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  • Highly parallel direct RNA sequencing on an array of nanopores
    Nat. Methods (IF 25.062) Pub Date : 2018-01-15
    Daniel R Garalde, Elizabeth A Snell, Daniel Jachimowicz, Botond Sipos, Joseph H Lloyd, Mark Bruce, Nadia Pantic, Tigist Admassu, Phillip James, Anthony Warland, Michael Jordan, Jonah Ciccone, Sabrina Serra, Jemma Keenan, Samuel Martin, Luke McNeill, E Jayne Wallace, Lakmal Jayasinghe, Chris Wright, Javier Blasco, Stephen Young, Denise Brocklebank, Sissel Juul, James Clarke, Andrew J Heron, Daniel J Turner

    Sequencing the RNA in a biological sample can unlock a wealth of information, including the identity of bacteria and viruses, the nuances of alternative splicing or the transcriptional state of organisms. However, current methods have limitations due to short read lengths and reverse transcription or amplification biases. Here we demonstrate nanopore direct RNA-seq, a highly parallel, real-time, single-molecule method that circumvents reverse transcription or amplification steps. This method yields full-length, strand-specific RNA sequences and enables the direct detection of nucleotide analogs in RNA.

    更新日期:2018-01-15
  • Detecting hierarchical genome folding with network modularity
    Nat. Methods (IF 25.062) Pub Date : 2018-01-15
    Heidi K Norton, Daniel J Emerson, Harvey Huang, Jesi Kim, Katelyn R Titus, Shi Gu, Danielle S Bassett, Jennifer E Phillips-Cremins

    Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Here, we describe 3DNetMod, a graph theory-based method for sensitive and accurate detection of chromatin domains across length scales in Hi-C data. We identify nested, partially overlapping TADs and subTADs genome wide by optimizing network modularity and varying a single resolution parameter. 3DNetMod can be applied broadly to understand genome reconfiguration in development and disease.

    更新日期:2018-01-15
  • Supermultiplexed optical imaging and barcoding with engineered polyynes
    Nat. Methods (IF 25.062) Pub Date : 2018-01-15
    Fanghao Hu, Chen Zeng, Rong Long, Yupeng Miao, Lu Wei, Qizhi Xu, Wei Min

    Optical multiplexing has a large impact in photonics, the life sciences and biomedicine. However, current technology is limited by a 'multiplexing ceiling' from existing optical materials. Here we engineered a class of polyyne-based materials for optical supermultiplexing. We achieved 20 distinct Raman frequencies, as 'Carbon rainbow', through rational engineering of conjugation length, bond-selective isotope doping and end-capping substitution of polyynes. With further probe functionalization, we demonstrated ten-color organelle imaging in individual living cells with high specificity, sensitivity and photostability. Moreover, we realized optical data storage and identification by combinatorial barcoding, yielding to our knowledge the largest number of distinct spectral barcodes to date. Therefore, these polyynes hold great promise in live-cell imaging and sorting as well as in high-throughput diagnostics and screening.

    更新日期:2018-01-15
  • GIGGLE: a search engine for large-scale integrated genome analysis
    Nat. Methods (IF 25.062) Pub Date : 2018-01-08
    Ryan M Layer, Brent S Pedersen, Tonya DiSera, Gabor T Marth, Jason Gertz, Aaron R Quinlan

    GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation.

    更新日期:2018-01-08
  • The new XFELs
    Nat. Methods (IF 25.062) Pub Date : 2018-01-03
    Allison Doerr

    The new XFELs The new XFELs, Published online: 03 January 2018; doi:10.1038/nmeth.4548 New X-ray free-electron (XFEL) facilities will broaden access to this technology, facilitate methods development, and push boundaries in structural biology.

    更新日期:2018-01-04
  • A profusion of confusion in NGS methods naming
    Nat. Methods (IF 25.062) Pub Date : 2018-01-03
    James Hadfield, Jacques Retief

    A profusion of confusion in NGS methods naming A profusion of confusion in NGS methods naming, Published online: 03 January 2018; doi:10.1038/nmeth.4558 A profusion of confusion in NGS methods naming

    更新日期:2018-01-04
  • Proteomics: Nascent proteome labeling in vivo
    Nat. Methods (IF 25.062) Pub Date : 2018-01-03

    Proteomics: Nascent proteome labeling in vivo Proteomics: Nascent proteome labeling in vivo, Published online: 03 January 2018; doi:10.1038/nmeth.4562 Proteomics: Nascent proteome labeling in vivo

    更新日期:2018-01-04
  • Mass spectrometry: False discovery rate estimation for metabolomics
    Nat. Methods (IF 25.062) Pub Date : 2018-01-03

