Mark Abney

Mark Abney

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Mark Abney

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Kinpute: Using identity by descent to improve genotype imputation.

Bioinformatics 2019 Mar 27. Epub 2019 Mar 27.

Department of Human Genetics, University of Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz221DOI Listing
March 2019

Observing the Effect of Soil-Applied Insecticides on Wireworm (Coleoptera: Elateridae) Behavior and Mortality Using Radiographic Imaging.

J Econ Entomol 2018 May 15. Epub 2018 May 15.

Department of Entomology, North Carolina State University, Raleigh, NC.

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http://dx.doi.org/10.1093/jee/toy130DOI Listing
May 2018

A LASSO penalized regression approach for genome-wide association analyses using related individuals: application to the Genetic Analysis Workshop 19 simulated data.

BMC Proc 2016 18;10(Suppl 7):221-226. Epub 2016 Oct 18.

Department of Human Genetics, University of Chicago, 920 E. 58th Street, CLSC 4th floor, Chicago, IL 60637 USA.

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http://dx.doi.org/10.1186/s12919-016-0034-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133525PMC
October 2016

Applying insecticides through drip irrigation to reduce wireworm (Coleoptera: Elateridae) feeding damage in sweet potato.

Pest Manag Sci 2016 Jun 7;72(6):1133-40. Epub 2015 Oct 7.

University of Georgia, Tifton, GA, USA.

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http://doi.wiley.com/10.1002/ps.4089
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http://dx.doi.org/10.1002/ps.4089DOI Listing
June 2016

Directional dominance on stature and cognition in diverse human populations.

