh Winer and colleagues review the techniques and outcomes of robotic-assisted pancreatic resections, focusing on robotic-assisted pancreaticoduodenectomy, robotic-assisted distal pancreatectomy and robotic-assisted central pancreatectomy.

    • Josh Winer
    • Mehmet F. Can
    • Amer H. Zureikat
    Reviews
    Nature Reviews Gastroenterology & Hepatology
    Volume: 9, P: 468-476
  • Rett syndrome is associated with impaired synaptic connectivity beginning in early development. Here the authors show in female mice heterozygous forMecp2, a model of Rett syndrome, that during adulthood, auditory cortex plasticity associated with a learned maternal behaviour is also impaired.

    • Keerthi Krishnan
    • Billy Y. B. Lau
    • Stephen D. Shea
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-13
  • How We Feel is a web and mobile-phone application for collecting de-identified self-reported COVID-19-related data. These data are used to map a diverse set of symptomatic, demographic, exposure and behavioural factors relevant to the ongoing pandemic.

    • William E. Allen
    • Han Altae-Tran
    • Xihong Lin
    Research
    Nature Human Behaviour
    Volume: 4, P: 972-982
  • SpatialData is a user-friendly computational framework for exploring, analyzing, annotating, aligning and storing spatial omics data that can seamlessly handle large multimodal datasets.

    • Luca Marconato
    • Giovanni Palla
    • Oliver Stegle
    ResearchOpen Access
    Nature Methods
    Volume: 22, P: 58-62
  • Chronic infection with SARS-CoV-2 leads to the emergence of viral variants that show reduced susceptibility to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma.

    • Steven A. Kemp
    • Dami A. Collier
    • Ravindra K. Gupta
    Research
    Nature
    Volume: 592, P: 277-282
  • Sera from vaccinated individuals and some monoclonal antibodies show a modest reduction in neutralizing activity against the B.1.1.7 variant of SARS-CoV-2; but the E484K substitution leads to a considerable loss of neutralizing activity.

    • Dami A. Collier
    • Anna De Marco
    • Ravindra K. Gupta
    Research
    Nature
    Volume: 593, P: 136-141
  • Data sharing is an important component of reproducible research, but meaningful data sharing can be difficult. Here authors describe a new open source tool, AFQ-Browser, that builds an interactive website allowing visualization and exploratory data analysis of published diffusion MRI data.

    • Jason D. Yeatman
    • Adam Richie-Halford
    • Ariel Rokem
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-10
  • Giuseppe Testa and colleagues report the generation and transcriptional characterization of patient-derived induced pluripotent stem cells (iPSCs) with copy number variants at 7q11.23, which cause syndromes including neurocognitive phenotypes. They find that the dosage of the transcription factor gene GTF2I accounts for 10–20% of the transcriptional dysregulation observed in these cells.

    • Antonio Adamo
    • Sina Atashpaz
    • Giuseppe Testa
    Research
    Nature Genetics
    Volume: 47, P: 132-141
  • The authors show that fear conditioning induces potentiation of excitatory synapses onto somatostatin-positive inhibitory neurons in the lateral division of the central amygdala. Preventing this synaptic potentiation impairs the formation of fear memories, and activation of these neurons is necessary and sufficient for expression of fear memories.

    • Haohong Li
    • Mario A Penzo
    • Bo Li
    Research
    Nature Neuroscience
    Volume: 16, P: 332-339
  • Drug target identification is a crucial step in drug development. Here, the authors introduce a Bayesian machine learning framework that integrates multiple data types to predict the targets of small molecules, enabling identification of a new set of microtubule inhibitors and the target of the anti-cancer molecule ONC201.

    • Neel S. Madhukar
    • Prashant K. Khade
    • Olivier Elemento
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-14
  • The crystal and cryo-electron microscopy structure analysis of the DCAF15–DDB1–DDA1–indisulam–RBM39 complex revealed the detailed mechanism of action of indisulam-induced RBM39 degradation and defined an α-helical degron motif in RBM39.

    • Dirksen E. Bussiere
    • Lili Xie
    • Joshiawa Paulk
    Research
    Nature Chemical Biology
    Volume: 16, P: 15-23
  • This Resource describes the Image Data Resource (IDR), a prototype online system for biological image data that links experimental and analytic data across multiple data sets and promotes image data sharing and reanalysis.

