Nanoscopy with more than 100,000 'doughnuts'.

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：: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：:Microarrays have been widely used for the analysis of gene expression, but the issue of reproducibility across platforms has yet to be fully resolved. To address this apparent problem, we compared gene expression between two microarray platforms: the short oligonucleotide Affymetrix Mouse Genome 430 2.0 GeneChip and a...

journal_title：Nature methods

authors： Larkin JE,Frank BC,Gavras H,Sultana R,Quackenbush J

更新日期：2005-05-01 00:00:00

abstract：:FLIRT (fast local infrared thermogenetics) is a microscopy-based technology to locally and reversibly manipulate protein function while simultaneously monitoring the effects in vivo. FLIRT locally inactivates fast-acting temperature-sensitive mutant proteins. We demonstrate that FLIRT can control temperature-sensitive...

journal_title：Nature methods

authors： Hirsch SM,Sundaramoorthy S,Davies T,Zhuravlev Y,Waters JC,Shirasu-Hiza M,Dumont J,Canman JC

更新日期：2018-11-01 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：: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：:CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome pro...

journal_title：Nature methods

authors： Datlinger P,Rendeiro AF,Schmidl C,Krausgruber T,Traxler P,Klughammer J,Schuster LC,Kuchler A,Alpar D,Bock C

更新日期：2017-03-01 00:00:00

abstract：:t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we ...

journal_title：Nature methods

authors： Linderman GC,Rachh M,Hoskins JG,Steinerberger S,Kluger Y

更新日期：2019-03-01 00:00:00

abstract：:The analysis of structure and dynamics of biomolecules is important for understanding their function. Toward this aim, we introduce a method called 'switchable FRET', which combines single-molecule fluorescence resonance energy transfer (FRET) with reversible photoswitching of fluorophores. Typically, single-molecule ...

journal_title：Nature methods

authors： Uphoff S,Holden SJ,Le Reste L,Periz J,van de Linde S,Heilemann M,Kapanidis AN

更新日期：2010-10-01 00:00:00

abstract：:The successful in vitro evolution of a DNA enzyme based on a ribozyme could offer insights into early evolutionary events and provide guidelines for designing hardier catalytic oligonucleotides. ...

journal_title：Nature methods

authors： Eisenstein M

更新日期：2006-06-01 00:00:00

abstract：:To engineer a stem cell genome, we developed a technology for targeted elimination of chromosomes from mouse embryonic stem (ES)-somatic hybrid cells. Here we demonstrate the use of a universal chromosome elimination cassette (CEC) for elimination of a single embryonic stem cell (ESC)-derived chromosome 11 or 12, and ...

journal_title：Nature methods

authors： Matsumura H,Tada M,Otsuji T,Yasuchika K,Nakatsuji N,Surani A,Tada T

更新日期：2007-01-01 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：: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：: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：:We report an atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) setup with a lateral resolution of 1.4 μm, a mass resolution greater than 100,000, and accuracy below ±2 p.p.m. We achieved this by coupling a focusing objective with a numerical aperture (NA) of ...

journal_title：Nature methods

authors： Kompauer M,Heiles S,Spengler B

更新日期：2017-01-01 00:00:00

abstract：:The complexities of tumor genomes are rapidly being uncovered, but how they are regulated into functional proteomes remains poorly understood. Standard proteomics workflows use databases of known proteins, but these databases do not capture the uniqueness of the cancer transcriptome, with its point mutations, unusual ...

journal_title：Nature methods

authors： Alfaro JA,Sinha A,Kislinger T,Boutros PC

更新日期：2014-11-01 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：:The analysis of synthetic genetic interaction networks can reveal how biological systems achieve a high level of complexity with a limited repertoire of components. Studies in yeast and bacteria have taken advantage of collections of deletion strains to construct matrices of quantitative interaction profiles and infer...

journal_title：Nature methods

authors： Horn T,Sandmann T,Fischer B,Axelsson E,Huber W,Boutros M

更新日期：2011-04-01 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：:The normalization of RNA-seq data is essential for accurate downstream inference, but the assumptions upon which most normalization methods are based are not applicable in the single-cell setting. Consequently, applying existing normalization methods to single-cell RNA-seq data introduces artifacts that bias downstrea...

journal_title：Nature methods

authors： Bacher R,Chu LF,Leng N,Gasch AP,Thomson JA,Stewart RM,Newton M,Kendziorski C

更新日期：2017-06-01 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：:We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced ...

journal_title：Nature methods

authors： Roth A,Khattra J,Yap D,Wan A,Laks E,Biele J,Ha G,Aparicio S,Bouchard-Côté A,Shah SP

更新日期：2014-04-01 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：:We demonstrate tracking of protein structural changes with time-resolved wide-angle X-ray scattering (TR-WAXS) with nanosecond time resolution. We investigated the tertiary and quaternary conformational changes of human hemoglobin under nearly physiological conditions triggered by laser-induced ligand photolysis. We a...

journal_title：Nature methods

authors： Cammarata M,Levantino M,Schotte F,Anfinrud PA,Ewald F,Choi J,Cupane A,Wulff M,Ihee H

更新日期：2008-10-01 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：:We combined rapid microfluidic mixing with single-molecule fluorescence resonance energy transfer to study the folding kinetics of the intrinsically disordered human protein α-synuclein. The time-resolution of 0.2 ms revealed initial collapse of the unfolded protein induced by binding with lipid mimics and subsequent ...

journal_title：Nature methods

authors： Gambin Y,VanDelinder V,Ferreon AC,Lemke EA,Groisman A,Deniz AA

更新日期：2011-03-01 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：:Quantification of cell-cycle state at a single-cell level is essential to understand fundamental three-dimensional (3D) biological processes such as tissue development and cancer. Analysis of 3D in vivo images, however, is very challenging. Today's best practice, manual annotation of select image events, generates arb...

journal_title：Nature methods

authors： Chittajallu DR,Florian S,Kohler RH,Iwamoto Y,Orth JD,Weissleder R,Danuser G,Mitchison TJ

更新日期：2015-06-01 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：:Understanding how cells maintain genome integrity when challenged with DNA double-strand breaks (DSBs) is of major importance, particularly since the discovery of multiple links of DSBs with genome instability and cancer-predisposition disorders. Ionizing radiation is the agent of choice to produce DSBs in cells; howe...

journal_title：Nature methods

authors： Stap J,Krawczyk PM,Van Oven CH,Barendsen GW,Essers J,Kanaar R,Aten JA

更新日期：2008-03-01 00:00:00