2026
A pharmacological modality to sequester homomeric proteins.
Livnah E , Suss O , Rogel A , Gilat A , Abdan Y , Villegas JA , Gabizon R , Nadir A , Shamir Y , Steinman NY , Tivon B , Albeck S , Unger T , Golani O , Goliand I , Elad N , Carvalho S , Shurrush K , Barr H , Margulies D , Levy ED , London N.
Nat Chem Biol
2026 Feb 5 ;
null
2025
Molecular armor: Simple rules to keep proteins (re)soluble.
Mathur S , Alexandrov AI , Radhakrishnan SR , Levy ED.
Cell Syst
2025 Oct 1 ;
16
(
10 ):
101428
Mutation-induced filaments of folded proteins are inert and non-toxic in a cellular system.
Levin T , Garcia-Seisdedos H , Lobov A , Wojtynek M , Alexandrov A , Jona G , Levi D , Medalia O , Levy ED.
Mol Syst Biol
2025 Sep 15 ;
21
(
10 ):
1306 -
1324
Principles of cotranslational mitochondrial protein import.
Zhu Z , Mallik S , Stevens TA , Huang R , Levy ED , Shan SO.
Cell
2025 Aug 11 ;
188
(
20 ):
5605 -
5617.e14
Uncovering the mechanism for polar sequestration of the major bacterial sugar regulator by high-throughput screens and 3D interaction modeling.
Albocher-Kedem N , Heidenreich M , Fadel A , Sirotkin E , Goldberger O , Nussbaum-Shochat A , Levy ED , Schueler-Furman O , Schuldiner M , Amster-Choder O.
Cell Rep
2025 Mar 17 ;
44
(
3 ):
115436
A pharmacological modality to sequester homomeric proteins
Livnah E , Suss O , Rogel A , Gilat A , Abdan Y , Villegas JD , Tivon B , Albeck S , Unger T , Golani O , Goliand I , Margulies D , Levy ED , London N.
Rapid and sensitive protein complex alignment with Foldseek-Multimer.
Kim W , Mirdita M , Levy Karin E , Gilchrist CLM , Schweke H , Söding J , Levy ED , Steinegger M.
Nat Methods
2025 Feb 5 ;
22
(
3 ):
469 -
472
Structural determinants of co-translational protein complex assembly.
Mallik S , Venezian J , Lobov A , Heidenreich M , Garcia-Seisdedos H , Yeates TO , Shiber A , Levy ED.
Cell
2024 Dec 20 ;
188
(
3 ):
764 -
777.e22
Co-translational assembly promotes functional diversification of paralogous proteins
Mallik S , Cisneros AF , Landry CR , Levy ED.
2024
The phase separation landscape of genome-wide genetic perturbations
Heidenreich M , Mathur S , Shu T , Xie Y , Sriker D , Dubreuil B , Holt L , Levy ED.
Mesoscale molecular assembly is favored by the active, crowded cytoplasm.
Shu T , Mitra G , Alberts J , Viana MP , Levy ED , Hocky GM , Holt LJ.
PRX Life
2024 Jul 10 ;
2
(
3 ):
033001
Mutational biases favor complexity increases in protein interaction networks after gene duplication.
Cisneros AF , Nielly-Thibault L , Mallik S , Levy ED , Landry CR.
Mol Syst Biol
2024 Mar 18 ;
20
(
5 ):
549 -
572
An atlas of protein homo-oligomerization across domains of life.
Schweke H , Pacesa M , Levin T , Goverde CA , Kumar P , Duhoo Y , Dornfeld LJ , Dubreuil B , Georgeon S , Ovchinnikov S , Woolfson DN , Correia BE , Dey S , Levy ED.
Cell
2024 Feb 6 ;
187
(
4 ):
999 -
1010.e15
2023
Mutational biases promote neutral increases in the complexity of protein interaction networks following gene duplication
Cisneros AF , Nielly-Thibault L , Mallik S , Levy ED , Landry CR.
CC+ : A searchable database of validated coiled coils in PDB structures and AlphaFold2 models.
Kumar P , Petrenas R , Dawson WM , Schweke H , Levy ED , Woolfson DN.
