Publisher Correction: Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl.

abstract：:We present a noninvasive approach to track activation of ATP-gated P2X receptors and potentially other transmitter-gated cation channels that show calcium fluxes. We genetically engineered rat P2X receptors to carry calcium sensors near the channel pore and tested this as a reporter for P2X(2) receptor opening. The me...

journal_title：Nature methods

authors： Richler E,Chaumont S,Shigetomi E,Sagasti A,Khakh BS

更新日期：2008-01-01 00:00:00

abstract：:Using a directed evolution approach, researchers demonstrate a way of creating 'designer' receptors that are specifically activated by a ligand with no other biological activity in the cell. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2007-05-01 00:00:00

abstract：:Genetically encoded unnatural amino acids provide powerful strategies for modulating the molecular functions of proteins in mammalian cells. However, this approach has not been coupled to genome-wide measurements, because efficient incorporation of unnatural amino acids is limited to transient expression settings that...

journal_title：Nature methods

authors： Elsässer SJ,Ernst RJ,Walker OS,Chin JW

更新日期：2016-02-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors：

更新日期：2018-12-01 00:00:00

abstract：:Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report th...

journal_title：Nature methods

authors： Radivojac P,Clark WT,Oron TR,Schnoes AM,Wittkop T,Sokolov A,Graim K,Funk C,Verspoor K,Ben-Hur A,Pandey G,Yunes JM,Talwalkar AS,Repo S,Souza ML,Piovesan D,Casadio R,Wang Z,Cheng J,Fang H,Gough J,Koskinen P,Törö

更新日期：2013-03-01 00:00:00

abstract：:We present functional ultrasound (fUS), a method for imaging transient changes in blood volume in the whole brain at better spatiotemporal resolution than with other functional brain imaging modalities. fUS uses plane-wave illumination at high frame rate and can measure blood volumes in smaller vessels than previous u...

journal_title：Nature methods

authors： Macé E,Montaldo G,Cohen I,Baulac M,Fink M,Tanter M

更新日期：2011-07-03 00:00:00

abstract：:Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses and disease, testing enhancer activity in animals remains tedious, with a minority of enhancers having been cha...

journal_title：Nature methods

authors： Gisselbrecht SS,Barrera LA,Porsch M,Aboukhalil A,Estep PW 3rd,Vedenko A,Palagi A,Kim Y,Zhu X,Busser BW,Gamble CE,Iagovitina A,Singhania A,Michelson AM,Bulyk ML

更新日期：2013-08-01 00:00:00

abstract：:Here we integrated multiphoton laser scanning microscopy and the registration of second harmonic generation images of collagen fibers to overcome difficulties in tracking stromal cell-matrix interactions for several days in live mice. We show that the matrix-modifying hormone relaxin increased tumor-associated fibrobl...

journal_title：Nature methods

authors： Perentes JY,McKee TD,Ley CD,Mathiew H,Dawson M,Padera TP,Munn LL,Jain RK,Boucher Y

更新日期：2009-02-01 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：: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：:Cortical information processing relies on synaptic interactions between diverse classes of neurons with distinct electrophysiological and connection properties. Uncovering the operational principles of these elaborate circuits requires the probing of electrical activity from selected populations of defined neurons. He...

journal_title：Nature methods

authors： Akemann W,Mutoh H,Perron A,Rossier J,Knöpfel T

更新日期：2010-08-01 00:00:00

abstract：:Biomolecular dynamics and stability are predominantly investigated in vitro and extrapolated to explain function in the living cell. We present fast relaxation imaging (FreI), which combines fluorescence microscopy and temperature jumps to probe biomolecular dynamics and stability inside a single living cell with high...

journal_title：Nature methods

authors： Ebbinghaus S,Dhar A,McDonald JD,Gruebele M

更新日期：2010-04-01 00:00:00

abstract：:We present general means to greatly increase the sensitivity of antibody-based assays. Augmentation relies on a 'tadpole' protein-DNA chimera whose protein moiety binds most classes of mammalian antibodies but not avian immunoglobulin Y (IgY). We used this tadpole in affinity capture assays followed by real-time PCR t...

journal_title：Nature methods

authors： Burbulis I,Yamaguchi K,Yu R,Resnekov O,Brent R

更新日期：2007-12-01 00:00:00

abstract：:The implementation of efficient technologies for the production of recombinant mammalian proteins remains an outstanding challenge in many structural and functional genomics programs. We have developed a new method for rapid identification of soluble protein expression in E. coli, based on a separation of soluble prot...

