A succinct list of references (under construction):
1. Molecular studies of evolution: A source of novel statistical problems.
J Neyman. in Statistical Decision Theory and Related Topics ed SS Gupta
and J Yackel, 1--27, Academic Press, New York (1971).
2. Inferring Phylogenies J Felsenstein, Sinauer Associates, Inc. (2004).
I am also developing interests in statistics education and health policies. How can statistics be taught effectively to students of different levels? How much mathematics should be included (roughly speaking, enough to make arguments sharp, but not so much as to obscure the conceptual subtleties)? How can the administration of healthcare, in particular, prescription drugs, be improved, so that it produces better clinical outcomes at lower financial costs?
A succinct list of references (under construction):
1. Statistics, 3e D Freedman, R Pisani and R Purves, WW Norton &
Company, Inc (1997).
2. Powerful Medicines: the benifits, risks, and costs of prescription drugs
J Avorn, AA Knorf (2004).
2. Association between divergence and interspersed repeats in mammalian
noncoding genomic DNA. F Chiaromonte, S Yang, L Elnitski, VB Yap, W Miller
and RC Hardison. Proceedings of the National Academy of Sciences of the
USA, 98:14503--14508 (2001).
3. Scoring pairwise genomic sequence alignments. F Chiaromonte, VB Yap and
W Miller. Proceedings of the Pacific Symposium on Biocomputing,
115--126 (2002).
4. Modeling genomic DNA base substitution. VB Yap and TP Speed. Proceedings of the American Statistical Association, 3855--3864 (2002).
5. Modeling DNA base substitution in large genomic regions from two organisms.
VB Yap and TP Speed. Journal of Molecular Evolution, 58:12--18
(2004).
6. Identification of evolutionary hotspots in the rodent genomes. VB Yap and
L Pachter. Genome Research, 14:574--579 (2004).
7. Genome sequence of the brown Norway rat yields insights into mammalian
evolution. The Rat Genome Sequencing Consortium. Nature, 428:493--521 (2004).
8. Comparative immunopeptidomics of humans and their pathogens. S Istrail, L
Florea, BV Halldorsson, O Kohlbacher, RS Schwartz, VB Yap, JW Yewdell and SL
Hoffman Proceedings of the National Academy of Sciences of the USA,
101:13268--13272 (2004).
9. Rooting a phylogenetic tree with nonreversible substitution models. VB Yap
and TP Speed. BMC Evolutionary Biology, 5:2 (2005).
10. Estimating substitution matrices. VB Yap and TP Speed. To appear in
Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen.
2. Developing a complete phylogenetics package with nonreversible substitution processes.
3. I am also interested in methods to incorporate gaps into various activities in molecular evolution, e.g., the estimation of distances, and of rates of evolution, and phylogenetic analysis. Some notes on the birth-and-death process are collected here.