High-resolution mass spectrometry of small molecules bound to membrane proteins.

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：:We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unk...

journal_title：Nature methods

authors： Newman AM,Liu CL,Green MR,Gentles AJ,Feng W,Xu Y,Hoang CD,Diehn M,Alizadeh AA

更新日期：2015-05-01 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：: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 applied pulse-shape analysis (PulSA) to monitor protein localization changes in mammalian cells by flow cytometry. PulSA enabled high-throughput tracking of protein aggregation, translocation from the cytoplasm to the nucleus and trafficking from the plasma membrane to the Golgi as well as stress-granule formation....

journal_title：Nature methods

authors： Ramdzan YM,Polling S,Chia CP,Ng IH,Ormsby AR,Croft NP,Purcell AW,Bogoyevitch MA,Ng DC,Gleeson PA,Hatters DM

更新日期：2012-03-18 00:00:00

abstract：:We developed a caged GABA (gamma-aminobutyric acid), which, when combined with an appropriate caged glutamate, allows bimodal control of neuronal membrane potential with subcellular resolution using optically independent two-photon uncaging of each neurotransmitter. We used two-color, two-photon uncaging to fire and b...

journal_title：Nature methods

authors： Kantevari S,Matsuzaki M,Kanemoto Y,Kasai H,Ellis-Davies GC

更新日期：2010-02-01 00:00:00

abstract：:Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then...

journal_title：Nature methods

authors： Gauchier M,van Mierlo G,Vermeulen M,Déjardin J

更新日期：2020-04-01 00:00:00

abstract：:The measurement of lifespan pervades aging research. Because lifespan results from complex interactions between genetic, environmental and stochastic factors, it varies widely even among isogenic individuals. The actions of molecular mechanisms on lifespan are therefore visible only through their statistical effects o...

journal_title：Nature methods

authors： Stroustrup N,Ulmschneider BE,Nash ZM,López-Moyado IF,Apfeld J,Fontana W

更新日期：2013-07-01 00:00:00

abstract：:Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are often kept in solution with detergent micelles and lipid nanodiscs that are locally disordered. Such spatial variability ne...

journal_title：Nature methods

authors： Punjani A,Zhang H,Fleet DJ

更新日期：2020-12-01 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：: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：: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：: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：:Although transcription activator-like effector nucleases (TALENs) can be designed to cleave chosen DNA sequences, TALENs have activity against related off-target sequences. To better understand TALEN specificity, we profiled 30 unique TALENs with different target sites, array length and domain sequences for their abil...

journal_title：Nature methods

authors： Guilinger JP,Pattanayak V,Reyon D,Tsai SQ,Sander JD,Joung JK,Liu DR

更新日期：2014-04-01 00:00:00

abstract：:Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems. ...

journal_title：Nature methods

authors： Mahmutovic A,Fange D,Berg OG,Elf J

更新日期：2012-12-01 00:00:00

abstract：:Recording light-microscopy images of large, nontransparent specimens, such as developing multicellular organisms, is complicated by decreased contrast resulting from light scattering. Early zebrafish development can be captured by standard light-sheet microscopy, but new imaging strategies are required to obtain high-...

journal_title：Nature methods

authors： Keller PJ,Schmidt AD,Santella A,Khairy K,Bao Z,Wittbrodt J,Stelzer EH

更新日期：2010-08-01 00:00:00

abstract：:X-ray free-electron lasers (XFELs) offer opportunities beyond classic X-ray crystallography, particularly for proteins that are difficult to crystallize. ...

journal_title：Nature methods

authors： Marx V

更新日期：2014-09-01 00:00:00

abstract：:RNA-guided Cas9 nucleases derived from clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have dramatically transformed our ability to edit the genomes of diverse organisms. We believe tools and techniques based on Cas9, a single unifying factor capable of colocalizing RNA, DNA and protein,...

journal_title：Nature methods

authors： Mali P,Esvelt KM,Church GM

更新日期：2013-10-01 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：:The shape of the genome is thought to play an important part in the coordination of transcription and other DNA-metabolic processes. Chromosome conformation capture (3C) technology allows us to analyze the folding of chromatin in the native cellular state at a resolution beyond that provided by current microscopy tech...

journal_title：Nature methods

authors： Simonis M,Kooren J,de Laat W

更新日期：2007-11-01 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：:Accurately modeling cellular response to perturbations is a central goal of computational biology. While such modeling has been based on statistical, mechanistic and machine learning models in specific settings, no generalization of predictions to phenomena absent from training data (out-of-sample) has yet been demons...

journal_title：Nature methods

authors： Lotfollahi M,Wolf FA,Theis FJ

更新日期：2019-08-01 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：: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：: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：: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：: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：:We present a method to robustly discriminate clustered from randomly distributed molecules detected with techniques based on single-molecule localization microscopy, such as PALM and STORM. The approach is based on deliberate variation of labeling density, such as titration of fluorescent antibody, combined with quant...

journal_title：Nature methods

authors： Baumgart F,Arnold AM,Leskovar K,Staszek K,Fölser M,Weghuber J,Stockinger H,Schütz GJ

更新日期：2016-08-01 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：:Targeted quantification of DNA methylation allows for interrogation of the most informative loci across many samples quickly and cost-effectively. Here we report improved bisulfite padlock probes (BSPPs) with a design algorithm to generate efficient padlock probes, a library-free protocol that dramatically reduces sam...

journal_title：Nature methods

authors： Diep D,Plongthongkum N,Gore A,Fung HL,Shoemaker R,Zhang K

更新日期：2012-02-05 00:00:00