Rational design of true monomeric and bright photoactivatable fluorescent proteins.

abstract：:Time resolution of current single-molecule fluorescence techniques is limited to milliseconds because of dye blinking and bleaching. Here we introduce a photoprotection strategy that affords microsecond resolution by combining efficient triplet quenching by oxygen and Trolox with minimized bleaching via the oxygen rad...

journal_title：Nature methods

authors： Campos LA,Liu J,Wang X,Ramanathan R,English DS,Muñoz V

更新日期：2011-02-01 00:00:00

abstract：:Tumor-initiating cells with stem cell properties are believed to sustain the growth of gliomas, but proposed markers such as CD133 cannot be used to identify these cells with sufficient specificity. We report an alternative isolation method purely based on phenotypic qualities of glioma-initiating cells (GICs), avoidi...

journal_title：Nature methods

authors： Clément V,Marino D,Cudalbu C,Hamou MF,Mlynarik V,de Tribolet N,Dietrich PY,Gruetter R,Hegi ME,Radovanovic I

更新日期：2010-03-01 00:00:00

abstract：:Cortical information processing relies on synaptic interactions between diverse classes of neurons with distinct electrophysiological and connection properties. Uncovering the operational principles of these elaborate circuits requires the probing of electrical activity from selected populations of defined neurons. He...

journal_title：Nature methods

authors： Akemann W,Mutoh H,Perron A,Rossier J,Knöpfel T

更新日期：2010-08-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors：

更新日期：2018-12-01 00:00:00

abstract：:Tumors from individuals with cancer are frequently genetically profiled for information about the driving forces behind the disease. We present the CancerMine resource, a text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer. All data are available online ( ...

journal_title：Nature methods

authors： Lever J,Zhao EY,Grewal J,Jones MR,Jones SJM

更新日期：2019-06-01 00:00:00

abstract：:We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30-90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic protein...

journal_title：Nature methods

authors： Jarzab A,Kurzawa N,Hopf T,Moerch M,Zecha J,Leijten N,Bian Y,Musiol E,Maschberger M,Stoehr G,Becher I,Daly C,Samaras P,Mergner J,Spanier B,Angelov A,Werner T,Bantscheff M,Wilhelm M,Klingenspor M,Lemeer S,Liebl W

更新日期：2020-05-01 00:00:00

abstract：:The reconstruction of neuronal populations, a key step in understanding neural circuits, remains a challenge in the presence of densely packed neurites. Here we achieved automatic reconstruction of neuronal populations by partially mimicking human strategies to separate individual neurons. For populations not resolvab...

journal_title：Nature methods

authors： Quan T,Zhou H,Li J,Li S,Li A,Li Y,Lv X,Luo Q,Gong H,Zeng S

更新日期：2016-01-01 00:00:00

abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

journal_title：Nature methods

authors： Singh A

更新日期：2019-12-01 00:00:00

abstract：:Dissecting the relationship between genotype and phenotype is one of the central goals in developmental biology and medicine. Transcriptome analysis is a powerful strategy to connect genotype to phenotype of a cell. Here we review the history, progress, potential applications and future developments of single-cell tra...

journal_title：Nature methods

authors： Tang F,Lao K,Surani MA

更新日期：2011-04-01 00:00:00

abstract：:We developed a highly sensitive parallel allele-specific sequencing (PASS) assay to simultaneously analyze a large number of viral genomes and detect minor drug-resistant populations at approximately 0.1-0.01% levels. Using this assay on samples from individuals infected with human immunodeficiency viruses (HIV), we s...

journal_title：Nature methods

authors： Cai F,Chen H,Hicks CB,Bartlett JA,Zhu J,Gao F

更新日期：2007-02-01 00:00:00

abstract：:Researchers show that to reliably establish protein interaction networks from microarray data it is necessary to measure saturation binding curves for each arrayed protein and its potential binding partners. ...

journal_title：Nature methods

authors： Rusk N

更新日期：2006-12-01 00:00:00

abstract：:To enable the detection of expression signatures specific to individual cells, we developed PLAYR (proximity ligation assay for RNA), a method for highly multiplexed transcript quantification by flow and mass cytometry that is compatible with standard antibody staining. When used with mass cytometry, PLAYR allowed for...

journal_title：Nature methods

authors： Frei AP,Bava FA,Zunder ER,Hsieh EW,Chen SY,Nolan GP,Gherardini PF

更新日期：2016-03-01 00:00:00

abstract：:Accurate identification of cell subsets in complex populations is key to discovering novelty in multidimensional single-cell experiments. We present X-shift (http://web.stanford.edu/~samusik/vortex/), an algorithm that processes data sets using fast k-nearest-neighbor estimation of cell event density and arranges popu...

journal_title：Nature methods

authors： Samusik N,Good Z,Spitzer MH,Davis KL,Nolan GP

更新日期：2016-06-01 00:00:00

abstract：:By combining activity-based proteomics and metabolomics, researchers have developed a new systems biology strategy for characterizing enzymes in the context of metabolic networks. ...

journal_title：Nature methods

authors： Doerr A

更新日期：2007-01-01 00:00:00

abstract：:The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-molecule linker that enables RNA to be cova...

journal_title：Nature methods

authors： Chen F,Wassie AT,Cote AJ,Sinha A,Alon S,Asano S,Daugharthy ER,Chang JB,Marblestone A,Church GM,Raj A,Boyden ES

更新日期：2016-08-01 00:00:00

abstract：:Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral overlap between fluorophores. Here we demonstrate a simple but general strategy to drastically increase the ...

journal_title：Nature methods

authors： Lubeck E,Cai L

更新日期：2012-06-03 00:00:00

abstract：:Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue frequencies to graphically scale character heights. We describe the pLogo, a motif visualization in which residue heights are scaled relative to their statistical significance. A pLogo generation tool is publicly available at...

