Imputing gene expression from selectively reduced probe sets.

abstract：:We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps o...

journal_title：Nature methods

authors： DiMaio F,Song Y,Li X,Brunner MJ,Xu C,Conticello V,Egelman E,Marlovits T,Cheng Y,Baker D

更新日期：2015-04-01 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：:Structure probing coupled with high-throughput sequencing could revolutionize our understanding of the role of RNA structure in regulation of gene expression. Despite recent technological advances, intrinsic noise and high sequence coverage requirements greatly limit the applicability of these techniques. Here we desc...

journal_title：Nature methods

authors： Selega A,Sirocchi C,Iosub I,Granneman S,Sanguinetti G

更新日期：2017-01-01 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：:We discuss unique features of lens-free computational imaging tools and report some of their emerging results for wide-field on-chip microscopy, such as the achievement of a numerical aperture (NA) of ∼0.8-0.9 across a field of view (FOV) of more than 20 mm(2) or an NA of ∼0.1 across a FOV of ∼18 cm(2), which correspo...

journal_title：Nature methods

authors： Greenbaum A,Luo W,Su TW,Göröcs Z,Xue L,Isikman SO,Coskun AF,Mudanyali O,Ozcan A

更新日期：2012-09-01 00:00:00

abstract：:Extracellular vesicles (EVs) are secreted nanosized particles with many biological functions and pathological associations. The inability to image EVs in fixed tissues has been a major limitation to understanding their role in healthy and diseased tissue microenvironments. Here, we show that crosslinking mammalian tis...

journal_title：Nature methods

authors： Gupta MP,Tandalam S,Ostrager S,Lever AS,Fung AR,Hurley DD,Alegre GB,Espinal JE,Remmel HL,Mukherjee S,Levine BM,Robins RP,Molina H,Dill BD,Kenific CM,Tuschl T,Lyden D,D'Amico DJ,Pena JTG

更新日期：2019-12-01 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：: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 shortcomi...

journal_title：Nature methods

authors： Beghin A,Kechkar A,Butler C,Levet F,Cabillic M,Rossier O,Giannone G,Galland R,Choquet D,Sibarita JB

更新日期：2017-12-01 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：:Circular RNAs (circRNAs) produced from back-spliced exons are widely expressed, but individual circRNA functions remain poorly understood owing to the lack of adequate methods for distinguishing circRNAs from cognate messenger RNAs with overlapping exons. Here, we report that CRISPR-RfxCas13d can effectively discrimin...

journal_title：Nature methods

authors： Li S,Li X,Xue W,Zhang L,Yang LZ,Cao SM,Lei YN,Liu CX,Guo SK,Shan L,Wu M,Tao X,Zhang JL,Gao X,Zhang J,Wei J,Li J,Yang L,Chen LL

更新日期：2021-01-01 00:00:00

abstract：:We report attainment of subdiffraction resolution using stimulated emission depletion (STED) microscopy with GFP-labeled samples. The approximately 70 nm lateral resolution attained in this study is demonstrated by imaging GFP-labeled viruses and the endoplasmic reticulum (ER) of a mammalian cell. Our results mark the...

journal_title：Nature methods

authors： Willig KI,Kellner RR,Medda R,Hein B,Jakobs S,Hell SW

更新日期：2006-09-01 00:00:00

abstract：:We must reliably map the interactomes of cellular macromolecular complexes in order to fully explore and understand biological systems. However, there are no methods to accurately predict how to capture a given macromolecular complex with its physiological binding partners. Here, we present a screening method that com...

journal_title：Nature methods

authors： Hakhverdyan Z,Domanski M,Hough LE,Oroskar AA,Oroskar AR,Keegan S,Dilworth DJ,Molloy KR,Sherman V,Aitchison JD,Fenyö D,Chait BT,Jensen TH,Rout MP,LaCava J

