abstract：:Numerous drugs and endogenous ligands bind to cell surface receptors leading to modulation of downstream signaling cascades and frequently to adaptation of the plasma membrane proteome. In-depth analysis of dynamic processes at the cell surface is challenging due to biochemical properties and low abundances of plasma ...

journal_title：Nature methods

authors： Kalxdorf M,Günthner I,Becher I,Kurzawa N,Knecht S,Savitski MM,Eberl HC,Bantscheff M

更新日期：2021-01-01 00:00:00

abstract：:Circular RNAs (circRNAs) produced from back-spliced exons are widely expressed, but individual circRNA functions remain poorly understood owing to the lack of adequate methods for distinguishing circRNAs from cognate messenger RNAs with overlapping exons. Here, we report that CRISPR-RfxCas13d can effectively discrimin...

journal_title：Nature methods

authors： Li S,Li X,Xue W,Zhang L,Yang LZ,Cao SM,Lei YN,Liu CX,Guo SK,Shan L,Wu M,Tao X,Zhang JL,Gao X,Zhang J,Wei J,Li J,Yang L,Chen LL

更新日期：2021-01-01 00:00:00

abstract：:Microfluidic channels provide a means to deliver barcodes encoding spatial information to a tissue, which allows co-profiling of gene expression and proteins of interest in a spatially resolved manner. ...

journal_title：Nature methods

authors： Tang L

更新日期：2021-01-01 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：:Despite the vital role of mechanical forces in biology, it still remains a challenge to image cellular force with sub-100-nm resolution. Here, we present tension points accumulation for imaging in nanoscale topography (tPAINT), integrating molecular tension probes with the DNA points accumulation for imaging in nanosc...

journal_title：Nature methods

authors： Brockman JM,Su H,Blanchard AT,Duan Y,Meyer T,Quach ME,Glazier R,Bazrafshan A,Bender RL,Kellner AV,Ogasawara H,Ma R,Schueder F,Petrich BG,Jungmann R,Li R,Mattheyses AL,Ke Y,Salaita K

更新日期：2020-10-01 00:00:00

abstract：:Chromosome segregation requires both compaction and disentanglement of sister chromatids. We describe SisterC, a chromosome conformation capture assay that distinguishes interactions between and along identical sister chromatids. SisterC employs 5-bromo-2'-deoxyuridine (BrdU) incorporation during S-phase to label newl...

journal_title：Nature methods

authors： Oomen ME,Hedger AK,Watts JK,Dekker J

更新日期：2020-10-01 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：: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 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：:Single-molecule localization microscopy is a powerful tool for visualizing subcellular structures, interactions and protein functions in biological research. However, inhomogeneous refractive indices inside cells and tissues distort the fluorescent signal emitted from single-molecule probes, which rapidly degrades res...

journal_title：Nature methods

authors： Xu F,Ma D,MacPherson KP,Liu S,Bu Y,Wang Y,Tang Y,Bi C,Kwok T,Chubykin AA,Yin P,Calve S,Landreth GE,Huang F

更新日期：2020-05-01 00:00:00

abstract：:Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then...

journal_title：Nature methods

authors： Gauchier M,van Mierlo G,Vermeulen M,Déjardin J

更新日期：2020-04-01 00:00:00

abstract：:Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. ...

journal_title：Nature methods

authors： Pintilie G,Zhang K,Su Z,Li S,Schmid MF,Chiu W

更新日期：2020-03-01 00:00:00

abstract：:Despite the widespread adoption of organoids as biomimetic tissue models, methods to comprehensively analyze cell-type-specific post-translational modification (PTM) signaling networks in organoids are absent. Here, we report multivariate single-cell analysis of such networks in organoids and organoid cocultures. Simu...

journal_title：Nature methods

authors： Qin X,Sufi J,Vlckova P,Kyriakidou P,Acton SE,Li VSW,Nitz M,Tape CJ

更新日期：2020-03-01 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： Caicedo JC,Goodman A,Karhohs KW,Cimini BA,Ackerman J,Haghighi M,Heng C,Becker T,Doan M,McQuin C,Rohban M,Singh S,Carpenter AE

更新日期：2020-02-01 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：:We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves the identification and quantification performance in conventional DIA ...

journal_title：Nature methods

authors： Demichev V,Messner CB,Vernardis SI,Lilley KS,Ralser M

更新日期：2020-01-01 00:00:00

abstract：:We demonstrate gas cluster ion beam scanning electron microscopy (SEM), in which wide-area ion milling is performed on a series of thick tissue sections. This three-dimensional electron microscopy technique acquires datasets with <10 nm isotropic resolution of each section, and these can then be stitched together to s...

journal_title：Nature methods

authors： Hayworth KJ,Peale D,Januszewski M,Knott GW,Lu Z,Xu CS,Hess HF

更新日期：2020-01-01 00:00:00

abstract：:Spontaneous and sensory-evoked activity propagates across varying spatial scales in the mammalian cortex, but technical challenges have limited conceptual links between the function of local neuronal circuits and brain-wide network dynamics. We present a method for simultaneous cellular-resolution two-photon calcium i...

journal_title：Nature methods

authors： Barson D,Hamodi AS,Shen X,Lur G,Constable RT,Cardin JA,Crair MC,Higley MJ

更新日期：2020-01-01 00:00:00

abstract：:Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and pr...

