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  • MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets
    Nat. Methods (IF 30.822) Pub Date : 2020-09-14
    Meena Choi; Jeremy Carver; Cristina Chiva; Manuel Tzouros; Ting Huang; Tsung-Heng Tsai; Benjamin Pullman; Oliver M. Bernhardt; Ruth Hüttenhain; Guo Ci Teo; Yasset Perez-Riverol; Jan Muntel; Maik Müller; Sandra Goetze; Maria Pavlou; Erik Verschueren; Bernd Wollscheid; Alexey I. Nesvizhskii; Lukas Reiter; Tom Dunkley; Eduard Sabidó; Nuno Bandeira; Olga Vitek

    MassIVE.quant is a repository infrastructure and data resource for reproducible quantitative mass spectrometry–based proteomics, which is compatible with all mass spectrometry data acquisition types and computational analysis tools. A branch structure enables MassIVE.quant to systematically store raw experimental data, metadata of the experimental design, scripts of the quantitative analysis workflow

    更新日期:2020-09-14
  • Live-cell super-resolved PAINT imaging of piconewton cellular traction forces
    Nat. Methods (IF 30.822) Pub Date : 2020-09-14
    Joshua M. Brockman; Hanquan Su; Aaron T. Blanchard; Yuxin Duan; Travis Meyer; M. Edward Quach; Roxanne Glazier; Alisina Bazrafshan; Rachel L. Bender; Anna V. Kellner; Hiroaki Ogasawara; Rong Ma; Florian Schueder; Brian G. Petrich; Ralf Jungmann; Renhao Li; Alexa L. Mattheyses; Yonggang Ke; Khalid Salaita

    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 nanoscale topography (DNA-PAINT) technique to map piconewton mechanical events with ~25-nm

    更新日期:2020-09-14
  • In vivo detection of antigen-specific CD8 + T cells by immuno-positron emission tomography
    Nat. Methods (IF 30.822) Pub Date : 2020-09-14
    Andrew W. Woodham; Stad H. Zeigler; Ella L. Zeyang; Stephen C. Kolifrath; Ross W. Cheloha; Mohammad Rashidian; Rodolfo J. Chaparro; Ronald D. Seidel; Scott J. Garforth; Jason L. Dearling; Maia Mesyngier; Phaneendra K. Duddempudi; Alan B. Packard; Steven C. Almo; Hidde L. Ploegh

    The immune system’s ability to recognize peptides on major histocompatibility molecules contributes to the eradication of cancers and pathogens. Tracking these responses in vivo could help evaluate the efficacy of immune interventions and improve mechanistic understanding of immune responses. For this purpose, we employ synTacs, which are dimeric major histocompatibility molecule scaffolds of defined

    更新日期:2020-09-14
  • Manu Prakash
    Nat. Methods (IF 30.822) Pub Date : 2020-09-10
    Vivien Marx

    Frugally built technology to study the ocean’s microbes, and engineering for societal good.

    更新日期:2020-09-11
  • Author Correction: Nested designs
    Nat. Methods (IF 30.822) Pub Date : 2020-09-09
    Martin Krzywinski; Naomi Altman; Paul Blainey

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-09-10
  • Reality check for organoids in neuroscience
    Nat. Methods (IF 30.822) Pub Date : 2020-09-09
    Vivien Marx

    To better study human neurodevelopment, researchers advance organoids as brain models.

