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\begin{center}
{\Large {\bf Papers for STAT 550 (DL) class, 2010}} 
\end{center}

{\Large{\bf Papers available}}

This list is neither necessary nor sufficient.

That is, it is a somewhat random collection compiled over the years of
teaching this class.  It contains some papers that were a reasonable choice
for a particular student, given their background or research direction,
but bear little relationship to the details of the 550 course.  Not all 
choices on the list are reasonable for all students.

Also, additions are welcome -- if you have a particular area/paper you would
like to choose, feel free to suggest.

The papers are listed first, somewhat sorted by category.  The references
follow on the last four pages (approx.)

{\bf Please note: in a given course offering, no two students may choose
the same paper.  To be fair, I operate on a first-come first-served basis,
although I have occasionally negotiated switches.\\
\centerline{
So if you have a particular choice you want, let me know right away.} }

\vspace*{1.0in}
{\bf I Population-related issues/studies, including LD and LD mapping}

\begin{rlist}{}

\item
\citeN{Abecasisetal05} -- Using LD in association mapping.

\item
\citeN{Carlsonetal04} -- selecting SNPs for Association Analysis.

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

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

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

\item
\citeN{Marthetal04} or \citeN{Pluzhnikovetal02}: Inference of human
history and demography from genetic data.

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

\item
\citeN{StoreyTibshirani03} -- significance for genome-wide studies.

\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

\item
\citeN{Voight06} or \citeN{LiStephens03} --selection and/or recombination
in the human genome.


\end{rlist}

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

\begin{rlist}{}

\item
\citeN{AndersonWeir07} -- estimating relationships in structured populations.

\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 and Segregation Analysis}

\begin{rlist}{}

\item
\citeN{Abecasisetal02} -- the original Merlin paper.

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


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

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

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


\end{rlist}

{\bf  IV  PHASE, Haplotyping, etc. }

\begin{rlist}{}

\item \citeN{Browning06} -- a newer and better model for haplotype clustering

\item \citeN{BrowningBrowning07} -- use of this model in imputation

\item \citeN{Browning08} - and in inferences for GWAS

\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}

\clearpage

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