Nanoscale resolution in GFP-based microscopy.

abstract：:We present the Single-Cell Clustering Assessment Framework, a method for the automated identification of putative cell types from single-cell RNA sequencing (scRNA-seq) data. By iteratively applying a machine learning approach to a given set of cells, we simultaneously identify distinct cell groups and a weighted list...

journal_title：Nature methods

authors： Miao Z,Moreno P,Huang N,Papatheodorou I,Brazma A,Teichmann SA

更新日期：2020-06-01 00:00:00

abstract：:We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unk...

journal_title：Nature methods

authors： Newman AM,Liu CL,Green MR,Gentles AJ,Feng W,Xu Y,Hoang CD,Diehn M,Alizadeh AA

更新日期：2015-05-01 00:00:00

abstract：:The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sens...

journal_title：Nature methods

authors： Thestrup T,Litzlbauer J,Bartholomäus I,Mues M,Russo L,Dana H,Kovalchuk Y,Liang Y,Kalamakis G,Laukat Y,Becker S,Witte G,Geiger A,Allen T,Rome LC,Chen TW,Kim DS,Garaschuk O,Griesinger C,Griesbeck O

更新日期：2014-02-01 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：:RNAs are ideal for the design of gene switches that can monitor and program cellular behavior because of their high modularity and predictable structure-function relationship. We have assembled an expression platform with an embedded modular ribozyme scaffold that correlates self-cleavage activity of designer ribozyme...

journal_title：Nature methods

authors： Ausländer S,Stücheli P,Rehm C,Ausländer D,Hartig JS,Fussenegger M

更新日期：2014-11-01 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：:Many protein interactions are mediated by small linear motifs interacting specifically with defined families of globular domains. Quantifying the specificity of a motif requires measuring and comparing its binding affinities to all its putative target domains. To this end, we developed the high-throughput holdup assay...

journal_title：Nature methods

authors： Vincentelli R,Luck K,Poirson J,Polanowska J,Abdat J,Blémont M,Turchetto J,Iv F,Ricquier K,Straub ML,Forster A,Cassonnet P,Borg JP,Jacob Y,Masson M,Nominé Y,Reboul J,Wolff N,Charbonnier S,Travé G

更新日期：2015-08-01 00:00:00

abstract：:APEX is an engineered peroxidase that functions as an electron microscopy tag and a promiscuous labeling enzyme for live-cell proteomics. Because limited sensitivity precludes applications requiring low APEX expression, we used yeast-display evolution to improve its catalytic efficiency. APEX2 is far more active in ce...

journal_title：Nature methods

authors： Lam SS,Martell JD,Kamer KJ,Deerinck TJ,Ellisman MH,Mootha VK,Ting AY

更新日期：2015-01-01 00:00:00

abstract：:The ability to selectively interfere with post-translationally modified proteins would have many biological and therapeutic applications. However, post-translational modifications cannot be selectively targeted by nucleic-acid-based interference approaches. Here we describe post-translational intracellular silencing a...

journal_title：Nature methods

authors： Chirichella M,Lisi S,Fantini M,Goracci M,Calvello M,Brandi R,Arisi I,D'Onofrio M,Di Primio C,Cattaneo A

更新日期：2017-03-01 00:00:00

abstract：:Massively parallel single-cell and single-nucleus RNA sequencing has opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so is the need for computational pipelines for scaled analysis. Here we developed Cumulus-a cloud-based framework for analyzing large-s...

journal_title：Nature methods

authors： Li B,Gould J,Yang Y,Sarkizova S,Tabaka M,Ashenberg O,Rosen Y,Slyper M,Kowalczyk MS,Villani AC,Tickle T,Hacohen N,Rozenblatt-Rosen O,Regev A

更新日期：2020-08-01 00:00:00

abstract：:We present DeNovoGear software for analyzing de novo mutations from familial and somatic tissue sequencing data. DeNovoGear uses likelihood-based error modeling to reduce the false positive rate of mutation discovery in exome analysis and fragment information to identify the parental origin of germ-line mutations. We ...

