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\begin{center}
{\Large {\bf Papers for STAT/BIOST550 class, 2007}} 
\end{center}

{\bf  This is an OLD list (2005). A somewhat updated one will appear soon,
and a more updated one later. The papers are listed first, and then the
full citations alphabetically after, on pages 3--5.\\
You do not have to choose a paper from this list. You may propose any paper,
but you do need to get your proposal approved.}

{\bf I Population-related issues}

\begin{rlist}{}

\item
\citeN{Ceppelinietal55} : the original ``Gene counting" paper

\item
\citeN{Clayton00} -- a review (as of that date) or
fine-scale disequilibrium mapping 

\item
\citeN{GrahamThompson98} -- disequilibrium mapping vi likelihoods

\item
\citeN{McpeekStrahs99}  -- another diseqilibrium mapping approach

\item
\citeN{Thompsonetal88} -- an interesting story about LD at three
tightly linked loci  

\item
\citeN{ThompsonNeel97} -- coalescent ancestry of a mutant allele and
implications for disequilibrium

\end{rlist}

{\bf II Gene ibd and use in sib pair analyses etc.}

\begin{rlist}{}

\item 
\citeN{BlackwelderElston85} -- classic paper on sib pair data.

\item
\citeN{BoehnkeCox97} -- errors in typing and relationship
and effects on sib pair studies.

\item
\citeN{Karigl81} recursive probabilities computations
  for more general IBD patterns

\item
\citeN{SpielmanEwens96} -- the original TDT test for linkage

\item
\citeN{SpielmanEwens98} -- the original extension TDT to S-TDT

\item
\citeN{Suarezetal78}  -- formalization of sib pair linkage tests

\item
\citeN{Thompson74} -- gene IBD for multiple individuals

\end{rlist}

\clearpage

{\bf III Linkage Analysis}

\begin{rlist}{}

\item
\citeN{Boehnke94} -- paper on limits of resolution of linkage mapping

\item 
\citeN{Botsteinetal80} -- the first ideas about genome-wide maps

\item
\citeN{ElstonStewart71}: a fundamental paper in computing likelihoods on 
pedigrees.

\item
\citeN{LanderBotstein87}: the basic ``Homozygosity mapping'' paper

\item
\citeN{LanderGreen87}; The orginal ``Mapmaker'' paper, which laid 
  methodological foundation for ``Genehunter'' programs.

\item
\citeN{Morton55} -- the classic introduction of the base-10 (!!!) lod
score

\item
\citeN{PloughmanBoehnke89} -- the basis of SIMLINK

\end{rlist}

{\bf  IV  And more .... -- not categorized yet}

\citeN{Boehnkeetal91} -- radiation hybrid mapping paper

\begin{rlist}

\item Schouten et al (Nov, 2005) Genetics -- combines haplotyping
   with "pedigrees" -- first solid study.

\item
\citeN{Smith76} : improvements in computing likelihoods on pedigrees
-- easier to understand than the more general Cannings et al. papers.

\item
\citeN{Thompson79}

\end{rlist}

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