Proteomic and phosphoproteomic comparison of human ES and iPS cells.

abstract：:We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial c...

journal_title：Nature methods

authors： Xu L,Brito IL,Alm EJ,Blainey PC

更新日期：2016-09-01 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：: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：:Fluorescent proteins have become extremely popular tools for in vivo imaging and especially for the study of localization, motility and interaction of proteins in living cells. Here we report TagRFP, a monomeric red fluorescent protein, which is characterized by high brightness, complete chromophore maturation, prolon...

journal_title：Nature methods

authors： Merzlyak EM,Goedhart J,Shcherbo D,Bulina ME,Shcheglov AS,Fradkov AF,Gaintzeva A,Lukyanov KA,Lukyanov S,Gadella TW,Chudakov DM

更新日期：2007-07-01 00:00:00

abstract：:Genetically encoded unnatural amino acids provide powerful strategies for modulating the molecular functions of proteins in mammalian cells. However, this approach has not been coupled to genome-wide measurements, because efficient incorporation of unnatural amino acids is limited to transient expression settings that...

journal_title：Nature methods

authors： Elsässer SJ,Ernst RJ,Walker OS,Chin JW

更新日期：2016-02-01 00:00:00

abstract：:As a result of recent improvements in mass spectrometry (MS), there is increased interest in data-independent acquisition (DIA) strategies in which all peptides are systematically fragmented using wide mass-isolation windows ('multiplex fragmentation'). DIA-Umpire (http://diaumpire.sourceforge.net/), a comprehensive c...

journal_title：Nature methods

authors： Tsou CC,Avtonomov D,Larsen B,Tucholska M,Choi H,Gingras AC,Nesvizhskii AI

更新日期：2015-03-01 00:00:00

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：:Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through their 3' untranslated regions, protein-coding RNAs interact with RNA-binding proteins and microRNAs, which regulate many properties, including RNA stability and subcellular localization....

journal_title：Nature methods

authors： Gruber AJ,Gypas F,Riba A,Schmidt R,Zavolan M

更新日期：2018-10-01 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：: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 self-renewal and differentiation of human pluripotent stem cells (hPSCs) have typically been studied in flat, two-dimensional (2D) environments. In this Perspective, we argue that 3D model systems may be needed in addition, as they mimic the natural 3D tissue organization more closely. We survey methods that have ...

journal_title：Nature methods

authors： Kraehenbuehl TP,Langer R,Ferreira LS

更新日期：2011-08-30 00:00:00

abstract：:Zinc-finger nucleases (ZFNs) have enabled highly efficient gene targeting in multiple cell types and organisms. Here we describe methods for using simple ssDNA oligonucleotides in tandem with ZFNs to efficiently produce human cell lines with three distinct genetic outcomes: (i) targeted point mutation, (ii) targeted g...

journal_title：Nature methods

authors： Chen F,Pruett-Miller SM,Huang Y,Gjoka M,Duda K,Taunton J,Collingwood TN,Frodin M,Davis GD

更新日期：2011-07-17 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：:Generation of complex libraries of defined nucleic acid sequences can greatly aid the functional analysis of protein and gene function. Previously, such studies relied either on individually synthesized oligonucleotides or on cellular nucleic acids as the starting material. As each method has disadvantages, we have de...

journal_title：Nature methods

authors： Cleary MA,Kilian K,Wang Y,Bradshaw J,Cavet G,Ge W,Kulkarni A,Paddison PJ,Chang K,Sheth N,Leproust E,Coffey EM,Burchard J,McCombie WR,Linsley P,Hannon GJ

更新日期：2004-12-01 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：: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：: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 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：:Firefly luciferase is the most widely used optical reporter for noninvasive bioluminescence imaging (BLI) in rodents. BLI relies on the ability of the injected luciferase substrate D-luciferin to access luciferase-expressing cells and tissues within the animal. Here we show that injection of mice with a synthetic luci...

journal_title：Nature methods

authors： Evans MS,Chaurette JP,Adams ST Jr,Reddy GR,Paley MA,Aronin N,Prescher JA,Miller SC

更新日期：2014-04-01 00:00:00

abstract：:The mechanical properties of the cellular microenvironment and their spatiotemporal variations are thought to play a central role in sculpting embryonic tissues, maintaining organ architecture and controlling cell behavior, including cell differentiation. However, no direct in vivo and in situ measurement of mechanica...

journal_title：Nature methods

authors： Serwane F,Mongera A,Rowghanian P,Kealhofer DA,Lucio AA,Hockenbery ZM,Campàs O

更新日期：2017-02-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors： Doerr A

更新日期：2019-03-01 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：:We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads f...

journal_title：Nature methods

authors： Robertson G,Schein J,Chiu R,Corbett R,Field M,Jackman SD,Mungall K,Lee S,Okada HM,Qian JQ,Griffith M,Raymond A,Thiessen N,Cezard T,Butterfield YS,Newsome R,Chan SK,She R,Varhol R,Kamoh B,Prabhu AL,Tam A,Zhao Y

更新日期：2010-11-01 00:00:00

abstract：:We introduce field synthesis, a theorem and method that can be used to synthesize any scanned or dithered light sheet, including those used in lattice light-sheet microscopy (LLSM), from an incoherent superposition of one-dimensional intensity distributions. Compared to LLSM, this user-friendly and modular approach of...

journal_title：Nature methods

authors： Chang BJ,Kittisopikul M,Dean KM,Roudot P,Welf ES,Fiolka R

更新日期：2019-03-01 00:00:00

abstract：:We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm for genome-wide association studies (GWAS) that scales linearly with cohort size in both run time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algo...

journal_title：Nature methods

authors： Lippert C,Listgarten J,Liu Y,Kadie CM,Davidson RI,Heckerman D

更新日期：2011-09-04 00:00:00

abstract：:Zinc-finger nucleases (ZFNs) drive efficient genome editing by introducing a double-strand break into the targeted gene. Cleavage is induced when two custom-designed ZFNs heterodimerize upon binding DNA to form a catalytically active nuclease complex. The importance of this dimerization event for subsequent cleavage a...

journal_title：Nature methods

authors： Doyon Y,Vo TD,Mendel MC,Greenberg SG,Wang J,Xia DF,Miller JC,Urnov FD,Gregory PD,Holmes MC

更新日期：2011-01-01 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：:We developed a general approach that allows unnatural amino acids with diverse physicochemical and biological properties to be genetically encoded in mammalian cells. A mutant Escherichia coli aminoacyl-tRNA synthetase (aaRS) is first evolved in yeast to selectively aminoacylate its tRNA with the unnatural amino acid ...

journal_title：Nature methods

authors： Liu W,Brock A,Chen S,Chen S,Schultz PG

更新日期：2007-03-01 00:00:00

abstract：:Achieving information content of satisfactory breadth and depth remains a formidable challenge for proteomics. This problem is particularly relevant to the study of primary human specimens, such as tumor biopsies, which are heterogeneous and of finite quantity. Here we present a functional proteomics strategy that uni...

journal_title：Nature methods

authors： Jessani N,Niessen S,Wei BQ,Nicolau M,Humphrey M,Ji Y,Han W,Noh DY,Yates JR 3rd,Jeffrey SS,Cravatt BF

更新日期：2005-09-01 00:00:00

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