Glycomics: an integrated systems approach to structure-function relationships of glycans.

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 biomedical application of human embryonic stem (hES) cells will increasingly depend on the availability of technologies for highly controlled genetic modification. In mouse genetics, conditional mutagenesis using site-specific recombinases has become an invaluable tool for gain- and loss-of-function studies. Here ...

journal_title：Nature methods

authors： Nolden L,Edenhofer F,Haupt S,Koch P,Wunderlich FT,Siemen H,Brüstle O

更新日期：2006-06-01 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：:Generation of complex libraries of defined nucleic acid sequences can greatly aid the functional analysis of protein and gene function. Previously, such studies relied either on individually synthesized oligonucleotides or on cellular nucleic acids as the starting material. As each method has disadvantages, we have de...

journal_title：Nature methods

authors： Cleary MA,Kilian K,Wang Y,Bradshaw J,Cavet G,Ge W,Kulkarni A,Paddison PJ,Chang K,Sheth N,Leproust E,Coffey EM,Burchard J,McCombie WR,Linsley P,Hannon GJ

更新日期：2004-12-01 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：:Electrically excitable cells are important in the normal functioning and in the pathophysiology of many biological processes. These cells are typically embedded in dense, heterogeneous tissues, rendering them difficult to target selectively with conventional electrical stimulation methods. The algal protein Channelrho...

journal_title：Nature methods

authors： Zhang F,Wang LP,Boyden ES,Deisseroth K

更新日期：2006-10-01 00:00:00

abstract：:RNAs are ideal for the design of gene switches that can monitor and program cellular behavior because of their high modularity and predictable structure-function relationship. We have assembled an expression platform with an embedded modular ribozyme scaffold that correlates self-cleavage activity of designer ribozyme...

journal_title：Nature methods

authors： Ausländer S,Stücheli P,Rehm C,Ausländer D,Hartig JS,Fussenegger M

更新日期：2014-11-01 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：:Tumor-initiating cells with stem cell properties are believed to sustain the growth of gliomas, but proposed markers such as CD133 cannot be used to identify these cells with sufficient specificity. We report an alternative isolation method purely based on phenotypic qualities of glioma-initiating cells (GICs), avoidi...

journal_title：Nature methods

authors： Clément V,Marino D,Cudalbu C,Hamou MF,Mlynarik V,de Tribolet N,Dietrich PY,Gruetter R,Hegi ME,Radovanovic I

更新日期：2010-03-01 00:00:00

abstract：:FLIRT (fast local infrared thermogenetics) is a microscopy-based technology to locally and reversibly manipulate protein function while simultaneously monitoring the effects in vivo. FLIRT locally inactivates fast-acting temperature-sensitive mutant proteins. We demonstrate that FLIRT can control temperature-sensitive...

journal_title：Nature methods

authors： Hirsch SM,Sundaramoorthy S,Davies T,Zhuravlev Y,Waters JC,Shirasu-Hiza M,Dumont J,Canman JC

更新日期：2018-11-01 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 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：: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：: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：:We have developed a single-plasmid system for the efficient bacterial expression of mutant proteins containing unnatural amino acids at specific sites designated by amber nonsense codons. In this system, multiple copies of a gene encoding an amber suppressor tRNA derived from a Methanocaldococcus jannaschii tyrosyl-tR...

journal_title：Nature methods

authors： Ryu Y,Schultz PG

更新日期：2006-04-01 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：: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：:Extracellular vesicles (EVs) are secreted nanosized particles with many biological functions and pathological associations. The inability to image EVs in fixed tissues has been a major limitation to understanding their role in healthy and diseased tissue microenvironments. Here, we show that crosslinking mammalian tis...

journal_title：Nature methods

authors： Gupta MP,Tandalam S,Ostrager S,Lever AS,Fung AR,Hurley DD,Alegre GB,Espinal JE,Remmel HL,Mukherjee S,Levine BM,Robins RP,Molina H,Dill BD,Kenific CM,Tuschl T,Lyden D,D'Amico DJ,Pena JTG

更新日期：2019-12-01 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：: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 normalization of RNA-seq data is essential for accurate downstream inference, but the assumptions upon which most normalization methods are based are not applicable in the single-cell setting. Consequently, applying existing normalization methods to single-cell RNA-seq data introduces artifacts that bias downstrea...

journal_title：Nature methods

authors： Bacher R,Chu LF,Leng N,Gasch AP,Thomson JA,Stewart RM,Newton M,Kendziorski C

更新日期：2017-06-01 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：:Transcription activator-like effector (TALE) proteins have gained broad appeal as a platform for targeted DNA recognition, largely owing to their simple rules for design. These rules relate the base specified by a single TALE repeat to the identity of two key residues (the repeat variable diresidue, or RVD) and enable...

journal_title：Nature methods

authors： Miller JC,Zhang L,Xia DF,Campo JJ,Ankoudinova IV,Guschin DY,Babiarz JE,Meng X,Hinkley SJ,Lam SC,Paschon DE,Vincent AI,Dulay GP,Barlow KA,Shivak DA,Leung E,Kim JD,Amora R,Urnov FD,Gregory PD,Rebar EJ

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：: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：: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： Fiolka R

更新日期：2019-10-01 00:00:00

abstract：:We present the Single-Cell Clustering Assessment Framework, a method for the automated identification of putative cell types from single-cell RNA sequencing (scRNA-seq) data. By iteratively applying a machine learning approach to a given set of cells, we simultaneously identify distinct cell groups and a weighted list...

journal_title：Nature methods

authors： Miao Z,Moreno P,Huang N,Papatheodorou I,Brazma A,Teichmann SA

更新日期：2020-06-01 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：: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：:Single-cell RNA sequencing (scRNA-seq) is a rich resource of cellular heterogeneity, opening new avenues in the study of complex tissues. We introduce Cell Population Mapping (CPM), a deconvolution algorithm in which reference scRNA-seq profiles are leveraged to infer the composition of cell types and states from bulk...

journal_title：Nature methods

authors： Frishberg A,Peshes-Yaloz N,Cohn O,Rosentul D,Steuerman Y,Valadarsky L,Yankovitz G,Mandelboim M,Iraqi FA,Amit I,Mayo L,Bacharach E,Gat-Viks I

更新日期：2019-04-01 00:00:00