deletions | additions
diff --git a/bibliography/biblio.bib b/bibliography/biblio.bib
index 15e7db9..ff4fa89 100644
--- a/bibliography/biblio.bib
+++ b/bibliography/biblio.bib
...
@article{Zou_2005,
doi = {10.1111/j.1467-9868.2005.00503.x},
url = {http://dx.doi.org/10.1111/j.1467-9868.2005.00503.x},
year = {2005},
month = {apr},
publisher = {Wiley-Blackwell},
volume = {67},
number = {2},
pages = {301--320},
author = {Zou, Hui and Hastie, Trevor},
title = {{Regularization and variable selection via the elastic net}},
journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
}
@article{Mailund_2006,
doi = {10.1186/1471-2105-7-454},
url = {http://dx.doi.org/10.1186/1471-2105-7-454},
year = {2006},
publisher = {Springer Science $\mathplus$ Business Media},
volume = {7},
number = {1},
pages = {454},
author = {Mailund, Thomas and Besenbacher, S{\o}ren and Schierup, Mikkel H},
journal = {{BMC} Bioinformatics},
}
@article{Eichler_2010,
doi = {10.1038/nrg2809},
url = {http://dx.doi.org/10.1038/nrg2809},
year = {2010},
month = {jun},
publisher = {Nature Publishing Group},
volume = {11},
number = {6},
pages = {446--450},
author = {Eichler, Evan E and Flint, Jonathan and Gibson, Greg and Kong, Augustine and Leal, Suzanne M and Moore, Jason H and Nadeau, Joseph H},
title = {{Missing heritability and strategies for finding the underlying causes of complex disease}},
journal = {Nat Rev Genet},
}
@article{Schork_2009,
doi = {10.1016/j.gde.2009.04.010},
url = {http://dx.doi.org/10.1016/j.gde.2009.04.010},
year = {2009},
month = {jun},
publisher = {Elsevier {BV}},
volume = {19},
number = {3},
pages = {212--219},
author = {Schork, Nicholas J and Murray, Sarah S and Frazer, Kelly A and Topol, Eric J},
title = {{Common vs. rare allele hypotheses for complex diseases}},
journal = {Current Opinion in Genetics {\&} Development},
}
@article{Pritchard_2001,
doi = {10.1086/321272},
url = {http://dx.doi.org/10.1086/321272},
year = {2001},
month = {jul},
publisher = {Elsevier {BV}},
volume = {69},
number = {1},
pages = {124--137},
author = {Pritchard, Jonathan K},
title = {{Are Rare Variants Responsible for Susceptibility to Complex Diseases?}},
journal = {The American Journal of Human Genetics},
}
@article{Li_2008,
doi = {10.1016/j.ajhg.2008.06.024},
url = {http://dx.doi.org/10.1016/j.ajhg.2008.06.024},
year = {2008},
month = {sep},
publisher = {Elsevier {BV}},
volume = {83},
number = {3},
pages = {311--321},
author = {Li, Bingshan and Leal, Suzanne M},
title = {{Methods for Detecting Associations with Rare Variants for Common Diseases: Application to Analysis of Sequence Data}},
journal = {The American Journal of Human Genetics},
}
@article{Excoffier_2011,
doi = {10.1093/bioinformatics/btr124},
url = {http://dx.doi.org/10.1093/bioinformatics/btr124},
year = {2011},
month = {mar},
publisher = {Oxford University Press ({OUP})},
volume = {27},
number = {9},
pages = {1332--1334},
author = {Excoffier, Laurent and Foll, Matthieu},
title = {{fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios}},
journal = {Bioinformatics},
}
@article{Excoffier_2013,
doi = {10.1371/journal.pgen.1003905},
url = {http://dx.doi.org/10.1371/journal.pgen.1003905},
...