    更新日期:2020-09-10
  • A temporal decomposition method for identifying venous effects in task-based fMRI
    Nat. Methods (IF 30.822) Pub Date : 2020-09-07
    Kendrick Kay; Keith W. Jamison; Ru-Yuan Zhang; Kamil Uğurbil

    The spatial resolution of functional magnetic resonance imaging (fMRI) is fundamentally limited by effects from large draining veins. Here we describe an analysis method that provides data-driven estimates of these effects in task-based fMRI. The method involves fitting a one-dimensional manifold that characterizes variation in response timecourses observed in a given dataset, and then using identified

    更新日期:2020-09-08
  • An expanded palette of dopamine sensors for multiplex imaging in vivo
    Nat. Methods (IF 30.822) Pub Date : 2020-09-07
    Tommaso Patriarchi; Ali Mohebi; Junqing Sun; Aaron Marley; Ruqiang Liang; Chunyang Dong; Kyle Puhger; Grace Or Mizuno; Carolyn M. Davis; Brian Wiltgen; Mark von Zastrow; Joshua D. Berke; Lin Tian

    Genetically encoded dopamine sensors based on green fluorescent protein (GFP) enable high-resolution imaging of dopamine dynamics in behaving animals. However, these GFP-based variants cannot be readily combined with commonly used optical sensors and actuators, due to spectral overlap. We therefore engineered red-shifted variants of dopamine sensors called RdLight1, based on mApple. RdLight1 can be

    更新日期:2020-09-08
  • Publisher Correction: Molecular motion on ice.
    Nat. Methods (IF 30.822) Pub Date : 2020-09-03
    Amber Dance

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-09-05
  • A dual-constriction biological nanopore.
    Nat. Methods (IF 30.822) Pub Date : 2020-09-01
    Arunima Singh

    Addition of a second constriction to CsgG-family nanopores improves the accuracy of homopolymer sequencing.

    更新日期:2020-09-01
  • Standardizing population genetics simulations.
    Nat. Methods (IF 30.822) Pub Date : 2020-09-01
    Lin Tang

    Stdpopsim facilitates realistic population genetics simulations with a catalog of widely used models.

    更新日期:2020-09-01
  • Extracellular protein degradation on demand.
    Nat. Methods (IF 30.822) Pub Date : 2020-09-01
    Rita Strack

    A protein degradation platform enables the targeted depletion of extracellular and membrane-bound proteins.

    更新日期:2020-09-01
  • Recreating the blood-CNS barrier in vitro.
    Nat. Methods (IF 30.822) Pub Date : 2020-09-01
    Madhura Mukhopadhyay

    Stem-cell-derived organoids reproduce the in vivo secretory and functional properties of the choroid plexus.

    更新日期:2020-09-01
  • Science on WeChat.
    Nat. Methods (IF 30.822) Pub Date : 2020-09-01

    We distributed an informal questionnaire to learn from scientists about their professional use of WeChat. We share some of their answers and discuss the multipurpose platform offered by WeChat.

    更新日期:2020-09-01
  • Connectomics in high throughput.
    Nat. Methods (IF 30.822) Pub Date : 2020-09-01
    Nina Vogt

    BRICseq provides access to brain-wide connectivity and can be combined with functional and transcriptomic studies for a comprehensive view of neuronal circuitry.

    更新日期:2020-09-01
  • 更新日期:2020-09-01
  • Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-31
    Qi Qiu,Peng Hu,Xiaojie Qiu,Kiya W Govek,Pablo G Cámara,Hao Wu

    Single-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal RNA dynamics. Here we present single-cell metabolically labeled new RNA tagging sequencing (scNT-seq), a method for massively parallel analysis of newly transcribed and pre-existing mRNAs from the same cell. This droplet microfluidics-based method enables high-throughput chemical conversion on barcoded beads

    更新日期:2020-08-31
  • Uncertainty and the management of epidemics.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-24
    Katriona Shea,Ottar N Bjørnstad,Martin Krzywinski,Naomi Altman

    “I have no idea what’s awaiting me, or what will happen when this all ends. For the moment I know this: there are sick people and they need curing.” ―Albert Camus, The Plague

