** denotes specific proposed papers
-- denotes proposed general topics.

Population Genetics
===================

** Population genetic basis of haplotype blocks in the 5q31 region.
    Anderson and Slatkin.   AJHG  74: 40-49.  2004

** Informativeness of genetic markers for inference of ancestry
   Rosenberg, Li, Ward, and Pritchard  AJHG 73: 1402-1422.  2003.

-- genetic variation across populations
    -- use of cross-species sequence variation to make inferences about
       biologically interesting phenomena (recombination, selection,
        functional elements, etc.)
** Clark et al. (2003)
   Inferring non-neutral evolutions from human-chimp-mouse
   orthologous gene trios.
   Science 302 1960-1963.

-- genetic variation within populations
     -- haplotype inference and analysis methods


Association tests
=================

** John Wakeley and Sabin Lessard
    Theory of the Effects of Population Structure and Sampling on 
    Patterns of Linkage Disequilibrium Applied to Genomic Data From Humans
      Genetics 2003 164: 1043-1053. 

http://www.genetics.org/cgi/reprint/162/2/987.pdf
Gilean A. T. McVean
A Genealogical Interpretation of Linkage Disequilibrium
Genetics, Vol. 162, 987-991, 

2002: Nature Genetics 32: 135-142
Human genome sequence variation and the influence of gene history, mutation and recombination 
D E Reich, S F Schaffner, M J Daly, G McVean, J C Mullikin, J M Higgins, D J Richter, E S Lander & D Altshuler

** Score tests for association between traits and haplotypes when
    linkage phase is ambiguous.
    Schaid et al.  AJHG  70: 425-434.      2002

** Haplotype block structure and its application to association studies:
    power and study designs.
   Zhang, Calabrese, Nordberg, Sun   AJHG 71: 1386-1394.  2002



Complex diseases:
================

** The allelic architecture of human disease genes:
    common disease -- common variant.  Or not?
    Pritchard and Cox.  Hum.Molec.Genet.  11: 2417-2423.  2002

--Allelic heterogeneity: implications for complex disease;
       methods to detect/methods that incorporate it

-- linkage analysis ideas for complex traits
       that involve biochemistry

Am. J. Hum. Genet., 73:711-719, 2003
http://www.journals.uchicago.edu/AJHG/journal/issues/v73n4/40440/40440.html
"Are We There Yet?": Deciding When One Has Demonstrated Specific Genetic
Causation in Complex Diseases and Quantitative Traits
(editorial)

Am. J. Hum. Genet., 72:1084-1087, 2003
http://www.journals.uchicago.edu/AJHG/journal/issues/v72n5/034908/034908.html
The Emperor's New Methods
(editorial)

Genetic mapping
===============

-- QTL mapping
-- LD mapping
-- ...


Software/algorithms
====================

-- Overview of analysis software.

-- Understanding linkage packages
        -- exact vs approximate
        -- inside the algorithm
        -- what they can and cannot do

DNA sequence stuff
==================

-- sequence analysis issues
      -- what is being done with the Human Genome Project
      -- "exon/intron stuff"
      -- gene finding

Microarrays
===========


-- Microarray data analysis