volume = {9},
number = {10},
pages = {e1003905},
author =
{Laurent Excoffier {Excoffier, Laurent and
Dupanloup, Isabelle
Dupanloup and
Huerta-S{\'a}nchez, Emilia
Huerta-S{\~{A}}{\textexclamdown}nchez and
Sousa, Vitor
C. Sousa C and
Matthieu Foll}, Foll, Matthieu},
editor = {Joshua M. Akey},
title = {{Robust Demographic Inference from Genomic and {SNP} Data}},
journal = {{PLoS} Genetics},
}
@article{Tenesa_2007,
doi = {10.1101/gr.6023607},
url = {http://dx.doi.org/10.1101/gr.6023607},
year = {2007},
month = {mar},
publisher = {Cold Spring Harbor Laboratory Press},
volume = {17},
number = {4},
pages = {520--526},
author = {A. Tenesa and P. Navarro and B. J. Hayes and D. L. Duffy and G. M. Clarke and M. E. Goddard and P. M. Visscher},
title = {{Recent human effective population size estimated from linkage disequilibrium}},
journal = {Genome Research},
}
@article{Price_2010,
doi =
{10.1016/j.ajhg.2010.05.014}, {10.1016/j.ajhg.2010.04.005},
url =
{http://dx.doi.org/10.1016/j.ajhg.2010.05.014}, {http://dx.doi.org/10.1016/j.ajhg.2010.04.005},
year = {2010},
month = {jun},
publisher = {Elsevier {BV}},
volume = {86},
number = {6},
pages =
{982}, {832--838},
author =
{Alkes L. Price {Price, Alkes L and
Kryukov, Gregory
V. Kryukov V and
Paul I.W. de
Bakker Bakker, Paul IW and
Purcell, Shaun
M. Purcell M and
Staples, Jeff
Staples and
Wei, Lee-Jen
Wei and
Sunyaev, Shamil
R. Sunyaev}, R},
title = {{Pooled Association Tests for Rare Variants in Exon-Resequencing Studies}},
journal = {The American Journal of Human Genetics},
}
@article{Neale_2011,
doi = {10.1371/journal.pgen.1001322},
url = {http://dx.doi.org/10.1371/journal.pgen.1001322},
year = {2011},
month = {mar},
publisher = {Public Library of Science ({PLoS})},
volume = {7},
number = {3},
pages = {e1001322},
author = {Neale, Benjamin M and Rivas, Manuel A and Voight, Benjamin F and Altshuler, David and Devlin, Bernie and Orho-Melander, Marju and Kathiresan, Sekar and Purcell, Shaun M and Roeder, Kathryn and Daly, Mark J},
editor = {Suzanne M. Leal},
title = {{Testing for an Unusual Distribution of Rare Variants}},
journal = {{PLoS} Genetics},
}
@article{Chen_2015,
doi = {10.1534/genetics.115.176107},
url = {http://dx.doi.org/10.1534/genetics.115.176107},
...
volume = {200},
number = {3},
pages = {719--736},
author =
{W. Chen {Chen, Wenan and
B. R. Larrabee Larrabee, Beth R and
I. G. Ovsyannikova Ovsyannikova, Inna G and
R. B. Kennedy Kennedy, Richard B and
I. H. Haralambieva Haralambieva, Iana H and
G. A. Poland Poland, Gregory A and
D. J. Schaid}, Schaid, Daniel J},
title = {{Fine Mapping Causal Variants with an Approximate Bayesian Method Using Marginal Test Statistics}},
journal = {Genetics},
}
@article{Servin_2005, @article{Servin_2007,
doi =
{10.1371/journal.pgen.0030114.eor}, {10.1371/journal.pgen.0030114},
url =
{http://dx.doi.org/10.1371/journal.pgen.0030114.eor}, {http://dx.doi.org/10.1371/journal.pgen.0030114},
year =
{2005}, {2007},
publisher = {Public Library of Science ({PLoS})},
volume =
{preprint}, {3},
number =
{2007}, {7},
pages = {e114},
author =
{Bertrand Servin {Servin, Bertrand and
Matthew Stephens}, Stephens, Matthew},
title =
{{Imputation-based analysis {{Imputation-Based Analysis of
association studies: candidate regions Association Studies: Candidate Regions and
quantitative traits}}, Quantitative Traits}},
journal = {{PLoS} Genetics},
}
@article{Zou_2005, @article{Scheet_2006,
doi =
{10.1111/j.1467-9868.2005.00503.x}, {10.1086/502802},
url =
{http://dx.doi.org/10.1111/j.1467-9868.2005.00503.x}, {http://dx.doi.org/10.1086/502802},
year =
{2005}, {2006},
month = {apr},
publisher =
{Wiley-Blackwell}, {Elsevier {BV}},
volume =
{67}, {78},
number = {4},
pages = {629--644},
author = {Paul Scheet and Matthew Stephens},
title = {{A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase}},
journal = {The American Journal of Human Genetics},
}
@article{Browning_2011,
doi = {10.1016/j.ajhg.2011.01.010},
url = {http://dx.doi.org/10.1016/j.ajhg.2011.01.010},
year = {2011},
month = {feb},
publisher = {Elsevier {BV}},
volume = {88},
number = {2},
pages =
{301--320}, {173--182},
author =
{Hui Zou {Brian L. Browning and
Trevor Hastie}, Sharon R. Browning},
title =
{{Regularization {{A Fast Powerful Method for Detecting Identity by Descent}},
journal = {The American Journal of Human Genetics},
}
@article{Howie_2009,
doi = {10.1371/journal.pgen.1000529},
