Statistical Genetics References

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• Abecasis GR (2000) GOLD--Graphical Overview of Linkage Disequilibrium . Bioinformatics 16: 182-183. [doi:10.1093/bioinformatics/16.2.182 | http://www.sph.umich.edu/csg/abecasis/GOLD]
• Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2002) Merlin--rapid analysis of dense genetic maps using sparse gene flow trees . Nature Genetics 30: 97-101. [doi:10.1038/ng786 | http://www.sph.umich.edu/csg/abecasis/Merlin]
• Almasy L, Blangero J (1998) Multipoint quantitative-trait linkage analysis in general pedigrees . American Journal of Human Genetics 62: 1198-1211. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1377101 | http://www.sfbr.org/sfbr/public/software/solar/index.html]
• Aulchenko YS, De Koning DJ, Haley C (2007) Genomewide Rapid Association Using Mixed Model and Regression: A fast and simple method For genomewide pedigree-based quantitative trait loci association analysis. Genetics 177: 577-585. [doi:10.1534/genetics.107.075614]

• Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics (Oxford, England) 21: 263-265. [doi:10.1093/bioinformatics/bth457 | http://www.broad.mit.edu/mpg/haploview]
• Basten CJ, Weir BS, Zeng ZB (1995) QTL Cartographer: A Reference Manual and Tutorial for QTL Mapping. Center for Quantitative Genetics, NC St U. [http://statgen.ncsu.edu/qtlcart/]
• Bhave SV, Hornbaker C, Phang TL, Saba L, Lapadat R, Kechris K, Gaydos J, McGoldrick D, Dolbey A, Leach S, Soriano B, Ellington A, Ellington E, Jones K, Mangion J, Belknap JK, Williams RW, Hunter LE, Hoffman PL, Tabakoff B (2007) The PhenoGen informatics website: tools for analyses of complex traits. BMC genetics 8: 59-NA. [doi:10.1186/1471-2156-8-59]
• Boldman KG, Kriese LA, Van Vleck LD, Van Tassell CP, Kachman SD (1995) A manual for use of MTDFREML. A set of programs to obtain estimates of variance and covariance. USDA Agriculture Research Service. [http://aipl.arsusda.gov/curtvt/mtdfreml.html]
• Borevitz JO, Maloof JN, Lutes J, Dabi T, Redfern JL, Trainer GT, Werner JD, Asami T, Berry CC, Weigel D, Chory J (2002) Quantitative Trait Loci Controlling Light and Hormone Response in Two Accessions of Arabidopsis thaliana. Genetics 160: 683-696. [http://www.genetics.org/cgi/content/abstract/160/2/683 | http://famprevmed.ucsd.edu/faculty/cberry/bqtl | http://cran.r-project.org/web/packages/bqtl]
• Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses . Bioinformatics 19: 889-890. [doi:10.1093/bioinformatics/btg112 | http://www.rqtl.org]
• Butcher A, Williams R, Whitaker D, Ling S, Speed P, Moran F (2002) Improving linkage analysis in outcrossed forest trees - an example from Acacia mangium. Theoretical and Applied Genetics 104: 1185-1191. [doi:10.1007/s00122-001-0820-1]

• Carter KW, McCaskie PA, Palmer LJ (2006) JLIN: a java based linkage disequilibrium plotter. BMC bioinformatics 7: 60-NA. [doi:10.1186/1471-2105-7-60 | http://www.genepi.org.au/jlin]
• Casstevens TM, Buckler ES (2004) GDPC: connecting researchers with multiple integrated data sources. Bioinformatics (Oxford, England) 20: 2839-2840. [doi:10.1093/bioinformatics/bth277]
• Clee SM, Yandell BS, Schueler KM, Rabaglia ME, Richards OC, Raines SM, Kabara EA, Klass DM, Mui ET, Stapleton DS, Gray-Keller MP, Young MB, Stoehr JP, Lan H, Boronenkov I, Raess PW, Flowers MT, Attie AD (2006) Positional cloning of Sorcs1, a type 2 diabetes quantitative trait locus . Nature Genetics 38: 688-693. [doi:10.1038/ng1796 | http://www.stat.wisc.edu/~yandell/qtl/software/subcon.zip]

