On the Robustness of Maximum Entropy Relationships for Complexity Distributions of Nucleotide Sequences. - Peter Salamon; John C. Wootton; Andrzej K. Konopka; Lars Kai Hansen (Comput. Chem., 1993)

Statistics of Local Complexity in Amino Acid Sequences and Sequence Databases. - John C. Wootton; Scott Federhen (Comput. Chem., 1993)

A Gibbs Sampler for the Detection of Subtle Motifs in Multiple Sequences. - Charles E. Lawrence; Stephen F. Altschul; John C. Wootton; Mark S. Boguski; Andrew F. Neuwald; Jun S. Liu (HICSS (5), 1994)

Non-globular Domains in Protein Sequences: Automated Segmentation Using Complexity Measures. - John C. Wootton (Comput. Chem., 1994)

Evaluating the Effectiveness of Sequence Analysis Algorithms Using Measures of Relevant Information. - John C. Wootton (Comput. Chem., 1997)

A Global Compositional Complexity Measure for Biological Sequences: AT-rich and GC-rich Genomes Encode Less Complex Proteins. - Honghui Wan; John C. Wootton (Comput. Chem., 2000)

Algorithms for computing lengths of chains in integral partition lattices. - Honghui Wan; John C. Wootton (Theor. Comput. Sci., 2002)

Discovering Simple Regions in Biological Sequences Associated with Scoring Schemes. - Honghui Wan; Lugang Li; Scott Federhen; John C. Wootton (J. Comput. Biol., 2003)

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment. - Stephen F. Altschul; John C. Wootton; Elena Zaslavsky; Yi-Kuo Yu (PLoS Comput. Biol., 2010)