url = {http://dx.doi.org/10.1371/journal.pgen.1000529},
year = {2009},
month = {jun},
publisher = {Public Library of Science ({PLoS})},
volume = {5},
number = {6},
pages = {e1000529},
author = {Bryan N. Howie and
variable selection via Peter Donnelly and Jonathan Marchini},
editor = {Nicholas J. Schork},
title = {{A Flexible and Accurate Genotype Imputation Method for the
elastic net}}, Next Generation of Genome-Wide Association Studies}},
journal = {{PLoS} Genetics},
}
@article{Li_2010,
doi = {10.1002/gepi.20533},
url = {http://dx.doi.org/10.1002/gepi.20533},
year = {2010},
month = {nov},
publisher = {Wiley-Blackwell},
volume = {34},
number = {8},
pages = {816--834},
author = {Yun Li and Cristen J. Willer and Jun Ding and Paul Scheet and Gon{\c{c}}alo R. Abecasis},
title = {{{MaCH}: using sequence and genotype data to estimate haplotypes and unobserved genotypes}},
journal = {Genetic Epidemiology},
}
@article{Li_2009,
doi = {10.1146/annurev.genom.9.081307.164242},
url = {http://dx.doi.org/10.1146/annurev.genom.9.081307.164242},
year = {2009},
month = {sep},
publisher = {Annual Reviews},
volume = {10},
number = {1},
pages = {387--406},
author = {Yun Li and Cristen Willer and Serena Sanna and Gon{\c{c}}alo Abecasis},
title = {{Genotype Imputation}},
journal =
{Journal {Annual Review of
the Royal Statistical Society: Series B (Statistical Methodology)}, Genomics and Human Genetics},
}
@article{Cho_2010,
doi = {10.1111/j.1469-1809.2010.00597.x},
url = {http://dx.doi.org/10.1111/j.1469-1809.2010.00597.x},
year = {2010},
month = {aug},
publisher = {Wiley-Blackwell},
volume = {74},
number = {5},
pages = {416--428},
author = {Seoae Cho and Kyunga Kim and Young Jin Kim and Jong-Keuk Lee and Yoon Shin Cho and Jong-Young Lee and Bok-Ghee Han and Heebal Kim and Jurg Ott and Taesung Park},
title = {{Joint Identification of Multiple Genetic Variants via Elastic-Net Variable Selection in a Genome-Wide Association Analysis}},
journal = {Annals of Human Genetics},
}
@article{Bardel_2005,
doi = {10.1186/1471-2156-6-24},
url = {http://dx.doi.org/10.1186/1471-2156-6-24},
year = {2005},
publisher = {Springer Nature},
volume = {6},
number = {1},
pages = {24},
author = {Claire Bardel and Vincent Danjean and Jean-Pierre Hugot and Pierre Darlu and Emmanuelle G{\'{e}}nin},
journal = {{BMC} Genet},
}
@article{Tenesa_2007,
doi = {10.1101/gr.6023607},
url = {http://dx.doi.org/10.1101/gr.6023607},
year = {2007},
month = {mar},
publisher = {Cold Spring Harbor Laboratory Press},
volume = {17},
number = {4},
pages = {520--526},
author = {A. Tenesa and P. Navarro and B. J. Hayes and D. L. Duffy and G. M. Clarke and M. E. Goddard and P. M. Visscher},
title = {{Recent human effective population size estimated from linkage disequilibrium}},
journal = {Genome Research},
}
@article{Asimit_2010,
doi = {10.1146/annurev-genet-102209-163421},
url = {http://dx.doi.org/10.1146/annurev-genet-102209-163421},
year = {2010},
month = {dec},
publisher = {Annual Reviews},
volume = {44},
number = {1},
pages = {293--308},
author = {Jennifer Asimit and Eleftheria Zeggini},
title = {{Rare Variant Association Analysis Methods for Complex Traits}},
journal = {Annu. Rev. Genet.},
}
...
}
@article{Mailund_2006, @article{Lee_2014,
doi =
{10.1186/1471-2105-7-454}, {10.1016/j.ajhg.2014.06.009},
url =
{http://dx.doi.org/10.1186/1471-2105-7-454}, {http://dx.doi.org/10.1016/j.ajhg.2014.06.009},
year =
{2006}, {2014},
month = {jul},
publisher =
{Springer Nature}, {Elsevier {BV}},
volume =
{7}, {95},
number = {1},
pages =
{454}, {5--23},
author =
{Thomas Mailund {Seunggeung Lee and
S{\o}ren Besenbacher Gon{\c{c}}alo~R. Abecasis and
Mikkel H Schierup}, Michael Boehnke and Xihong Lin},
title = {{Rare-Variant Association Analysis: Study Designs and Statistical Tests}},
journal =
{{BMC} Bioinformatics}, {The American Journal of Human Genetics},
}
@article{Burkett_2013, @article{Xu_2012,
doi =
{10.3389/fgene.2013.00260}, {10.1371/journal.pone.0041694},
url =
{http://dx.doi.org/10.3389/fgene.2013.00260}, {http://dx.doi.org/10.1371/journal.pone.0041694},
year =
{2013}, {2012},
month = {aug},
publisher =
{Frontiers Media {SA}}, {Public Library of Science ({PLoS})},
volume =
{4}, {7},
number = {8},
pages = {e41694},
author =
{Kelly M. Burkett {ChangJiang Xu and Martin Ladouceur and Zari Dastani and J. Brent Richards and Antonio Ciampi and Celia M. T.