更新日期：2015-06-01 00:00:00

abstract：:The occurrence of multiple strains of prions may reflect conformational variability of PrP(Sc), a disease-associated, aggregated variant of the cellular prion protein, PrP(C). Here we used luminescent conjugated polymers (LCPs), which emit conformation-dependent fluorescence spectra, for characterizing prion strains. ...

journal_title：Nature methods

authors： Sigurdson CJ,Nilsson KP,Hornemann S,Manco G,Polymenidou M,Schwarz P,Leclerc M,Hammarström P,Wüthrich K,Aguzzi A

更新日期：2007-12-01 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：:Our Patterning on Topography (PoT) printing technique enables fibronectin, laminin and other proteins to be applied to biomaterial surfaces in complex geometries that are inaccessible using traditional soft lithography techniques. Engineering combinatorial surfaces that integrate topographical and biochemical micropat...

journal_title：Nature methods

authors： Sun Y,Jallerat Q,Szymanski JM,Feinberg AW

更新日期：2015-02-01 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：:Despite the vital role of mechanical forces in biology, it still remains a challenge to image cellular force with sub-100-nm resolution. Here, we present tension points accumulation for imaging in nanoscale topography (tPAINT), integrating molecular tension probes with the DNA points accumulation for imaging in nanosc...

journal_title：Nature methods

authors： Brockman JM,Su H,Blanchard AT,Duan Y,Meyer T,Quach ME,Glazier R,Bazrafshan A,Bender RL,Kellner AV,Ogasawara H,Ma R,Schueder F,Petrich BG,Jungmann R,Li R,Mattheyses AL,Ke Y,Salaita K

更新日期：2020-10-01 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：: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：: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：:Despite the widespread adoption of organoids as biomimetic tissue models, methods to comprehensively analyze cell-type-specific post-translational modification (PTM) signaling networks in organoids are absent. Here, we report multivariate single-cell analysis of such networks in organoids and organoid cocultures. Simu...

journal_title：Nature methods

authors： Qin X,Sufi J,Vlckova P,Kyriakidou P,Acton SE,Li VSW,Nitz M,Tape CJ

更新日期：2020-03-01 00:00:00

abstract：:A robust method for simultaneous visualization of all four cell cycle phases in living cells is highly desirable. We developed an intensiometric reporter of the transition from S to G2 phase and engineered a far-red fluorescent protein, mMaroon1, to visualize chromatin condensation in mitosis. We combined these new re...

journal_title：Nature methods

authors： Bajar BT,Lam AJ,Badiee RK,Oh YH,Chu J,Zhou XX,Kim N,Kim BB,Chung M,Yablonovitch AL,Cruz BF,Kulalert K,Tao JJ,Meyer T,Su XD,Lin MZ

更新日期：2016-12-01 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：: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：: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：: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：: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：:We describe an engineered family of highly antigenic molecules based on GFP-like fluorescent proteins. These molecules contain numerous copies of peptide epitopes and simultaneously bind IgG antibodies at each location. These 'spaghetti monster' fluorescent proteins (smFPs) distributed well in neurons, notably into sm...

journal_title：Nature methods

authors： Viswanathan S,Williams ME,Bloss EB,Stasevich TJ,Speer CM,Nern A,Pfeiffer BD,Hooks BM,Li WP,English BP,Tian T,Henry GL,Macklin JJ,Patel R,Gerfen CR,Zhuang X,Wang Y,Rubin GM,Looger LL

更新日期：2015-06-01 00:00:00

abstract：:Phenotype-based small-molecule screening is a powerful method to identify molecules that regulate cellular functions. However, such screens are generally performed in vitro under conditions that do not necessarily model complex physiological conditions or disease states. Here, we use molecular cell barcoding to enable...

journal_title：Nature methods

authors： Grüner BM,Schulze CJ,Yang D,Ogasawara D,Dix MM,Rogers ZN,Chuang CH,McFarland CD,Chiou SH,Brown JM,Cravatt BF,Bogyo M,Winslow MM

更新日期：2016-10-01 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