    更新日期:2020-08-24
  • Feature-based molecular networking in the GNPS analysis environment.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-24
    Louis-Félix Nothias,Daniel Petras,Robin Schmid,Kai Dührkop,Johannes Rainer,Abinesh Sarvepalli,Ivan Protsyuk,Madeleine Ernst,Hiroshi Tsugawa,Markus Fleischauer,Fabian Aicheler,Alexander A Aksenov,Oliver Alka,Pierre-Marie Allard,Aiko Barsch,Xavier Cachet,Andres Mauricio Caraballo-Rodriguez,Ricardo R Da Silva,Tam Dang,Neha Garg,Julia M Gauglitz,Alexey Gurevich,Giorgis Isaac,Alan K Jarmusch,Zdeněk Kameník

    Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution

    更新日期:2020-08-24
  • METLIN MS2 molecular standards database: a broad chemical and biological resource.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-24
    Jingchuan Xue,Carlos Guijas,H Paul Benton,Benedikt Warth,Gary Siuzdak

    更新日期:2020-08-24
  • Publisher Correction: High-sensitivity and high-specificity biomechanical imaging by stimulated Brillouin scattering microscopy.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-20
    Itay Remer,Roni Shaashoua,Netta Shemesh,Anat Ben-Zvi,Alberto Bilenca

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-08-21
  • Molecular motion on ice.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-19
    Amber Dance

    With advanced approaches to sample preparation and data analysis, scientists doing cryo-EM are starting to infer molecular movements from samples that are, literally, frozen.

    更新日期:2020-08-19
  • Uri Manor.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-18
    Vivien Marx

    A new way to see actin in action, hearing as others don’t, and saved by the guitar.

    更新日期:2020-08-19
  • Plankton in a hamster wheel.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-17
    Katja M Taute

    Plankton regularly travel vast distances up and down in the ocean. A water-filled hamster wheel with glass windows now enables detailed microscopic lab observations of individual aquatic microorganisms during their vertical migrations.

    更新日期:2020-08-17
  • Scale-free vertical tracking microscopy.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-17
    Deepak Krishnamurthy,Hongquan Li,François Benoit du Rey,Pierre Cambournac,Adam G Larson,Ethan Li,Manu Prakash

    The behavior and microscale processes associated with freely suspended organisms, along with sinking particles underlie key ecological processes in the ocean. Mechanistically studying such multiscale processes in the laboratory presents a considerable challenge for microscopy: how to measure single cells at microscale resolution, while allowing them to freely move hundreds of meters in the vertical

    更新日期:2020-08-17
  • Optimizing imaging speed and excitation intensity for single-molecule localization microscopy.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-17
    Robin Diekmann,Maurice Kahnwald,Andreas Schoenit,Joran Deschamps,Ulf Matti,Jonas Ries

    High laser powers are common practice in single-molecule localization microscopy to speed up data acquisition. Here we systematically quantified how excitation intensity influences localization precision and labeling density, the two main factors determining data quality. We found a strong trade-off between imaging speed and quality and present optimized imaging protocols for high-throughput, multicolor

    更新日期:2020-08-17
  • ReDU: a framework to find and reanalyze public mass spectrometry data.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-17
    Alan K Jarmusch,Mingxun Wang,Christine M Aceves,Rohit S Advani,Shaden Aguirre,Alexander A Aksenov,Gajender Aleti,Allegra T Aron,Anelize Bauermeister,Sanjana Bolleddu,Amina Bouslimani,Andres Mauricio Caraballo Rodriguez,Rama Chaar,Roxana Coras,Emmanuel O Elijah,Madeleine Ernst,Julia M Gauglitz,Emily C Gentry,Makhai Husband,Scott A Jarmusch,Kenneth L Jones,Zdenek Kamenik,Audrey Le Gouellec,Aileen Lu

    We present ReDU (https://redu.ucsd.edu/), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one’s own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different

    更新日期:2020-08-17
  • Improvement of cryo-EM maps by density modification.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-17
    Thomas C Terwilliger,Steven J Ludtke,Randy J Read,Paul D Adams,Pavel V Afonine

    A density-modification procedure for improving maps from single-particle electron cryogenic microscopy (cryo-EM) is presented. The theoretical basis of the method is identical to that of maximum-likelihood density modification, previously used to improve maps from macromolecular X-ray crystallography. Key differences from applications in crystallography are that the errors in Fourier coefficients are

