Emmanuel Levy

Publications

2024

An atlas of protein homo-oligomerization across domains of life.
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Cell,2024 Feb 15187(4):

2023

CC(+) : A searchable database of validated coiled coils in PDB structures and AlphaFold2 models.
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Protein Sci,2023 Nov32(11):
Mesoscale molecular assembly is favored by the active, crowded cytoplasm.
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bioRxiv,2023 Sep 21:
Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.
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Proteomics,2023 Sep23(17):

2022

Molecular and environmental determinants of biomolecular condensate formation.
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Nat Chem Biol,2022 Dec18(12):
How gene duplication diversifies the landscape of protein oligomeric state and function.
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Curr Opin Genet Dev,2022 Oct76:
Affinity and Valence Impact the Extent and Symmetry of Phase Separation of Multivalent Proteins.
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Phys Rev Lett,2022 Sep 16129(12):
A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates.
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Protein Sci,2022 Jul31(7):
Synthetic condensate size correlates with yeast replicative cell age.
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MicroPubl Biol,20222022:
Mutant libraries reveal negative design shielding proteins from supramolecular self-assembly and relocalization in cells.
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Proc Natl Acad Sci U S A,2022 Feb 1119(5):
PDBe-KB: collaboratively defining the biological context of structural data.
Nucleic Acids Res,2022 Jan 750(D1):
QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure.
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Front Mol Biosci,20218:

2021

PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry.
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Structure,2021 Nov 429(11):
Altered Protein Abundance and Localization Inferred from Sites of Alternative Modification by Ubiquitin and SUMO.
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J Mol Biol,2021 Oct 15433(21):
Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins.
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Front Mol Biosci,20218:
"Structuromics": another step toward a holistic view of the cell.
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Cell,2021 Jan 21184(2):

2020

Not Going with the Flow: How Cells Adapt Internal Physics.
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Cell,2020 Dec 10183(6):
Designer protein assemblies with tunable phase diagrams in living cells.
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Nat Chem Biol,2020 Sep16(9):
Proteomic analysis reveals the direct recruitment of intrinsically disordered regions to stress granules in S. cerevisiae.
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J Cell Sci,2020 Jul 9133(13):
PDBe-KB: a community-driven resource for structural and functional annotations.
Nucleic Acids Res,2020 Jan 848(D1):

2019

Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions.
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J Mol Biol,2019 Dec 6431(24):
Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast.
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Nat Commun,2019 Jul 410(1):
Geometric description of self-interaction potential in symmetric protein complexes.
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Sci Data,2019 May 176(1):
Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering.
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Angew Chem Int Ed Engl,2019 Apr 1658(17):
Evolthon: A community endeavor to evolve lab evolution.
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PLoS Biol,2019 Mar17(3):
YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries.
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Nucleic Acids Res,2019 Jan 847(D1):

2018

Genome-wide C-SWAT library for high-throughput yeast genome tagging.
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Nat Methods,2018 Aug15(8):
Genome-wide SWAp-Tag yeast libraries for proteome exploration.
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Nat Methods,2018 Aug15(8):
Inferring and Using Protein Quaternary Structure Information from Crystallographic Data.
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Methods Mol Biol,20181764:
PDB-wide identification of biological assemblies from conserved quaternary structure geometry.
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Nat Methods,2018 Jan15(1):

2017

Proteins evolve on the edge of supramolecular self-assembly.
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Nature,2017 Aug 10548(7666):
Exhaustive search of linear information encoding protein-peptide recognition.
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PLoS Comput Biol,2017 Apr13(4):

2016

Protein-Fragment Complementation Assays for Large-Scale Analysis, Functional Dissection, and Spatiotemporal Dynamic Studies of Protein-Protein Interactions in Living Cells.
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Cold Spring Harb Protoc,2016 Nov 12016(11):
The Dihydrofolate Reductase Protein-Fragment Complementation Assay: A Survival-Selection Assay for Large-Scale Analysis of Protein-Protein Interactions.
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Cold Spring Harb Protoc,2016 Nov 12016(11):
Young phosphorylation is functionally silent.
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Science,2016 Oct 14354(6309):
Evolution of domain-peptide interactions to coadapt specificity and affinity to functional diversity.
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Proc Natl Acad Sci U S A,2016 Jul 5113(27):

2015

Decoding a neural circuit controlling global animal state in C. elegans.
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Elife,2015 Mar 114:
Symmetry breaking in homo-oligomers: the curious case of mega-hemocyanin.
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Structure,2015 Jan 623(1):

2014

Fast and accurate discovery of degenerate linear motifs in protein sequences.
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PLoS One,20149(9):
Different subunits belonging to the same protein complex often exhibit discordant expression levels and evolutionary properties.
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Curr Opin Struct Biol,2014 Jun26:
High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation.
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Cell Rep,2014 May 227(4):

2013

Extracting insight from noisy cellular networks.
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Cell,2013 Nov 21155(5):
Structural, evolutionary, and assembly principles of protein oligomerization.
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Prog Mol Biol Transl Sci,2013117:

2012

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.
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Proc Natl Acad Sci U S A,2012 Dec 11109(50):
Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information.
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Philos Trans R Soc Lond B Biol Sci,2012 Sep 19367(1602):

2010

A simple definition of structural regions in proteins and its use in analyzing interface evolution.
J Mol Biol,2010 Nov 5403(4):
Molecular characterization of the evolution of phagosomes.
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Mol Syst Biol,2010 Oct 196:
Homomeric protein complexes: evolution and assembly.
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Biochem Soc Trans,2010 Aug38(4):
Systemizing the structures and structuring the system.
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Expert Rev Proteomics,2010 Jun7(3):
Cell signaling. Signaling through cooperation.
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Science,2010 May 21328(5981):

2009

Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins.
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Proc Natl Acad Sci U S A,2009 Jun 23106(25):
Weak functional constraints on phosphoproteomes.
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Trends Genet,2009 May25(5):
Self-assembly and evolution of homomeric protein complexes.
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Phys Rev Lett,2009 Mar 20102(11):
How perfect can protein interactomes be?
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Sci Signal,2009 Mar 32(60):

2008

Assembly reflects evolution of protein complexes.
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Nature,2008 Jun 26453(7199):
Evolution and dynamics of protein interactions and networks.
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Curr Opin Struct Biol,2008 Jun18(3):

2007

CORRIE: enzyme sequence annotation with confidence estimates.
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BMC Bioinformatics,2007 May 228 Suppl 4(Suppl 4):
Evolution of protein complexes by duplication of homomeric interactions.
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Genome Biol,20078(4):

2006

3D complex: a structural classification of protein complexes.
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PLoS Comput Biol,2006 Nov 172(11):
The origins and evolution of functional modules: lessons from protein complexes.
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Philos Trans R Soc Lond B Biol Sci,2006 Mar 29361(1467):

2005

Probabilistic annotation of protein sequences based on functional classifications.
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BMC Bioinformatics,2005 Dec 146: