### Abstract

- Top of page
- Abstract
- Introduction
- Milestones in Graphical Bioinformatics
- D/D Matrix
- Lattice Representations of DNA without Loss of Information
- Spectral Representation of DNA
- Graphical Approach to the Alignment of DNA
- Graphical Approach to the Alignment of Proteins
- Hormesis at the Proteome Level
- Proteomics Map and Their Numerical Characterization
- Canonical Labels for Maps
- Modified Labeling Algorithm for General Maps
- Characterization of Maps Based on Canonical Labels
- Dual of the Map
- Route to the Exact Solution to the Alignment of DNA and Proteins
- AAA Matrix
- Sequential AAA Matrix
- Exact Solution to the Protein Alignment Problem
- Comment on the Exact Solution of the Protein Alignment Problem
- Very Efficient Search for Nucleotide Alignment (VESNA)
- Milestones and Beyond
- Other Voices
- Other Directions
- Concluding Remarks
- Acknowledgments

After reviewing the field of graphical bioinformatics, we have selected two dozen of the most significant publications that represent milestones of graphical bioinformatics. These publications can be viewed as forming the backbone of graphical bioinformatics, the branch of bioinformatics that initiates analysis of DNA, RNA, and proteins by considering various graphical representations of these sequences. Graphical bioinformatics, a division of bioinformatics that analyzes sequences of DNA, RNA, proteins, and proteomics maps by developing and using tools of discrete mathematics and graph theory in particular, has expanded since the year 2000, although pioneering contributions date back to Hamory (1983) and Jeffrey (1990). We chronologically follow the development of graphical bioinformatics, without assuming that readers are familiar with discrete mathematics or graph theory. Readers unfamiliar with graph theory may even have some advantage over those who have been only superficially exposed to graph theory, inview of wide misconceptions and misinformation about chemical graph theory among quantum chemists, physical chemists, and medicinal chemists in past decades. © 2013 Wiley Periodicals, Inc.