EcoCyc: a comprehensive database resource for Escherichia coli. - Ingrid M. Keseler; Julio Collado-Vides; Socorro Gama-Castro; John Ingraham; Suzanne M. Paley; Ian T. Paulsen; Martín Peralta-Gil; Peter D. Karp (Nucleic Acids Res., 2005)

MetaCyc: a multiorganism database of metabolic pathways and enzymes. - Ron Caspi; Hartmut Foerster; Carol A. Fulcher; Rebecca Hopkinson; John Ingraham; Pallavi Kaipa; Markus Krummenacker; Suzanne M. Paley; John Pick; Seung Yon Rhee; Christophe Tissier; Peifen Zhang; et al. (Nucleic Acids Res., 2006)

CTArcade: learning computational thinking while training virtual characters through game play. - Tak Yeon Lee; Matthew Louis Mauriello; John Ingraham; Awalin Sopan; June Ahn; Benjamin B. Bederson (CHI Extended Abstracts, 2012)

Variational Inference for Sparse and Undirected Models. - John Ingraham; Debora S. Marks (ICML, 2017)

Learning Protein Structure with a Differentiable Simulator. - John Ingraham; Adam J. Riesselman; Chris Sander; Debora S. Marks (ICLR, 2019)

Generative Models for Graph-Based Protein Design. - John Ingraham; Vikas K. Garg 001; Regina Barzilay; Tommi S. Jaakkola (NeurIPS, 2019)

The EVcouplings Python framework for coevolutionary sequence analysis. - Thomas A. Hopf; Anna G. Green; Benjamin Schubert; Sophia Mersmann; Charlotta Schärfe; John Ingraham; Ágnes Tóth-Petróczy; Kelly Brock; Adam J. Riesselman; Perry Palmedo; Chan Kang; Robert P. Sheridan; et al. (Bioinform., 2019)