Protein Sci
2023 Nov 1 ;
32
(
11 ):
e4789
Mesoscale molecular assembly is favored by the active, crowded cytoplasm.
Shu T , Mitra G , Alberts J , Viana MP , Levy ED , Hocky GM , Holt LJ
Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.
Schweke H , Xu Q , Tauriello G , Pantolini L , Schwede T , Cazals F , Lhéritier A , Fernandez-Recio J , Rodríguez-Lumbreras LA , Schueler-Furman O , Varga JK , Jiménez-García B , Réau MF , Bonvin AMJJ , Savojardo C , Martelli PL , Casadio R , Tubiana J , Wolfson HJ , Oliva R , Barradas-Bautista D , Ricciardelli T , Cavallo L , Venclovas Č , Olechnovič K , Guerois R , Andreani J , Martin J , Wang X , Terashi G , Sarkar D , Christoffer C , Aderinwale T , Verburgt J , Kihara D , Marchand A , Correia BE , Duan R , Qiu L , Xu X , Zhang S , Zou X , Dey S , Dunbrack RL , Levy ED , Wodak SJ.
Proteomics
2023 Jun 27 ;
23
(
17 ):
e2200323
Mapping interactions between disordered regions reveals promiscuity in biomolecular condensate formation
Gilat A , Dubrueil B , Levy ED.
2022
Molecular and environmental determinants of biomolecular condensate formation.
Villegas JA , Heidenreich M , Levy ED.
Nat Chem Biol
2022 Nov 18 ;
18
(
12 ):
1319 -
1329
How gene duplication diversifies the landscape of protein oligomeric state and function.
Mallik S , Tawfik DS , Levy ED.
Curr Opin Genet Dev
2022 Aug 22 ;
76
:
101966
Affinity and Valence Impact the Extent and Symmetry of Phase Separation of Multivalent Proteins.
Nandi SK , Österle D , Heidenreich M , Levy ED , Safran SA.
Phys Rev Lett
2022 Sep 1 ;
129
(
12 ):
128102
A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates.
Villegas JA , Levy ED.
Protein Sci
2022 Jul 1 ;
31
(
7 ):
e4361
Synthetic condensate size correlates with yeast replicative cell age.
Heidenreich M , Georgeson JM , Nadav Y , Levy ED.
MicroPubl Biol
2022 Jun 3 ;
2022
The modular cell gets connected.
Michnick SW , Levy ED.
Science
2022 Mar 10 ;
375
(
6585 ):
1093 -
1094
Mutant libraries reveal negative design shielding proteins from supramolecular self-assembly and relocalization in cells.
Garcia Seisdedos H , Levin T , Shapira G , Freud S , Levy ED.
Proc Natl Acad Sci U S A
2022 Feb 1 ;
119
(
5 ):
e2101117119
PDBe-KB: collaboratively defining the biological context of structural data.
PDBe-KB consortium.
Nucleic Acids Res
2022 Jan 1 ;
50
(
d1 ):
D534 -
D542
QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure.
Dey S , Prilusky J , Levy ED.
Front Mol Biosci
2022 Jan 5 ;
8
:
787510
2021
PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry.
Dey S , Levy ED.
Structure
2021 Sep 13 ;
29
(
11 ):
1303 -
1311.e3
Altered Protein Abundance and Localization Inferred from Sites of Alternative Modification by Ubiquitin and SUMO.
Ulman A , Levin T , Dassa B , Javitt A , Kacen A , Shmueli MD , Eisenberg-Lerner A , Sheban D , Fishllevich S , Levy ED , Merbl Y.
J Mol Biol
2021 Aug 28 ;
433
(
21 ):
167219
Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins.
Dubreuil B , Levy ED.
Front Mol Biosci
2021 Apr 30 ;
8
:
626729
"Structuromics": another step toward a holistic view of the cell.
Levy ED , Vogel C.
Cell
2021 Jan 1 ;
184
(
2 ):
301 -
303
2020
Not Going with the Flow: How Cells Adapt Internal Physics.
Garcia-Seisdedos H , Heidenreich M , Levy ED.
Cell
2020 Dec 1 ;
183
(
6 ):
1462 -
1463
Designer protein assemblies with tunable phase diagrams in living cells.