journal_title：Nature methods

authors： Ramu A,Noordam MJ,Schwartz RS,Wuster A,Hurles ME,Cartwright RA,Conrad DF

更新日期：2013-10-01 00:00:00

abstract：:We describe a GFP-based RNA reporter system (lambdaN-GFP) to visualize RNA molecules in live mammalian cells. It consists of GFP fused to an arginine-rich peptide derived from the phage lambda N protein, lambdaN22, which binds a unique minimal RNA motif and can be used to tag any RNA molecule. LambdaN-GFP uses a small...

journal_title：Nature methods

authors： Daigle N,Ellenberg J

更新日期：2007-08-01 00:00:00

abstract：:Monomeric (m)Eos2 is an engineered photoactivatable fluorescent protein widely used for super-resolution microscopy. We show that mEos2 forms oligomers at high concentrations and forms aggregates when labeling membrane proteins, limiting its application as a fusion partner. We solved the crystal structure of tetrameri...

journal_title：Nature methods

authors： Zhang M,Chang H,Zhang Y,Yu J,Wu L,Ji W,Chen J,Liu B,Lu J,Liu Y,Zhang J,Xu P,Xu T

更新日期：2012-05-13 00:00:00

abstract：:A new system for lineage ablation is based on transgenic expression of a diphtheria toxin receptor (DTR) in mouse cells and application of diphtheria toxin (DT). To streamline this approach, we generated Cre-inducible DTR transgenic mice (iDTR) in which Cre-mediated excision of a STOP cassette renders cells sensitive ...

journal_title：Nature methods

authors： Buch T,Heppner FL,Tertilt C,Heinen TJ,Kremer M,Wunderlich FT,Jung S,Waisman A

更新日期：2005-06-01 00:00:00

abstract：:Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. ...

journal_title：Nature methods

authors： Pintilie G,Zhang K,Su Z,Li S,Schmid MF,Chiu W

更新日期：2020-03-01 00:00:00

abstract：:Using a line-scanning method during functional magnetic resonance imaging (fMRI), we obtained high temporal (50-ms) and spatial (50-μm) resolution information along the cortical thickness and showed that the laminar position of fMRI onset coincides with distinct neural inputs in rat somatosensory and motor cortices. T...

journal_title：Nature methods

authors： Yu X,Qian C,Chen DY,Dodd SJ,Koretsky AP

更新日期：2014-01-01 00:00:00

abstract：:A 'paired-end ditag' (PET) strategy for pinpointing protein binding sites can reveal a wealth of information about transcription factors and other DNA-binding proteins. ...

journal_title：Nature methods

authors： Eisenstein M

更新日期：2006-05-01 00:00:00

abstract：:We describe a simple method for efficiently labeling cell-surface sialic acid-containing glycans on living animal cells. The method uses mild periodate oxidation to generate an aldehyde on sialic acids, followed by aniline-catalyzed oxime ligation with a suitable tag. Aniline catalysis dramatically accelerates oxime l...

journal_title：Nature methods

authors： Zeng Y,Ramya TN,Dirksen A,Dawson PE,Paulson JC

更新日期：2009-03-01 00:00:00

abstract：:Precisely defining the roles of specific cell types is an intriguing frontier in the study of intact biological systems and has stimulated the rapid development of genetically encoded tools for observation and control. However, targeting these tools with adequate specificity remains challenging: most cell types are be...

journal_title：Nature methods

authors： Fenno LE,Mattis J,Ramakrishnan C,Hyun M,Lee SY,He M,Tucciarone J,Selimbeyoglu A,Berndt A,Grosenick L,Zalocusky KA,Bernstein H,Swanson H,Perry C,Diester I,Boyce FM,Bass CE,Neve R,Huang ZJ,Deisseroth K

更新日期：2014-07-01 00:00:00

abstract：:We present a method to robustly discriminate clustered from randomly distributed molecules detected with techniques based on single-molecule localization microscopy, such as PALM and STORM. The approach is based on deliberate variation of labeling density, such as titration of fluorescent antibody, combined with quant...