    Mass spectrometry: False discovery rate estimation for metabolomics Mass spectrometry: False discovery rate estimation for metabolomics, Published online: 03 January 2018; doi:10.1038/nmeth.4564 Mass spectrometry: False discovery rate estimation for metabolomics

    更新日期:2018-01-04
  • Genomics: Annotating full-length long noncoding RNAs
    Nat. Methods (IF 25.062) Pub Date : 2018-01-03

    Genomics: Annotating full-length long noncoding RNAs Genomics: Annotating full-length long noncoding RNAs, Published online: 03 January 2018; doi:10.1038/nmeth.4566 Genomics: Annotating full-length long noncoding RNAs

    更新日期:2018-01-04
  • Imaging: Reflecting on light sheets
    Nat. Methods (IF 25.062) Pub Date : 2018-01-03
    Christian Schnell

    Imaging: Reflecting on light sheets Imaging: Reflecting on light sheets, Published online: 03 January 2018; doi:10.1038/nmeth.4570 Reflective coverslips can improve spatiotemporal resolution and collection efficiency in diSPIM light-sheet fluorescence microscopy.

    更新日期:2018-01-04
  • Bioinformatics: Fast curve fitting on a graphics processing unit
    Nat. Methods (IF 25.062) Pub Date : 2018-01-03

    Bioinformatics: Fast curve fitting on a graphics processing unit Bioinformatics: Fast curve fitting on a graphics processing unit, Published online: 03 January 2018; doi:10.1038/nmeth.4568 Bioinformatics: Fast curve fitting on a graphics processing unit

    更新日期:2018-01-04
  • Genomics: High-resolution mapping of R loops
    Nat. Methods (IF 25.062) Pub Date : 2018-01-03
    Vesna Todorovic

    Genomics: High-resolution mapping of R loops Genomics: High-resolution mapping of R loops, Published online: 03 January 2018; doi:10.1038/nmeth.4572 Two novel techniques refine genome-wide mapping of R loops.

    更新日期:2018-01-04
  • Interactome INSIDER: a structural interactome browser for genomic studies
    Nat. Methods (IF 25.062) Pub Date : 2018-01-01
    Michael J Meyer, Juan Felipe Beltrán, Siqi Liang, Robert Fragoza, Aaron Rumack, Jin Liang, Xiaomu Wei, Haiyuan Yu

    We present Interactome INSIDER, a tool to link genomic variant information with structural protein–protein interactomes. Underlying this tool is the application of machine learning to predict protein interaction interfaces for 185,957 protein interactions with previously unresolved interfaces in human and seven model organisms, including the entire experimentally determined human binary interactome. Predicted interfaces exhibit functional properties similar to those of known interfaces, including enrichment for disease mutations and recurrent cancer mutations. Through 2,164 de novo mutagenesis experiments, we show that mutations of predicted and known interface residues disrupt interactions at a similar rate and much more frequently than mutations outside of predicted interfaces. To spur functional genomic studies, Interactome INSIDER (http://interactomeinsider.yulab.org) enables users to identify whether variants or disease mutations are enriched in known and predicted interaction interfaces at various resolutions. Users may explore known population variants, disease mutations, and somatic cancer mutations, or they may upload their own set of mutations for this purpose.

    更新日期:2018-01-01
  • Biotinylation by antibody recognition—a method for proximity labeling
    Nat. Methods (IF 25.062) Pub Date : 2017-12-18
    Daniel Z Bar, Kathleen Atkatsh, Urraca Tavarez, Michael R Erdos, Yosef Gruenbaum, Francis S Collins

    Biotinylation by antibody recognition—a method for proximity labeling Biotinylation by antibody recognition—a method for proximity labeling, Published online: 18 December 2017; doi:10.1038/nmeth.4533 Proximity-based labeling represents a useful approach for mapping protein environment, but current methods for this are limited to application to cell lines. This approach is now extended to primary human tissues with a method that uses antibodies to guide proximity labeling.

    更新日期:2017-12-18
  • Resolving systematic errors in widely used enhancer activity assays in human cells
    Nat. Methods (IF 25.062) Pub Date : 2017-12-11
    Felix Muerdter, Łukasz M Boryń, Ashley R Woodfin, Christoph Neumayr, Martina Rath, Muhammad A Zabidi, Michaela Pagani, Vanja Haberle, Tomáš Kazmar, Rui R Catarino, Katharina Schernhuber, Cosmas D Arnold, Alexander Stark

    Resolving systematic errors in widely used enhancer activity assays in human cells Resolving systematic errors in widely used enhancer activity assays in human cells, Published online: 11 December 2017; doi:10.1038/nmeth.4534 Using the ORI of plasmids used in enhancer assays as the sole core promoter and inhibiting the interferon I response triggered by plasmid transfection greatly reduces false positive and negative results in single-candidate and massively parallel enhancer assays and enables genome-wide enhancer screens.