Heidenreich M , Georgeson JM , Locatelli E , Rovigatti L , Nandi SK , Steinberg A , Nadav Y , Shimoni E , Safran SA , Doye JPK , Levy ED.
Nat Chem Biol
2020 Jul 13 ;
16
(
9 ):
939 -
945
Proteomic analysis reveals the direct recruitment of intrinsically disordered regions to stress granules in S. cerevisiae .
Zhu M , Kuechler ER , Zhang J , Matalon O , Dubreuil B , Hofmann A , Loewen C , Levy ED , Gsponer J , Mayor T.
J Cell Sci
2020 Jul 9 ;
133
(
13 ):
jcs244657
PDBe-KB: a community-driven resource for structural and functional annotations.
PDBe-KB consortium.
Nucleic Acids Res
2020 Jan 1 ;
48
(
d1 ):
D344 -
D353
2019
Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions.
Dubreuil B , Matalon O , Levy ED.
J Mol Biol
2019 Aug 20 ;
431
(
24 ):
4978 -
4992
Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast.
Buchmuller BC , Herbst K , Meurer M , Kirrmaier D , Sass E , Levy ED , Knop M.
Nat Commun
2019 Jul 4 ;
10
(
1 ):
2960
Geometric description of self-interaction potential in symmetric protein complexes.
Empereur-Mot C , Garcia-Seisdedos H , Elad N , Dey S , Levy ED.
Sci Data
2019 May 17 ;
6
(
1 ):
64
Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering.
Garcia-Seisdedos H , Villegas JA , Levy ED.
Angew Chem Int Ed Engl
2019 Feb 20 ;
58
(
17 ):
5514 -
5531
Evolthon: A community endeavor to evolve lab evolution.
Kaminski Strauss S , Schirman D , Jona G , Brooks AN , Kunjapur AM , Nguyen Ba AN , Flint A , Solt A , Mershin A , Dixit A , Yona AH , Csörgő B , Busby BP , Hennig BP , Pál C , Schraivogel D , Schultz D , Wernick DG , Agashe D , Levi D , Zabezhinsky D , Russ D , Sass E , Tamar E , Herz E , Levy ED , Church GM , Yelin I , Nachman I , Gerst JE , Georgeson JM , Adamala KP , Steinmetz LM , Rübsam M , Ralser M , Klutstein M , Desai MM , Walunjkar N , Yin N , Aharon Hefetz N , Jakimo N , Snitser O , Adini O , Kumar P , Soo Hoo Smith R , Zeidan R , Hazan R , Rak R , Kishony R , Johnson S , Nouriel S , Vonesch SC , Foster S , Dagan T , Wein T , Karydis T , Wannier TM , Stiles T , Olin-Sandoval V , Mueller WF , Bar-On YM , Dahan O , Pilpel Y.
PLoS Biol
2019 Mar 29 ;
17
(
3 ):
e3000182
Author Correction: Genome-wide SWAp-Tag yeast libraries for proteome exploration.
Weill U , Yofe I , Sass E , Stynen B , Davidi D , Natarajan J , Ben-Menachem R , Avihou Z , Goldman O , Harpaz N , Chuartzman S , Kniazev K , Knoblach B , Laborenz J , Boos F , Kowarzyk J , Ben-Dor S , Zalckvar E , Herrmann JM , Rachubinski RA , Pines O , Rapaport D , Michnick SW , Levy ED , Schuldiner M.
Nat Methods
2019 Feb 1 ;
16
(
2 ):
205
YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries.
Dubreuil B , Sass E , Nadav Y , Heidenreich M , Georgeson JM , Weill U , Duan Y , Meurer M , Schuldiner M , Knop M , Levy ED.
Nucleic Acids Res
2019 Jan 1 ;
47
(
d1 ):
D1245 -
D1249
2018
Genome-wide SWAp-Tag yeast libraries for proteome exploration.
Weill U , Yofe I , Sass E , Stynen B , Davidi D , Natarajan J , Ben-Menachem R , Avihou Z , Goldman O , Harpaz N , Chuartzman S , Kniazev K , Knoblach B , Laborenz J , Boos F , Kowarzyk J , Ben-Dor S , Zalckvar E , Herrmann JM , Rachubinski RA , Pines O , Rapaport D , Michnick SW , Levy ED , Schuldiner M.