Greenwood and Brad McNeney and Jinko Graham}, Greenwood},
editor = {Zhaoxia Yu},
title =
{{Gene genealogies {{Multiple Regression Methods Show Great Potential for
genetic association mapping with application to Crohn{\textquotesingle}s disease}}, Rare Variant Association Tests}},
journal =
{Front. Genet.}, {{PLoS} {ONE}},
}
@article{Cho_2009, @article{Friedman_2010,
doi =
{10.1186/1753-6561-3-s7-s25}, {10.18637/jss.v033.i01},
url =
{http://dx.doi.org/10.1186/1753-6561-3-s7-s25}, {http://dx.doi.org/10.18637/jss.v033.i01},
year =
{2009}, {2010},
publisher =
{Springer Nature}, {Foundation for Open Access Statistic},
volume =
{3}, {33},
number =
{Suppl 7},
pages = {S25}, {1},
author =
{Seoae Cho and Haseong Kim {Jerome Friedman and
Sohee Oh Trevor Hastie and
Kyunga Kim and Taesung Park}, Robert Tibshirani},
title =
{{Elastic-net regularization approaches {{Regularization Paths for
genome-wide association studies of rheumatoid arthritis}}, Generalized Linear Models via Coordinate Descent}},
journal =
{{BMC} Proc}}, {Journal of Statistical Software},
}
@article{Neale_2011, @article{Simon_2011,
doi =
{10.1371/journal.pgen.1001322}, {10.18637/jss.v039.i05},
url =
{http://dx.doi.org/10.1371/journal.pgen.1001322}, {http://dx.doi.org/10.18637/jss.v039.i05},
year = {2011},
publisher = {Foundation for Open Access Statistic},
volume = {39},
number = {5},
author = {Noah Simon and Jerome Friedman and Trevor Hastie and Rob Tibshirani},
title = {{Regularization Paths for Cox{\textquotesingle}s Proportional Hazards Model via Coordinate Descent}},
journal = {Journal of Statistical Software},
}
@article{Tibshirani_2011a,
doi = {10.1111/j.1467-9868.2011.01004.x},
url = {http://dx.doi.org/10.1111/j.1467-9868.2011.01004.x},
year = {2011},
month =
{mar}, {nov},
publisher =
{Public Library of Science ({PLoS})}, {Wiley-Blackwell},
volume =
{7}, {74},
number =
{3}, {2},
pages =
{e1001322}, {245--266},
author =
{Benjamin M. Neale {Robert Tibshirani and Jacob Bien and
Manuel A. Rivas Jerome Friedman and
Benjamin F. Voight Trevor Hastie and
David Altshuler Noah Simon and
Bernie Devlin Jonathan Taylor and
Marju Orho-Melander Ryan J. Tibshirani},
title = {{Strong rules for discarding predictors in lasso-type problems}},
journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
}
@article{,
title = {{SKAT: SNP-Set (Sequence) Kernel Association Test}},
author = {Seunggeun Lee and
Sekar Kathiresan with contributions from Larisa Miropolsky and
Shaun M. Purcell Michael Wu},
year = {2015},
note = {R package version 1.0.9},
url = {{http://CRAN.R-project.org/package=SKAT}},
}
@misc{lee2014skat,
title = {{SKAT: SNP-set (Sequence) Kernel Association Test. R package version 1.0. 5}},
author = {Lee, Seunggeun and
Kathryn Roeder Miropolsky, Larisa and
Mark J. Daly},
editor Wu, Micheal},
year = {2014},
}
@article{Burkett_2014,
doi = {10.1159/000363443},
url = {http://dx.doi.org/10.1159/000363443},
year = {2014},
month = {aug},
publisher = {S. Karger {AG}},
volume = {78},
number = {3-4},
pages = {117--130},
author =
{Suzanne {Kelly M.
Leal}, Burkett and Brad McNeney and Jinko Graham and Celia M.T. Greenwood},
title =
{{Testing for an Unusual Distribution of {{Using Gene Genealogies to Detect Rare
Variants}}, Variants Associated with Complex Traits}},
journal =
{PLoS} Genetics}, {Human Heredity},
}
