Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos.

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：: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：: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： Martinez-Sanchez A,Kochovski Z,Laugks U,Meyer Zum Alten Borgloh J,Chakraborty S,Pfeffer S,Baumeister W,Lučić V

更新日期：2020-02-01 00:00:00

abstract：:Focused-ion-beam scanning electron microscopy (FIB-SEM) has become an essential tool for studying neural tissue at resolutions below 10 nm × 10 nm × 10 nm, producing data sets optimized for automatic connectome tracing. We present a technical advance, ultrathick sectioning, which reliably subdivides embedded tissue sa...

journal_title：Nature methods

authors： Hayworth KJ,Xu CS,Lu Z,Knott GW,Fetter RD,Tapia JC,Lichtman JW,Hess HF

更新日期：2015-04-01 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：: ...

journal_title：Nature methods

authors：

更新日期：2018-12-01 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：:Despite widespread use of CRISPR, comprehensive data on the frequency and impact of Cas9-mediated off-targets in modified rodents are limited. Here we present deep-sequencing data from 81 genome-editing projects on mouse and rat genomes at 1,423 predicted off-target sites, 32 of which were confirmed, and show that hig...

journal_title：Nature methods

authors： Anderson KR,Haeussler M,Watanabe C,Janakiraman V,Lund J,Modrusan Z,Stinson J,Bei Q,Buechler A,Yu C,Thamminana SR,Tam L,Sowick MA,Alcantar T,O'Neil N,Li J,Ta L,Lima L,Roose-Girma M,Rairdan X,Durinck S,Warming S

更新日期：2018-07-01 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：: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：:Preprocessing of functional magnetic resonance imaging (fMRI) involves numerous steps to clean and standardize the data before statistical analysis. Generally, researchers create ad hoc preprocessing workflows for each dataset, building upon a large inventory of available tools. The complexity of these workflows has s...

journal_title：Nature methods

authors： Esteban O,Markiewicz CJ,Blair RW,Moodie CA,Isik AI,Erramuzpe A,Kent JD,Goncalves M,DuPre E,Snyder M,Oya H,Ghosh SS,Wright J,Durnez J,Poldrack RA,Gorgolewski KJ

更新日期：2019-01-01 00:00:00

abstract：:Researchers designed an enzyme to carry out the Diels-Alder reaction, an activity not found in nature. ...

journal_title：Nature methods

authors： Doerr A

更新日期：2010-09-01 00:00:00

abstract：:Because of ever-increasing throughput requirements of sequencing data, most existing short-read aligners have been designed to focus on speed at the expense of accuracy. The Genome Multitool (GEM) mapper can leverage string matching by filtration to search the alignment space more efficiently, simultaneously deliverin...

journal_title：Nature methods

authors： Marco-Sola S,Sammeth M,Guigó R,Ribeca P

更新日期：2012-12-01 00:00:00

abstract：:Optimism about biomedicine is challenged by the increasingly complex ethical, legal and social issues it raises. Reporting of scientific methods is no longer sufficient to address the complex relationship between science and society. To promote 'ethical reproducibility', we call for transparent reporting of research e...

journal_title：Nature methods

authors： Anderson JA,Eijkholt M,Illes J

更新日期：2013-09-01 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：: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：:Infrared fluorescent proteins (IFPs) provide an additional color to GFP and its homologs in protein labeling. Drawing on structural analysis of the dimer interface, we identified a bacteriophytochrome in the sequence database that is monomeric in truncated form and engineered it into a naturally monomeric IFP (mIFP). ...

journal_title：Nature methods

authors： Yu D,Baird MA,Allen JR,Howe ES,Klassen MP,Reade A,Makhijani K,Song Y,Liu S,Murthy Z,Zhang SQ,Weiner OD,Kornberg TB,Jan YN,Davidson MW,Shu X

更新日期：2015-08-01 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：: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：: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 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：:Protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We and others previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectromet...

journal_title：Nature methods

authors： Hu LZ,Goebels F,Tan JH,Wolf E,Kuzmanov U,Wan C,Phanse S,Xu C,Schertzberg M,Fraser AG,Bader GD,Emili A

更新日期：2019-08-01 00:00:00

abstract：:Spatiotemporal activity patterns in three-dimensionally organized cellular networks are fundamental to the function of the nervous system. Despite advances in functional imaging of cell populations, a method to resolve local network activity in three dimensions has been lacking. Here we introduce a three-dimensional (...

journal_title：Nature methods

authors： Göbel W,Kampa BM,Helmchen F

更新日期：2007-01-01 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：: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：:The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and b...

journal_title：Nature methods

authors： Ewing AD,Houlahan KE,Hu Y,Ellrott K,Caloian C,Yamaguchi TN,Bare JC,P'ng C,Waggott D,Sabelnykova VY,ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants.,Kellen MR,Norman TC,Haussler D,Friend SH,Stolovitzky G,Ma

更新日期：2015-07-01 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：:New methods to quantify protein kinase activities directly from complex cellular mixtures are critical for understanding biological regulatory pathways. Herein, a fluorescence-based chemosensor strategy for the direct measurement of kinase activities in crude mammalian cell lysates is described. We first designed a ne...

journal_title：Nature methods

authors： Shults MD,Janes KA,Lauffenburger DA,Imperiali B

更新日期：2005-04-01 00:00:00

abstract：:The complexity of the angiogenic cascade limits cellular approaches to studying angiogenic endothelial cells (ECs). In turn, in vivo assays do not allow the analysis of the distinct cellular behavior of ECs during angiogenesis. Here we show that ECs can be grafted as spheroids into a matrix to give rise to a complex t...

journal_title：Nature methods

authors： Alajati A,Laib AM,Weber H,Boos AM,Bartol A,Ikenberg K,Korff T,Zentgraf H,Obodozie C,Graeser R,Christian S,Finkenzeller G,Stark GB,Héroult M,Augustin HG

更新日期：2008-05-01 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