Nat Methods
2018 Jul 9 ;
15
(
8 ):
617 -
622
Genome-wide C-SWAT library for high-throughput yeast genome tagging.
Meurer M , Duan Y , Sass E , Kats I , Herbst K , Buchmuller BC , Dederer V , Huber F , Kirrmaier D , Štefl M , Van Laer K , Dick TP , Lemberg MK , Khmelinskii A , Levy ED , Knop M.
Nat Methods
2018 Jul 9 ;
15
(
8 ):
598 -
600
Reprogramming protein abundance fluctuations in single cells by degradation
Matalon O , Steinberg A , Sass E , Hausser J , Levy E.
PDB-wide identification of biological assemblies from conserved quaternary structure geometry.
Dey S , Ritchie DW , Levy ED.
Nat Methods
2017 Nov 20 ;
15
(
1 ):
67 -
72
Inferring and Using Protein Quaternary Structure Information from Crystallographic Data.
Dey S , Levy ED.
Methods Mol Biol
2018 Jan 1 ;
1764
:
357 -
375
2017
Proteins evolve on the edge of supramolecular self-assembly.
Garcia-Seisdedos H , Empereur-Mot C , Elad N , Levy ED.
Nature
2017 Aug 2 ;
548
(
7666 ):
244 -
247
Exhaustive search of linear information encoding protein-peptide recognition.
Kelil A , Kelil A , Dubreuil B , Levy ED , Michnick SW.
PLoS Comput Biol
2017 Apr 20 ;
13
(
4 ):
e1005499
2016
Protein-Fragment Complementation Assays for Large-Scale Analysis, Functional Dissection, and Spatiotemporal Dynamic Studies of Protein-Protein Interactions in Living Cells.
Michnick SW , Landry CR , Levy ED , Diss G , Ear PH , Kowarzyk J , Malleshaiah MK , Messier V , Tchekanda E.
Cold Spring Harb Protoc
2016 Nov 1 ;
2016
(
11 )
The Dihydrofolate Reductase Protein-Fragment Complementation Assay: A Survival-Selection Assay for Large-Scale Analysis of Protein-Protein Interactions.
Michnick SW , Levy ED , Landry CR , Kowarzyk J , Messier V.
Cold Spring Harb Protoc
2016 Nov 1 ;
2016
(
11 )
Young phosphorylation is functionally silent.
Matalon O , Dubreuil B , Levy ED.
Science
2016 Oct 1 ;
354
(
6309 ):
176 -
177
Evolution of domain-peptide interactions to coadapt specificity and affinity to functional diversity.
Kelil A , Levy ED , Michnick SW.
Proc Natl Acad Sci U S A
2016 Jun 17 ;
113
(
27 ):
E3862 -
E3871
2015
Decoding a neural circuit controlling global animal state in C. elegans.
Laurent P , Soltesz Z , Nelson GM , Chen C , Arellano-Carbajal F , Levy E , de Bono M
Symmetry breaking in homo-oligomers: the curious case of mega-hemocyanin.
Garcia Seisdedos H , Steinberg A , Levy ED.
Structure
2015 Jan 1 ;
23
(
1 ):
3 -
5
2014
Fast and accurate discovery of degenerate linear motifs in protein sequences.
Kelil A , Dubreuil B , Levy ED , Michnick SW.
PLoS One
2014 Sep 10 ;
9
(
9 ):
e106081
Different subunits belonging to the same protein complex often exhibit discordant expression levels and evolutionary properties.
Matalon O , Horovitz A , Levy ED.
Curr Opin Struct Biol
2014 Jun 1 ;
26
:
113 -
120
High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation.
Levy ED , Kowarzyk J , Michnick SW.
Cell Rep
2014 May 10 ;
7
(
4 ):
1333 -
1340
2013
Extracting insight from noisy cellular networks.
Landry CR , Levy ED , Abd Rabbo D , Tarassov K , Michnick SW.
