Quantitative multiplexed profiling of cellular signaling networks using phosphotyrosine-specific DNA-tagged SH2 domains.

abstract：:We present DeNovoGear software for analyzing de novo mutations from familial and somatic tissue sequencing data. DeNovoGear uses likelihood-based error modeling to reduce the false positive rate of mutation discovery in exome analysis and fragment information to identify the parental origin of germ-line mutations. We ...

journal_title：Nature methods

authors： Ramu A,Noordam MJ,Schwartz RS,Wuster A,Hurles ME,Cartwright RA,Conrad DF

更新日期：2013-10-01 00:00:00

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：:We report attainment of subdiffraction resolution using stimulated emission depletion (STED) microscopy with GFP-labeled samples. The approximately 70 nm lateral resolution attained in this study is demonstrated by imaging GFP-labeled viruses and the endoplasmic reticulum (ER) of a mammalian cell. Our results mark the...

journal_title：Nature methods

authors： Willig KI,Kellner RR,Medda R,Hein B,Jakobs S,Hell SW

更新日期：2006-09-01 00:00:00

abstract：:Recent efforts in neuroscience research have been aimed at obtaining detailed anatomical neuronal wiring maps as well as information on how neurons in these networks engage in dynamic activities. Although the entire connectivity map of the nervous system of Caenorhabditis elegans has been known for more than 25 years,...

journal_title：Nature methods

authors： Schrödel T,Prevedel R,Aumayr K,Zimmer M,Vaziri A

更新日期：2013-10-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors：

更新日期：2018-12-01 00:00:00

abstract：:Thermodynamic stability is fundamental to the biology of proteins. Information on protein stability is essential for studying protein structure and folding and can also be used indirectly to monitor protein-ligand or protein-protein interactions. While clearly valuable, the experimental determination of a protein's st...

journal_title：Nature methods

authors： Park C,Marqusee S

更新日期：2005-03-01 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：: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：:Next-generation sequencing technology is a powerful tool for transcriptome analysis. However, under certain conditions, only a small amount of material is available, which requires more sensitive techniques that can preferably be used at the single-cell level. Here we describe a single-cell digital gene expression pro...

journal_title：Nature methods

authors： Tang F,Barbacioru C,Wang Y,Nordman E,Lee C,Xu N,Wang X,Bodeau J,Tuch BB,Siddiqui A,Lao K,Surani MA

更新日期：2009-05-01 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：:The Q system is a repressible binary expression system for transgenic manipulations in living organisms. Through protein engineering and in vivo functional tests, we report here variants of the Q-system transcriptional activator, including QF2, for driving strong and ubiquitous expression in all Drosophila tissues. Ou...

journal_title：Nature methods

authors： Riabinina O,Luginbuhl D,Marr E,Liu S,Wu MN,Luo L,Potter CJ

更新日期：2015-03-01 00:00:00

abstract：:We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads f...

journal_title：Nature methods

authors： Robertson G,Schein J,Chiu R,Corbett R,Field M,Jackman SD,Mungall K,Lee S,Okada HM,Qian JQ,Griffith M,Raymond A,Thiessen N,Cezard T,Butterfield YS,Newsome R,Chan SK,She R,Varhol R,Kamoh B,Prabhu AL,Tam A,Zhao Y

更新日期：2010-11-01 00:00:00

abstract：:An uncharged CoA precursor that can enter the cell is used for covalent, site-specific labeling of proteins inside living cells. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2006-11-01 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：:We report a technique to selectively and continuously label the proteomes of individual cell types in coculture, named cell type-specific labeling using amino acid precursors (CTAP). Through transgenic expression of exogenous amino acid biosynthesis enzymes, vertebrate cells overcome their dependence on supplemented e...

journal_title：Nature methods

authors： Gauthier NP,Soufi B,Walkowicz WE,Pedicord VA,Mavrakis KJ,Macek B,Gin DY,Sander C,Miller ML

更新日期：2013-08-01 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 have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30-90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic protein...

journal_title：Nature methods

authors： Jarzab A,Kurzawa N,Hopf T,Moerch M,Zecha J,Leijten N,Bian Y,Musiol E,Maschberger M,Stoehr G,Becher I,Daly C,Samaras P,Mergner J,Spanier B,Angelov A,Werner T,Bantscheff M,Wilhelm M,Klingenspor M,Lemeer S,Liebl W

更新日期：2020-05-01 00:00:00

abstract：:Quantitative measurements of cell-generated forces have heretofore required that cells be cultured on two-dimensional substrates. We describe a technique to quantitatively measure three-dimensional traction forces exerted by cells fully encapsulated in well-defined elastic hydrogel matrices. Using this approach we mea...

journal_title：Nature methods

authors： Legant WR,Miller JS,Blakely BL,Cohen DM,Genin GM,Chen CS

更新日期：2010-12-01 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：: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：: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：: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

abstract：:Small interfering RNAs (siRNAs) have been widely exploited for sequence-specific gene knockdown, predominantly to investigate gene function in cultured vertebrate cells, and also hold promise as therapeutic agents. Because not all siRNAs that are cognate to a given target mRNA are equally effective, computational tool...

journal_title：Nature methods

authors： Pei Y,Tuschl T

更新日期：2006-09-01 00:00:00

abstract：:A label-free microscopy technique based on electrochemical impedance offers a new way of studying electrochemical processes in single cells. ...

journal_title：Nature methods

authors： Doerr A

更新日期：2011-03-01 00:00:00

abstract：:We describe an engineered family of highly antigenic molecules based on GFP-like fluorescent proteins. These molecules contain numerous copies of peptide epitopes and simultaneously bind IgG antibodies at each location. These 'spaghetti monster' fluorescent proteins (smFPs) distributed well in neurons, notably into sm...

journal_title：Nature methods

authors： Viswanathan S,Williams ME,Bloss EB,Stasevich TJ,Speer CM,Nern A,Pfeiffer BD,Hooks BM,Li WP,English BP,Tian T,Henry GL,Macklin JJ,Patel R,Gerfen CR,Zhuang X,Wang Y,Rubin GM,Looger LL

更新日期：2015-06-01 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：: ...

journal_title：Nature methods

authors： Strack R

更新日期：2019-02-01 00:00:00

abstract：:An outstanding challenge of epigenome-wide association studies (EWASs) performed in complex tissues is the identification of the specific cell type(s) responsible for the observed differential DNA methylation. Here we present a statistical algorithm called CellDMC ( https://github.com/sjczheng/EpiDISH ), which can ide...

journal_title：Nature methods

authors： Zheng SC,Breeze CE,Beck S,Teschendorff AE

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：: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