• Ding K (2003) LDA--a java-based linkage disequilibrium analyzer. Bioinformatics 19: 2147-2148. [doi:10.1093/bioinformatics/btg276 | http://www.chgb.org.cn/lda/lda.htm]
• Dudbridge F (2003) Pedigree disequilibrium tests for multilocus haplotypes. Genetic epidemiology 25: 115-121. [doi:10.1002/gepi.10252 | http://www.litbio.org/]
• Durinck S (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21: 3439-3440. [doi:10.1093/bioinformatics/bti525 | http://www.biomart.org]

• Gaunt TR, Rodriguez S, Zapata C, Day IN (2006) MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers. BMC bioinformatics 7: 227-NA. [doi:10.1186/1471-2105-7-227 | http://www.genes.org.uk/software/midas]
• Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya O (2007) A genome-wide functional network for the laboratory mouse. Princeton University. [http://mousenet.princeton.edu | http://avis.princeton.edu/mouseNET/supplement/supplement_index.html]

• Hardy OJ, Vekemans X (2002) Spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2: 618-620. [http://www.ulb.ac.be/sciences/lagev/spagedi.html]

• Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447-1455. [http://www.genetics.org/cgi/content/abstract/136/4/1447 | http://www.plant.dlo.nl/default.asp?section=products&page=/products/mapping/]
• Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, DeGreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A (2007) The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology 25: 1127-1133. [doi:10.1038/nbt1347]

• Lander E, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181. [doi:10.1016/0888-7543(87)90010-3]
• Lander ES, Abrahamson J, Barlow A (1987) MAPMAKER: a computer package for constructing genetic linkage maps. Cytogenetic and Cell Genetics 46: 642-NA. [doi:10.1159/000132491]
• Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics (Oxford, England) 21: 2128-2129. [doi:10.1093/bioinformatics/bti282 | http://www.powermarker.net/]
• Ljungberg K, Holmgren S, Carlborg O (2004) Simultaneous search for multiple QTL using the global optimization algorithm DIRECT. Bioinformatics (Oxford, England) 20: 1887-1895. [doi:10.1093/bioinformatics/bth175 | http://user.it.uu.se/~kl/qtl_software.html]

• Meer JM, Cudmore JRH, Manly K (2004) MapManager/QTX: software for complex trait analysis. [http://www.mapmanager.org/mmQTX.html]
• Mester D, Ronin Y, Nevo E, Korol A (2004) Fast and high precision algorithms for optimization in large-scale genomic problems. Computational Biology and Chemistry 28: 281-290. [doi:10.1016/j.compbiolchem.2004.08.003 | http://www.multiqtl.com/]
• Meyer M, Munzner T, Pfister H (2009) MizBee: A Multiscale Synteny Browser . [http://mizbee.org/More_Info_files/mizbee.pdf | http://mizbee.org | http://vis.computer.org/VisWeek2009/infovis]
• Mott R, Talbot CJ, Turri MG, Collins AC, Flint J (2000) A method for fine mapping quantitative trait loci in outbred animal stocks . Proceedings of the National Academy of Sciences of the United States of America 97: 12649-12654. [doi:10.1073/pnas.230304397 | http://www.well.ox.ac.uk/~rmott/happy.html]

• Perez-Enciso M, Misztal I (2004) Qxpak: a versatile mixed model application for genetical genomics and QTL analyses. Bioinformatics (Oxford, England) 20: 2792-2798. [doi:10.1093/bioinformatics/bth331 | http://www.icrea.es/pag.asp?id=Miguel.Perez]
• Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959. [http://www.genetics.org/cgi/content/abstract/155/2/945 | http://pritch.bsd.uchicago.edu/software.html]

• Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, States D, Hanash S, Paulovich A, McIntosh MW (2006) Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. Journal of proteome research 5: 112-121. [doi:10.1021/pr0503533]
• Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A (2006) A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC bioinformatics 7: 489-NA. [doi:10.1186/1471-2105-7-489]
• Richardson S (2008) Bayesian Gene Expression. [http://www.bgx.org.uk/]

