Research Groups

Selected Key Publications

Toth-Petroczy A*, Palmedo P*, John Ingraham JI, Thomas A. Hopf TA, Berger B, Sander C, Marks DS. Structured states of disordered proteins from genomic sequences. Cell 2016, 167(1):158-70.

Rockah-Shmuel L, Toth-Petroczy A, Sela A, Wurtzel O, Sorek R and Tawfik DS. The Occurrence and Bypass of Frame-shifting Insertion-Deletions (InDels) to give Functional Proteins are correlated. PloS Genetics 2013 (10) e1003882

Dellus-Gur E*, Toth-Petroczy A*, Elias M, Tawfik DS. What makes a protein fold amenable to functional innovations? Fold polarity and stability trade-offs. J Mol Biol 2013; 425(14):2609-21.

Toth-Petroczy A and Tawfik DS. Protein insertions and deletions enabled by neutral roaming in sequence space. Mol Biol Evol 2013; 30(4):761-71.

Tóth-Petróczy A and Tawfik DS. Slow protein evolutionary rates are dictated by surface-core association. PNAS 2011, 108(27):11151-6.

* equal contribution



Anwoy Kumar Mohanty, Dana Vuzman, Laurent Francioli, Christopher Cassa, Christopher null, Christopher null, Christopher null, Agnes Toth-Petroczy, Shamil Sunyaev
novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data.
Bioinformatics, 35(7) 1174-1180 (2019)
Mirna Bilus, Maja Semanjski, Marko Mocibob, Igor Zivkovic, Nevena Cvetesic, Dan S Tawfik, Agnes Toth-Petroczy, Boris Macek, Ita Gruic-Sovulj
On the Mechanism and Origin of Isoleucyl-tRNA Synthetase Editing against Norvaline.
J Mol Biol, 431(6) 1284-1297 (2019)


Maria Luisa Romero Romero, Fan Yang, Yu-Ru Lin, Agnes Toth-Petroczy, Igor N. Berezovsky, Alexander Goncearenco, Wen Yang, Alon Wellner, Fanindra Kumar-Deshmukh, Michal Sharon, David Baker, Gabriele Varani, Dan S Tawfik
Simple yet functional phosphate-loop proteins.
Proc Natl Acad Sci U.S.A., 115(51) 11943-11950 (2018)
Thomas A Hopf, Anna G Green, Benjamin Schubert, Sophia Mersmann, Charlotta P I Schärfe, John Ingraham, Agnes Toth-Petroczy, Kelly Brock, Adam J Riesselman, Perry Palmedo, ChulHee Kang, Robert Sheridan, Eli J Draizen, Christian Dallago, Chris Sander, Debora S Marks
The EVcouplings Python framework for coevolutionary sequence analysis.
Bioinformatics, Art. No. doi: 10.1093/bioinformatics/bty862 (2018)
Alireza Haghighi, Joel B Krier, Agnes Toth-Petroczy, Christopher Cassa, Natasha Y Frank, Nikkola Carmichael, Elizabeth Fieg, Andrew Bjonnes, Anwoy Kumar Mohanty, Lauren C Briere, Sharyn Lincoln, Stephanie Lucia, Vandana A Gupta, Onuralp Söylemez, Sheila Sutti, Kameron Kooshesh, Haiyan Qiu, Christopher J Fay, Victoria Perroni, Jamie Valerius, Meredith Hanna, Alexander Frank, Jodie Ouahed, Scott B Snapper, Angeliki Pantazi, Sameer S Chopra, Ignaty Leshchiner, Nathan O Stitziel, Anna Feldweg, Michael Mannstadt, Joseph Loscalzo, David A Sweetser, Eric Liao, Joan M Stoler, Catherine B Nowak, Pedro A Sanchez-Lara, Ophir D. Klein, Hazel Perry, Nikolaos A Patsopoulos, Soumya Raychaudhuri, Wolfram Goessling, Robert C Green, Christine E Seidman, Calum A MacRae, Shamil Sunyaev, Richard L Maas, Dana Vuzman, Dana null
An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery.
NPJ Genom Med, 3 21-21 (2018)


Agnes Toth-Petroczy, Perry Palmedo, John Ingraham, Thomas A Hopf, Bonnie Berger, Chris Sander, Debora S Marks
Structured States of Disordered Proteins from Genomic Sequences.
Cell, 167(1) 158-170 (2016)
Paola Laurino, Ágnes Tóth-Petróczy, Rubén Meana-Pañeda, Wei Lin, Donald G Truhlar, Dan S Tawfik
An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors.
PLoS Biol, 14(3) Art. No. e1002396 (2016)


Liat Rockah-Shmuel, Ágnes Tóth-Petróczy, Dan S Tawfik
Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations.
PLoS Comput Biol, 11(8) Art. No. e1004421 (2015)


Monika Fuxreiter, Ágnes Tóth-Petróczy, Daniel A Kraut, Andreas Matouschek, Roderick Y H Lim, Bin Xue, Lukasz Kurgan, Vladimir N Uversky
Disordered proteinaceous machines.
Chem. Rev., 114(13) 6806-6843 (2014)
Agnes Tóth-Petróczy, Dan S Tawfik
Hopeful (protein InDel) monsters?
Structure, 22(6) 803-804 (2014)
Agnes Tóth-Petróczy, Dan S Tawfik
The robustness and innovability of protein folds.
Curr. Opin. Struct. Biol., 26 131-138 (2014)


Liat Rockah-Shmuel, Ágnes Tóth-Petróczy, Asaf Sela, Omri Wurtzel, Rotem Sorek, Dan S Tawfik
Correlated occurrence and bypass of frame-shifting insertion-deletions (InDels) to give functional proteins.
PLoS Genet, 9(10) Art. No. e1003882 (2013)
Eynat Dellus-Gur, Agnes Toth-Petroczy, Mikael Elias, Dan S Tawfik
What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs.
J Mol Biol, 425(14) 2609-2621 (2013)
Agnes Tóth-Petróczy, Dan S Tawfik
Protein insertions and deletions enabled by neutral roaming in sequence space.
Mol Biol Evol, 30(4) 761-771 (2013)


Tzachi Hagai, Ágnes Tóth-Petróczy, Ariel Azia, Yaakov Levy
The origins and evolution of ubiquitination sites.
Mol Biosyst, 8(7) 1865-1877 (2012)


Tzachi Hagai, Ariel Azia, Ágnes Tóth-Petróczy, Yaakov Levy
Intrinsic disorder in ubiquitination substrates.
J Mol Biol, 412(3) 319-324 (2011)
Agnes Tóth-Petróczy, Dan S Tawfik
Slow protein evolutionary rates are dictated by surface-core association.
Proc Natl Acad Sci U.S.A., 108(27) 11151-11156 (2011)


Agnes Tóth-Petróczy, Istvan Simon, Monika Fuxreiter, Yaakov Levy
Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding.
J Am Chem Soc, 131(42) 15084-15085 (2009)


Agnes Tóth-Petróczy, Christopher J Oldfield, István Simon, Yuichiro Takagi, A. Keith Dunker, Vladimir N Uversky, Monika Fuxreiter
Malleable machines in transcription regulation: the mediator complex.
PLoS Comput Biol, 4(12) Art. No. e1000243 (2008)


Agnes Toth-Petroczy, Agnes Szilagyi, Zsolt Ronai, Maria Sasvari-Szekely, András Guttman
Validation of a tentative microsatellite marker for the dopamine D4 receptor gene by capillary gel electrophoresis.
J Chromatogr A, 1130(2) 201-205 (2006)