Nature Search

Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins

Using cryo-EM, the authors identified 42 MIPs, including outer junction protein CFAP77 and outer dense fibers, in native doublet microtubules of Tetrahymena thermophila. Knockout of CFAP77 reduced ciliary beat frequency and led to outer junction damage.

Shintaroh Kubo
Corbin S. Black
Khanh Huy Bui
ResearchOpen Access15 Apr 2023
Nature Communications

Volume: 14, P: 1-16
X-ray structure of an anti-fungal chitosanase from streptomyces N174

Edward M. Marcotte
Arthur F. Monzingo
Jon D. Robertas
Research01 Feb 1996
Nature Structural Biology

Volume: 3, P: 155-162
The human ciliopathy protein RSG1 links the CPLANE complex to transition zone architecture

The CPLANE complex is essential for ciliogenesis, and mutations to all but one subunit have been associated with ciliopathies. Here they identify three familial mutations in the final subunit, RSG1, that cause ciliopathy and add to our understanding of ciliary transition zone assembly.

Neftalí Vazquez
Chanjae Lee
John B. Wallingford
ResearchOpen Access01 Jul 2025
Nature Communications

Volume: 16, P: 1-16
Panorama of ancient metazoan macromolecular complexes

Using biochemical fractionation and mass spectrometry, animal protein complexes are identified from nine species in parallel, and, along with genome sequence information, complex conservation is investigated and over one million protein–protein interactions are predicted in 122 eukaryotes.

Cuihong Wan
Blake Borgeson
Andrew Emili
Research07 Sept 2015
Nature

Volume: 525, P: 339-344
Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core

Arthur F. Monzingo
Edward M. Marcotte
Jon D. Robertas
Research01 Feb 1996
Nature Structural Biology

Volume: 3, P: 133-140
Absolute abundance for the masses

Mass spectrometry can now measure the absolute concentrations of the majority of cellular proteins without labeling.

Christine Vogel
Edward M Marcotte
News & Views01 Sept 2009
Nature Biotechnology

Volume: 27, P: 825-826
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

Recent large-scale quantitative assessment of the proteome and transcriptome has revealed that transcript abundances only partially predict protein abundances. This article discusses ways in which such studies are informing our knowledge of protein expression regulation.

Christine Vogel
Edward M. Marcotte
Reviews13 Mar 2012
Nature Reviews Genetics

Volume: 13, P: 227-232
Temporal stability and molecular persistence of the bone marrow plasma cell antibody repertoire

Longevity of antibody responses has been attributed to persistence of plasma cells in mice. Here the authors provide human data in support of this model by immunoglobulin sequencing bone marrow sections from two human donors over 6.5 years to show temporal stability of plasma cell clonotypes, but not other B cells.

Gabriel C. Wu
Nai-Kong V. Cheung
Gregory C. Ippolito
ResearchOpen Access21 Dec 2016
Nature Communications

Volume: 7, P: 1-9
Correction: Corrigendum: The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery

Michinori Toriyama
Chanjae Lee
John B Wallingford
Amendments and Corrections27 Jul 2016
Nature Genetics

Volume: 48, P: 970
A combined algorithm for genome-wide prediction of protein function

Edward M. Marcotte
Matteo Pellegrini
David Eisenberg
Research04 Nov 1999
Nature

Volume: 402, P: 83-86
How do shotgun proteomics algorithms identify proteins?

Instrumentation aside, algorithms for matching mass spectra to proteins are at the heart of shotgun proteomics. How do these algorithms work, what can we expect of them and why is it so difficult to find protein modifications?

Edward M Marcotte
Reviews01 Jul 2007
Nature Biotechnology

Volume: 25, P: 755-757
Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination

Antibodies that bind to both H1 and H3 influenza strains exist in the pre-vaccination serum repertoire of healthy adults; most vaccine-elicited clonotypes bind either H1 or H3 strains.

Jiwon Lee
Daniel R Boutz
George Georgiou
Research07 Nov 2016
Nature Medicine

Volume: 22, P: 1456-1464
Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness

Translational reprogramming, which enables site-specific incorporation of non-natural amino acids into proteins, offers practical tools for studying protein function but also provides insights into the genetic code. Bacteriophages engineered with a 21-amino-acid genetic code make use of the additional noncanonical amino acid during in vitro evolution.

Michael J Hammerling
Jared W Ellefson
Jeffrey E Barrick
Research02 Feb 2014
Nature Chemical Biology

Volume: 10, P: 178-180
Engineering Escherichia coli to see light

These smart bacteria ‘photograph’ a light pattern as a high-definition chemical image.

