Single-cell genomics.

abstract：: ...

journal_title：Nature methods

authors： Doerr A

更新日期：2019-01-01 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

abstract：:Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are often kept in solution with detergent micelles and lipid nanodiscs that are locally disordered. Such spatial variability ne...

journal_title：Nature methods

authors： Punjani A,Zhang H,Fleet DJ

更新日期：2020-12-01 00:00:00

abstract：:We describe a GFP-based RNA reporter system (lambdaN-GFP) to visualize RNA molecules in live mammalian cells. It consists of GFP fused to an arginine-rich peptide derived from the phage lambda N protein, lambdaN22, which binds a unique minimal RNA motif and can be used to tag any RNA molecule. LambdaN-GFP uses a small...

journal_title：Nature methods

authors： Daigle N,Ellenberg J

更新日期：2007-08-01 00:00:00

abstract：:Despite its biological importance, tRNA has not been adequately sequenced by standard methods because of its abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. We achieved efficient and quantitative tRNA sequencing in HEK293T cells by using engineered demethylases to...

journal_title：Nature methods

authors： Zheng G,Qin Y,Clark WC,Dai Q,Yi C,He C,Lambowitz AM,Pan T

更新日期：2015-09-01 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

abstract：:Current extracellular multisite recordings suffer from low signal-to-noise ratio, limiting the monitoring to action potentials, and preclude detection of subthreshold synaptic potentials. Here we report an approach to induce Aplysia californica neurons to actively engulf protruding microelectrodes, providing 'in-cell ...

journal_title：Nature methods

authors： Hai A,Shappir J,Spira ME

更新日期：2010-03-01 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：:To enable the detection of expression signatures specific to individual cells, we developed PLAYR (proximity ligation assay for RNA), a method for highly multiplexed transcript quantification by flow and mass cytometry that is compatible with standard antibody staining. When used with mass cytometry, PLAYR allowed for...

journal_title：Nature methods

authors： Frei AP,Bava FA,Zunder ER,Hsieh EW,Chen SY,Nolan GP,Gherardini PF

更新日期：2016-03-01 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：:We developed a microarray hybridization-based method, 'comparative genome sequencing' (CGS), to find mutations in bacterial genomes and used it to study metronidazole resistance in H. pylori. CGS identified mutations in several genes, most likely affecting metronidazole activation, and produced no false positives in a...

journal_title：Nature methods

authors： Albert TJ,Dailidiene D,Dailide G,Norton JE,Kalia A,Richmond TA,Molla M,Singh J,Green RD,Berg DE

更新日期：2005-12-01 00:00:00

abstract：:We must reliably map the interactomes of cellular macromolecular complexes in order to fully explore and understand biological systems. However, there are no methods to accurately predict how to capture a given macromolecular complex with its physiological binding partners. Here, we present a screening method that com...

journal_title：Nature methods

authors： Hakhverdyan Z,Domanski M,Hough LE,Oroskar AA,Oroskar AR,Keegan S,Dilworth DJ,Molloy KR,Sherman V,Aitchison JD,Fenyö D,Chait BT,Jensen TH,Rout MP,LaCava J

更新日期：2015-06-01 00:00:00

abstract：:Caenorhabditis elegans is an important model organism in biology, but until now no antibiotic selection markers have been successfully demonstrated for this species. We have developed a selection system using puromycin that allows the rapid and easy isolation of large populations of transgenic worms. This approach is ...

journal_title：Nature methods

authors： Semple JI,Garcia-Verdugo R,Lehner B

更新日期：2010-09-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors： Doerr A

更新日期：2018-11-01 00:00:00

abstract：:A new system for lineage ablation is based on transgenic expression of a diphtheria toxin receptor (DTR) in mouse cells and application of diphtheria toxin (DT). To streamline this approach, we generated Cre-inducible DTR transgenic mice (iDTR) in which Cre-mediated excision of a STOP cassette renders cells sensitive ...

journal_title：Nature methods

authors： Buch T,Heppner FL,Tertilt C,Heinen TJ,Kremer M,Wunderlich FT,Jung S,Waisman A

更新日期：2005-06-01 00:00:00

abstract：:Despite widespread use of CRISPR, comprehensive data on the frequency and impact of Cas9-mediated off-targets in modified rodents are limited. Here we present deep-sequencing data from 81 genome-editing projects on mouse and rat genomes at 1,423 predicted off-target sites, 32 of which were confirmed, and show that hig...

journal_title：Nature methods

authors： Anderson KR,Haeussler M,Watanabe C,Janakiraman V,Lund J,Modrusan Z,Stinson J,Bei Q,Buechler A,Yu C,Thamminana SR,Tam L,Sowick MA,Alcantar T,O'Neil N,Li J,Ta L,Lima L,Roose-Girma M,Rairdan X,Durinck S,Warming S

更新日期：2018-07-01 00:00:00

abstract：:Accurately modeling cellular response to perturbations is a central goal of computational biology. While such modeling has been based on statistical, mechanistic and machine learning models in specific settings, no generalization of predictions to phenomena absent from training data (out-of-sample) has yet been demons...

journal_title：Nature methods

authors： Lotfollahi M,Wolf FA,Theis FJ

更新日期：2019-08-01 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：: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：: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：:Fluorescent proteins have become extremely popular tools for in vivo imaging and especially for the study of localization, motility and interaction of proteins in living cells. Here we report TagRFP, a monomeric red fluorescent protein, which is characterized by high brightness, complete chromophore maturation, prolon...

journal_title：Nature methods

authors： Merzlyak EM,Goedhart J,Shcherbo D,Bulina ME,Shcheglov AS,Fradkov AF,Gaintzeva A,Lukyanov KA,Lukyanov S,Gadella TW,Chudakov DM

更新日期：2007-07-01 00:00:00

abstract：:Cells adjust to changes in environmental conditions using complex regulatory programs. These cellular programs are the result of an intricate interplay between gene expression, cellular growth and protein degradation. Technologies that enable simultaneous and time-resolved measurements of these variables are necessary...

journal_title：Nature methods

authors： Zuleta IA,Aranda-Díaz A,Li H,El-Samad H

更新日期：2014-04-01 00:00:00

abstract：:Structure probing coupled with high-throughput sequencing could revolutionize our understanding of the role of RNA structure in regulation of gene expression. Despite recent technological advances, intrinsic noise and high sequence coverage requirements greatly limit the applicability of these techniques. Here we desc...

journal_title：Nature methods

authors： Selega A,Sirocchi C,Iosub I,Granneman S,Sanguinetti G

更新日期：2017-01-01 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 need for automated and efficient systems for tracking full animal pose has increased with the complexity of behavioral data and analyses. Here we introduce LEAP (LEAP estimates animal pose), a deep-learning-based method for predicting the positions of animal body parts. This framework consists of a graphical inter...

journal_title：Nature methods

authors： Pereira TD,Aldarondo DE,Willmore L,Kislin M,Wang SS,Murthy M,Shaevitz JW

更新日期：2019-01-01 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：: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：:Gene expression is extensively regulated at the levels of mRNA stability, localization and translation. However, decoding functional RNA-regulatory features remains a limitation to understanding post-transcriptional regulation in vivo. Here, we developed RNA-element selection assay (RESA), a method that selects RNA el...

journal_title：Nature methods

authors： Yartseva V,Takacs CM,Vejnar CE,Lee MT,Giraldez AJ

更新日期：2017-02-01 00:00:00

abstract：:The complexity of the angiogenic cascade limits cellular approaches to studying angiogenic endothelial cells (ECs). In turn, in vivo assays do not allow the analysis of the distinct cellular behavior of ECs during angiogenesis. Here we show that ECs can be grafted as spheroids into a matrix to give rise to a complex t...

journal_title：Nature methods

authors： Alajati A,Laib AM,Weber H,Boos AM,Bartol A,Ikenberg K,Korff T,Zentgraf H,Obodozie C,Graeser R,Christian S,Finkenzeller G,Stark GB,Héroult M,Augustin HG

更新日期：2008-05-01 00:00:00

abstract：:We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. On seven published data sets, we benchmark SIMLR against state-of-the-art met...

journal_title：Nature methods

authors： Wang B,Zhu J,Pierson E,Ramazzotti D,Batzoglou S

更新日期：2017-04-01 00:00:00