    更新日期:2020-08-17
  • Publisher Correction: Change-makers bring on recombinant antibodies.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-14
    Vivien Marx

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-08-14
  • Time-resolved cryo-EM using Spotiton.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-10
    Venkata P Dandey,William C Budell,Hui Wei,Daija Bobe,Kashyap Maruthi,Mykhailo Kopylov,Edward T Eng,Peter A Kahn,Jenny E Hinshaw,Nidhi Kundu,Crina M Nimigean,Chen Fan,Nattakan Sukomon,Seth A Darst,Ruth M Saecker,James Chen,Brandon Malone,Clinton S Potter,Bridget Carragher

    We present an approach for preparing cryo-electron microscopy (cryo-EM) grids to study short-lived molecular states. Using piezoelectric dispensing, two independent streams of ~50-pl droplets of sample are deposited within 10 ms of each other onto the surface of a nanowire EM grid, and the mixing reaction stops when the grid is vitrified in liquid ethane ~100 ms later. We demonstrate this approach

    更新日期:2020-08-10
  • Actin chromobody imaging reveals sub-organellar actin dynamics.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-10
    Cara R Schiavon,Tong Zhang,Bing Zhao,Andrew S Moore,Pauline Wales,Leonardo R Andrade,Melissa Wu,Tsung-Chang Sung,Yelena Dayn,Jasmine W Feng,Omar A Quintero,Gerald S Shadel,Robert Grosse,Uri Manor

    The actin cytoskeleton plays multiple critical roles in cells, from cell migration to organelle dynamics. The small and transient actin structures regulating organelle dynamics are challenging to detect with fluorescence microscopy, making it difficult to determine whether actin filaments are directly associated with specific membranes. To address these limitations, we developed fluorescent-protein-tagged

    更新日期:2020-08-10
  • Genetically encoded tags for direct synthesis of EM-visible gold nanoparticles in cells.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-10
    Zhaodi Jiang,Xiumei Jin,Yuhua Li,Sitong Liu,Xiao-Man Liu,Ying-Ying Wang,Pei Zhao,Xinbin Cai,Ying Liu,Yaqi Tang,Xiaobin Sun,Yan Liu,Yanyong Hu,Ming Li,Gaihong Cai,Xiangbing Qi,She Chen,Li-Lin Du,Wanzhong He

    Genetically encoded tags for single-molecule imaging in electron microscopy (EM) are long-awaited. Here, we report an approach for directly synthesizing EM-visible gold nanoparticles (AuNPs) on cysteine-rich tags for single-molecule visualization in cells. We first uncovered an auto-nucleation suppression mechanism that allows specific synthesis of AuNPs on isolated tags. Next, we exploited this mechanism

    更新日期:2020-08-10
  • Author Correction: Analysis of the Human Protein Atlas Image Classification competition.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-05
    Wei Ouyang,Casper F Winsnes,Martin Hjelmare,Anthony J Cesnik,Lovisa Åkesson,Hao Xu,Devin P Sullivan,Shubin Dai,Jun Lan,Park Jinmo,Shaikat M Galib,Christof Henkel,Kevin Hwang,Dmytro Poplavskiy,Bojan Tunguz,Russel D Wolfinger,Yinzheng Gu,Chuanpeng Li,Jinbin Xie,Dmitry Buslov,Sergei Fironov,Alexander Kiselev,Dmytro Panchenko,Xuan Cao,Runmin Wei,Yuanhao Wu,Xun Zhu,Kuan-Lun Tseng,Zhifeng Gao,Cheng Ju,Xiaohan

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-08-05
  • Rational design and implementation of a chemically inducible heterotrimerization system.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-03
    Helen D Wu,Masaki Kikuchi,Onur Dagliyan,Adam K Aragaki,Hideki Nakamura,Nikolay V Dokholyan,Takashi Umehara,Takanari Inoue

    Chemically inducible dimerization (CID) uses a small molecule to induce binding of two different proteins. CID tools such as the FK506-binding protein–FKBP–rapamycin-binding– (FKBP–FRB)–rapamycin system have been widely used to probe molecular events inside and outside cells. While various CID tools are available, chemically inducible trimerization (CIT) does not exist, due to inherent challenges in

    更新日期:2020-08-03
  • High-sensitivity and high-specificity biomechanical imaging by stimulated Brillouin scattering microscopy.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-03
    Itay Remer,Roni Shaashoua,Netta Shemesh,Anat Ben-Zvi,Alberto Bilenca

    Label-free, non-contact imaging with mechanical contrast and optical sectioning is a substantial challenge in microscopy. Spontaneous Brillouin scattering microscopy meets this challenge, but encounters a trade-off between acquisition speed and the specificity for biomechanical constituents with overlapping Brillouin bands. Stimulated Brillouin scattering microscopy overcomes this trade-off and enables

    更新日期:2020-08-03
  • Animal-derived-antibody generation faces strict reform in accordance with European Union policy on animal use.
    Nat. Methods (IF 30.822) Pub Date : 2020-08-01
    Alison C Gray,Andrew R M Bradbury,Achim Knappik,Andreas Plückthun,Carl A K Borrebaeck,Stefan Dübel

    更新日期:2020-08-01
  • Trapping fluorescence in the soma.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-31
    Nina Vogt

    Tethering fluorescent proteins to ribosomes clears up background signals when imaging neural circuits.

    更新日期:2020-07-31
  • Printing in vivo.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-31
    Lei Tang

    Intravital three-dimensional bioprinting enables the biofabrication of constructs in a pre-existing 3D matrix, such as inside tissues of live animals.

    更新日期:2020-07-31
  • Mapping RNA-RNA interactions.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-31
    Lin Tang

    RIC-seq enables in situ mapping of intra- and intermolecular RNA–RNA interactions.

    更新日期:2020-07-31
  • Multiplex fate mapping.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-31
    Madhura Mukhopadhyay

    barRNAseq allows detailed explorations of signaling pathways that control embryonic differentiation.

    更新日期:2020-07-31
  • Imaging single glycan molecules.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-31
    Arunima Singh

    Direct imaging of carbohydrates using electrospray ion beam deposition and scanning tunneling microscopy.

    更新日期:2020-07-31
  • Content type revamp.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-31

    We’ve made some recent updates to our various content type offerings at Nature Methods. Here is a cheat sheet.

    更新日期:2020-07-31
  • Author Correction: Comparing phenotypic variation between inbred and outbred mice.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-29
    Alexander H Tuttle,Vivek M Philip,Elissa J Chesler,Jeffrey S Mogil

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-07-30
  • Supervised enhancer prediction with epigenetic pattern recognition and targeted validation.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-29
    Anurag Sethi,Mengting Gu,Emrah Gumusgoz,Landon Chan,Koon-Kiu Yan,Joel Rozowsky,Iros Barozzi,Veena Afzal,Jennifer A Akiyama,Ingrid Plajzer-Frick,Chengfei Yan,Catherine S Novak,Momoe Kato,Tyler H Garvin,Quan Pham,Anne Harrington,Brandon J Mannion,Elizabeth A Lee,Yoko Fukuda-Yuzawa,Axel Visel,Diane E Dickel,Kevin Y Yip,Richard Sutton,Len A Pennacchio,Mark Gerstein

    Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays allows the characterization of large numbers of enhancers for the first time. Here, we developed a framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features. We integrated these features

    更新日期:2020-07-29
  • Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-27
    Bo Li,Joshua Gould,Yiming Yang,Siranush Sarkizova,Marcin Tabaka,Orr Ashenberg,Yanay Rosen,Michal Slyper,Monika S Kowalczyk,Alexandra-Chloé Villani,Timothy Tickle,Nir Hacohen,Orit Rozenblatt-Rosen,Aviv Regev

