Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.

abstract：:All-optical electrophysiology-spatially resolved simultaneous optical perturbation and measurement of membrane voltage-would open new vistas in neuroscience research. We evolved two archaerhodopsin-based voltage indicators, QuasAr1 and QuasAr2, which show improved brightness and voltage sensitivity, have microsecond r...

journal_title：Nature methods

authors： Hochbaum DR,Zhao Y,Farhi SL,Klapoetke N,Werley CA,Kapoor V,Zou P,Kralj JM,Maclaurin D,Smedemark-Margulies N,Saulnier JL,Boulting GL,Straub C,Cho YK,Melkonian M,Wong GK,Harrison DJ,Murthy VN,Sabatini BL,Boyden ES,C

更新日期：2014-08-01 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：:Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatica...

journal_title：Nature methods

authors： Alneberg J,Bjarnason BS,de Bruijn I,Schirmer M,Quick J,Ijaz UZ,Lahti L,Loman NJ,Andersson AF,Quince C

更新日期：2014-11-01 00:00:00

abstract：:Plants have evolved a unique system in which the plant hormone auxin directly induces rapid degradation of the AUX/IAA family of transcription repressors by a specific form of the SCF E3 ubiquitin ligase. Other eukaryotes lack the auxin response but share the SCF degradation pathway, allowing us to transplant the auxi...

journal_title：Nature methods

authors： Nishimura K,Fukagawa T,Takisawa H,Kakimoto T,Kanemaki M

更新日期：2009-12-01 00:00:00

abstract：:To trace cell lineages in a developing vertebrate and to observe, in vivo, how behaviors of individual cells are affected by the genes they express, we created a zebrafish line containing a transgene called mosaic analysis in zebrafish (MAZe), built around a self-excising hsp70:Cre cassette. Heat shock triggers Cre re...

journal_title：Nature methods

authors： Collins RT,Linker C,Lewis J

更新日期：2010-03-01 00:00:00

abstract：:MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular r...

journal_title：Nature methods

authors： Alberti C,Manzenreither RA,Sowemimo I,Burkard TR,Wang J,Mahofsky K,Ameres SL,Cochella L

更新日期：2018-04-01 00:00:00

abstract：:To enable sophisticated optogenetic manipulation of neural circuits throughout the nervous system with limited disruption of animal behavior, light-delivery systems beyond fiber optic tethering and large, head-mounted wireless receivers are desirable. We report the development of an easy-to-construct, implantable wire...

journal_title：Nature methods

authors： Montgomery KL,Yeh AJ,Ho JS,Tsao V,Mohan Iyer S,Grosenick L,Ferenczi EA,Tanabe Y,Deisseroth K,Delp SL,Poon AS

更新日期：2015-10-01 00:00:00

abstract：:Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical samples: here we outline how restriction digestion targets bisulfite sequencing to hotspots of...

journal_title：Nature methods

authors： Gu H,Bock C,Mikkelsen TS,Jäger N,Smith ZD,Tomazou E,Gnirke A,Lander ES,Meissner A

更新日期：2010-02-01 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：:The biomedical application of human embryonic stem (hES) cells will increasingly depend on the availability of technologies for highly controlled genetic modification. In mouse genetics, conditional mutagenesis using site-specific recombinases has become an invaluable tool for gain- and loss-of-function studies. Here ...

journal_title：Nature methods

authors： Nolden L,Edenhofer F,Haupt S,Koch P,Wunderlich FT,Siemen H,Brüstle O

更新日期：2006-06-01 00:00:00

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：: ...

journal_title：Nature methods

authors： Strack R

更新日期：2019-02-01 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：:It remains particularly problematic to define the structures of native macromolecular assemblies, which are often of low abundance. Here we present a strategy for isolating complexes at endogenous levels from GFP-tagged transgenic cell lines. Using cross-linking mass spectrometry, we extracted distance restraints that...

journal_title：Nature methods

authors： Shi Y,Pellarin R,Fridy PC,Fernandez-Martinez J,Thompson MK,Li Y,Wang QJ,Sali A,Rout MP,Chait BT

更新日期：2015-12-01 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： Caicedo JC,Goodman A,Karhohs KW,Cimini BA,Ackerman J,Haghighi M,Heng C,Becker T,Doan M,McQuin C,Rohban M,Singh S,Carpenter AE

更新日期：2020-02-01 00:00:00

abstract：:Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses and disease, testing enhancer activity in animals remains tedious, with a minority of enhancers having been cha...

journal_title：Nature methods

authors： Gisselbrecht SS,Barrera LA,Porsch M,Aboukhalil A,Estep PW 3rd,Vedenko A,Palagi A,Kim Y,Zhu X,Busser BW,Gamble CE,Iagovitina A,Singhania A,Michelson AM,Bulyk ML

更新日期：2013-08-01 00:00:00

abstract：:We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. On seven published data sets, we benchmark SIMLR against state-of-the-art met...

journal_title：Nature methods

authors： Wang B,Zhu J,Pierson E,Ramazzotti D,Batzoglou S

更新日期：2017-04-01 00:00:00

abstract：:The importance of locating proteins in their context within cells has been heightened recently by the accomplishments in molecular structure and systems biology. Although light microscopy (LM) has been extensively used for mapping protein localization, many studies require the additional resolution of the electron mic...

