CoC: a database of universally conserved residues in protein folds. - Jason E. Donald; Isaac A. Hubner; Veronica Rotemberg; Eugene I. Shakhnovich; Leonid A. Mirny (Bioinform., 2005)

Intricate Knots in Proteins: Function and Evolution. - Peter Virnau; Leonid A. Mirny; Mehran Kardar (PLoS Comput. Biol., 2006)

Protein knot server: detection of knots in protein structures. - Grigory Kolesov; Peter Virnau; Mehran Kardar; Leonid A. Mirny (Nucleic Acids Res., 2007)

Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering. - Carlos Gomez-Uribe; George C. Verghese; Leonid A. Mirny (PLoS Comput. Biol., 2007)

A Stevedore's Protein Knot. - Daniel Bölinger; Joanna I. Sulkowska; Hsiao-Ping Hsu; Leonid A. Mirny; Mehran Kardar; José N. Onuchic; Peter Virnau (PLoS Comput. Biol., 2010)

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization. - Marc A. Martí-Renom; Leonid A. Mirny (PLoS Comput. Biol., 2011)

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions. - Boryana Doyle; Geoffrey Fudenberg; Maxim Imakaev; Leonid A. Mirny (PLoS Comput. Biol., 2014)

History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. - Ekaterina Khrameeva; Geoffrey Fudenberg; Mikhail S. Gelfand; Leonid A. Mirny (J. Bioinform. Comput. Biol., 2016)

Cooler: scalable storage for Hi-C data and other genomically labeled arrays. - Nezar Abdennur; Leonid A. Mirny (Bioinform., 2020)