    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-scale single-cell and single-nucleus RNA sequencing datasets. Cumulus combines the

    更新日期:2020-07-27
  • A general method to optimize and functionalize red-shifted rhodamine dyes.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-27
    Jonathan B Grimm,Ariana N Tkachuk,Liangqi Xie,Heejun Choi,Boaz Mohar,Natalie Falco,Kathy Schaefer,Ronak Patel,Qinsi Zheng,Zhe Liu,Jennifer Lippincott-Schwartz,Timothy A Brown,Luke D Lavis

    Expanding the palette of fluorescent dyes is vital to push the frontier of biological imaging. Although rhodamine dyes remain the premier type of small-molecule fluorophore owing to their bioavailability and brightness, variants excited with far-red or near-infrared light suffer from poor performance due to their propensity to adopt a lipophilic, nonfluorescent form. We report a framework for rationalizing

    更新日期:2020-07-27
  • 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-27
    Huy Q Nguyen,Shyamtanu Chattoraj,David Castillo,Son C Nguyen,Guy Nir,Antonios Lioutas,Elliot A Hershberg,Nuno M C Martins,Paul L Reginato,Mohammed Hannan,Brian J Beliveau,George M Church,Evan R Daugharthy,Marc A Marti-Renom,C-Ting Wu

    There is a need for methods that can image chromosomes with genome-wide coverage, as well as greater genomic and optical resolution. We introduce OligoFISSEQ, a suite of three methods that leverage fluorescence in situ sequencing (FISSEQ) of barcoded Oligopaint probes to enable the rapid visualization of many targeted genomic regions. Applying OligoFISSEQ to human diploid fibroblast cells, we show

    更新日期:2020-07-27
  • Author Correction: Highly specific multiplexed RNA imaging in tissues with split-FISH.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-26
    Jolene Jie Lin Goh,Nigel Chou,Wan Yi Seow,Norbert Ha,Chung Pui Paul Cheng,Yun-Ching Chang,Ziqing Winston Zhao,Kok Hao Chen

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-07-27
  • Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-23
    Ismael Rodríguez-Espigares,Mariona Torrens-Fontanals,Johanna K S Tiemann,David Aranda-García,Juan Manuel Ramírez-Anguita,Tomasz Maciej Stepniewski,Nathalie Worp,Alejandro Varela-Rial,Adrián Morales-Pastor,Brian Medel-Lacruz,Gáspár Pándy-Szekeres,Eduardo Mayol,Toni Giorgino,Jens Carlsson,Xavier Deupi,Slawomir Filipek,Marta Filizola,José Carlos Gómez-Tamayo,Angel Gonzalez,Hugo Gutiérrez-de-Terán,Mireia

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-07-24
  • Change-makers bring on recombinant antibodies.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-22
    Vivien Marx

    There’s a growing affinity for recombinant antibodies. Some say it’s also high time for animal-free recombinants.

    更新日期:2020-07-22
  • Jana Selent.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-21
    Vivien Marx

    A platform for exploring GPCR secrets, powered by community, music and sports.

    更新日期:2020-07-21
  • Philosopher: a versatile toolkit for shotgun proteomics data analysis.
    Nat. Methods (IF 30.822) Pub Date : 2020-09-01
    Felipe da Veiga Leprevost,Sarah E Haynes,Dmitry M Avtonomov,Hui-Yin Chang,Avinash K Shanmugam,Dattatreya Mellacheruvu,Andy T Kong,Alexey I Nesvizhskii

    更新日期:2020-07-15
  • Investigating higher-order interactions in single-cell data with scHOT.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-13
    Shila Ghazanfar,Yingxin Lin,Xianbin Su,David Ming Lin,Ellis Patrick,Ze-Guang Han,John C Marioni,Jean Yee Hwa Yang

    Single-cell genomics has transformed our ability to examine cell fate choice. Examining cells along a computationally ordered ‘pseudotime’ offers the potential to unpick subtle changes in variability and covariation among key genes. We describe an approach, scHOT—single-cell higher-order testing—which provides a flexible and statistically robust framework for identifying changes in higher-order interactions