    更新日期:2017-12-11
  • Mapping the 3D orientation of piconewton integrin traction forces
    Nat. Methods (IF 25.062) Pub Date : 2017-12-11
    Joshua M Brockman, Aaron T Blanchard, Victor Pui-Yan Ma, Wallace D Derricotte, Yun Zhang, Meredith E Fay, Wilbur A Lam, Francesco A Evangelista, Alexa L Mattheyses, Khalid Salaita

    Mapping the 3D orientation of piconewton integrin traction forces Mapping the 3D orientation of piconewton integrin traction forces, Published online: 11 December 2017; doi:10.1038/nmeth.4536 Molecular force microscopy employs a combination of fluorescence polarization microscopy and molecular tension sensors to determine the orientation of cellular forces. The technology is demonstrated for integrin-mediated forces in platelets and fibroblasts.

    更新日期:2017-12-11
  • BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance
    Nat. Methods (IF 25.062) Pub Date : 2017-12-11
    Alexandra A Duarte, Ewa Gogola, Norman Sachs, Marco Barazas, Stefano Annunziato, Julian R de Ruiter, Arno Velds, Sohvi Blatter, Julia M Houthuijzen, Marieke van de Ven, Hans Clevers, Piet Borst, Jos Jonkers, Sven Rottenberg

    BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance, Published online: 11 December 2017; doi:10.1038/nmeth.4535 Mouse tumor organoids are characterized as a model to study tumor biology and drug resistance.

    更新日期:2017-12-11
  • NetSig: network-based discovery from cancer genomes
    Nat. Methods (IF 25.062) Pub Date : 2017-12-04
    Heiko Horn, Michael S Lawrence, Candace R Chouinard, Yashaswi Shrestha, Jessica Xin Hu, Elizabeth Worstell, Emily Shea, Nina Ilic, Eejung Kim, Atanas Kamburov, Alireza Kashani, William C Hahn, Joshua D Campbell, Jesse S Boehm, Gad Getz, Kasper Lage

    NetSig: network-based discovery from cancer genomes NetSig: network-based discovery from cancer genomes, Published online: 04 December 2017; doi:10.1038/nmeth.4514 NetSig is a network-based statistic that identifies cancer driver genes with high accuracy and can be combined with gene-based statistical tests; results are validated with a large-scale in vivo tumorigenesis assay.

    更新日期:2017-12-05
  • Programmable full-adder computations in communicating three-dimensional cell cultures
    Nat. Methods (IF 25.062) Pub Date : 2017-12-04
    David Ausländer, Simon Ausländer, Xavier Pierrat, Leon Hellmann, Leila Rachid, Martin Fussenegger

    Programmable full-adder computations in communicating three-dimensional cell cultures Programmable full-adder computations in communicating three-dimensional cell cultures, Published online: 04 December 2017; doi:10.1038/nmeth.4505 Designer cells executing rationally assembled genetic programs that can process input signals with programmable logic are combined in a 3D cell culture that performs three-input, two-output full-adder computations.

    更新日期:2017-12-05
  • The new 2D Superresolution mode for ZEISS Airyscan
    Nat. Methods (IF 25.062) Pub Date : 2017-11-30
    Joseph Huff, Annette Bergter, Jan Birkenbeil, Ingo Kleppe, Ralf Engelmann

    The new 2D Superresolution mode for ZEISS Airyscan The new 2D Superresolution mode for ZEISS Airyscan, Published online: 30 November 2017; doi:10.1038/nmeth.f.404 The new 2D Superresolution mode for ZEISS Airyscan

    更新日期:2017-12-05
  • LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data
    Nat. Methods (IF 25.062) Pub Date : 2017-11-30
    David Sehnal, Mandar Deshpande, Radka Svobodová Vařeková, Saqib Mir, Karel Berka, Adam Midlik, Lukáš Pravda, Sameer Velankar, Jaroslav Koča

    LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data, Published online: 30 November 2017; doi:10.1038/nmeth.4499 LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data

    更新日期:2017-12-01
  • Hardware triggering: maximizing speed and efficiency for live cell imaging
    Nat. Methods (IF 25.062) Pub Date : 2017-11-30
    Michael A Davis

    Hardware triggering: maximizing speed and efficiency for live cell imaging Hardware triggering: maximizing speed and efficiency for live cell imaging, Published online: 30 November 2017; doi:10.1038/nmeth.f.402 Hardware triggering: maximizing speed and efficiency for live cell imaging

