23.6k citations · 23.7k across the 5 of their papers we have counts for
5 papers
Phylogenetic Corrections and Higher-Order Sequence Statistics in Protein Families: The Potts Model vs MSA Transformer
Kisan Khatri, Ronald M. Levy, Allan Haldane
Recent generative learning models applied to protein multiple sequence alignment (MSA) datasets include simple and interpretable physics-based Potts covariation models and other ma…
Generative Capacity of Probabilistic Protein Sequence Models
Francisco McGee, Quentin Novinger, Ronald M. Levy +2
Potts models and variational autoencoders (VAEs) have recently gained popularity as generative protein sequence models (GPSMs) to explore fitness landscapes and predict the effect…
Array Programming with NumPy
Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt +23
Array programming provides a powerful, compact, expressive syntax for accessing, manipulating, and operating on data in vectors, matrices, and higher-dimensional arrays. NumPy is t…
Influence of Multiple Sequence Alignment Depth on Potts Statistical Models of Protein Covariation
Allan Haldane, Ronald M. Levy
Potts statistical models have become a popular and promising way to analyze mutational covariation in protein Multiple Sequence Alignments (MSAs) in order to understand protein str…
Biophysical Fitness Landscapes for Transcription Factor Binding Sites
Allan Haldane, Michael Manhart, Alexandre V. Morozov
Evolutionary trajectories and phenotypic states available to cell populations are ultimately dictated by intermolecular interactions between DNA, RNA, proteins, and other molecular…