    更新日期:2020-07-13
  • Novel NanoLuc substrates enable bright two-population bioluminescence imaging in animals.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-13
    Yichi Su,Joel R Walker,Yunhee Park,Thomas P Smith,Lan Xiang Liu,Mary P Hall,Louai Labanieh,Robin Hurst,David C Wang,Lance P Encell,Namdoo Kim,Feijie Zhang,Mark A Kay,Kerriann M Casey,Robbie G Majzner,Jennifer R Cochran,Crystal L Mackall,Thomas A Kirkland,Michael Z Lin

    Sensitive detection of two biological events in vivo has long been a goal in bioluminescence imaging. Antares, a fusion of the luciferase NanoLuc to the orange fluorescent protein CyOFP, has emerged as a bright bioluminescent reporter with orthogonal substrate specificity to firefly luciferase (FLuc) and its derivatives such as AkaLuc. However, the brightness of Antares in mice is limited by the poor

    更新日期:2020-07-13
  • GPCRmd uncovers the dynamics of the 3D-GPCRome.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-13
    Ismael Rodríguez-Espigares,Mariona Torrens-Fontanals,Johanna K S Tiemann,David Aranda-García,Juan Manuel Ramírez-Anguita,Tomasz Maciej Stepniewski,Nathalie Worp,Alejandro Varela-Rial,Adrián Morales-Pastor,Brian Medel-Lacruz,Gáspár Pándy-Szekeres,Eduardo Mayol,Toni Giorgino,Jens Carlsson,Xavier Deupi,Slawomir Filipek,Marta Filizola,José Carlos Gómez-Tamayo,Angel Gonzalez,Hugo Gutiérrez-de-Terán,Mireia

    G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations

    更新日期:2020-07-13
  • On the cutting edge: protease-based methods for sensing and controlling cell biology.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-13
    H Kay Chung,Michael Z Lin

    Sequence-specific proteases have proven to be versatile building blocks for tools that report or control cellular function. Reporting methods link protease activity to biochemical signals, whereas control methods rely on engineering proteases to respond to exogenous inputs such as light or chemicals. In turn, proteases have inherent control abilities, as their native functions are to release, activate

    更新日期:2020-07-13
  • ZipSeq: barcoding for real-time mapping of single cell transcriptomes.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-06
    Kenneth H Hu,John P Eichorst,Chris S McGinnis,David M Patterson,Eric D Chow,Kelly Kersten,Stephen C Jameson,Zev J Gartner,Arjun A Rao,Matthew F Krummel

    Spatial transcriptomics seeks to integrate single cell transcriptomic data within the three-dimensional space of multicellular biology. Current methods to correlate a cell’s position with its transcriptome in living tissues have various limitations. We developed an approach, called ‘ZipSeq’, that uses patterned illumination and photocaged oligonucleotides to serially print barcodes (‘zipcodes’) onto

    更新日期:2020-07-06
  • T cell antigen discovery.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-06
    Alok V Joglekar,Guideng Li

    T cells respond to threats in an antigen-specific manner using T cell receptors (TCRs) that recognize short peptide antigens presented on major histocompatibility complex (MHC) proteins. The TCR–peptide-MHC interaction mediated between a T cell and its target cell dictates its function and thereby influences its role in disease. A lack of approaches for antigen discovery has limited the fundamental

    更新日期:2020-07-06
  • Selective cell-surface N-glycan editing.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-02
    Arunima Singh

    A two-step chemoenzymatic method for N-glycan subtype-selective editing.

    更新日期:2020-07-02
  • Tuning transparency in human cells.
    Nat. Methods (IF 30.822) Pub Date : 2020-07-02
    Rita Strack

    Proteins that control the optical properties of cephalopod skin cells can modulate the transparency of mammalian cells.

    更新日期:2020-07-02
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