Genetic incorporation of unnatural amino acids into proteins in mammalian cells.

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：: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：:Database searching is an essential element of large-scale proteomics. Because these methods are widely used, it is important to understand the rationale of the algorithms. Most algorithms are based on concepts first developed in SEQUEST and PeptideSearch. Four basic approaches are used to determine a match between a s...

journal_title：Nature methods

authors： Sadygov RG,Cociorva D,Yates JR 3rd

更新日期：2004-12-01 00:00:00

abstract：:Spontaneous and sensory-evoked activity propagates across varying spatial scales in the mammalian cortex, but technical challenges have limited conceptual links between the function of local neuronal circuits and brain-wide network dynamics. We present a method for simultaneous cellular-resolution two-photon calcium i...

journal_title：Nature methods

authors： Barson D,Hamodi AS,Shen X,Lur G,Constable RT,Cardin JA,Crair MC,Higley MJ

更新日期：2020-01-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors： Doerr A

更新日期：2019-01-01 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：: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：: ...

journal_title：Nature methods

authors： Vogt N

更新日期：2019-02-01 00:00:00

abstract：:Combining high-mass-accuracy mass spectrometry, isobaric tagging and software for multiplexed, large-scale protein quantification, we report deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate. This 24-sample comparison resulted in a very larg...

journal_title：Nature methods

authors： Phanstiel DH,Brumbaugh J,Wenger CD,Tian S,Probasco MD,Bailey DJ,Swaney DL,Tervo MA,Bolin JM,Ruotti V,Stewart R,Thomson JA,Coon JJ

更新日期：2011-09-11 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：: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：:High-speed, large-scale three-dimensional (3D) imaging of neuronal activity poses a major challenge in neuroscience. Here we demonstrate simultaneous functional imaging of neuronal activity at single-neuron resolution in an entire Caenorhabditis elegans and in larval zebrafish brain. Our technique captures the dynamic...

journal_title：Nature methods

authors： Prevedel R,Yoon YG,Hoffmann M,Pak N,Wetzstein G,Kato S,Schrödel T,Raskar R,Zimmer M,Boyden ES,Vaziri A

更新日期：2014-07-01 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：:Single-cell transcriptomics provides an opportunity to characterize cell-type-specific transcriptional networks, intercellular signaling pathways and cellular diversity with unprecedented resolution by profiling thousands of cells in a single experiment. However, owing to the unique statistical properties of scRNA-seq...

journal_title：Nature methods

authors： Skinnider MA,Squair JW,Foster LJ

更新日期：2019-05-01 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：: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：: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：: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：: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：:Macromolecular crowding in cells influences processes such as folding, association and diffusion of proteins and polynucleic acids. Direct spatiotemporal readout of crowding would be a powerful approach for unraveling the structure of the cytoplasm and determining the impact of excluded volume on protein function in l...

journal_title：Nature methods

authors： Boersma AJ,Zuhorn IS,Poolman B

更新日期：2015-03-01 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：:We show that nanoscopy based on the principle called RESOLFT (reversible saturable optical fluorescence transitions) or nonlinear structured illumination can be effectively parallelized using two incoherently superimposed orthogonal standing light waves. The intensity minima of the resulting pattern act as 'doughnuts'...

journal_title：Nature methods

authors： Chmyrov A,Keller J,Grotjohann T,Ratz M,d'Este E,Jakobs S,Eggeling C,Hell SW

更新日期：2013-08-01 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：:We have developed a versatile, potent technique for imaging cells in culture and in vivo by expressing a metabolically biotinylated cell-surface receptor and visualizing it with labeled streptavidin moieties. The recombinant reporter protein, which incorporates a biotin acceptor peptide (BAP) between an N-terminal sig...

journal_title：Nature methods

authors： Tannous BA,Grimm J,Perry KF,Chen JW,Weissleder R,Breakefield XO

更新日期：2006-05-01 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：: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：:Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and pr...

journal_title：Nature methods

authors： Ouyang W,Winsnes CF,Hjelmare M,Cesnik AJ,Åkesson L,Xu H,Sullivan DP,Dai S,Lan J,Jinmo P,Galib SM,Henkel C,Hwang K,Poplavskiy D,Tunguz B,Wolfinger RD,Gu Y,Li C,Xie J,Buslov D,Fironov S,Kiselev A,Panchenko D,C

更新日期：2019-12-01 00:00:00

abstract：:The ability to apply precise inputs to signaling species in live cells would be transformative for interrogating and understanding complex cell-signaling systems. Here we report an 'optogenetic' method for applying custom signaling inputs using feedback control of a light-gated protein-protein interaction. We applied ...

journal_title：Nature methods

authors： Toettcher JE,Gong D,Lim WA,Weiner OD

更新日期：2011-09-11 00:00:00

abstract：:Existing methods for human induced pluripotent stem cell (hiPSC) cardiac differentiation are efficient but require complex, undefined medium constituents that hinder further elucidation of the molecular mechanisms of cardiomyogenesis. Using hiPSCs derived under chemically defined conditions on synthetic matrices, we s...

journal_title：Nature methods

authors： Burridge PW,Matsa E,Shukla P,Lin ZC,Churko JM,Ebert AD,Lan F,Diecke S,Huber B,Mordwinkin NM,Plews JR,Abilez OJ,Cui B,Gold JD,Wu JC

更新日期：2014-08-01 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