pLogo: a probabilistic approach to visualizing sequence motifs.

Abstract:

:Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue frequencies to graphically scale character heights. We describe the pLogo, a motif visualization in which residue heights are scaled relative to their statistical significance. A pLogo generation tool is publicly available at http://plogo.uconn.edu/ and supports real-time conditional probability calculations and visualizations.

journal_name

Nat Methods

journal_title

Nature methods

authors

O'Shea JP,Chou MF,Quader SA,Ryan JK,Church GM,Schwartz D

doi

10.1038/nmeth.2646

subject

Has Abstract

pub_date

2013-12-01 00:00:00

pages

1211-2

issue

12

eissn

1548-7091

issn

1548-7105

pii

nmeth.2646

journal_volume

10

pub_type

杂志文章
  • Anna Moroni.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 评论,新闻

    doi:10.1038/s41592-018-0192-y

    authors: Marx V

    更新日期:2018-11-01 00:00:00

  • High-speed nanoscopic tracking of the position and orientation of a single virus.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth.1395

    authors: Kukura P,Ewers H,Müller C,Renn A,Helenius A,Sandoghdar V

    更新日期:2009-12-01 00:00:00

  • Independence and reproducibility across microarray platforms.

    abstract::Microarrays have been widely used for the analysis of gene expression, but the issue of reproducibility across platforms has yet to be fully resolved. To address this apparent problem, we compared gene expression between two microarray platforms: the short oligonucleotide Affymetrix Mouse Genome 430 2.0 GeneChip and a...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth757

    authors: Larkin JE,Frank BC,Gavras H,Sultana R,Quackenbush J

    更新日期:2005-05-01 00:00:00

  • Structural modeling of protein-RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS.

    abstract::Ribonucleoproteins (RNPs) are key regulators of cellular function. We established an efficient approach, crosslinking of segmentally isotope-labeled RNA and tandem mass spectrometry (CLIR-MS/MS), to localize protein-RNA interactions simultaneously at amino acid and nucleotide resolution. The approach was tested on pol...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.4235

    authors: Dorn G,Leitner A,Boudet J,Campagne S,von Schroetter C,Moursy A,Aebersold R,Allain FH

    更新日期:2017-05-01 00:00:00

  • Identification of differentially methylated cell types in epigenome-wide association studies.

    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

    pub_type: 杂志文章

    doi:10.1038/s41592-018-0213-x

    authors: Zheng SC,Breeze CE,Beck S,Teschendorff AE

    更新日期:2018-12-01 00:00:00

  • The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells.

    abstract::Cell signaling, one of key processes in both normal cellular function and disease, is coordinated by numerous interactions between membrane proteins that change in response to stimuli. We present a split ubiquitin-based method for detection of integral membrane protein-protein interactions (PPIs) in human cells, terme...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2895

    authors: Petschnigg J,Groisman B,Kotlyar M,Taipale M,Zheng Y,Kurat CF,Sayad A,Sierra JR,Mattiazzi Usaj M,Snider J,Nachman A,Krykbaeva I,Tsao MS,Moffat J,Pawson T,Lindquist S,Jurisica I,Stagljar I

    更新日期:2014-05-01 00:00:00

  • Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering.

    abstract::We demonstrate tracking of protein structural changes with time-resolved wide-angle X-ray scattering (TR-WAXS) with nanosecond time resolution. We investigated the tertiary and quaternary conformational changes of human hemoglobin under nearly physiological conditions triggered by laser-induced ligand photolysis. We a...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1255

    authors: Cammarata M,Levantino M,Schotte F,Anfinrud PA,Ewald F,Choi J,Cupane A,Wulff M,Ihee H

    更新日期:2008-10-01 00:00:00

  • High-resolution mass spectrometry of small molecules bound to membrane proteins.

    abstract::Small molecules are known to stabilize membrane proteins and to modulate their function and oligomeric state, but such interactions are often hard to precisely define. Here we develop and apply a high-resolution, Orbitrap mass spectrometry-based method for analyzing intact membrane protein-ligand complexes. Using this...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3771

    authors: Gault J,Donlan JA,Liko I,Hopper JT,Gupta K,Housden NG,Struwe WB,Marty MT,Mize T,Bechara C,Zhu Y,Wu B,Kleanthous C,Belov M,Damoc E,Makarov A,Robinson CV

    更新日期:2016-04-01 00:00:00

  • Conditional genome engineering in Toxoplasma gondii uncovers alternative invasion mechanisms.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth.2301

    authors: Andenmatten N,Egarter S,Jackson AJ,Jullien N,Herman JP,Meissner M

    更新日期:2013-02-01 00:00:00

  • High-speed volumetric imaging of neuronal activity in freely moving rodents.

    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

    pub_type: 杂志文章

    doi:10.1038/s41592-018-0008-0

    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

  • Membrane-protein structure determination by solid-state NMR spectroscopy of microcrystals.

    abstract::Membrane proteins are largely underrepresented among available atomic-resolution structures. The use of detergents in protein purification procedures hinders the formation of well-ordered crystals for X-ray crystallography and leads to slower molecular tumbling, impeding the application of solution-state NMR. Solid-st...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2248

    authors: Shahid SA,Bardiaux B,Franks WT,Krabben L,Habeck M,van Rossum BJ,Linke D

    更新日期:2012-12-01 00:00:00

  • Harnessing fungal bioluminescence.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-019-0311-4

    authors: Strack R

    更新日期:2019-02-01 00:00:00

  • FaST linear mixed models for genome-wide association studies.

    abstract::We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm for genome-wide association studies (GWAS) that scales linearly with cohort size in both run time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algo...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1681

    authors: Lippert C,Listgarten J,Liu Y,Kadie CM,Davidson RI,Heckerman D

    更新日期:2011-09-04 00:00:00

  • Highly efficient Cas9-mediated transcriptional programming.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth.3312

    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

  • Targeted chromosome elimination from ES-somatic hybrid cells.

    abstract::To engineer a stem cell genome, we developed a technology for targeted elimination of chromosomes from mouse embryonic stem (ES)-somatic hybrid cells. Here we demonstrate the use of a universal chromosome elimination cassette (CEC) for elimination of a single embryonic stem cell (ESC)-derived chromosome 11 or 12, and ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth973

    authors: Matsumura H,Tada M,Otsuji T,Yasuchika K,Nakatsuji N,Surani A,Tada T

    更新日期:2007-01-01 00:00:00

  • Author Correction: Resolution upgrades for light-sheet microscopy.