journal_title：Nature methods

authors： O'Shea JP,Chou MF,Quader SA,Ryan JK,Church GM,Schwartz D

更新日期：2013-12-01 00:00:00

abstract：:t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we ...

journal_title：Nature methods

authors： Linderman GC,Rachh M,Hoskins JG,Steinerberger S,Kluger Y

更新日期：2019-03-01 00:00:00

abstract：:Rational protein engineering requires a holistic understanding of protein function. Here, we apply deep learning to unlabeled amino-acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically rich and structurally, evolutionarily and biophysically grounded. We...

journal_title：Nature methods

authors： Alley EC,Khimulya G,Biswas S,AlQuraishi M,Church GM

更新日期：2019-12-01 00:00:00

abstract：:We developed a caged GABA (gamma-aminobutyric acid), which, when combined with an appropriate caged glutamate, allows bimodal control of neuronal membrane potential with subcellular resolution using optically independent two-photon uncaging of each neurotransmitter. We used two-color, two-photon uncaging to fire and b...

journal_title：Nature methods

authors： Kantevari S,Matsuzaki M,Kanemoto Y,Kasai H,Ellis-Davies GC

更新日期：2010-02-01 00:00:00

abstract：:Current extracellular multisite recordings suffer from low signal-to-noise ratio, limiting the monitoring to action potentials, and preclude detection of subthreshold synaptic potentials. Here we report an approach to induce Aplysia californica neurons to actively engulf protruding microelectrodes, providing 'in-cell ...

journal_title：Nature methods

authors： Hai A,Shappir J,Spira ME

更新日期：2010-03-01 00:00:00

abstract：:The need for automated and efficient systems for tracking full animal pose has increased with the complexity of behavioral data and analyses. Here we introduce LEAP (LEAP estimates animal pose), a deep-learning-based method for predicting the positions of animal body parts. This framework consists of a graphical inter...

journal_title：Nature methods

authors： Pereira TD,Aldarondo DE,Willmore L,Kislin M,Wang SS,Murthy M,Shaevitz JW

更新日期：2019-01-01 00:00:00

abstract：:We achieve simultaneous two-photon excitation of three chromophores with distinct absorption spectra using synchronized pulses from a femtosecond laser and an optical parametric oscillator. The two beams generate separate multiphoton processes, and their spatiotemporal overlap provides an additional two-photon excitat...

journal_title：Nature methods

authors： Mahou P,Zimmerley M,Loulier K,Matho KS,Labroille G,Morin X,Supatto W,Livet J,Débarre D,Beaurepaire E

更新日期：2012-07-08 00:00:00

abstract：:Protein-RNA networks are ubiquitous and central in biological control. We present an approach termed RNA Tagging that enables the user to identify protein-RNA interactions in vivo by analyzing purified cellular RNA, without protein purification or cross-linking. An RNA-binding protein of interest is fused to an enzyme...

journal_title：Nature methods

authors： Lapointe CP,Wilinski D,Saunders HA,Wickens M

更新日期：2015-12-01 00:00:00

abstract：:Circuit mapping requires knowledge of both structural and functional connectivity between cells. Although optical tools have been made to assess either the morphology and projections of neurons or their activity and functional connections, few probes integrate this information. We have generated a family of photoactiv...

journal_title：Nature methods

authors： Berlin S,Carroll EC,Newman ZL,Okada HO,Quinn CM,Kallman B,Rockwell NC,Martin SS,Lagarias JC,Isacoff EY

更新日期：2015-09-01 00:00:00

abstract：:Existing methods for human induced pluripotent stem cell (hiPSC) cardiac differentiation are efficient but require complex, undefined medium constituents that hinder further elucidation of the molecular mechanisms of cardiomyogenesis. Using hiPSCs derived under chemically defined conditions on synthetic matrices, we s...

journal_title：Nature methods

authors： Burridge PW,Matsa E,Shukla P,Lin ZC,Churko JM,Ebert AD,Lan F,Diecke S,Huber B,Mordwinkin NM,Plews JR,Abilez OJ,Cui B,Gold JD,Wu JC

更新日期：2014-08-01 00:00:00

abstract：:Single-molecule localization microscopy is a powerful tool for visualizing subcellular structures, interactions and protein functions in biological research. However, inhomogeneous refractive indices inside cells and tissues distort the fluorescent signal emitted from single-molecule probes, which rapidly degrades res...

journal_title：Nature methods

authors： Xu F,Ma D,MacPherson KP,Liu S,Bu Y,Wang Y,Tang Y,Bi C,Kwok T,Chubykin AA,Yin P,Calve S,Landreth GE,Huang F

更新日期：2020-05-01 00:00:00

abstract：:We report a technique to selectively and continuously label the proteomes of individual cell types in coculture, named cell type-specific labeling using amino acid precursors (CTAP). Through transgenic expression of exogenous amino acid biosynthesis enzymes, vertebrate cells overcome their dependence on supplemented e...

journal_title：Nature methods

authors： Gauthier NP,Soufi B,Walkowicz WE,Pedicord VA,Mavrakis KJ,Macek B,Gin DY,Sander C,Miller ML

更新日期：2013-08-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors： Strack R

更新日期：2019-02-01 00:00:00

abstract：:Microarrays have been widely used for the analysis of gene expression, but the issue of reproducibility across platforms has yet to be fully resolved. To address this apparent problem, we compared gene expression between two microarray platforms: the short oligonucleotide Affymetrix Mouse Genome 430 2.0 GeneChip and a...

journal_title：Nature methods

authors： Larkin JE,Frank BC,Gavras H,Sultana R,Quackenbush J

更新日期：2005-05-01 00:00:00