    更新日期:2017-12-01
  • Accessible virtual reality of biomolecular structural models using the Autodesk Molecule Viewer
    Nat. Methods (IF 25.062) Pub Date : 2017-11-30
    Aidin R Balo, Merry Wang, Oliver P Ernst

    Accessible virtual reality of biomolecular structural models using the Autodesk Molecule Viewer Accessible virtual reality of biomolecular structural models using the Autodesk Molecule Viewer, Published online: 30 November 2017; doi:10.1038/nmeth.4506 Accessible virtual reality of biomolecular structural models using the Autodesk Molecule Viewer

    更新日期:2017-12-01
  • Microscopy: hello, adaptive optics
    Nat. Methods (IF 25.062) Pub Date : 2017-11-30
    Vivien Marx

    Microscopy: hello, adaptive optics Microscopy: hello, adaptive optics, Published online: 30 November 2017; doi:10.1038/nmeth.4508 Aberrations hinder clear imaging, but an array of options help to correct much distortion.

    更新日期:2017-12-01
  • Stem cells: Stem cells tip toward totipotency
    Nat. Methods (IF 25.062) Pub Date : 2017-11-30

    Stem cells: Stem cells tip toward totipotency Stem cells: Stem cells tip toward totipotency, Published online: 30 November 2017; doi:10.1038/nmeth.4516 Stem cells: Stem cells tip toward totipotency

    更新日期:2017-12-01
  • Neuroscience: Genome editing in the brain
    Nat. Methods (IF 25.062) Pub Date : 2017-11-30

    Neuroscience: Genome editing in the brain Neuroscience: Genome editing in the brain, Published online: 30 November 2017; doi:10.1038/nmeth.4520 Neuroscience: Genome editing in the brain

    更新日期:2017-12-01
  • Genomics: Haplobank of mutated mouse stem cell clones
    Nat. Methods (IF 25.062) Pub Date : 2017-11-30

    Genomics: Haplobank of mutated mouse stem cell clones Genomics: Haplobank of mutated mouse stem cell clones, Published online: 30 November 2017; doi:10.1038/nmeth.4518 Genomics: Haplobank of mutated mouse stem cell clones

    更新日期:2017-12-01
  • Cell biology: Measuring cellular mass with a picobalance
    Nat. Methods (IF 25.062) Pub Date : 2017-11-30

    Cell biology: Measuring cellular mass with a picobalance Cell biology: Measuring cellular mass with a picobalance, Published online: 30 November 2017; doi:10.1038/nmeth.4522 Cell biology: Measuring cellular mass with a picobalance

    更新日期:2017-12-01
  • A permanent window for the murine lung enables high-resolution imaging of cancer metastasis
    Nat. Methods (IF 25.062) Pub Date : 2017-11-27
    David Entenberg, Sonia Voiculescu, Peng Guo, Lucia Borriello, Yarong Wang, George S Karagiannis, Joan Jones, Francis Baccay, Maja Oktay, John Condeelis

    A permanent window for the murine lung enables high-resolution imaging of cancer metastasis A permanent window for the murine lung enables high-resolution imaging of cancer metastasis, Published online: 27 November 2017; doi:10.1038/nmeth.4511 The window for high-resolution imaging of the lung (WHRIL) enables longitudinal imaging of the same region of murine lung tissue over a period of weeks, and this enables the visualization of spontaneous cancer metastasis from the earliest stages.

    更新日期:2017-11-28
  • Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics
    Nat. Methods (IF 25.062) Pub Date : 2017-11-27
    Zijuan Lai, Hiroshi Tsugawa, Gert Wohlgemuth, Sajjan Mehta, Matthew Mueller, Yuxuan Zheng, Atsushi Ogiwara, John Meissen, Megan Showalter, Kohei Takeuchi, Tobias Kind, Peter Beal, Masanori Arita, Oliver Fiehn

    Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics, Published online: 27 November 2017; doi:10.1038/nmeth.4512 An integrated cheminformatics workflow aids the functional and structural annotation of unknown metabolites found across multiple biological systems.

    更新日期:2017-11-28
  • Systematic characterization of maturation time of fluorescent proteins in living cells
    Nat. Methods (IF 25.062) Pub Date : 2017-11-20
    Enrique Balleza, J Mark Kim, Philippe Cluzel

    Systematic characterization of maturation time of fluorescent proteins in living cells Systematic characterization of maturation time of fluorescent proteins in living cells, Published online: 20 November 2017; doi:10.1038/nmeth.4509 This work characterizes the maturation kinetics of 50 cyan to far-red fluorescent proteins and provides evidence that proteins that mature faster than their brighter but slower counterparts are more useful for quantitative evaluation of fast processes.

    更新日期:2017-11-21
  • PDB-wide identification of biological assemblies from conserved quaternary structure geometry
    Nat. Methods (IF 25.062) Pub Date : 2017-11-20
    Sucharita Dey, David W Ritchie, Emmanuel D Levy

    PDB-wide identification of biological assemblies from conserved quaternary structure geometry PDB-wide identification of biological assemblies from conserved quaternary structure geometry, Published online: 20 November 2017; doi:10.1038/nmeth.4510 Monomeric and homo-oligomeric protein quaternary structure states are predicted on a PDB-wide scale using a method that approaches the accuracy of manual annotation.

    更新日期:2017-11-21
  • Systematic characterization of maturation time of fluorescent proteins in living cells
    Nat. Methods (IF 25.062) Pub Date : 2017-11-20
    Enrique Balleza, J Mark Kim, Philippe Cluzel

    Systematic characterization of maturation time of fluorescent proteins in living cells Systematic characterization of maturation time of fluorescent proteins in living cells, Published online: 20 November 2017; doi:10.1038/nmeth.4509 This work characterizes the maturation kinetics of 50 cyan to far-red fluorescent proteins and provides evidence that proteins that mature faster than their brighter but slower counterparts are more useful for quantitative evaluation of fast processes.

    更新日期:2017-11-21
  • PDB-wide identification of biological assemblies from conserved quaternary structure geometry
    Nat. Methods (IF 25.062) Pub Date : 2017-11-20
    Sucharita Dey, David W Ritchie, Emmanuel D Levy

    PDB-wide identification of biological assemblies from conserved quaternary structure geometry PDB-wide identification of biological assemblies from conserved quaternary structure geometry, Published online: 20 November 2017; doi:10.1038/nmeth.4510 Monomeric and homo-oligomeric protein quaternary structure states are predicted on a PDB-wide scale using a method that approaches the accuracy of manual annotation.

    更新日期:2017-11-21
  • Multicolor quantitative confocal imaging cytometry
    Nat. Methods (IF 25.062) Pub Date : 2017-11-13
    Daniel L Coutu, Konstantinos D Kokkaliaris, Leo Kunz, Timm Schroeder

    Multicolor 3D quantitative imaging of large tissue volumes is necessary to understand tissue development and organization as well as interactions between distinct cell types in situ. However, tissue imaging remains technically challenging, particularly imaging of bone and marrow. Here, we describe a pipeline to reproducibly generate high-dimensional quantitative data from bone and bone marrow that may be extended to any tissue. We generate thick bone sections from adult mouse femurs with preserved tissue microarchitecture and demonstrate eight-color imaging using confocal microscopy without linear unmixing. We introduce XiT, an open-access software for fast and easy data curation, exploration and quantification of large imaging data sets with single-cell resolution. We describe how XiT can be used to correct for potential artifacts in quantitative 3D imaging, and we use the pipeline to measure the spatial relationship between hematopoietic cells, bone matrix and marrow Schwann cells.

    更新日期:2017-11-13
  • Profiling the transcriptome with RNA SPOTs
    Nat. Methods (IF 25.062) Pub Date : 2017-11-13
    Chee-Huat Linus Eng, Sheel Shah, Julian Thomassie, Long Cai

    Profiling the transcriptome with RNA SPOTs Profiling the transcriptome with RNA SPOTs, Published online: 13 November 2017; doi:10.1038/nmeth.4500 NatureArticleSnippet(type=short-summary, markup= RNA SPOTs adapts sequential fluorescence in situ hybridization (seqFISH) for highly accurate and inexpensive transcriptome-scale or targeted RNA quantification in vitro . , isJats=true)

    更新日期:2017-11-13
  • An improved MS2 system for accurate reporting of the mRNA life cycle
    Nat. Methods (IF 25.062) Pub Date : 2017-11-13
    Evelina Tutucci, Maria Vera, Jeetayu Biswas, Jennifer Garcia, Roy Parker, Robert H Singer

    An improved MS2 system for accurate reporting of the mRNA life cycle An improved MS2 system for accurate reporting of the mRNA life cycle, Published online: 13 November 2017; doi:10.1038/nmeth.4502 NatureArticleSnippet(type=short-summary, markup= An improved MS2-tagging system for live-cell RNA imaging allows faithful monitoring of the mRNA life cycle, overcoming degradation artifacts associated with previous versions and having implications regarding mRNA regulation in yeast. , isJats=true)

