abstract：:Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue frequencies to graphically scale character heights. We describe the pLogo, a motif visualization in which residue heights are scaled relative to their statistical significance. A pLogo generation tool is publicly available at...

journal_title：Nature methods

authors： O'Shea JP,Chou MF,Quader SA,Ryan JK,Church GM,Schwartz D

更新日期：2013-12-01 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：: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：: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：:Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active-site conformations and consequently alter protein function. Observing alternative conformations at low levels of electron density, in addition to comparison of in...

journal_title：Nature methods

authors： van den Bedem H,Bhabha G,Yang K,Wright PE,Fraser JS

更新日期：2013-09-01 00:00:00

abstract：:Optimism about biomedicine is challenged by the increasingly complex ethical, legal and social issues it raises. Reporting of scientific methods is no longer sufficient to address the complex relationship between science and society. To promote 'ethical reproducibility', we call for transparent reporting of research e...

journal_title：Nature methods

authors： Anderson JA,Eijkholt M,Illes J

更新日期：2013-09-01 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 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：: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：: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：:With potential relevance for brain-mapping work, hydrogel-based structures can now be built from within biological tissue to allow subsequent removal of lipids without mechanical disassembly of the tissue. This process creates a tissue-hydrogel hybrid that is physically stable, that preserves fine structure, proteins ...

journal_title：Nature methods

authors： Chung K,Deisseroth K

更新日期：2013-06-01 00:00:00

abstract：:We describe a protein quantification method called neutron encoding that exploits the subtle mass differences caused by nuclear binding energy variation in stable isotopes. These mass differences are synthetically encoded into amino acids and incorporated into yeast and mouse proteins via metabolic labeling. Mass spec...

journal_title：Nature methods

authors： Hebert AS,Merrill AE,Bailey DJ,Still AJ,Westphall MS,Strieter ER,Pagliarini DJ,Coon JJ

更新日期：2013-04-01 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 established a conditional site-specific recombination system based on dimerizable Cre recombinase-mediated recombination in the apicomplexan parasite Toxoplasma gondii. Using a new single-vector strategy that allows ligand-dependent, efficient removal of a gene of interest, we generated three knockouts of apicomple...

journal_title：Nature methods

authors： Andenmatten N,Egarter S,Jackson AJ,Jullien N,Herman JP,Meissner M

更新日期：2013-02-01 00:00:00

abstract：:We present eXpress, a software package for efficient probabilistic assignment of ambiguously mapping sequenced fragments. eXpress uses a streaming algorithm with linear run time and constant memory use. It can determine abundances of sequenced molecules in real time and can be applied to ChIP-seq, metagenomics and oth...

journal_title：Nature methods

authors： Roberts A,Pachter L

更新日期：2013-01-01 00:00:00

abstract：:Membrane proteins are largely underrepresented among available atomic-resolution structures. The use of detergents in protein purification procedures hinders the formation of well-ordered crystals for X-ray crystallography and leads to slower molecular tumbling, impeding the application of solution-state NMR. Solid-st...

journal_title：Nature methods

authors： Shahid SA,Bardiaux B,Franks WT,Krabben L,Habeck M,van Rossum BJ,Linke D

更新日期：2012-12-01 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：: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：:Measuring complete gene expression profiles for a large number of experiments is costly. We propose an approach in which a small subset of probes is selected based on a preliminary set of full expression profiles. In subsequent experiments, only the subset is measured, and the missing values are inputed. We developed ...

journal_title：Nature methods

authors： Donner Y,Feng T,Benoist C,Koller D

更新日期：2012-11-01 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 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：:We discuss the advantages and challenges of the open-source strategy in biological image analysis and argue that its full impact will not be realized without better support and recognition of software engineers' contributions to the biological sciences and more support of this development model from funders and instit...

journal_title：Nature methods

authors： Cardona A,Tomancak P

更新日期：2012-06-28 00:00:00

abstract：:Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral overlap between fluorophores. Here we demonstrate a simple but general strategy to drastically increase the ...