journal_title：Nature methods

authors： Cornvik T,Dahlroth SL,Magnusdottir A,Herman MD,Knaust R,Ekberg M,Nordlund P

更新日期：2005-07-01 00:00:00

abstract：:In mass-spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily rely on sequence database searching or spectral library matching. The lack of accurate predictive models for fragment ion intensities impairs the realization of the full potential of these approaches. Here, we...

journal_title：Nature methods

authors： Gessulat S,Schmidt T,Zolg DP,Samaras P,Schnatbaum K,Zerweck J,Knaute T,Rechenberger J,Delanghe B,Huhmer A,Reimer U,Ehrlich HC,Aiche S,Kuster B,Wilhelm M

更新日期：2019-06-01 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：:Glycosylation, which represents the most complex posttranslational modification (PTM) event during protein maturation, has a vital role in biological processes. Glycan biosynthesis is orchestrated by numerous glycosyltransferases, each displaying different selectivities for multiple reaction sites. The precise specifi...

journal_title：Nature methods

authors： Ito H,Kameyama A,Sato T,Sukegawa M,Ishida HK,Narimatsu H

更新日期：2007-07-01 00:00:00

abstract：:We describe an efficient, accurate and robust whole-genome genotyping (WGG) assay based on a two-color, single-base extension (SBE), single-nucleotide polymorphism (SNP)-scoring step. We report genotyping results for biallelic International HapMap quality control (QC) SNPs using a single probe per locus. We show scala...

journal_title：Nature methods

authors： Steemers FJ,Chang W,Lee G,Barker DL,Shen R,Gunderson KL

更新日期：2006-01-01 00:00:00

abstract：:Identifying groups of similar objects is a popular first step in biomedical data analysis, but it is error-prone and impossible to perform manually. Many computational methods have been developed to tackle this problem. Here we assessed 13 well-known methods using 24 data sets ranging from gene expression to protein d...

journal_title：Nature methods

authors： Wiwie C,Baumbach J,Röttger R

更新日期：2015-11-01 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：: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：:We introduce a method for sequencing peptides by mass spectrometry using a metalloendopeptidase that cleaves proteins at the amino side of lysine (Lys-N). When analyzed by electron transfer dissociation (ETD)-based mass spectrometric sequencing, Lys-N-digested peptides that contain a single lysine residue produce spec...

journal_title：Nature methods

authors： Taouatas N,Drugan MM,Heck AJ,Mohammed S

更新日期：2008-05-01 00:00:00

abstract：:Live-cell single mRNA imaging is a powerful tool but has been restricted in higher eukaryotes to artificial cell lines and reporter genes. We describe an approach that enables live-cell imaging of single endogenous labeled mRNA molecules transcribed in primary mammalian cells and tissue. We generated a knock-in mouse ...

journal_title：Nature methods

authors： Lionnet T,Czaplinski K,Darzacq X,Shav-Tal Y,Wells AL,Chao JA,Park HY,de Turris V,Lopez-Jones M,Singer RH

更新日期：2011-02-01 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 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：:To enable sophisticated optogenetic manipulation of neural circuits throughout the nervous system with limited disruption of animal behavior, light-delivery systems beyond fiber optic tethering and large, head-mounted wireless receivers are desirable. We report the development of an easy-to-construct, implantable wire...

journal_title：Nature methods

authors： Montgomery KL,Yeh AJ,Ho JS,Tsao V,Mohan Iyer S,Grosenick L,Ferenczi EA,Tanabe Y,Deisseroth K,Delp SL,Poon AS

更新日期：2015-10-01 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：:Photoconvertible fluorescent proteins are potential tools for investigating dynamic processes in living cells and for emerging super-resolution microscopy techniques. Unfortunately, most probes in this class are hampered by oligomerization, small photon budgets or poor photostability. Here we report an EosFP variant t...

journal_title：Nature methods

authors： McKinney SA,Murphy CS,Hazelwood KL,Davidson MW,Looger LL

更新日期：2009-02-01 00:00:00

abstract：:By combining activity-based proteomics and metabolomics, researchers have developed a new systems biology strategy for characterizing enzymes in the context of metabolic networks. ...

journal_title：Nature methods

authors： Doerr A

更新日期：2007-01-01 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