Multiomics sequencing goes spatial.

abstract：:Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation ...

journal_title：Nature methods

authors： de la Cruz MJ,Hattne J,Shi D,Seidler P,Rodriguez J,Reyes FE,Sawaya MR,Cascio D,Weiss SC,Kim SK,Hinck CS,Hinck AP,Calero G,Eisenberg D,Gonen T

更新日期：2017-02-13 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 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：:Time resolution of current single-molecule fluorescence techniques is limited to milliseconds because of dye blinking and bleaching. Here we introduce a photoprotection strategy that affords microsecond resolution by combining efficient triplet quenching by oxygen and Trolox with minimized bleaching via the oxygen rad...

journal_title：Nature methods

authors： Campos LA,Liu J,Wang X,Ramanathan R,English DS,Muñoz V

更新日期：2011-02-01 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：:Massively parallel single-cell and single-nucleus RNA sequencing has opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so is the need for computational pipelines for scaled analysis. Here we developed Cumulus-a cloud-based framework for analyzing large-s...

journal_title：Nature methods

authors： Li B,Gould J,Yang Y,Sarkizova S,Tabaka M,Ashenberg O,Rosen Y,Slyper M,Kowalczyk MS,Villani AC,Tickle T,Hacohen N,Rozenblatt-Rosen O,Regev A

更新日期：2020-08-01 00:00:00

abstract：:The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sens...

journal_title：Nature methods

authors： Thestrup T,Litzlbauer J,Bartholomäus I,Mues M,Russo L,Dana H,Kovalchuk Y,Liang Y,Kalamakis G,Laukat Y,Becker S,Witte G,Geiger A,Allen T,Rome LC,Chen TW,Kim DS,Garaschuk O,Griesinger C,Griesbeck O

更新日期：2014-02-01 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：: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：:We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced ...

journal_title：Nature methods

authors： Roth A,Khattra J,Yap D,Wan A,Laks E,Biele J,Ha G,Aparicio S,Bouchard-Côté A,Shah SP

更新日期：2014-04-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors：

更新日期：2018-12-01 00:00:00

abstract：:Researchers show that to reliably establish protein interaction networks from microarray data it is necessary to measure saturation binding curves for each arrayed protein and its potential binding partners. ...

journal_title：Nature methods

authors： Rusk N

更新日期：2006-12-01 00:00:00

abstract：:The importance of locating proteins in their context within cells has been heightened recently by the accomplishments in molecular structure and systems biology. Although light microscopy (LM) has been extensively used for mapping protein localization, many studies require the additional resolution of the electron mic...

journal_title：Nature methods

authors： Giepmans BN,Deerinck TJ,Smarr BL,Jones YZ,Ellisman MH

更新日期：2005-10-01 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：: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：: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：:Understanding how cells maintain genome integrity when challenged with DNA double-strand breaks (DSBs) is of major importance, particularly since the discovery of multiple links of DSBs with genome instability and cancer-predisposition disorders. Ionizing radiation is the agent of choice to produce DSBs in cells; howe...

journal_title：Nature methods

authors： Stap J,Krawczyk PM,Van Oven CH,Barendsen GW,Essers J,Kanaar R,Aten JA

更新日期：2008-03-01 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：:The RNA-guided nuclease Cas9 can be reengineered as a programmable transcription factor. However, modest levels of gene activation have limited potential applications. We describe an improved transcriptional regulator obtained through the rational design of a tripartite activator, VP64-p65-Rta (VPR), fused to nuclease...

journal_title：Nature methods

authors： Chavez A,Scheiman J,Vora S,Pruitt BW,Tuttle M,P R Iyer E,Lin S,Kiani S,Guzman CD,Wiegand DJ,Ter-Ovanesyan D,Braff JL,Davidsohn N,Housden BE,Perrimon N,Weiss R,Aach J,Collins JJ,Church GM

更新日期：2015-04-01 00:00:00

abstract：:The reconstruction of neuronal populations, a key step in understanding neural circuits, remains a challenge in the presence of densely packed neurites. Here we achieved automatic reconstruction of neuronal populations by partially mimicking human strategies to separate individual neurons. For populations not resolvab...

journal_title：Nature methods

authors： Quan T,Zhou H,Li J,Li S,Li A,Li Y,Lv X,Luo Q,Gong H,Zeng S

更新日期：2016-01-01 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：:The self-reconstructing properties of Bessel beams provide healing benefits in highly scattering media. ...

journal_title：Nature methods

authors： Evanko D

更新日期：2010-11-01 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 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：: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 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：:A quantitative high-throughput FRET-based method of screening fluorescent protein fusion libraries brings the promise of more detailed interactome maps. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2007-02-01 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：:In the originally published paper, the "before" image for the afatinib condition in Fig. 6c was incorrect. Instead of an image displaying a GBM-3 neoplastic organoid before afatinib treatment, this panel showed an image from the GBM-2 control (DMSO) group before treatment. This error has now been corrected in the HTML...

journal_title：Nature methods

authors： Bian S,Repic M,Guo Z,Kavirayani A,Burkard T,Bagley JA,Krauditsch C,Knoblich JA

更新日期：2018-09-01 00:00:00

abstract：:To enhance the repertoire of molecular tools for studying malaria parasite biology, we adapted a ligand-regulatable FKBP protein destabilization domain (ddFKBP) for use in P. falciparum. We destabilized the reporter yellow fluorescent protein (YFP) and the P. falciparum protease falcipain-2 in a ligand-reversible mann...

journal_title：Nature methods

authors： Armstrong CM,Goldberg DE

更新日期：2007-12-01 00:00:00