Cell
2013 Nov 1 ;
155
(
5 ):
983 -
989
Structural, evolutionary, and assembly principles of protein oligomerization.
Levy ED , Teichmann S.
Prog Mol Biol Transl Sci
2013 Jan 1 ;
117
:
25 -
51
2012
Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.
Levy ED , De S , Teichmann SA.
Proc Natl Acad Sci U S A
2012 Nov 26 ;
109
(
50 ):
20461 -
20466
Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information.
Levy ED , Michnick SW , Landry CR.
Philos Trans R Soc Lond B Biol Sci
2012 Sep 1 ;
367
(
1602 ):
2594 -
2606
2010
A simple definition of structural regions in proteins and its use in analyzing interface evolution.
Levy ED.
J Mol Biol
2010 Sep 22 ;
403
(
4 ):
660 -
670
Molecular characterization of the evolution of phagosomes.
Boulais J , Trost M , Landry CR , Dieckmann R , Levy ED , Soldati T , Michnick SW , Thibault P , Desjardins M.
Mol Syst Biol
2010 Oct 1 ;
6
:
423
Homomeric protein complexes: evolution and assembly.
Venkatakrishnan AJ , Levy ED , Teichmann SA.
Biochem Soc Trans
2010 Aug 1 ;
38
(
4 ):
879 -
882
Systemizing the structures and structuring the system.
Levy ED , Teichmann SA.
Expert Rev Proteomics
2010 Jun 1 ;
7
(
3 ):
319 -
322
Cell signaling. Signaling through cooperation.
Levy ED , Landry CR , Michnick SW.
Science
2010 May 1 ;
328
(
5981 ):
983 -
984
2009
Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins.
Pechmann S , Levy ED , Tartaglia GG , Vendruscolo M.
Proc Natl Acad Sci U S A
2009 Jun 5 ;
106
(
25 ):
10159 -
10164
Weak functional constraints on phosphoproteomes.
Landry CR , Levy ED , Michnick SW.
Trends Genet
2009 Apr 6 ;
25
(
5 ):
193 -
197
Self-assembly and evolution of homomeric protein complexes.
Villar G , Wilber AW , Williamson AJ , Thiara P , Doye JP , Louis AA , Jochum MN , Lewis AC , Levy ED.
Phys Rev Lett
2009 Mar 18 ;
102
(
11 ):
118106
How perfect can protein interactomes be?
Levy ED , Landry CR , Michnick SW.
Sci Signal
2009 Mar 3 ;
2
(
60 ):
pe11
2008
Assembly reflects evolution of protein complexes.
Levy ED , Boeri Erba E , Robinson CV , Teichmann SA.
Nature
2008 Jun 18 ;
453
(
7199 ):
1262 -
1265
Evolution and dynamics of protein interactions and networks.
Levy ED , Pereira-Leal JB.
Curr Opin Struct Biol
2008 Apr 28 ;
18
(
3 ):
349 -
357
2007
PiQSi: protein quaternary structure investigation.
Levy ED.
Structure
2007 Nov 1 ;
15
(
11 ):
1364 -
1367
CORRIE: enzyme sequence annotation with confidence estimates.
Audit B , Levy ED , Gilks WR , Goldovsky L , Ouzounis CA.
BMC Bioinformatics
2007 May 22 ;
8 Suppl 4
:
S3
Evolution of protein complexes by duplication of homomeric interactions.
Pereira-Leal JB , Levy ED , Kamp C , Teichmann SA.
Genome Biol
2007 Jan 1 ;
8
(
4 ):
R51
2006
3D complex: a structural classification of protein complexes.
Levy ED , Pereira-Leal JB , Chothia C , Teichmann SA.
PLoS Comput Biol
2006 Oct 5 ;
2
(
11 ):
e155
The origins and evolution of functional modules: lessons from protein complexes.
Pereira-Leal JB , Levy ED , Teichmann SA.
Philos Trans R Soc Lond B Biol Sci
2006 Mar 1 ;
361
(
1467 ):
507 -
517
2005
Probabilistic annotation of protein sequences based on functional classifications.
Levy ED , Ouzounis CA , Gilks WR , Audit B.
BMC Bioinformatics
2005 Dec 14 ;
6
:
302