Anselm Levskaya
Aaron A. Chevalier
Christopher A. Voigt
Research23 Nov 2005
Nature

Volume: 438, P: 441-442
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation

Peng Lu
Christine Vogel
Edward M Marcotte
Research24 Dec 2006
Nature Biotechnology

Volume: 25, P: 117-124
Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

Single-protein molecules are identified in parallel through fluorescence monitoring of Edman degradation.

Jagannath Swaminathan
Alexander A Boulgakov
Edward M Marcotte
Research22 Oct 2018
Nature Biotechnology

Volume: 36, P: 1076-1082
The genome sequence of the filamentous fungus Neurospora crassa

James E. Galagan
Sarah E. Calvo
Bruce Birren
ResearchOpen Access24 Apr 2003
Nature

Volume: 422, P: 859-868
Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism

Motile cilia are hair-like structures that are found on the surface of eukaryotic cells providing cell motility. Here, authors reveal the twelve components of nexin-dynein regulatory complex and associated proteins in cilia from Tetrahymena thermophila.

Avrin Ghanaeian
Sumita Majhi
Khanh Huy Bui
ResearchOpen Access15 Sept 2023
Nature Communications

Volume: 14, P: 1-15
Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols

The yeast Saccharomyces cerevisiae is powerful for studying human G protein-coupled receptors as they can be coupled to its mating pathway. Here the authors engineer baker’s yeast to produce human sterols and show that vertebrate G protein coupled receptors are more sensitive in this membrane environment.

Björn D. M. Bean
Colleen J. Mulvihill
Vincent J. J. Martin
ResearchOpen Access24 May 2022
Nature Communications

Volume: 13, P: 1-15
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages

Shailesh V Date
Edward M Marcotte
Research17 Aug 2003
Nature Biotechnology

Volume: 21, P: 1055-1062
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans

Insuk Lee
Ben Lehner
Edward M Marcotte
Research27 Jan 2008
Nature Genetics

Volume: 40, P: 181-188
Genome evolution in the allotetraploid frog Xenopus laevis

The two homoeologous subgenomes in the allotetraploid frog Xenopus laevis evolved asymmetrically; one often retained the ancestral state, whereas the other experienced gene loss, deletion, rearrangement and reduced gene expression.

Adam M. Session
Yoshinobu Uno
Daniel S. Rokhsar
ResearchOpen Access19 Oct 2016
Nature

Volume: 538, P: 336-343
Long-term neural and physiological phenotyping of a single human

Large-scale, multimodal phenotypic characterisation is a valuable tool to explore brain function. Poldrack et al. collect and relate MRI, psychological, physiological, metabolic and gene expression data from a single human over an 18 month period, providing a rich resource for future studies.

Russell A. Poldrack
Timothy O. Laumann
Jeanette A. Mumford
ResearchOpen Access09 Dec 2015
Nature Communications

Volume: 6, P: 1-15
Flaws in evaluation schemes for pair-input computational predictions

Yungki Park
Edward M Marcotte
Correspondence07 Dec 2012
Nature Methods

Volume: 9, P: 1134-1136
The path not taken

If known pathways represent preferred paths through global protein networks, large-scale experiments should focus on how to recognize these paths among all of the alternatives.

Edward M. Marcotte
News & Views01 Jul 2001
Nature Biotechnology

Volume: 19, P: 626-627
Systematic comparison of variant calling pipelines using gold standard personal exome variants

Sohyun Hwang
Eiru Kim
Edward M. Marcotte
ResearchOpen Access07 Dec 2015
Scientific Reports

Volume: 5, P: 1-8
The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery

John Wallingford and colleagues combine proteomics, in vivo imaging and genetic analyses to identify a new ciliopathy-associated protein module, which they call CPLANE. They show that CPLANE proteins, which include Fuzzy, Inturned and Wdpcp, interact with Jbts17 at basal bodies, where they act to recruit a specific subset of intraflagellar transport proteins.

Michinori Toriyama
Chanjae Lee
John B Wallingford
Research09 May 2016
Nature Genetics

Volume: 48, P: 648-656
Protein function in the post-genomic era

David Eisenberg
Edward M. Marcotte
Todd O. Yeates
Reviews15 Jun 2000
Nature

Volume: 405, P: 823-826
The need for a public proteomics repository

John T Prince
Mark W Carlson
Edward M Marcotte
Comments & Opinion01 Apr 2004
Nature Biotechnology

Volume: 22, P: 471-472
An open invitation to the Understudied Proteins Initiative

Georg Kustatscher
Tom Collins
Juri Rappsilber
Correspondence09 May 2022
Nature Biotechnology

Volume: 40, P: 815-817
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

Lee et al. have created the largest functional gene network for plants by combining existing data on Arabidopsis thaliana with data gathered from other organisms. Although the genetics of many A. thaliana traits has been thoroughly studied, the authors succeed in discovering new genes associated with root development and drought resistance.

