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

\noindent
{\bf Already selected papers}

\begin{rlist}{}

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

\item
{\bf Dao-Fu Dai:}
\citeN{Marthetal04} or \citeN{Pluzhnikovetal02}: Inference of human
history and demography from genetic data.

\item
{\bf  Patrick Danaher:}  
\citeN{Abecasisetal02} -- the original Merlin paper.

\item
{\bf Louis Grothaus:} 
\citeN{Clayton00} -- a review (as of that date) of
fine-scale disequilibrium mapping 

\item
{\bf Michal Juraska:}   
\citeN{Thompsonetal88} -- an interesting story about LD at three
tightly linked loci  ?

\item
{\bf Fredrik Karlsson:}   \\
\citeN{LuoLin03}-- information from using marker data in fitting genetic
models.

\item
{\bf Yi-Ting Lin:}  
\citeN{Schoutenetal05} -- combines haplotyping
   with "pedigrees" -- first solid study.

\item
{\bf Sarah Ng:}  
\citeN{AndersonWeir07} -- estimating relationships in structured populations.

\item
{\bf Brian Piening:}
\citeN{LanderGreen87}; The orginal ``Mapmaker'' paper, which laid 
methodological foundation for ``Genehunter'' programs.
                
\item
{\bf Terry Shen:}   
\citeN{Carlsonetal04} -- selecting SNPs for Association Analysis.

\item
{\bf Veronika Skrivankova:}   \citeN{StoreyTibshirani03} --
significance for genome-wide studies.

\item
{\bf Hui-Hun Tseng:} 
\citeN{Voight06} or \citeN{LiStephens03} --selection and/or recombination
in the human genome.

\item
{\bf Kayleen Williams:}  
\citeN{SpielmanEwens96} -- the original TDT test for linkage

\item
{\bf Quenna Wong:}  
\citeN{MeesterSjerps03} -- DNA Forensics -- a two-stain problem.

\item
{\bf Xiuwen Zheng:}  
\citeN{Abecasisetal05} -- Using LD in association mapping.

\end{rlist}


\clearpage

{\Large{\bf Papers still available}}

This list has been updated with info from my 2006 lists, but is still
somwhat rough.  It will improve.  Thank you for your patience.

Elizabeth.  11/13/2007.

{\bf I Population-related issues}

\begin{rlist}{}

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

\item
\citeN{Falushetal03} -- 
   another Stephens/Pritchard popn structure paper

\item
\citeN {Pritchardetal00} --
   the first Stephens/Pritchard popn structure paper


\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{DudoitSpeed00} -- a score test for linkage based on ibd in sib pairs

\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}

{\bf III Linkage Analysis}

\begin{rlist}{}

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

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

\item
\citeN{Georgeetal05} -- an application of new MCMC methods to estimate
lod scores on some extended pedigrees.

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

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

\end{rlist}

{\bf  IV  PHASE, Haplotyping, etc. }

\begin{rlist}{}

%% \item \citeN{Schoutenetal05} -- combines haplotyping
%%    with "pedigrees" -- first solid study.

\item
\citeN{StephensDonnelly03}-- a comparison of alternaive computational
algorithms/models for phasing

\item 
\citeN{Stephensetal01} -- Mathhew Stephens original PHASE paper 

\item
\citeN{ScheetStephens06} The FastPHASE paper 

\end{rlist}

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

\begin{rlist}{}

\item
\citeN{Kaplanetal95}  -- the first likelihood approach to
disequilibrium mapping.

\item
\citeN{McpeekStrahs99}


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

\item
\citeN{Thompson79}

\item
\citeN{LevyLahadetal95a}

\item
\citeN{LevyLahadetal95}

\end{rlist}

\clearpage
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\clearpage

{\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}

\begin{rlist}


\item
\citeN{Boehnkeetal91} -- radiation hybrid mapping paper

\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}

\clearpage
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