journal_title：Nature methods

authors： Baumgart F,Arnold AM,Leskovar K,Staszek K,Fölser M,Weghuber J,Stockinger H,Schütz GJ

更新日期：2016-08-01 00:00:00

abstract：:The self-reconstructing properties of Bessel beams provide healing benefits in highly scattering media. ...

journal_title：Nature methods

authors： Evanko D

更新日期：2010-11-01 00:00:00

abstract：:Biomolecular dynamics and stability are predominantly investigated in vitro and extrapolated to explain function in the living cell. We present fast relaxation imaging (FreI), which combines fluorescence microscopy and temperature jumps to probe biomolecular dynamics and stability inside a single living cell with high...

journal_title：Nature methods

authors： Ebbinghaus S,Dhar A,McDonald JD,Gruebele M

更新日期：2010-04-01 00:00:00

abstract：:We developed a method that allows release of intact membrane protein complexes from amphipols, bicelles and nanodiscs in the gas phase for observation by mass spectrometry (MS). Current methods involve release of membrane protein complexes from detergent micelles, which reveals subunit composition and lipid binding. W...

journal_title：Nature methods

authors： Hopper JT,Yu YT,Li D,Raymond A,Bostock M,Liko I,Mikhailov V,Laganowsky A,Benesch JL,Caffrey M,Nietlispach D,Robinson CV

更新日期：2013-12-01 00:00:00

abstract：:The commonly used, monomeric EYFP enabled imaging of intracellular protein structures beyond the optical resolution limit ('super-resolution' imaging) in living cells. By combining photoinduced activation of single EYFP fusions and time-lapse imaging, we obtained sub-40 nm resolution images of the filamentous superstr...

journal_title：Nature methods

authors： Biteen JS,Thompson MA,Tselentis NK,Bowman GR,Shapiro L,Moerner WE

更新日期：2008-11-01 00:00:00

abstract：:Electron cryotomography is currently the only method capable of visualizing cells in three dimensions at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information, data processing is very labor intensive and the results are often limited...

journal_title：Nature methods

authors： Chen M,Bell JM,Shi X,Sun SY,Wang Z,Ludtke SJ

更新日期：2019-11-01 00:00:00

abstract：:The protein ubiquitin is an important post-translational modifier that regulates a wide variety of biological processes. In cells, ubiquitin is apportioned among distinct pools, which include a variety of free and conjugated species. Although maintenance of a dynamic and complex equilibrium among ubiquitin pools is cr...

journal_title：Nature methods

authors： Kaiser SE,Riley BE,Shaler TA,Trevino RS,Becker CH,Schulman H,Kopito RR

更新日期：2011-07-10 00:00:00

abstract：:Ribonucleoproteins (RNPs) are key regulators of cellular function. We established an efficient approach, crosslinking of segmentally isotope-labeled RNA and tandem mass spectrometry (CLIR-MS/MS), to localize protein-RNA interactions simultaneously at amino acid and nucleotide resolution. The approach was tested on pol...

journal_title：Nature methods

authors： Dorn G,Leitner A,Boudet J,Campagne S,von Schroetter C,Moursy A,Aebersold R,Allain FH

更新日期：2017-05-01 00:00:00

abstract：:Systems biology conceptualizes biological systems as dynamic networks of interacting elements, whereby functionally important properties are thought to emerge from the structure of such networks. Owing to the ubiquitous role of complexes of interacting proteins in biological systems, their subunit composition and temp...

journal_title：Nature methods

authors： Beck M,Malmström JA,Lange V,Schmidt A,Deutsch EW,Aebersold R

更新日期：2009-11-01 00:00:00

abstract：:Electrically excitable cells are important in the normal functioning and in the pathophysiology of many biological processes. These cells are typically embedded in dense, heterogeneous tissues, rendering them difficult to target selectively with conventional electrical stimulation methods. The algal protein Channelrho...

journal_title：Nature methods

authors： Zhang F,Wang LP,Boyden ES,Deisseroth K

更新日期：2006-10-01 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