    更新日期:2017-11-13
  • The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power
    Nat. Methods (IF 25.062) Pub Date : 2017-11-13
    Melissa K Passarelli, Alexander Pirkl, Rudolf Moellers, Dmitry Grinfeld, Felix Kollmer, Rasmus Havelund, Carla F Newman, Peter S Marshall, Henrik Arlinghaus, Morgan R Alexander, Andy West, Stevan Horning, Ewald Niehuis, Alexander Makarov, Colin T Dollery, Ian S Gilmore

    The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power, Published online: 13 November 2017; doi:10.1038/nmeth.4504 NatureArticleSnippet(type=short-summary, markup= The high spatial resolution of secondary ion mass spectrometry and the high resolving power of the Orbitrap mass spectrometer are combined in a single imaging platform, the 3D OrbiSIMS. The instrument's capabilities for resolving lipids and neurotransmitters in the brain with subcellular spatial resolution, and a drug in a single cell in three dimensions is demonstrated. , isJats=true)

    更新日期:2017-11-13
  • Multicolor quantitative confocal imaging cytometry
    Nat. Methods (IF 25.062) Pub Date : 2017-11-13
    Daniel L Coutu, Konstantinos D Kokkaliaris, Leo Kunz, Timm Schroeder

    Multicolor quantitative confocal imaging cytometry Multicolor quantitative confocal imaging cytometry, Published online: 13 November 2017; doi:10.1038/nmeth.4503 NatureArticleSnippet(type=short-summary, markup= This resource paper describes the steps involved in carrying out quantitative multicolour imaging in tissue. It is applied to cleared mouse bone and plots the spatial distribution of specific cell populations within the marrow. , isJats=true)

    更新日期:2017-11-13
  • Profiling the transcriptome with RNA SPOTs
    Nat. Methods (IF 25.062) Pub Date : 2017-11-13
    Chee-Huat Linus Eng, Sheel Shah, Julian Thomassie, Long Cai

    Profiling the transcriptome with RNA SPOTs Profiling the transcriptome with RNA SPOTs, Published online: 13 November 2017; doi:10.1038/nmeth.4500 NatureArticleSnippet(type=short-summary, markup= RNA SPOTs adapts sequential fluorescence in situ hybridization (seqFISH) for highly accurate and inexpensive transcriptome-scale or targeted RNA quantification in vitro . , isJats=true)

    更新日期:2017-11-13
  • An improved MS2 system for accurate reporting of the mRNA life cycle
    Nat. Methods (IF 25.062) Pub Date : 2017-11-13
    Evelina Tutucci, Maria Vera, Jeetayu Biswas, Jennifer Garcia, Roy Parker, Robert H Singer

    An improved MS2 system for accurate reporting of the mRNA life cycle An improved MS2 system for accurate reporting of the mRNA life cycle, Published online: 13 November 2017; doi:10.1038/nmeth.4502 NatureArticleSnippet(type=short-summary, markup= An improved MS2-tagging system for live-cell RNA imaging allows faithful monitoring of the mRNA life cycle, overcoming degradation artifacts associated with previous versions and having implications regarding mRNA regulation in yeast. , isJats=true)

    更新日期:2017-11-13
  • The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power
    Nat. Methods (IF 25.062) Pub Date : 2017-11-13
    Melissa K Passarelli, Alexander Pirkl, Rudolf Moellers, Dmitry Grinfeld, Felix Kollmer, Rasmus Havelund, Carla F Newman, Peter S Marshall, Henrik Arlinghaus, Morgan R Alexander, Andy West, Stevan Horning, Ewald Niehuis, Alexander Makarov, Colin T Dollery, Ian S Gilmore

    We report the development of a 3D OrbiSIMS instrument for label-free biomedical imaging. It combines the high spatial resolution of secondary ion mass spectrometry (SIMS; under 200 nm for inorganic species and under 2 μm for biomolecules) with the high mass-resolving power of an Orbitrap (>240,000 at m/z 200). This allows exogenous and endogenous metabolites to be visualized in 3D with subcellular resolution. We imaged the distribution of neurotransmitters—gamma-aminobutyric acid, dopamine and serotonin—with high spectroscopic confidence in the mouse hippocampus. We also putatively annotated and mapped the subcellular localization of 29 sulfoglycosphingolipids and 45 glycerophospholipids, and we confirmed lipid identities with tandem mass spectrometry. We demonstrated single-cell metabolomic profiling using rat alveolar macrophage cells incubated with different concentrations of the drug amiodarone, and we observed that the upregulation of phospholipid species and cholesterol is correlated with the accumulation of amiodarone.