    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

    pub_type: 已发布勘误

    doi:10.1038/s41592-019-0588-3

    authors: Fiolka R

    更新日期:2019-10-01 00:00:00

  • Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth724

    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

  • Tracking the wily transcription factor.

    abstract::A 'paired-end ditag' (PET) strategy for pinpointing protein binding sites can reveal a wealth of information about transcription factors and other DNA-binding proteins. ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth0506-341

    authors: Eisenstein M

    更新日期:2006-05-01 00:00:00

  • Enhanced antibody validation.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 评论,杂志文章

    doi:10.1038/s41592-018-0248-z

    authors: Doerr A

    更新日期:2018-12-01 00:00:00

  • Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light.

    abstract::Recent efforts in neuroscience research have been aimed at obtaining detailed anatomical neuronal wiring maps as well as information on how neurons in these networks engage in dynamic activities. Although the entire connectivity map of the nervous system of Caenorhabditis elegans has been known for more than 25 years,...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2637

    authors: Schrödel T,Prevedel R,Aumayr K,Zimmer M,Vaziri A

    更新日期:2013-10-01 00:00:00

  • Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval.

    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

    pub_type: 杂志文章

    doi:10.1038/s41592-020-0816-x

    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

  • Annotating the unannotated.

    abstract::By combining activity-based proteomics and metabolomics, researchers have developed a new systems biology strategy for characterizing enzymes in the context of metabolic networks. ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth0107-8b

    authors: Doerr A

    更新日期:2007-01-01 00:00:00

  • De novo assembly and analysis of RNA-seq data.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth.1517

    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

  • The GEM mapper: fast, accurate and versatile alignment by filtration.

    abstract::Because of ever-increasing throughput requirements of sequencing data, most existing short-read aligners have been designed to focus on speed at the expense of accuracy. The Genome Multitool (GEM) mapper can leverage string matching by filtration to search the alignment space more efficiently, simultaneously deliverin...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2221

    authors: Marco-Sola S,Sammeth M,Guigó R,Ribeca P

    更新日期:2012-12-01 00:00:00

  • An FKBP destabilization domain modulates protein levels in Plasmodium falciparum.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth1132

    authors: Armstrong CM,Goldberg DE

    更新日期:2007-12-01 00:00:00

  • Mapping of signaling networks through synthetic genetic interaction analysis by RNAi.

    abstract::The analysis of synthetic genetic interaction networks can reveal how biological systems achieve a high level of complexity with a limited repertoire of components. Studies in yeast and bacteria have taken advantage of collections of deletion strains to construct matrices of quantitative interaction profiles and infer...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1581

    authors: Horn T,Sandmann T,Fischer B,Axelsson E,Huber W,Boutros M

    更新日期:2011-04-01 00:00:00

  • Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins.

    abstract::We examined cell cycle-dependent changes in the proteome of human cells by systematically measuring protein dynamics in individual living cells. We used time-lapse microscopy to measure the dynamics of a random subset of 20 nuclear proteins, each tagged with yellow fluorescent protein (YFP) at its endogenous chromosom...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth892

    authors: Sigal A,Milo R,Cohen A,Geva-Zatorsky N,Klein Y,Alaluf I,Swerdlin N,Perzov N,Danon T,Liron Y,Raveh T,Carpenter AE,Lahav G,Alon U

    更新日期:2006-07-01 00:00:00

  • Imaging cellular ultrastructures using expansion microscopy (U-ExM).

    abstract::Determining the structure and composition of macromolecular assemblies is a major challenge in biology. Here we describe ultrastructure expansion microscopy (U-ExM), an extension of expansion microscopy that allows the visualization of preserved ultrastructures by optical microscopy. This method allows for near-native...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-018-0238-1

    authors: Gambarotto D,Zwettler FU,Le Guennec M,Schmidt-Cernohorska M,Fortun D,Borgers S,Heine J,Schloetel JG,Reuss M,Unser M,Boyden ES,Sauer M,Hamel V,Guichard P

    更新日期:2019-01-01 00:00:00

  • A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates.

    abstract::New methods to quantify protein kinase activities directly from complex cellular mixtures are critical for understanding biological regulatory pathways. Herein, a fluorescence-based chemosensor strategy for the direct measurement of kinase activities in crude mammalian cell lysates is described. We first designed a ne...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth747

    authors: Shults MD,Janes KA,Lauffenburger DA,Imperiali B

    更新日期:2005-04-01 00:00:00

  • Onco-proteogenomics: cancer proteomics joins forces with genomics.

    abstract::The complexities of tumor genomes are rapidly being uncovered, but how they are regulated into functional proteomes remains poorly understood. Standard proteomics workflows use databases of known proteins, but these databases do not capture the uniqueness of the cancer transcriptome, with its point mutations, unusual ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3138

    authors: Alfaro JA,Sinha A,Kislinger T,Boutros PC

    更新日期:2014-11-01 00:00:00