• Schneider A, Dessimoz C, Gonnet GH (2007) OMA Browser--exploring orthologous relations across 352 complete genomes. Bioinformatics (Oxford, England) 23: 2180-2182. [doi:10.1093/bioinformatics/btm295 | http://www.omabrowser.org]
• Seaton G, Hernandez J, Grunchec JA, White I, Allen J, De Koning DJ, Wei W, Berry D, Haley C, Knott S (2006) GRIDQTL: a grid portal for QTL mapping of compute intensive datasets. Belo Horizonte, MG. [http://www.gridqtl.org.uk/publications/wcgalp27_633-916.pdf | http://www.gridqtl.org.uk]
• Sen S, Churchill GA (2001) A statistical framework for quantitative trait mapping. Genetics 159: 371-387. [http://www.genetics.org/cgi/content/abstract/159/1/371 | http://www.jax.org/research/churchill/research/qtl/pseudomarker.html]
• Sillanpää M, Arjas E (1998) Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373-1388. [http://www.genetics.org/cgi/content/abstract/148/3/1373 | http://www.rni.helsinki.fi/~mjs/]
• Sillanpää MJ, Arjas E (1999) Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. Genetics 151: 1605-1619. [http://www.genetics.org/cgi/content/abstract/151/4/1605 | http://www.rni.helsinki.fi/~mjs/]
• Sun W, Yuan S, Li KC (2008) Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study. BMC genomics 9: 242-NA. [doi:10.1186/1471-2164-9-242 | http://www.bios.unc.edu/~wsun/software.htm]
• Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T (2008) eQED: an efficient method for interpreting eQTL associations using protein networks. Molecular systems biology 4: 162-NA. [doi:10.1038/msb.2008.4]

• Utz HF, Melchinger AE (1996) PLABQTL: a program for composite interval mapping of QTL . J Quant Trait Loci 2: 000. [http://www.uni-hohenheim.de/ipspwww/soft.html]

• van Ooijen JW, Maliepaard C (2996) MapQTL version 3.0: software for the calculation of QTL positions on genetic maps. CPRO-DLO. [http://www.kyazma.nl/]

• Wang J, W.Williams R, Manly KF (2003) WebQTL: Web-Based Complex Trait Analysis . Neuroinformatics 1: 299-308. [doi:10.1385/NI:1:4:299 | http://www.genenetwork.org]
• Wu B, Liu N, Zhao H (2006) PSMIX: an R package for population structure inference via maximum likelihood method. BMC bioinformatics 7: 317-NA. [doi:10.1186/1471-2105-7-317 | http://bioinformatics.med.yale.edu/PSMIX]
• Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, Su AI (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome biology 10: R130-NA. [doi:10.1186/gb-2009-10-11-r130 | http://biogps.gnf.org]

• Xu Z, Zou F, Vision TJ (2005) Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples. Genetics 170: 401-408. [doi:10.1534/genetics.104.033746 | http://www.bio.unc.edu/faculty/vision/lab/mappop/]

• Yandell BS, Bradbury P (2007) Computing strategies and software for gene mapping . In: Kole C (ed.) . Science Publishers, Inc.: Enfield, New Hampshire, pp. 329-377. [http://www.stat.wisc.edu/~yandell/doc/2007/E11.PlantMap.pdf]
• Yandell BS, Mehta T, Banerjee S, Shriner D, Venkataraman R, Moon JY, Neely WW, Wu H, von Smith R, Yi N (2007) R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses . Bioinformatics (Oxford, England) 23: 641-643. [doi:10.1093/bioinformatics/btm011 | http://www.qtlbim.org]
• Yang J, Hu C, Ye X, Zhu J (2006) QTLNetwork 2.0 Software for Mapping QTL with Epistatic and QE interaction effects in Experimental Populations . [http://ibi.zju.edu.cn/software/qtlnetwork]
• Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness . Nature Genetics 38: 203-208. [doi:10.1038/ng1702 | http://www.maizegenetics.net/bioinformatics/tassel]

• Zhang Z, Todhunter RJ, Buckler ES, Van Vleck LD (2007) Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood . Journal of animal science 85: 881-885. [doi:10.2527/jas.2006-656 | http://aipl.arsusda.gov/curtvt/mtdfreml.html]
• Zhang ZD, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M (2007) Tilescope: online analysis pipeline for high-density tiling microarray data. Genome biology 8: R81-NA. [doi:10.1186/gb-2007-8-5-r81 | http://tilescope.gersteinlab.org/]
• Zou W, Aylor DL, Zeng ZB (2007) eQTL Viewer: visualizing how sequence variation affects genome-wide transcription . BMC bioinformatics 8: 7-NA. [doi:10.1186/1471-2105-8-7 | http://statgen.ncsu.edu/eQTLViewer/svgHome.html]

Last modified: Tue Mar 30 15:46:54 2010 by Brian S. Yandell