    更新日期:2017-11-13
  • Isolation and 3D expansion of multipotent Sox9+ mouse lung progenitors
    Nat. Methods (IF 25.062) Pub Date : 2017-11-06
    Massimo Nichane, Asif Javed, V Sivakamasundari, Monisha Ganesan, Lay Teng Ang, Petra Kraus, Thomas Lufkin, Kyle M Loh, Bing Lim

    Multiple adult tissues are maintained by stem cells of restricted developmental potential which can only form a subset of lineages within the tissue. For instance, the two adult lung epithelial compartments (airways and alveoli) are separately maintained by distinct lineage-restricted stem cells. A challenge has been to obtain multipotent stem cells and/or progenitors that can generate all epithelial cell types of a given tissue. Here we show that mouse Sox9+ multipotent embryonic lung progenitors can be isolated and expanded long term in 3D culture. Cultured Sox9+ progenitors transcriptionally resemble their in vivo counterparts and generate both airway and alveolar cell types in vitro. Sox9+ progenitors that were transplanted into injured adult mouse lungs differentiated into all major airway and alveolar lineages in vivo in a region-appropriate fashion. We propose that a single expandable embryonic lung progenitor population with broader developmental competence may eventually be used as an alternative for region-restricted adult tissue stem cells in regenerative medicine.

    更新日期:2017-11-10
  • The Author File: Alice C. McHardy
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Vivien Marx

    The Author File: Alice C. McHardy The Author File: Alice C. McHardy, Published online: 31 October 2017; doi:10.1038/nmeth.4485 NatureArticleSnippet(type=standfirst, markup= How to run a computational competition energized by modern dance. , isJats=true)

    更新日期:2017-11-10
  • DNA sequencing: Packing, trapping and sequencing
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Zachary J Lapin

    DNA sequencing: Packing, trapping and sequencing DNA sequencing: Packing, trapping and sequencing, Published online: 31 October 2017; doi:10.1038/nmeth.4487 NatureArticleSnippet(type=standfirst, markup= Ultralow concentrations of DNA can be optically sequenced with SMRT DNA sequencing. , isJats=true)

    更新日期:2017-11-10
  • Stem cells: Antibodies trigger reprogramming
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Nicole Rusk

    Stem cells: Antibodies trigger reprogramming Stem cells: Antibodies trigger reprogramming, Published online: 31 October 2017; doi:10.1038/nmeth.4491 NatureArticleSnippet(type=standfirst, markup= Antibodies that initiate signaling cascades and thereby replace reprogramming factors promise an efficient and safe way to produce pluripotent stem cells. , isJats=true)

    更新日期:2017-11-10
  • Microscopy: Laser-emission microscopy
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Rita Strack

    Microscopy: Laser-emission microscopy Microscopy: Laser-emission microscopy, Published online: 31 October 2017; doi:10.1038/nmeth.4489 NatureArticleSnippet(type=standfirst, markup= An optical setup for observing targeted fluorophores lasing from within tissue. , isJats=true)

    更新日期:2017-11-10
  • Genomics: A function-first look at tumor heterogeneity
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Tal Nawy

    Genomics: A function-first look at tumor heterogeneity Genomics: A function-first look at tumor heterogeneity, Published online: 31 October 2017; doi:10.1038/nmeth.4493 NatureArticleSnippet(type=standfirst, markup= Fate maps of human brain cancer cells, transplanted in mouse, challenge traditional views of tumor genomic heterogeneity. , isJats=true)

    更新日期:2017-11-10
  • Accessible, curated metagenomic data through ExperimentHub
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer B Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, Levi Waldron

    Accessible, curated metagenomic data through ExperimentHub Accessible, curated metagenomic data through ExperimentHub, Published online: 31 October 2017; doi:10.1038/nmeth.4468

    更新日期:2017-11-10
  • Neurobiology: gene expression captured on-site
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Vivien Marx

    Neurobiology: gene expression captured on-site Neurobiology: gene expression captured on-site, Published online: 31 October 2017; doi:10.1038/nmeth.4472 NatureArticleSnippet(type=standfirst, markup= A wealth of spatial techniques capture the 'where' of gene expression. , isJats=true)

    更新日期:2017-11-10
  • Isolation and 3D expansion of multipotent Sox9+ mouse lung progenitors
    Nat. Methods (IF 25.062) Pub Date : 2017-11-06
    Massimo Nichane, Asif Javed, V Sivakamasundari, Monisha Ganesan, Lay Teng Ang, Petra Kraus, Thomas Lufkin, Kyle M Loh, Bing Lim

    Multiple adult tissues are maintained by stem cells of restricted developmental potential which can only form a subset of lineages within the tissue. For instance, the two adult lung epithelial compartments (airways and alveoli) are separately maintained by distinct lineage-restricted stem cells. A challenge has been to obtain multipotent stem cells and/or progenitors that can generate all epithelial cell types of a given tissue. Here we show that mouse Sox9+ multipotent embryonic lung progenitors can be isolated and expanded long term in 3D culture. Cultured Sox9+ progenitors transcriptionally resemble their in vivo counterparts and generate both airway and alveolar cell types in vitro. Sox9+ progenitors that were transplanted into injured adult mouse lungs differentiated into all major airway and alveolar lineages in vivo in a region-appropriate fashion. We propose that a single expandable embryonic lung progenitor population with broader developmental competence may eventually be used as an alternative for region-restricted adult tissue stem cells in regenerative medicine.

