The genome sequences of multiple species has enabled functional inferences from comparative
genomics. A primary objective is to infer biological functions from the conservation of …

Surveys of gene expression reveal extensive variability both within and between a wide range
of species. Compelling cases have been made for adaptive changes in gene regulation, …

Positive selection can be inferred from its effect on linked neutral variation. In the restrictive
case when there is no recombination, all linked variation is removed. If recombination is …

… We thank members of the Fay laboratory and S. Sunyaev for helpful suggestions, S.
Sunyaev for sending us the PolyPhen algorithm, and The International HapMap Consortium for …

Preterm birth affects approximately 1 out of every 10 births in the United States, leading to
high rates of mortality and long-term negative health consequences. To investigate the …

The distinction between deleterious, neutral, and adaptive mutations is a fundamental
problem in the study of molecular evolution. Two significant quantities are the fraction of DNA …

… Fay; CDB and PR from Red Star, Berkeley, California, United States; K1–K15 from N. Goto-…
Sniegowski and members of the Fay lab for comments and suggestions. We also thank B. …

Although positive selection has been detected in many genes, its overall contribution to
protein evolution is debatable 1 . If the bulk of molecular evolution is neutral, then the ratio of …

… Gasch and members of the Fay laboratory for comments and discussions. We also thank two
… Doniger SW, Fay JC (2007) Frequent gain and loss of functional transcription factor binding …

Whether or not humans have experienced a reduction in population size in the recent past
is a controversial issue germane to the origin and colonization of our own species (Stringer …