Explanipedia

Topiary: Pruning the manual labor from ancestral sequence reconstruction Open

Kona N. Orlandi, Sophia R. Phillips, Zachary R. Sailer, Joseph Harman, Michael J. Harms · 2022

Ancestral sequence reconstruction (ASR) is a powerful tool to study the evolution of proteins and thus gain deep insight into the relationships among protein sequence, structure, and function. A major barrier to its broad use is the comple…

Comparative Analysis and Ancestral Sequence Reconstruction of Bacterial Sortase Family Proteins Generates Functional Ancestral Mutants with Different Sequence Specificities Open

Jordan D. Valgardson, Sarah A. Struyvenberg, Zachary R. Sailer, Isabel M. Piper, Justin E. Svendsen , et al. · 2022

Gram-positive bacteria are some of the earliest known life forms, diverging from gram-negative bacteria 2 billion years ago. These organisms utilize sortase enzymes to attach proteins to their peptidoglycan cell wall, a structural feature …

Exploring the Evolutionary History of Kinetic Stability in the α-Lytic Protease Family Open

Charlotte Nixon, Shion A. Lim, Zachary R. Sailer, Ivan N. Zheludev, Christine L. Gee , et al. · 2021

In addition to encoding the tertiary fold and stability, the primary sequence of a protein encodes the folding trajectory and kinetic barriers that determine the speed of folding. How these kinetic barriers are encoded is not well understo…

Inferring a complete genotype-phenotype map from a small number of measured phenotypes Open

Zachary R. Sailer, Sarah H. Shafik, Robert L. Summers, Alex Joule, Alice Patterson‐Robert , et al. · 2020

Understanding evolution requires detailed knowledge of genotype-phenotype maps; however, it can be a herculean task to measure every phenotype in a combinatorial map. We have developed a computational strategy to predict the missing phenot…

Exploring the evolutionary history of kinetic stability in the alpha-lytic protease family Open

Charlotte Nixon, Shion A. Lim, Zachary R. Sailer, Ivan N. Zheludev, Christine L. Gee , et al. · 2020

In addition to encoding the final tertiary fold and stability, the primary sequence of a protein encodes the folding trajectory and kinetic barriers that determines the speed of folding. How these kinetic barriers are encoded by the sequen…

eaton-lab/toytree: v1.0 publication release Open

Eaton Lab, Deren A. R. Eaton, Zachary R. Sailer · 2019

This version corresponds to the final submission of the toytree manuscript to Methods in Ecology and Evolution.

jupyter/jupyter-book: v0.5 Open

Chris Holdgraf, Jan Kleinert, Elizabeth DuPré, Mainak Jas, Alexander Morley , et al. · 2019

Create an online book with Jupyter Notebooks and Jekyll

pyjanitor: A Cleaner API for Cleaning Data Open

Eric Ma, Zachary Barry, S. L. Zuckerman, Zachary R. Sailer · 2019

The pandas library has become the de facto library for data wrangling in the Python programming language. However, inconsistencies in the pandas application programming interface (API), while idiomatic due to historical use, prevent use of…

Uninterpretable interactions: epistasis as uncertainty Open

Zachary R. Sailer, Michael J. Harms · 2018

Epistasis is a common feature of genotype-phenotype maps. Understanding the patterns of epistasis is critical for predicting unmeasured phenotypes, explaining evolutionary trajectories, and for inferring the biological mechanisms that dete…

Molecular Ensembles Shape Evolutionary Trajectories Open

Michael J. Harms, Zachary R. Sailer, Lucas C. Wheeler · 2018

Using Ancestral Proteins to Probe the Thermodynamic and Kinetic Properties of the Alpha-Lytic Protease Family Open

Charlotte Nixon, Shion A. Lim, Zachary R. Sailer, Michael J. Harms, Susan Marqusee · 2018

Molecular ensembles make evolution unpredictable Open

Zachary R. Sailer, Michael J. Harms · 2017

Significance A long-standing goal in evolutionary biology is predicting evolution. Here, we show that the architecture of macromolecules fundamentally limits evolutionary predictability. Under physiological conditions, macromolecules, like…

High-order epistasis shapes evolutionary trajectories Open

Zachary R. Sailer, Michael J. Harms · 2017

High-order epistasis-where the effect of a mutation is determined by interactions with two or more other mutations-makes small, but detectable, contributions to genotype-fitness maps. While epistasis between pairs of mutations is known to …

Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps Open

Zachary R. Sailer, Michael J. Harms · 2017

High-order epistasis has been observed in many genotype-phenotype maps. These multi-way interactions between mutations may be useful for dissecting complex traits and could have profound implications for evolution. Alternatively, they coul…

harmslab/epistasis: Added unlicense Open

Zachary R. Sailer, M. Harms · 2017

First release with DOI.

Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps Open

Zachary R. Sailer, Michael J. Harms · 2016

High-order epistasis has been observed in many genotype-phenotype maps. These multi-way interactions between mutations may be useful for dissecting complex traits and could have profound implications for evolution. Alternatively, they coul…

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