Authors:
Peter K Joshi Tonu Esko Hannele Mattsson Niina Eklund Ilaria Gandin Teresa Nutile Anne U Jackson Claudia Schurmann Albert V Smith Weihua Zhang Yukinori Okada Alena Stančáková Jessica D Faul Wei Zhao Traci M Bartz Maria Pina Concas Nora Franceschini Stefan Enroth Veronique Vitart Stella Trompet Xiuqing Guo Daniel I Chasman Jeffery R O'Connel Tanguy Corre Suraj S Nongmaithem Yuning Chen Massimo Mangino Daniela Ruggiero Michela Traglia Aliki-Eleni Farmaki Tim Kacprowski Andrew Bjonnes Ashley van der Spek Ying Wu Anil K Giri Lisa R Yanek Lihua Wang Edith Hofer Cornelius A Rietveld Olga McLeod Marilyn C Cornelis Cristian Pattaro Niek Verweij Clemens Baumbach Abdel Abdellaoui Helen R Warren Dragana Vuckovic Hao Mei Claude Bouchard John R B Perry Stefania Cappellani Saira S Mirza Miles C Benton Ulrich Broeckel Sarah E Medland Penelope A Lind Giovanni Malerba Alexander Drong Loic Yengo Lawrence F Bielak Degui Zhi Peter J van der Most Daniel Shriner Reedik Mägi Gibran Hemani Tugce Karaderi Zhaoming Wang Tian Liu Ilja Demuth Jing Hua Zhao Weihua Meng Lazaros Lataniotis Sander W van der Laan Jonathan P Bradfield Andrew R Wood Amelie Bonnefond Tarunveer S Ahluwalia Leanne M Hall Erika Salvi Seyhan Yazar Lisbeth Carstensen Hugoline G de Haan Mark Abney Uzma Afzal Matthew A Allison Najaf Amin Folkert W Asselbergs Stephan J L Bakker R Graham Barr Sebastian E Baumeister Daniel J Benjamin Sven Bergmann Eric Boerwinkle Erwin P Bottinger Archie Campbell Aravinda Chakravarti Yingleong Chan Stephen J Chanock Constance Chen Y-D Ida Chen Francis S Collins John Connell Adolfo Correa L Adrienne Cupples George Davey Smith Gail Davies Marcus Dörr Georg Ehret Stephen B Ellis Bjarke Feenstra Mary F Feitosa Ian Ford Caroline S Fox Timothy M Frayling Nele Friedrich Frank Geller Generation Scotland Irina Gillham-Nasenya Omri Gottesman Misa Graff Francine Grodstein Charles Gu Chris Haley Christopher J Hammond Sarah E Harris Tamara B Harris Nicholas D Hastie Nancy L Heard-Costa Kauko Heikkilä Lynne J Hocking Georg Homuth Jouke-Jan Hottenga Jinyan Huang Jennifer E Huffman Pirro G Hysi M Arfan Ikram Erik Ingelsson Anni Joensuu Åsa Johansson Pekka Jousilahti J Wouter Jukema Mika Kähönen Yoichiro Kamatani Stavroula Kanoni Shona M Kerr Nazir M Khan Philipp Koellinger Heikki A Koistinen Manraj K Kooner Michiaki Kubo Johanna Kuusisto Jari Lahti Lenore J Launer Rodney A Lea Benjamin Lehne Terho Lehtimäki David C M Liewald Lars Lind Marie Loh Marja-Liisa Lokki Stephanie J London Stephanie J Loomis Anu Loukola Yingchang Lu Thomas Lumley Annamari Lundqvist Satu Männistö Pedro Marques-Vidal Corrado Masciullo Angela Matchan Rasika A Mathias Koichi Matsuda James B Meigs Christa Meisinger Thomas Meitinger Cristina Menni Frank D Mentch Evelin Mihailov Lili Milani May E Montasser Grant W Montgomery Alanna Morrison Richard H Myers Rajiv Nadukuru Pau Navarro Mari Nelis Markku S Nieminen Ilja M Nolte George T O'Connor Adesola Ogunniyi Sandosh Padmanabhan Walter R Palmas James S Pankow Inga Patarcic Francesca Pavani Patricia A Peyser Kirsi Pietilainen Neil Poulter Inga Prokopenko Sarju Ralhan Paul Redmond Stephen S Rich Harri Rissanen Antonietta Robino Lynda M Rose Richard Rose Cinzia Sala Babatunde Salako Veikko Salomaa Antti-Pekka Sarin Richa Saxena Helena Schmidt Laura J Scott William R Scott Bengt Sennblad Sudha Seshadri Peter Sever Smeeta Shrestha Blair H Smith Jennifer A Smith Nicole Soranzo Nona Sotoodehnia Lorraine Southam Alice V Stanton Maria G Stathopoulou Konstantin Strauch Rona J Strawbridge Matthew J Suderman Nikhil Tandon Sian-Tsun Tang Kent D Taylor Bamidele O Tayo Anna Maria Töglhofer Maciej Tomaszewski Natalia Tšernikova Jaakko Tuomilehto Andre G Uitterlinden Dhananjay Vaidya Astrid van Hylckama Vlieg Jessica van Setten Tuula Vasankari Sailaja Vedantam Efthymia Vlachopoulou Diego Vozzi Eero Vuoksimaa Melanie Waldenberger Erin B Ware William Wentworth-Shields John B Whitfield Sarah Wild Gonneke Willemsen Chittaranjan S Yajnik Jie Yao Gianluigi Zaza Xiaofeng Zhu The BioBank Japan Project Rany M Salem Mads Melbye Hans Bisgaard Nilesh J Samani Daniele Cusi David A Mackey Richard S Cooper Philippe Froguel Gerard Pasterkamp Struan F A Grant Hakon Hakonarson Luigi Ferrucci Robert A Scott Andrew D Morris Colin N A Palmer George Dedoussis Panos Deloukas Lars Bertram Ulman Lindenberger Sonja I Berndt Cecilia M Lindgren Nicholas J Timpson Anke Tönjes Patricia B Munroe Thorkild I A Sørensen Charles N Rotimi Donna K Arnett Albertine J Oldehinkel Sharon L R Kardia Beverley Balkau Giovanni Gambaro Andrew P Morris Johan G Eriksson Margie J Wright Nicholas G Martin Steven C Hunt John M Starr Ian J Deary Lyn R Griffiths Henning Tiemeier Nicola Pirastu Jaakko Kaprio Nicholas J Wareham Louis Pérusse James G Wilson Giorgia Girotto Mark J Caulfield Olli Raitakari Dorret I Boomsma Christian Gieger Pim van der Harst Andrew A Hicks Peter Kraft Juha Sinisalo Paul Knekt Magnus Johannesson Patrik K E Magnusson Anders Hamsten Reinhold Schmidt Ingrid B Borecki Erkki Vartiainen Diane M Becker Dwaipayan Bharadwaj Karen L Mohlke Michael Boehnke Cornelia M van Duijn Dharambir K Sanghera Alexander Teumer Eleftheria Zeggini Andres Metspalu Paolo Gasparini Sheila Ulivi Carole Ober Daniela Toniolo Igor Rudan David J Porteous Marina Ciullo Tim D Spector Caroline Hayward Josée Dupuis Ruth J F Loos Alan F Wright Giriraj R Chandak Peter Vollenweider Alan Shuldiner Paul M Ridker Jerome I Rotter Naveed Sattar Ulf Gyllensten Kari E North Mario Pirastu Bruce M Psaty David R Weir Markku Laakso Vilmundur Gudnason Atsushi Takahashi John C Chambers Jaspal S Kooner David P Strachan Harry Campbell Joel N Hirschhorn Markus Perola Ozren Polašek James F Wilson

Nature 2015 Jul 1;523(7561):459-462. Epub 2015 Jul 1.

Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland.

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http://dx.doi.org/10.1038/nature14618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516141PMC
July 2015

Permutation testing in the presence of polygenic variation.

Authors:
Mark Abney

Genet Epidemiol 2015 May 10;39(4):249-58. Epub 2015 Mar 10.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1002/gepi.21893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634896PMC
May 2015

PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population.

PLoS Comput Biol 2015 Mar 3;11(3):e1004139. Epub 2015 Mar 3.

Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America; Departments of Medicine, and Statistics, The University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4348507PMC
March 2015

Effects of Thrips Density, Mode of Inoculation, and Plant Age on Tomato Spotted Wilt Virus Transmission in Peanut Plants.

Environ Entomol 2015 Feb 21;44(1):136-43. Epub 2015 Jan 21.

Department of Entomology, University of Georgia, Tifton, GA 31793.

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http://dx.doi.org/10.1093/ee/nvu013DOI Listing
February 2015

High-resolution genetic mapping of complex traits from a combined analysis of F2 and advanced intercross mice.

Genetics 2014 Sep;198(1):103-16

Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637 Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, Illinois 60637

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http://dx.doi.org/10.1534/genetics.114.167056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174923PMC
September 2014

Practical considerations regarding the use of genotype and pedigree data to model relatedness in the context of genome-wide association studies.

G3 (Bethesda) 2013 Oct 3;3(10):1861-7. Epub 2013 Oct 3.

Department of Human Genetics, The University of Chicago, Illinois 60637.

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http://dx.doi.org/10.1534/g3.113.007948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789811PMC
October 2013

A spatial ecology study on the effects of field conditions and crop rotation on the incidence of Plectris aliena (Coleoptera: Scarabaeidae) grub damage to sweetpotato roots.

Environ Entomol 2013 Oct;42(5):1046-51

Syngenta Seeds, Inc., 128 Federal Walk, Kennett Square, PA 19348, USA.

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http://dx.doi.org/10.1603/EN13123DOI Listing
October 2013

Using identity by descent estimation with dense genotype data to detect positive selection.

Authors:
Lide Han Mark Abney

Eur J Hum Genet 2013 Feb 11;21(2):205-11. Epub 2012 Jul 11.

Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1038/ejhg.2012.148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548265PMC
February 2013

GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations.

Bioinformatics 2012 Jun 19;28(11):1553-4. Epub 2012 Apr 19.

Department of Human Genetics, University of Chicago, 920 E. 58th St., Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356846PMC
June 2012

Effectiveness of tomato-spotted wilt virus management tactics.

J Econ Entomol 2012 Jun;105(3):943-8

Department of Agriculture & Applied Economics, University of Georgia, 301 Corner Hall, Room 309, Athmens, GA 30605, USA.

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http://dx.doi.org/10.1603/ec11272DOI Listing
June 2012

Rising prevalence of asthma is sex-specific in a US farming population.

J Allergy Clin Immunol 2011 Oct 15;128(4):774-9. Epub 2011 Aug 15.

Department of Medicine, Section of Pulmonary and Critical Care, The University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1016/j.jaci.2011.06.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401412PMC
October 2011

Identity by descent estimation with dense genome-wide genotype data.

Authors:
Lide Han Mark Abney

Genet Epidemiol 2011 Sep 18;35(6):557-67. Epub 2011 Jul 18.

Department of Human Genetics, University of Chicago, Illinois, USA.

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http://home.uchicago.edu/~abney/abney_web/Publications_files
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http://doi.wiley.com/10.1002/gepi.20606
Publisher Site
http://dx.doi.org/10.1002/gepi.20606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587128PMC
September 2011

Genetic variance components estimation for binary traits using multiple related individuals.

Genet Epidemiol 2011 Jul 4;35(5):291-302. Epub 2011 Apr 4.

Department of Mathematics, Physics, and Statistics, University of the Sciences, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1002/gepi.20577DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612980PMC
July 2011

QTLRel: an R package for genome-wide association studies in which relatedness is a concern.

BMC Genet 2011 Jul 27;12:66. Epub 2011 Jul 27.

Department of Human Genetics, The University of Chicago, IL 60637, USA.

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http://dx.doi.org/10.1186/1471-2156-12-66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160955PMC
July 2011

Relative susceptibility of two sweetpotato varieties to storage root damage by sweetpotato flea beetle (Coleoptera: Chrysomelidae) and wireworm (Coleoptera: Elateridae).

J Econ Entomol 2011 Feb;104(1):143-8

Department of Entomology, Campus Box 7630, North Carolina State University, Raleigh, NC 27695, USA.

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http://dx.doi.org/10.1603/ec10196DOI Listing
February 2011

Influence of preceding crop on wireworm (Coleoptera: Elateridae) abundance in the coastal plain of North Carolina.

J Econ Entomol 2010 Dec;103(6):2087-93

Department of Entomology, Box 7630, North Carolina State University, Raleigh, NC 27695-7630, USA.

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http://dx.doi.org/10.1603/ec10184DOI Listing
December 2010

Survey of wireworms (Coleoptera: Elateridae) in North Carolina sweetpotato fields and seasonal abundance of Conoderus vespertinus.

J Econ Entomol 2010 Aug;103(4):1268-76

Department of Entomology, Box 7630, North Carolina State University, Raleigh, NC 27695-7630, USA.

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http://dx.doi.org/10.1603/ec09174DOI Listing
August 2010

Colloquium papers: Heritability of reproductive fitness traits in a human population.

Proc Natl Acad Sci U S A 2010 Jan 12;107 Suppl 1:1772-8. Epub 2009 Oct 12.

Department of Human Genetics and Obstetrics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1073/pnas.0906196106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868280PMC
January 2010

Confidence intervals for putative quantitative trait loci - development and applications of new linkage methods.

BMC Proc 2007 18;1 Suppl 1:S91. Epub 2007 Dec 18.

Department of Human Genetics, University of Chicago, 920 East 57th Street, Chicago, Illinois 60637, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367503PMC
http://dx.doi.org/10.1186/1753-6561-1-s1-s91DOI Listing
December 2009

A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients.

Authors:
Mark Abney

Bioinformatics 2009 Jun 9;25(12):1561-3. Epub 2009 Apr 9.

Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687941PMC
June 2009

Influence of soil temperature, rainfall, and planting and harvest dates on Chaetocnema confinis (Coleoptera: Chrysomelidae) damage to sweetpotato roots.

J Econ Entomol 2008 Aug;101(4):1238-43

Department of Entomology, North Carolina State University, Raleigh NC 27695-7630, USA.

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http://dx.doi.org/10.1603/0022-0493(2008)101[1238:iostra]2.0.co;2DOI Listing
August 2008

Identity-by-descent estimation and mapping of qualitative traits in large, complex pedigrees.

Authors:
Mark Abney

Genetics 2008 Jul 13;179(3):1577-90. Epub 2008 Jul 13.

Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1534/genetics.108.089912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475756PMC
July 2008

Rise and fall of cotton aphid (Hemiptera: Aphididae) populations in southeastern cotton production systems.

J Econ Entomol 2008 Feb;101(1):23-35

Department of Entomology, North Carolina State University, Raleigh, NC, USA.

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http://dx.doi.org/10.1603/0022-0493(2008)101[23:rafoca]2.0.co;2DOI Listing
February 2008

Heritability estimation of sex-specific effects on human quantitative traits.

Genet Epidemiol 2007 May;31(4):338-47

Department of Human Genetics, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.

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http://home.uchicago.edu/~abney/abney_web/Publications_files
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http://doi.wiley.com/10.1002/gepi.20214
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http://dx.doi.org/10.1002/gepi.20214DOI Listing
May 2007

The sex-specific genetic architecture of quantitative traits in humans.

Nat Genet 2006 Feb 22;38(2):218-22. Epub 2006 Jan 22.

[1] Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1038/ng1726DOI Listing
February 2006

Sex differences in the genetic basis of morning serum cortisol levels: genome-wide screen identifies two novel loci specific to women.

J Clin Endocrinol Metab 2005 Aug 7;90(8):4747-52. Epub 2005 Jun 7.

Department of Health Studies, The University of Chicago, 5841 South Maryland Avenue, MC2007, Chicago, Illinois 60637, USA.

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https://academic.oup.com/jcem/article-lookup/doi/10.1210/jc.
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http://dx.doi.org/10.1210/jc.2005-0384DOI Listing
August 2005

Sex-specific genetic architecture of whole blood serotonin levels.

Am J Hum Genet 2005 Jan 3;76(1):33-41. Epub 2004 Nov 3.

Department of Human Genetics, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1086/426697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1196431PMC
January 2005

Testing for Hardy-Weinberg equilibrium in samples with related individuals.

Genetics 2004 Dec 15;168(4):2349-61. Epub 2004 Sep 15.

INSERM U535, 94817 Villejuif Cedex, France.

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http://dx.doi.org/10.1534/genetics.104.031617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448754PMC
December 2004

Genome-wide association study identifies ITGB3 as a QTL for whole blood serotonin.

Eur J Hum Genet 2004 Nov;12(11):949-54

Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1038/sj.ejhg.5201239DOI Listing
November 2004

Major loci influencing serum triglyceride levels on 2q14 and 9p21 localized by homozygosity-by-descent mapping in a large Hutterite pedigree.

Hum Mol Genet 2003 Jan;12(2):137-44

Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/hmg/ddg012DOI Listing
January 2003

Quantitative-trait homozygosity and association mapping and empirical genomewide significance in large, complex pedigrees: fasting serum-insulin level in the Hutterites.

Am J Hum Genet 2002 Apr 4;70(4):920-34. Epub 2002 Mar 4.

Department of Human Genetics, University of Chicago, 920 East 85th Street, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1086/339705DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC379120PMC
April 2002