A DNA and restriction enzyme implementation of Turing machines. - Paul Wilhelm Karl Rothemund (DNA Based Computers, 1995)

A Sticker-Based Model for DNA Computation. - Sam T. Roweis; Erik Winfree; Richard Burgoyne; Nickolas V. Chelyapov; Myron F. Goodman; Paul W. K. Rothemund; Leonard M. Adleman (J. Comput. Biol., 1998)

On Applying Molecular Computation to the Data Encryption Standard. - Leonard M. Adleman; Paul W. K. Rothemund; Sam T. Roweis; Erik Winfree (J. Comput. Biol., 1999)

Solution of a Satisfiability Problem on a Gel-Based DNA Computer. - Ravinderjit S. Braich; Cliff Johnson; Paul W. K. Rothemund; Darryl Hwang; Nickolas V. Chelyapov; Leonard M. Adleman (DNA Computing, 2000)

The program-size complexity of self-assembled squares (extended abstract). - Paul W. K. Rothemund; Erik Winfree (STOC, 2000)

Using lateral capillary forces to compute by self-assembly. - Paul W. K. Rothemund (Proc. Natl. Acad. Sci. USA, 2000)

Combinatorial optimization problems in self-assembly. - Leonard M. Adleman; Qi Cheng 001; Ashish Goel; Ming-Deh A. Huang; David Kempe 001; Pablo Moisset de Espanés; Paul W. K. Rothemund (STOC, 2002)

Self-Assembled Circuit Patterns. - Matthew Cook 001; Paul W. K. Rothemund; Erik Winfree (DNA, 2003)

Design of DNA origami. - Paul W. K. Rothemund (ICCAD, 2005)

Scaffolded DNA Origami: from Generalized Multicrossovers to Polygonal Networks. - Paul W. K. Rothemund (Nanotechnology: Science and Computation, 2006)

Beyond Watson and Crick: Programming DNA self-assembly for nanofabrication. - Paul W. K. Rothemund (NEMS, 2012)

Progressive Alignment of Shapes. - Ashwin Gopinath; David G. Kirkpatrick; Paul W. K. Rothemund; Chris Thachuk (CCCG, 2016)