    更新日期:2017-11-06
  • The Author File: Alice C. McHardy
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Vivien Marx

    The Author File: Alice C. McHardy The Author File: Alice C. McHardy, Published online: 31 October 2017; doi:10.1038/nmeth.4485 NatureArticleSnippet(type=standfirst, markup= How to run a computational competition energized by modern dance. , isJats=true)

    更新日期:2017-11-01
  • DNA sequencing: Packing, trapping and sequencing
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Zachary J Lapin

    DNA sequencing: Packing, trapping and sequencing DNA sequencing: Packing, trapping and sequencing, Published online: 31 October 2017; doi:10.1038/nmeth.4487 NatureArticleSnippet(type=standfirst, markup= Ultralow concentrations of DNA can be optically sequenced with SMRT DNA sequencing. , isJats=true)

    更新日期:2017-11-01
  • Stem cells: Antibodies trigger reprogramming
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Nicole Rusk

    Stem cells: Antibodies trigger reprogramming Stem cells: Antibodies trigger reprogramming, Published online: 31 October 2017; doi:10.1038/nmeth.4491 NatureArticleSnippet(type=standfirst, markup= Antibodies that initiate signaling cascades and thereby replace reprogramming factors promise an efficient and safe way to produce pluripotent stem cells. , isJats=true)

    更新日期:2017-11-01
  • Microscopy: Laser-emission microscopy
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Rita Strack

    Microscopy: Laser-emission microscopy Microscopy: Laser-emission microscopy, Published online: 31 October 2017; doi:10.1038/nmeth.4489 NatureArticleSnippet(type=standfirst, markup= An optical setup for observing targeted fluorophores lasing from within tissue. , isJats=true)

    更新日期:2017-11-01
  • Genomics: A function-first look at tumor heterogeneity
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Tal Nawy

    Genomics: A function-first look at tumor heterogeneity Genomics: A function-first look at tumor heterogeneity, Published online: 31 October 2017; doi:10.1038/nmeth.4493 NatureArticleSnippet(type=standfirst, markup= Fate maps of human brain cancer cells, transplanted in mouse, challenge traditional views of tumor genomic heterogeneity. , isJats=true)

    更新日期:2017-11-01
  • Accessible, curated metagenomic data through ExperimentHub
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer B Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, Levi Waldron

    Accessible, curated metagenomic data through ExperimentHub Accessible, curated metagenomic data through ExperimentHub, Published online: 31 October 2017; doi:10.1038/nmeth.4468

    更新日期:2017-11-01
  • Neurobiology: gene expression captured on-site
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Vivien Marx

    Neurobiology: gene expression captured on-site Neurobiology: gene expression captured on-site, Published online: 31 October 2017; doi:10.1038/nmeth.4472 NatureArticleSnippet(type=standfirst, markup= A wealth of spatial techniques capture the 'where' of gene expression. , isJats=true)

    更新日期:2017-11-01
  • Tracking microscopy enables whole-brain imaging in freely moving zebrafish
    Nat. Methods (IF 25.062) Pub Date : 2017-11-01
    Olivier Thouvenin, Claire Wyart

    Tracking microscopy enables whole-brain imaging in freely moving zebrafish Tracking microscopy enables whole-brain imaging in freely moving zebrafish, Published online: 31 October 2017; doi:10.1038/nmeth.4474 NatureArticleSnippet(type=standfirst, markup= Efficient tracking and optical whole-brain imaging at single-cell resolution in freely behaving zebrafish larvae pave the way for quantitative investigation of circuits underlying complex behaviors. , isJats=true)

    更新日期:2017-11-01
  • Localization-based super-resolution imaging meets high-content screening
    Nat. Methods (IF 25.062) Pub Date : 2017-10-30
    Anne Beghin, Adel Kechkar, Corey Butler, Florian Levet, Marine Cabillic, Olivier Rossier, Gregory Giannone, Rémi Galland, Daniel Choquet, Jean-Baptiste Sibarita

    Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.

    更新日期:2017-10-30
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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