journal_title：Nature methods

authors： Lubeck E,Cai L

更新日期：2012-06-03 00:00:00

abstract：:Monomeric (m)Eos2 is an engineered photoactivatable fluorescent protein widely used for super-resolution microscopy. We show that mEos2 forms oligomers at high concentrations and forms aggregates when labeling membrane proteins, limiting its application as a fusion partner. We solved the crystal structure of tetrameri...

journal_title：Nature methods

authors： Zhang M,Chang H,Zhang Y,Yu J,Wu L,Ji W,Chen J,Liu B,Lu J,Liu Y,Zhang J,Xu P,Xu T

更新日期：2012-05-13 00:00:00

abstract：:We introduce a nonintrusive method exploiting single-cell variability after cell division to validate protein localization. We found that Clp proteases, widely reported to form biologically relevant foci, were uniformly distributed in Escherichia coli cells, and that many commonly used fluorescent proteins caused seve...

journal_title：Nature methods

authors： Landgraf D,Okumus B,Chien P,Baker TA,Paulsson J

更新日期：2012-04-08 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：: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：:We report a simple and generic method for the direct transfer of protein complexes separated by native gel electrophoresis to electron microscopy grids. After transfer, sufficient material remains in the gel for identification and characterization by mass spectrometry. The method should facilitate higher-throughput si...

journal_title：Nature methods

authors： Knispel RW,Kofler C,Boicu M,Baumeister W,Nickell S

更新日期：2012-01-08 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：: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：:We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm for genome-wide association studies (GWAS) that scales linearly with cohort size in both run time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algo...

journal_title：Nature methods

authors： Lippert C,Listgarten J,Liu Y,Kadie CM,Davidson RI,Heckerman D

更新日期：2011-09-04 00:00:00

abstract：:Engineering precise genetic changes in a genome is powerful way to study gene function, and several recent papers describe new applications of gene-editing tools. Working with researchers at Sangamo BioSciences, Howard Hughes Medical Institute investigator Barbara Meyer and her colleagues at the University of Californ...

journal_title：Nature methods

authors： Baker M

更新日期：2011-09-01 00:00:00

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：: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：:The protein ubiquitin is an important post-translational modifier that regulates a wide variety of biological processes. In cells, ubiquitin is apportioned among distinct pools, which include a variety of free and conjugated species. Although maintenance of a dynamic and complex equilibrium among ubiquitin pools is cr...

journal_title：Nature methods

authors： Kaiser SE,Riley BE,Shaler TA,Trevino RS,Becker CH,Schulman H,Kopito RR

更新日期：2011-07-10 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：:We developed a multiplex sequencing-by-synthesis method combining terminal phosphate-labeled fluorogenic nucleotides (TPLFNs) and resealable polydimethylsiloxane (PDMS) microreactors. In the presence of phosphatase, primer extension by DNA polymerase using nonfluorescent TPLFNs generates fluorophores, which are confin...

journal_title：Nature methods

authors： Sims PA,Greenleaf WJ,Duan H,Xie XS

更新日期：2011-06-12 00:00:00

abstract：:Dissecting the relationship between genotype and phenotype is one of the central goals in developmental biology and medicine. Transcriptome analysis is a powerful strategy to connect genotype to phenotype of a cell. Here we review the history, progress, potential applications and future developments of single-cell tra...

journal_title：Nature methods

authors： Tang F,Lao K,Surani MA

更新日期：2011-04-01 00:00:00

abstract：:Methods for genomic analysis at single-cell resolution enable new understanding of complex biological phenomena. Single-cell techniques, ranging from flow cytometry and microfluidics to PCR and sequencing, are used to understand the cellular composition of complex tissues, find new microbial species and perform genome...

journal_title：Nature methods

authors： Kalisky T,Quake SR

更新日期：2011-04-01 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