journal_title：Nature methods

authors： Giepmans BN,Deerinck TJ,Smarr BL,Jones YZ,Ellisman MH

更新日期：2005-10-01 00:00:00

abstract：:The ability to apply precise inputs to signaling species in live cells would be transformative for interrogating and understanding complex cell-signaling systems. Here we report an 'optogenetic' method for applying custom signaling inputs using feedback control of a light-gated protein-protein interaction. We applied ...

journal_title：Nature methods

authors： Toettcher JE,Gong D,Lim WA,Weiner OD

更新日期：2011-09-11 00:00:00

abstract：:Thus far, optical recording of neuronal activity in freely behaving animals has been limited to a thin axial range. We present a head-mounted miniaturized light-field microscope (MiniLFM) capable of capturing neuronal network activity within a volume of 700 × 600 × 360 µm3 at 16 Hz in the hippocampus of freely moving ...

journal_title：Nature methods

authors： Skocek O,Nöbauer T,Weilguny L,Martínez Traub F,Xia CN,Molodtsov MI,Grama A,Yamagata M,Aharoni D,Cox DD,Golshani P,Vaziri A

更新日期：2018-06-01 00:00:00

abstract：:Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report th...

journal_title：Nature methods

authors： Radivojac P,Clark WT,Oron TR,Schnoes AM,Wittkop T,Sokolov A,Graim K,Funk C,Verspoor K,Ben-Hur A,Pandey G,Yunes JM,Talwalkar AS,Repo S,Souza ML,Piovesan D,Casadio R,Wang Z,Cheng J,Fang H,Gough J,Koskinen P,Törö

更新日期：2013-03-01 00:00:00

abstract：:The understanding of integral membrane protein (IMP) structure and function is hampered by the difficulty of handling these proteins. Aqueous solubilization, necessary for many types of biophysical analysis, generally requires a detergent to shield the large lipophilic surfaces of native IMPs. Many proteins remain dif...

journal_title：Nature methods

authors： Chae PS,Rasmussen SG,Rana RR,Gotfryd K,Chandra R,Goren MA,Kruse AC,Nurva S,Loland CJ,Pierre Y,Drew D,Popot JL,Picot D,Fox BG,Guan L,Gether U,Byrne B,Kobilka B,Gellman SH

更新日期：2010-12-01 00:00:00

abstract：:High-resolution optical imaging is critical to understanding brain function. We demonstrate that three-photon microscopy at 1,300-nm excitation enables functional imaging of GCaMP6s-labeled neurons beyond the depth limit of two-photon microscopy. We record spontaneous activity from up to 150 neurons in the hippocampal...

journal_title：Nature methods

authors： Ouzounov DG,Wang T,Wang M,Feng DD,Horton NG,Cruz-Hernández JC,Cheng YT,Reimer J,Tolias AS,Nishimura N,Xu C

更新日期：2017-04-01 00:00:00

abstract：:A quantitative high-throughput FRET-based method of screening fluorescent protein fusion libraries brings the promise of more detailed interactome maps. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2007-02-01 00:00:00

abstract：:We report a simple and generic method for the direct transfer of protein complexes separated by native gel electrophoresis to electron microscopy grids. After transfer, sufficient material remains in the gel for identification and characterization by mass spectrometry. The method should facilitate higher-throughput si...

journal_title：Nature methods

authors： Knispel RW,Kofler C,Boicu M,Baumeister W,Nickell S

更新日期：2012-01-08 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：:Drug-inducible systems allowing the control of gene expression in mammalian cells are invaluable tools for genetic research, and could also fulfill essential roles in gene- and cell-based therapy. Currently available systems, however, often have limited in vivo functionality because of leakiness, insufficient levels o...

journal_title：Nature methods

authors： Szulc J,Wiznerowicz M,Sauvain MO,Trono D,Aebischer P

更新日期：2006-02-01 00:00:00

abstract：:Optical studies have revealed that, after binding, virions move laterally on the plasma membrane, but the complexity of the cellular environment and the drawbacks of fluorescence microscopy have prevented access to the molecular dynamics of early virus-host couplings, which are important for cell infection. Here we pr...

journal_title：Nature methods

authors： Kukura P,Ewers H,Müller C,Renn A,Helenius A,Sandoghdar V

更新日期：2009-12-01 00:00:00

abstract：:The dynamic reshaping of tissues during morphogenesis results from a combination of individual cell behaviors and collective cell rearrangements. However, a comprehensive framework to unambiguously measure and link cell behavior to tissue morphogenesis is lacking. Here we introduce such a kinematic framework, bridging...

journal_title：Nature methods

authors： Blanchard GB,Kabla AJ,Schultz NL,Butler LC,Sanson B,Gorfinkiel N,Mahadevan L,Adams RJ

更新日期：2009-06-01 00:00:00

abstract：:An uncharged CoA precursor that can enter the cell is used for covalent, site-specific labeling of proteins inside living cells. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2006-11-01 00:00:00