Insuk Lee
Bindu Ambaru
Seung Y Rhee
Research31 Jan 2010
Nature Biotechnology

Volume: 28, P: 149-156
Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection

Streptococcal para-amino benzoic acid enhances Porphyromonas gingivalis colonization while reducing virulence during polymicrobial oral infection.

Masae Kuboniwa
John R. Houser
Richard J. Lamont
Research18 Sept 2017
Nature Microbiology

Volume: 2, P: 1493-1499
Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus

In hybrid inviability between Xenopus laevis and Xenopus tropicalis, genomic regions on two X. laevis chromosomes are incompatible with the X. tropicalis cytoplasm and are mis-segregated during mitosis, leading to unbalanced gene expression at the maternal to zygotic transition, followed by cell-autonomous catastrophic embryo death.

Romain Gibeaux
Rachael Acker
Rebecca Heald
Research10 Jan 2018
Nature

Volume: 553, P: 337-341
The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis and mouse embryonic development

The planar cell polarity (PCP) effector Fuz had not been studied in mice. Due to disrupted ciliogenesis, Fuz mutant mice show neural tube and skeletal defects. Fuz regulates trafficking of membrane cargoes to cilia through its interaction with a GTPase of the Rab family.

Ryan S. Gray
Philip B. Abitua
Richard H. Finnell
Research20 Sept 2009
Nature Cell Biology

Volume: 11, P: 1225-1232
A probabilistic view of gene function

Andrew G Fraser
Edward M Marcotte
Reviews27 May 2004
Nature Genetics

Volume: 36, P: 559-564
Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins

Structure determination of intracellular ciliary proteins using cross-linking mass spectrometry and AlphaFold2 (AF2) reveal that AF2 predictions with lower predicted align error scores correspond to more correct native structures.

Caitlyn L. McCafferty
Erin L. Pennington
Edward M. Marcotte
ResearchOpen Access15 Apr 2023
Communications Biology

Volume: 6, P: 1-10
The emerging landscape of single-molecule protein sequencing technologies

This Perspective describes new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell proteomics.

Javier Antonio Alfaro
Peggy Bohländer
Chirlmin Joo
Reviews07 Jun 2021
Nature Methods

Volume: 18, P: 604-617
Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

Sohyun Hwang
Seung Y Rhee
Insuk Lee
Protocols25 Aug 2011
Nature Protocols

Volume: 6, P: 1429-1442
Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data

Christine Vogel
Edward M Marcotte
Protocols21 Aug 2008
Nature Protocols

Volume: 3, P: 1444-1451
SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode

This manuscript investigates the binding mode of a potent SARS-CoV-2 neutralizing antibody. N3-1 is escaped by Omicron variants due to altered spike dynamics. This work suggests the need for innovative vaccine designs to combat evolving variants.

Jule Goike
Ching-Lin Hsieh
Jimmy D. Gollihar
ResearchOpen Access11 Dec 2023
Communications Biology

Volume: 6, P: 1-13
The E. coli molecular phenotype under different growth conditions

Mehmet U. Caglar
John R. Houser
Claus O. Wilke
ResearchOpen Access18 Apr 2017
Scientific Reports

Volume: 7, P: 1-15
Understudied proteins: opportunities and challenges for functional proteomics

Most research aiming at understanding the molecular foundations of life and disease has focused on a limited set of increasingly well-known proteins while the biological functions of many others remain poorly understood. We propose to form the Understudied Protein Initiative with the objective of reducing the annotation gap by systematically associating uncharacterized proteins with proteins of known function, thereby laying the groundwork for future detailed mechanistic studies.

Georg Kustatscher
Tom Collins
Juri Rappsilber
Comments & Opinion09 May 2022
Nature Methods

Volume: 19, P: 774-779
Potent PDZ-Domain PICK1 Inhibitors that Modulate Amyloid Beta-Mediated Synaptic Dysfunction

Edward Y. S. Lin
Laura F. Silvian
Kevin M. Guckian
ResearchOpen Access07 Sept 2018
Scientific Reports

Volume: 8, P: 1-10

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