    • Eleanor Williams
    • Josh Moore
    • Jason R Swedlow
    ResearchOpen Access
    Nature Methods
    Volume: 14, P: 775-781
  • In this study, Massachusetts Consortium for Pathogen Readiness (MassCPR) investigators assess the relationship between SARS-CoV-2 viral load and COVID-19 disease severity and report that the levels of detectable viral RNA, especially in plasma, correlates with severity of respiratory disease, inflammatory markers and predicted risk of death.

    • Jesse Fajnzylber
    • James Regan
    • Alex Zhu
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-9
  • Developmental disorders (DDs) are more prevalent in males, thought to be due to X-linked genetic variation. Here, the authors investigate the burden of X-linked coding variants in 11,044 DD patients, showing that this contributes to ~6% of both male and female cases and therefore does not solely explain male bias in DDs.

    • Hilary C. Martin
    • Eugene J. Gardner
    • Matthew E. Hurles
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-13
  • High-resolution contact maps of active enhancers and target genes generated by H3K27ac HiChIP in primary human cells provide rational guides to link noncoding disease-associated risk variants to candidate causal genes. Genes are validated by CRISPR activation and interference at connected enhancers and eQTL analysis, leading to a fourfold increase in the number of potential target genes for autoimmune and cardiovascular diseases.

    • Maxwell R Mumbach
    • Ansuman T Satpathy
    • Howard Y Chang
    Research
    Nature Genetics
    Volume: 49, P: 1602-1612
  • Larsson Omberg and colleagues write a Commentary describing the collaborative model used by the Pan-Cancer Working Group of The Cancer Genome Atlas. Pan-Cancer members used the Synapse software platform to share and evolve data, results and methods to perform integrative analyses of genome-wide molecular data for 12 cancer types.

    • Larsson Omberg
    • Kyle Ellrott
    • Adam A Margolin
    Comments & OpinionOpen Access
    Nature Genetics
    Volume: 45, P: 1121-1126
  • To investigate the sensory contributions of barrel cortex, the authors estimate spatiotemporal receptive fields by reverse correlation of multi-whisker stimulation to synaptic inputs. Complex stimuli revealed dramatically sharpened receptive fields, largely due to adaptation, and suggest the potential importance of surround facilitation through adaptation for discriminating complex shapes and textures during natural sensing.

    • Alejandro Ramirez
    • Eftychios A Pnevmatikakis
    • Randy M Bruno
    Research
    Nature Neuroscience
    Volume: 17, P: 866-875
  • The Impact of Genomic Variation on Function Consortium is combining single-cell mapping, genomic perturbations and predictive modelling to investigate relationships between human genomic variation, genome function and phenotypes and will provide an open resource to the community.

    • Jesse M. Engreitz
    • Heather A. Lawson
    • Ella K. Samer
    Reviews
    Nature
    Volume: 633, P: 47-57
  • Environmental DNA studies focus more on microbes, invertebrates, and temperate ecosystems, compared to biodiversity-focused forest carbon projects, and both areas need to align to facilitate improved biodiversity monitoring in the forest carbon market, according to the three-phase systematic analysis.

    • Michael C. Allen
    • Julie L. Lockwood
    • Benjamin D. Jaffe
    ResearchOpen Access
    Communications Earth & Environment
    Volume: 5, P: 1-10
  • To understand the function of cortical circuits, it is necessary to catalog their cellular diversity. Past attempts to do so using anatomical, physiological or molecular features of cortical cells have not resulted in a unified taxonomy of neuronal or glial cell types, partly due to limited data. Single-cell transcriptomics is enabling, for the first time, systematic high-throughput measurements of cortical cells and generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data reveal clusters that often correspond to cell types previously defined by morphological or physiological criteria and that appear conserved across cortical areas and species. To capitalize on these new methods, we propose the adoption of a transcriptome-based taxonomy of cell types for mammalian neocortex. This classification should be hierarchical and use a standardized nomenclature. It should be based on a probabilistic definition of a cell type and incorporate data from different approaches, developmental stages and species. A community-based classification and data aggregation model, such as a knowledge graph, could provide a common foundation for the study of cortical circuits. This community-based classification, nomenclature and data aggregation could serve as an example for cell type atlases in other parts of the body.

    • Rafael Yuste
    • Michael Hawrylycz
    • Ed Lein
    Comments & OpinionOpen Access
    Nature Neuroscience
    Volume: 23, P: 1456-1468
  • For several cancer types analyzed by The Cancer Genome Atlas project, predictions of patient survival were not substantially improved by using common data mining approaches to combine traditional clinical variables with molecular profiling data.

    • Yuan Yuan
    • Eliezer M Van Allen
    • Han Liang
    Research
    Nature Biotechnology
    Volume: 32, P: 644-652