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

 

* joined first author # joined corresponding author

2021

Jodie Ouahed✳︎#, Judith R Kelsen✳︎#, Waldo A Spessott, Kameron Kooshesh, Maria L Sanmillan, Noor Dawany, Kathleen E Sullivan, Kathryn Hamilton, Voytek Slowik, Sergey Nejentsev, João Farela Neves, Helena Flores, Wendy K Chung, Ashley Wilson, Kwame Anyane Yeboa, Karen Wou, Preti Jain, Michael Field, Sophia Tollefson, Maiah H Dent, Dalin Li, Takeo Naito, Dermot P B McGovern, Andrew C Kwong, Faith Taliaferro, Jose Ordovas-Montanes, Bruce Horwitz, Daniel Kotlarz, Christoph Klein, Jonathan Evans, Jill Dorsey, Neil Warner, Abdul Elkadri, Aleixo M Muise, Jeffrey Goldsmith, Benjamin Thompson, Karin R Engelhardt, Andrew J Cant, Sophie Hambleton, Andrew Barclay, Agnes Toth-Petroczy, Dana Vuzman, Nikkola Carmichael, Corneliu Bodea, Christopher Cassa, Marcella Devoto, Richard L Maas, Edward M Behrens, Claudio G Giraudo#, Scott B Snapper#
Variants in STXBP3 Are Associated With Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation.
J Crohns Colitis, Art. No. 10.1093/ecco-jcc/jjab077 (2021)
DOI

2019

Anwoy Kumar Mohanty, Dana Vuzman, Laurent Francioli, Christopher Cassa, 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)
DOI
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Jose Velilla✳︎, Michael Mario Marchetti✳︎, Agnes Toth-Petroczy, Claire Grosgogeat, Alexis H Bennett, Nikkola Carmichael, Elicia Estrella, Basil T Darras, Natasha Y Frank, Joel B Krier, Rachelle Gaudet, Vandana A Gupta
Homozygous TRPV4 mutation causes congenital distal spinal muscular atrophy and arthrogryposis.
Neurol Genet, 5(2) Art. No. e312 (2019)
Open Access   DOI
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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)
DOI

2018

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)
DOI
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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)
DOI
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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)
DOI

2016

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)
DOI
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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)
Open Access   DOI

2015

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)
Open Access   DOI

2014

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)
DOI
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Agnes Tóth-Petróczy, Dan S Tawfik
Hopeful (protein InDel) monsters?
Structure, 22(6) 803-804 (2014)
DOI
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Agnes Tóth-Petróczy, Dan S Tawfik
The robustness and innovability of protein folds.
Curr. Opin. Struct. Biol., 26 131-138 (2014)
DOI

2013

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)
Open Access   DOI
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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)
DOI
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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)
DOI

2012

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

2011

Tzachi Hagai, Ariel Azia, Ágnes Tóth-Petróczy, Yaakov Levy
Intrinsic disorder in ubiquitination substrates.
J Mol Biol, 412(3) 319-324 (2011)
DOI
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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)
DOI

2009

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)
DOI

2008

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)
Open Access   DOI

2006

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)
DOI