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He is the author of the first texts in the field of molecular evolution, Molecular Evolution and Fundamentals of Molecular Evolution (co-authored with Dan Graur), and an author on more than 200 peer-reviewed publications.
Emanuel Margoliash's first publication of sequence data for cytochrome c allowed comparison of the rates of molecular evolution for different proteins (cytochrome c seemed to evolve faster than hemoglobin), which Zuckerkandl discussed at a 1964 conference in Bruges.
In 1999, under the new joint editorship of Martin Kreitman (the current editor-in-chief), Takashi Gojobori, and Giorgio Bernardi, the journal made explicit its focus on "the fundamental issues in molecular evolution", to the exclusion of molecular phylogenetics (the purview of several other molecular evolution journals, most significantly Molecular Phylogenetics and Evolution) and origin of life research, except in cases that have "a special significance and impact".