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2025	The Impact of Disorder–Order Switching on Protein Sequence Evolution Biochemistry Avital Sharir-Ivry, Yu Xia
2025	CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure Bioinformatics Lucas Chivot, Noé Mathieux, Anna Cosson, Antoine Bridier-Nahmias, Loïc Favennec, Jean-Christophe Gelly, Jérôme Clain, Romain Coppée
2024	Improved prediction of site‐rates from structure with averaging across homologs Protein Science Christoffer Norn, Fábio Oliveira, Ingemar André
2023	Toxic Determination of Cry11 Mutated Proteins Obtained Using Rational Design and Its Computational Analysis International Journal of Molecular Sciences Miguel O. Suárez-Barrera, Diego F. Herrera-Pineda, Paola Rondón-Villarreal, Efraín Hernando Pinzón-Reyes, Rodrigo Ochoa, Lydia Visser, Nohora Juliana Rueda-Forero
2022	Evolution of Amino Acid Propensities under Stability-Mediated Epistasis Molecular Biology and Evolution Noor Youssef, Edward Susko, Andrew J Roger, Joseph P Bielawski
2022	ZINC40099027 promotes monolayer circular defect closure by a novel pathway involving cytosolic activation of focal adhesion kinase and downstream paxillin and ERK1/2 Cell and Tissue Research Sema Oncel, Marc D. Basson
2022	Possible Co-Evolution of Polyglutamine and Polyproline in Huntingtin Protein: Proline-Rich Domain as Transient Folding Chaperone The Journal of Physical Chemistry Letters Leili Zhang, Hongsuk Kang, Jose Manuel Perez-Aguilar, Ruhong Zhou
2021	Evolutionary coupling range varies widely among enzymes depending on selection pressure Biophysical Journal Julian Echave
2021	Quantifying evolutionary importance of protein sites: A Tale of two measures PLOS Genetics Avital Sharir-Ivry, Yu Xia
2021	Learning the local landscape of protein structures with convolutional neural networks Journal of Biological Physics Anastasiya V. Kulikova, Daniel J. Diaz, James M. Loy, Andrew D. Ellington, Claus O. Wilke
2020	Consequences of Stability-Induced Epistasis for Substitution Rates Molecular Biology and Evolution Noor Youssef, Edward Susko, Joseph P Bielawski
2020	Computational reconstruction of atomistic protein structures from coarse-grained models Computational and Structural Biotechnology Journal Aleksandra E. Badaczewska-Dawid, Andrzej Kolinski, Sebastian Kmiecik
2019	Evolutionary couplings detect side-chain interactions PeerJ Adam J. Hockenberry, Claus O. Wilke
2019	Analyzing Change in Protein Stability Associated with Single Point Deletions in a Newly Defined Protein Structure Database Journal of Proteome Research Anupam Banerjee, Yaakov Levy, Pralay Mitra
2019	Beyond Stability Constraints: A Biophysical Model of Enzyme Evolution with Selection on Stability and Activity Molecular Biology and Evolution Julian Echave
2019	The Site-Specific Amino Acid Preferences of Homologous Proteins Depend on Sequence Divergence Genome Biology and Evolution Evandro Ferrada
2019	Non-catalytic Binding Sites Induce Weaker Long-Range Evolutionary Rate Gradients than Catalytic Sites in Enzymes Journal of Molecular Biology Avital Sharir-Ivry, Yu Xia
2019	Using Pseudoenzymes to Probe Evolutionary Design Principles of Enzymes Evolutionary Bioinformatics Avital Sharir-Ivry, Yu Xia
2019	Fitness Effects of Single Amino Acid Insertions and Deletions in TEM-1 β-Lactamase Journal of Molecular Biology Courtney E. Gonzalez, Paul Roberts, Marc Ostermeier
2018	Relationships between residue Voronoi volume and sequence conservation in proteins Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Jen-Wei Liu, Chih-Wen Cheng, Yu-Feng Lin, Shao-Yu Chen, Jenn-Kang Hwang, Shih-Chung Yen
2018	Nature of Long-Range Evolutionary Constraint in Enzymes: Insights from Comparison to Pseudoenzymes with Similar Structures Molecular Biology and Evolution Avital Sharir-Ivry, Yu Xia
2018	Measuring evolutionary rates of proteins in a structural context F1000Research Dariya K. Sydykova, Benjamin R. Jack, Stephanie J. Spielman, Claus O. Wilke
2017	On the relationship between residue structural environment and sequence conservation in proteins Proteins: Structure, Function, and Bioinformatics Jen-Wei Liu, Jau-Ji Lin, Chih-Wen Cheng, Yu-Feng Lin, Jenn-Kang Hwang, Tsun-Tsao Huang
2017	Measuring evolutionary rates of proteins in a structural context F1000Research Dariya K. Sydykova, Benjamin R. Jack, Stephanie J. Spielman, Claus O. Wilke
2017	The Impact of Native State Switching on Protein Sequence Evolution Molecular Biology and Evolution Avital Sharir-Ivry, Yu Xia
2017	Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein PLOS ONE Eleisha L. Jackson, Stephanie J. Spielman, Claus O. Wilke
2017	Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence Annual Review of Biophysics Julian Echave, Claus O. Wilke
2016	Causes of evolutionary rate variation among protein sites Nature Reviews Genetics Julian Echave, Stephanie J. Spielman, Claus O. Wilke
2016	Alpha Helices Are More Robust to Mutations than Beta Strands PLOS Computational Biology György Abrusán, Joseph A. Marsh
2016	Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes PLOS Biology Benjamin R. Jack, Austin G. Meyer, Julian Echave, Claus O. Wilke
2016	Quantifying side-chain conformational variations in protein structure Scientific Reports Zhichao Miao, Yang Cao
2016	Intermediate divergence levels maximize the strength of structure–sequence correlations in enzymes and viral proteins Protein Science Eleisha L. Jackson, Amir Shahmoradi, Stephanie J. Spielman, Benjamin R. Jack, Claus O. Wilke
2016	Dissecting the roles of local packing density and longer‐range effects in protein sequence evolution Proteins: Structure, Function, and Bioinformatics Amir Shahmoradi, Claus O. Wilke
2015	Genetically modified proteins: functional improvement and chimeragenesis Bioengineered Larissa Balabanova, Vasily Golotin, Anna Podvolotskaya, Valery Rasskazov
2015	The utility of protein structure as a predictor of site-wise dN/dSvaries widely among HIV-1 proteins Journal of The Royal Society Interface Austin G. Meyer, Claus O. Wilke
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