journal_title：Nature methods

authors： Ouyang W,Winsnes CF,Hjelmare M,Cesnik AJ,Åkesson L,Xu H,Sullivan DP,Dai S,Lan J,Jinmo P,Galib SM,Henkel C,Hwang K,Poplavskiy D,Tunguz B,Wolfinger RD,Gu Y,Li C,Xie J,Buslov D,Fironov S,Kiselev A,Panchenko D,C

更新日期：2019-12-01 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： Singh A

更新日期：2019-12-01 00:00:00

abstract：:Rational protein engineering requires a holistic understanding of protein function. Here, we apply deep learning to unlabeled amino-acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically rich and structurally, evolutionarily and biophysically grounded. We...

journal_title：Nature methods

authors： Alley EC,Khimulya G,Biswas S,AlQuraishi M,Church GM

更新日期：2019-12-01 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：:Human cortical organoids (hCOs), derived from human embryonic stem cells (hESCs), provide a platform to study human brain development and diseases in complex three-dimensional tissue. However, current hCOs lack microvasculature, resulting in limited oxygen and nutrient delivery to the inner-most parts of hCOs. We engi...

journal_title：Nature methods

authors： Cakir B,Xiang Y,Tanaka Y,Kural MH,Parent M,Kang YJ,Chapeton K,Patterson B,Yuan Y,He CS,Raredon MSB,Dengelegi J,Kim KY,Sun P,Zhong M,Lee S,Patra P,Hyder F,Niklason LE,Lee SH,Yoon YS,Park IH

更新日期：2019-11-01 00:00:00

abstract：:Electron cryotomography is currently the only method capable of visualizing cells in three dimensions at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information, data processing is very labor intensive and the results are often limited...

journal_title：Nature methods

authors： Chen M,Bell JM,Shi X,Sun SY,Wang Z,Ludtke SJ

更新日期：2019-11-01 00:00:00

abstract：:Single-cell RNA sequencing has enabled the decomposition of complex tissues into functionally distinct cell types. Often, investigators wish to assign cells to cell types through unsupervised clustering followed by manual annotation or via 'mapping' to existing data. However, manual interpretation scales poorly to lar...

journal_title：Nature methods

authors： Zhang AW,O'Flanagan C,Chavez EA,Lim JLP,Ceglia N,McPherson A,Wiens M,Walters P,Chan T,Hewitson B,Lai D,Mottok A,Sarkozy C,Chong L,Aoki T,Wang X,Weng AP,McAlpine JN,Aparicio S,Steidl C,Campbell KR,Shah SP

更新日期：2019-10-01 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：:Protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We and others previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectromet...

journal_title：Nature methods

authors： Hu LZ,Goebels F,Tan JH,Wolf E,Kuzmanov U,Wan C,Phanse S,Xu C,Schertzberg M,Fraser AG,Bader GD,Emili A

更新日期：2019-08-01 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：:In mass-spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily rely on sequence database searching or spectral library matching. The lack of accurate predictive models for fragment ion intensities impairs the realization of the full potential of these approaches. Here, we...

journal_title：Nature methods

authors： Gessulat S,Schmidt T,Zolg DP,Samaras P,Schnatbaum K,Zerweck J,Knaute T,Rechenberger J,Delanghe B,Huhmer A,Reimer U,Ehrlich HC,Aiche S,Kuster B,Wilhelm M

更新日期：2019-06-01 00:00:00

abstract：:Tumors from individuals with cancer are frequently genetically profiled for information about the driving forces behind the disease. We present the CancerMine resource, a text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer. All data are available online ( ...

journal_title：Nature methods

authors： Lever J,Zhao EY,Grewal J,Jones MR,Jones SJM

更新日期：2019-06-01 00:00:00

abstract：:Single-cell transcriptomics provides an opportunity to characterize cell-type-specific transcriptional networks, intercellular signaling pathways and cellular diversity with unprecedented resolution by profiling thousands of cells in a single experiment. However, owing to the unique statistical properties of scRNA-seq...

journal_title：Nature methods

authors： Skinnider MA,Squair JW,Foster LJ

更新日期：2019-05-01 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：:Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the 'texture' formed by cellular organization, to defi...

journal_title：Nature methods

authors： Chen Y,McElvain LE,Tolpygo AS,Ferrante D,Friedman B,Mitra PP,Karten HJ,Freund Y,Kleinfeld D

更新日期：2019-04-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors： Doerr A

更新日期：2019-03-01 00:00:00

abstract：:We introduce field synthesis, a theorem and method that can be used to synthesize any scanned or dithered light sheet, including those used in lattice light-sheet microscopy (LLSM), from an incoherent superposition of one-dimensional intensity distributions. Compared to LLSM, this user-friendly and modular approach of...

journal_title：Nature methods

authors： Chang BJ,Kittisopikul M,Dean KM,Roudot P,Welf ES,Fiolka R

更新日期：2019-03-01 00:00:00

abstract：:t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we ...

journal_title：Nature methods

authors： Linderman GC,Rachh M,Hoskins JG,Steinerberger S,Kluger Y

更新日期：2019-03-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors： Vogt N

更新日期：2019-02-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors： Strack R

更新日期：2019-02-01 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：: ...

journal_title：Nature methods

authors： Doerr A

更新日期：2019-01-01 00:00:00