Publications
2024
An atlas of protein homo-oligomerization across domains of life.
Cell,2024 Feb 15187(4):
2023
CC(+) : A searchable database of validated coiled coils in PDB structures and AlphaFold2 models.
Protein Sci,2023 Nov32(11):
DOI: 10.1002/pro.4789
Mesoscale molecular assembly is favored by the active, crowded cytoplasm.
bioRxiv,2023 Sep 21:
Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.
Proteomics,2023 Sep23(17):
2022
Molecular and environmental determinants of biomolecular condensate formation.
Nat Chem Biol,2022 Dec18(12):
How gene duplication diversifies the landscape of protein oligomeric state and function.
Curr Opin Genet Dev,2022 Oct76:
Affinity and Valence Impact the Extent and Symmetry of Phase Separation of Multivalent Proteins.
Phys Rev Lett,2022 Sep 16129(12):
A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates.
Protein Sci,2022 Jul31(7):
DOI: 10.1002/pro.4361
Synthetic condensate size correlates with yeast replicative cell age.
MicroPubl Biol,20222022:
The modular cell gets connected.
Science,2022 Mar 11375(6585):
Mutant libraries reveal negative design shielding proteins from supramolecular self-assembly and relocalization in cells.
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):
DOI: 10.1093/nar/gkab988
QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure.
Front Mol Biosci,20218:
2021
PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry.
Structure,2021 Nov 429(11):
Altered Protein Abundance and Localization Inferred from Sites of Alternative Modification by Ubiquitin and SUMO.
J Mol Biol,2021 Oct 15433(21):
Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins.
Front Mol Biosci,20218:
"Structuromics": another step toward a holistic view of the cell.
Cell,2021 Jan 21184(2):
2020
Not Going with the Flow: How Cells Adapt Internal Physics.
Cell,2020 Dec 10183(6):
Designer protein assemblies with tunable phase diagrams in living cells.
Nat Chem Biol,2020 Sep16(9):
Proteomic analysis reveals the direct recruitment of intrinsically disordered regions to stress granules in S. cerevisiae.
J Cell Sci,2020 Jul 9133(13):
DOI: 10.1242/jcs.244657
PDBe-KB: a community-driven resource for structural and functional annotations.
Nucleic Acids Res,2020 Jan 848(D1):
DOI: 10.1093/nar/gkz853
2019
Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions.
J Mol Biol,2019 Dec 6431(24):
Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast.
Nat Commun,2019 Jul 410(1):
Geometric description of self-interaction potential in symmetric protein complexes.
Sci Data,2019 May 176(1):
Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering.
Angew Chem Int Ed Engl,2019 Apr 1658(17):
Evolthon: A community endeavor to evolve lab evolution.
PLoS Biol,2019 Mar17(3):
YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries.
Nucleic Acids Res,2019 Jan 847(D1):
DOI: 10.1093/nar/gky941
2018
Genome-wide C-SWAT library for high-throughput yeast genome tagging.
Nat Methods,2018 Aug15(8):
Genome-wide SWAp-Tag yeast libraries for proteome exploration.
Nat Methods,2018 Aug15(8):
Inferring and Using Protein Quaternary Structure Information from Crystallographic Data.
Methods Mol Biol,20181764:
PDB-wide identification of biological assemblies from conserved quaternary structure geometry.
Nat Methods,2018 Jan15(1):
DOI: 10.1038/nmeth.4510
2017
Proteins evolve on the edge of supramolecular self-assembly.
Nature,2017 Aug 10548(7666):
DOI: 10.1038/nature23320
Exhaustive search of linear information encoding protein-peptide recognition.
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.
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.
Cold Spring Harb Protoc,2016 Nov 12016(11):
Young phosphorylation is functionally silent.
Science,2016 Oct 14354(6309):
Evolution of domain-peptide interactions to coadapt specificity and affinity to functional diversity.
Proc Natl Acad Sci U S A,2016 Jul 5113(27):
2015
Decoding a neural circuit controlling global animal state in C. elegans.
Elife,2015 Mar 114:
DOI: 10.7554/eLife.04241
Symmetry breaking in homo-oligomers: the curious case of mega-hemocyanin.
Structure,2015 Jan 623(1):
2014
Fast and accurate discovery of degenerate linear motifs in protein sequences.
PLoS One,20149(9):
Different subunits belonging to the same protein complex often exhibit discordant expression levels and evolutionary properties.
Curr Opin Struct Biol,2014 Jun26:
High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation.
Cell Rep,2014 May 227(4):
2013
Extracting insight from noisy cellular networks.
Cell,2013 Nov 21155(5):
Structural, evolutionary, and assembly principles of protein oligomerization.
Prog Mol Biol Transl Sci,2013117:
2012
Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.
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.
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.
Mol Syst Biol,2010 Oct 196:
DOI: 10.1038/msb.2010.80
Homomeric protein complexes: evolution and assembly.
Biochem Soc Trans,2010 Aug38(4):
DOI: 10.1042/BST0380879
Systemizing the structures and structuring the system.
Expert Rev Proteomics,2010 Jun7(3):
DOI: 10.1586/epr.10.33
Cell signaling. Signaling through cooperation.
Science,2010 May 21328(5981):
2009
Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins.
Proc Natl Acad Sci U S A,2009 Jun 23106(25):
Weak functional constraints on phosphoproteomes.
Trends Genet,2009 May25(5):
Self-assembly and evolution of homomeric protein complexes.
Phys Rev Lett,2009 Mar 20102(11):
How perfect can protein interactomes be?
Sci Signal,2009 Mar 32(60):
2008
Assembly reflects evolution of protein complexes.
Nature,2008 Jun 26453(7199):
DOI: 10.1038/nature06942
Evolution and dynamics of protein interactions and networks.
Curr Opin Struct Biol,2008 Jun18(3):
2007
PiQSi: protein quaternary structure investigation.
Structure,2007 Nov15(11):
CORRIE: enzyme sequence annotation with confidence estimates.
BMC Bioinformatics,2007 May 228 Suppl 4(Suppl 4):
Evolution of protein complexes by duplication of homomeric interactions.
Genome Biol,20078(4):
2006
3D complex: a structural classification of protein complexes.
PLoS Comput Biol,2006 Nov 172(11):
The origins and evolution of functional modules: lessons from protein complexes.
Philos Trans R Soc Lond B Biol Sci,2006 Mar 29361(1467):
2005
Probabilistic annotation of protein sequences based on functional classifications.
BMC Bioinformatics,2005 Dec 146: