Publications

Our group publishes papers presenting new methodologies, describing the results of studies that use our software, and reviewing current topics in the field of Bioinformatics. Scroll down or click here for a complete list of papers produced by our lab. Since 2013, we write blog posts summarizing new research papers and review articles:

GWAS

Mouse Genetics

Population Structure

Review Articles

Publications

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2016

Lusis, Aldons J; Seldin, Marcus; Allayee, Hooman; Bennett, Brian J; Civelek, Mete; Davis, Richard C; Eskin, Eleazar; Farber, Charles; Hui, Simon T; Mehrabian, Margarete; Norheim, Frode; Pan, Calvin; Parks, Brian; Rau, Christoph; Smith, Desmond J; Vallim, Thomas; Wang, Yibin; Wang, Jessica

The Hybrid Mouse Diversity Panel: A Resource for Systems Genetics Analyses of Metabolic and Cardiovascular Traits. Journal Article

J Lipid Res, 2016, ISSN: 1539-7262.

Abstract | Links | BibTeX | Tags: genome-wide association studies, Hybrid Mouse Diversity Panel, Mouse Genetics

Hasin-Brumshtein, Yehudit; Khan, Arshad H; Hormozdiari, Farhad; Pan, Calvin; Parks, Brian W; Petyuk, Vladislav A; Piehowski, Paul D; Brümmer, Anneke; Pellegrini, Matteo; Xiao, Xinshu; Eskin, Eleazar; Smith, Richard D; Lusis, Aldons J; Smith, Desmond J

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes. Journal Article

Elife, 5 , 2016, ISSN: 2050-084X.

Abstract | Links | BibTeX | Tags: Expression QTLs, Mouse Genetics

Lavinsky, Joel; Ge, Marshall; Crow, Amanda L; Pan, Calvin; Wang, Juemei; Dermanaki, Pehzman Salehi; Myint, Anthony; Eskin, Eleazar; Allayee, Hooman; Lusis, Aldons J; Friedman, Rick A

The Genetic Architecture of Noise-induced Hearing Loss: Evidence for a Gene-by-Environment Interaction. Journal Article

G3 (Bethesda), 2016, ISSN: 2160-1836.

Abstract | Links | BibTeX | Tags: Mouse Genetics

2015

Rau, Christoph D; Parks, Brian; Wang, Yibin; Eskin, Eleazar; Simecek, Petr; Churchill, Gary A; Lusis, Aldons J

High Density Genotypes of Inbred Mouse Strains: Improved Power and Precision of Association Mapping. Journal Article

G3 (Bethesda), 5 (10), pp. 2021-6, 2015, ISSN: 2160-1836.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

2014

Kang, Eun Yong; Han, Buhm; Furlotte, Nicholas; Joo, Jong Wha J; Shih, Diana; Davis, Richard C; Lusis, Aldons J; Eskin, Eleazar

Meta-Analysis Identifies Gene-by-Environment Interactions as Demonstrated in a Study of 4,965 Mice Journal Article

PLoS Genet, 10 (1), pp. e1004022, 2014, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: Genes By Environment, Meta-Analysis, Mouse Genetics

Ohmen, Jeffrey; Kang, Eun Yong ; Li, Xin ; Joo, Jong Wha ; Hormozdiari, Farhad ; Zheng, Qing Yin ; Davis, Richard C; Lusis, Aldons J; Eskin, Eleazar ; Friedman, Rick A

Genome-Wide Association Study for Age-Related Hearing Loss (AHL) in the Mouse: A Meta-Analysis. Journal Article

J Assoc Res Otolaryngol, 15 (3), pp. 335-52, 2014, ISSN: 1438-7573.

Abstract | Links | BibTeX | Tags: HMDP, Meta-Analysis, Mouse Genetics

2013

Leikauf, George D; Concel, Vincent J; Bein, Kiflai ; Liu, Pengyuan ; Berndt, Annerose ; Martin, Timothy M; Ganguly, Koustav ; Jang, An-Soo S; Brant, Kelly A; Jr, Richard Dopico A; Upadhyay, Swapna ; Cario, Clinton L; Di, Yp Peter ; Vuga, Louis J; Kostem, Emrah ; Eskin, Eleazar ; You, Ming ; Kaminski, Naftali ; Prows, Daniel R; Knoell, Daren L; Fabisiak, James P

Functional Genomic Assessment of Phosgene-induced Acute Lung Injury in Mice. Journal Article

Am J Respir Cell Mol Biol, 2013, ISSN: 1535-4989.

Abstract | Links | BibTeX | Tags: Mouse Genetics

Parks, Brian W; Nam, Elizabeth ; Org, Elin ; Kostem, Emrah ; Norheim, Frode ; Hui, Simon T; Pan, Calvin ; Civelek, Mete ; Rau, Christoph D; Bennett, Brian J; Mehrabian, Margarete ; Ursell, Luke K; He, Aiqing ; Castellani, Lawrence W; Zinker, Bradley ; Kirby, Mark ; Drake, Thomas A; Drevon, Christian A; Knight, Rob ; Gargalovic, Peter ; Kirchgessner, Todd ; Eskin, Eleazar ; Lusis, Aldons J

Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Journal Article

Cell Metab, 17 (1), pp. 141-52, 2013, ISSN: 1932-7420.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

Davis, Richard C; van Nas, Atila ; Bennett, Brian ; Orozco, Luz ; Pan, Calvin ; Rau, Christoph D; Eskin, Eleazar ; Lusis, Aldons J

Genome-wide association mapping of blood cell traits in mice. Journal Article

Mamm Genome, 2013, ISSN: 1432-1777.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

2012

Flint, Jonathan; Eskin, Eleazar

Genome-wide association studies in mice Journal Article

Nature Reviews Genetics, 13 (11), pp. 807-17, 2012, ISSN: 1471-0064.

Abstract | Links | BibTeX | Tags: Mouse Genetics

Bennett, Brian J; Orozco, Luz ; Kostem, Emrah ; Erbilgin, Ayca ; Dallinga, Marchien ; Neuhaus, Isaac ; Guan, Bo ; Wang, Xuping ; Eskin, Eleazar ; Lusis, Aldons J

High-Resolution Association Mapping of Atherosclerosis Loci in Mice. Journal Article

Arterioscler Thromb Vasc Biol, 2012, ISSN: 1524-4636.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

Ghazalpour, Anatole; Rau, Christoph D; Farber, Charles R; Bennett, Brian J; Orozco, Luz D; van Nas, Atila; Pan, Calvin; Allayee, Hooman; Beaven, Simon W; Civelek, Mete; Davis, Richard C; Drake, Thomas A; Friedman, Rick A; Furlotte, Nick; Hui, Simon T; Jentsch, David J; Kostem, Emrah; Kang, Hyun Min; Kang, Eun Yong; Joo, Jong Wha; Korshunov, Vyacheslav A; Laughlin, Rick E; Martin, Lisa J; Ohmen, Jeffrey D; Parks, Brian W; Pellegrini, Matteo; Reue, Karen; Smith, Desmond J; Tetradis, Sotirios; Wang, Jessica; Wang, Yibin; N, James

Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits. Journal Article

Mamm Genome, 2012, ISSN: 1432-1777.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

Hersch, Micha; Peter, Bastian ; Kang, Hyun Min ; Schüpfer, Fanny ; Abriel, Hugues ; Pedrazzini, Thierry ; Eskin, Eleazar ; Beckmann, Jacques S; Bergmann, Sven ; Maurer, Fabienne

Mapping genetic variants associated with Beta-adrenergic responses in inbred mice. Journal Article

PLoS One, 7 (7), pp. e41032, 2012, ISSN: 1932-6203.

Abstract | Links | BibTeX | Tags: Mouse Genetics

Calabrese, Gina; Bennett, Brian J; Orozco, Luz ; Kang, Hyun M; Eskin, Eleazar ; Dombret, Carlos ; Backer, Olivier De ; Lusis, Aldons J; Farber, Charles R

Systems genetic analysis of osteoblast-lineage cells. Journal Article

PLoS Genet, 8 (12), pp. e1003150, 2012, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

Furlotte, Nicholas A; Kang, Eun Yong; Nas, Atila Van; Farber, Charles R; Lusis, Aldons J; Eskin, Eleazar

Increasing Association Mapping Power and Resolution in Mouse Genetic Studies Through the Use of Meta-analysis for Structured Populations. Journal Article

Genetics, 191 (3), pp. 959-67, 2012, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: Meta-Analysis, Meta-Analysis Grant, Mouse Genetics

2011

Ghazalpour, Anatole; Bennett, Brian; Petyuk, Vladislav A; Orozco, Luz; Hagopian, Raffi; Mungrue, Imran N; Farber, Charles R; Sinsheimer, Janet; Kang, Hyun M; Furlotte, Nicholas; Park, Christopher C; Wen, Ping-Zi; Brewer, Heather; Weitz, Karl; Camp, David G; Pan, Calvin; Yordanova, Roumyana; Neuhaus, Isaac; Tilford, Charles; Siemers, Nathan; Gargalovic, Peter; Eskin, Eleazar; Kirchgessner, Todd; Smith, Desmond J; Smith, Richard D; Lusis, Aldons J

Comparative analysis of proteome and transcriptome variation in mouse. Journal Article

PLoS Genet, 7 (6), pp. e1001393, 2011, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

Park, Christopher C; Gale, Greg D; de Jong, Simone ; Ghazalpour, Anatole ; Bennett, Brian J; Farber, Charles R; Langfelder, Peter ; Lin, Andy ; Khan, Arshad H; Eskin, Eleazar ; Horvath, Steve ; Lusis, Aldons J; Ophoff, Roel A; Smith, Desmond J

Gene networks associated with conditional fear in mice identified using a systems genetics approach. Journal Article

BMC Syst Biol, 5 , pp. 43, 2011, ISSN: 1752-0509.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

Farber, Charles R; Bennett, Brian J; Orozco, Luz; Zou, Wei; Lira, Ana; Kostem, Emrah; Kang, Hyun Min; Furlotte, Nicholas; Berberyan, Ani; Ghazalpour, Anatole; Suwanwela, Jaijam; Drake, Thomas A; Eskin, Eleazar; Wang, Tian Q; Teitelbaum, Steven L; Lusis, Aldons J

Mouse genome-wide association and systems genetics identify asxl2 as a regulator of bone mineral density and osteoclastogenesis. Journal Article

PLoS Genet, 7 (4), pp. e1002038, 2011, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

Keane, Thomas M; Goodstadt, Leo; Danecek, Petr; White, Michael A; Wong, Kim; Yalcin, Binnaz; Heger, Andreas; Agam, Avigail; Slater, Guy; Goodson, Martin; Furlotte, Nicholas A; Eskin, Eleazar; Nellåker, Christoffer; Whitley, Helen; Cleak, James; Janowitz, Deborah; Hernandez-Pliego, Polinka; Edwards, Andrew; Belgard, Grant T; Oliver, Peter L; McIntyre, Rebecca E; Bhomra, Amarjit; Nicod, Jérôme; Gan, Xiangchao; Yuan, Wei; van der Weyden, Louise; Steward, Charles A; Bala, Sendu; Stalker, Jim; Mott, Richard; Durbin, Richard

Mouse genomic variation and its effect on phenotypes and gene regulation. Journal Article

Nature, 477 (7364), pp. 289-94, 2011, ISSN: 1476-4687.

Abstract | Links | BibTeX | Tags: Mouse Genetics

2010

Bennett, Brian J; Farber, Charles R; Orozco, Luz; Kang, Hyun Min; Ghazalpour, Anatole; Siemers, Nathan; Neubauer, Michael; Neuhaus, Isaac; Yordanova, Roumyana; Guan, Bo; Truong, Amy; Yang, Wen-Pin; He, Aiqing; Kayne, Paul; Gargalovic, Peter; Kirchgessner, Todd; Pan, Calvin; Castellani, Lawrence W; Kostem, Emrah; Furlotte, Nicholas; Drake, Thomas A; Eskin, Eleazar; Lusis, Aldons J

A high-resolution association mapping panel for the dissection of complex traits in mice. Journal Article

Genome Res, 20 (2), pp. 281-90, 2010, ISSN: 1549-5469.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

Kang, Hyun Min; Zaitlen, Noah A; Eskin, Eleazar

EMINIM: an adaptive and memory-efficient algorithm for genotype imputation. Journal Article

J Comput Biol, 17 (3), pp. 547-60, 2010, ISSN: 1557-8666.

Abstract | Links | BibTeX | Tags: Imputation, Mouse Genetics

Kirby, Andrew; Kang, Hyun Min; Wade, Claire M; Cotsapas, Chris J; Kostem, Emrah; Han, Buhm; Furlotte, Nick; Kang, Eun Yong; Rivas, Manuel; Bogue, Molly A; Frazer, Kelly A; Johnson, Frank M; Beilharz, Erica J; Cox, David R; Eskin, Eleazar; Daly, Mark J

Fine Mapping in 94 Inbred Mouse Strains Using a High-density Haplotype Resource. Journal Article

Genetics, 2010, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: Mouse Genetics

McLachlan, Stela; Lee, Seung-Min M; Steele, Teresa M; Hawthorne, Paula L; Zapala, Matthew A; Eskin, Eleazar ; Schork, Nicholas J; Anderson, Gregory J; Vulpe, Chris D

In silico QTL mapping of basal liver iron levels in inbred mouse strains. Journal Article

Physiol Genomics, 2010, ISSN: 1531-2267.

Abstract | Links | BibTeX | Tags: Mouse Genetics

2009

Yang, Ivana V; Wade, Claire M; Kang, Hyun Min ; Alper, Scott ; Rutledge, Holly ; Lackford, Brad ; Eskin, Eleazar ; Daly, Mark J; Schwartz, David A

Identification of novel genes that mediate innate immunity using inbred mice. Journal Article

Genetics, 183 (4), pp. 1535-44, 2009, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: Mouse Genetics

2008

Kang, Hyun Min; Zaitlen, Noah A; Wade, Claire M; Kirby, Andrew ; Heckerman, David ; Daly, Mark J; Eskin, Eleazar

Efficient control of population structure in model organism association mapping. Journal Article

Genetics, 178 (3), pp. 1709-23, 2008, ISSN: 0016-6731.

Abstract | Links | BibTeX | Tags: Mouse Genetics, Population Structure Methods

Ghazalpour, Anatole; Doss, Sudheer ; Kang, Hyun ; Farber, Charles ; Wen, Ping-Zi Z; Brozell, Alec ; Castellanos, Ruth ; Eskin, Eleazar ; Smith, Desmond J; Drake, Thomas A; Lusis, Aldons J

High-resolution mapping of gene expression using association in an outbred mouse stock. Journal Article

PLoS Genet, 4 (8), pp. e1000149, 2008, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: Mouse Genetics

2007

Frazer, Kelly A; Eskin, Eleazar ; Kang, Hyun Min ; Bogue, Molly A; Hinds, David A; Beilharz, Erica J; Gupta, Robert V; Montgomery, Julie ; Morenzoni, Matt M; Nilsen, Geoffrey B; Pethiyagoda, Charit L; Stuve, Laura L; Johnson, Frank M; Daly, Mark J; Wade, Claire M; Cox, David R

A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Journal Article

Nature, 448 (7157), pp. 1050-3, 2007, ISSN: 1476-4687.

Abstract | Links | BibTeX | Tags: Mouse Genetics