Mouse

Collaborative Cross

Genome-Wide Association Study in Two Cohorts from a Multi-generational Mouse Advanced Intercross Line Highlights the Difficulty of Replication Due to Study-Specific Heterogeneity
Xinzhu Zhou, Celine L. St. Pierre, Natalia M. Gonzales, Jennifer Zou, Riyan Cheng, Apurva S. Chitre, Greta Sokoloff, Abraham A. Palmer

G3: Genes, Genomes, Genetics March 2020 10: 951-965; https://doi.org/10.1534/g3.119.400763
A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size
John R. Shorter, Paul L. Maurizio, Timothy A. Bell, Ginger D. Shaw, Darla R. Miller, Terry J. Gooch, Jason S. Spence, Leonard McMillan, William Valdar, Fernando Pardo-Manuel de Villena

G3: Genes, Genomes, Genetics May 2019 9: 1613-1622; https://doi.org/10.1534/g3.118.200847
Determinants of QTL Mapping Power in the Realized Collaborative Cross
Gregory R. Keele, Wesley L. Crouse, Samir N. P. Kelada, William Valdar

G3: Genes, Genomes, Genetics May 2019 9: 1707-1727; https://doi.org/10.1534/g3.119.400194
Bayesian Diallel Analysis Reveals Mx1-Dependent and Mx1-Independent Effects on Response to Influenza A Virus in Mice
Paul L. Maurizio, Martin T. Ferris, Gregory R. Keele, Darla R. Miller, Ginger D. Shaw, Alan C. Whitmore, Ande West, Clayton R. Morrison, Kelsey E. Noll, Kenneth S. Plante, Adam S. Cockrell, David W. Threadgill, Fernando Pardo-Manuel de Villena, Ralph S. Baric, Mark T. Heise, William Valdar

G3: Genes, Genomes, Genetics February 2018 8: 427-445; https://doi.org/10.1534/g3.117.300438
Joint Analysis of Strain and Parent-of-Origin Effects for Recombinant Inbred Intercrosses Generated from Multiparent Populations with the Collaborative Cross as an Example
Yanyan Liu, Sican Xiong, Wei Sun, Fei Zou

G3: Genes, Genomes, Genetics February 2018 8: 599-605; https://doi.org/10.1534/g3.117.300483
Structural Variation Shapes the Landscape of Recombination in Mouse

Andrew P. Morgan, Daniel M. Gatti, Maya L. Najarian, Thomas M. Keane, Raymond J. Galante, Allan I. Pack, Richard Mott, Gary A. Churchill, Fernando Pardo-Manuel de Villena

Genetics June 2017 206: 603-619; https://doi.org/10.1534/genetics.116.197988
Genomes of the Mouse Collaborative Cross
Open Access

Anuj Srivastava, Andrew P. Morgan, Maya L. Najarian, Vishal Kumar Sarsani, J. Sebastian Sigmon, John R. Shorter, Anwica Kashfeen, Rachel C. McMullan, Lucy H. Williams, Paola Giusti-Rodríguez, Martin T. Ferris, Patrick Sullivan, Pablo Hock, Darla R. Miller, Timothy A. Bell, Leonard McMillan, Gary A. Churchill, Fernando Pardo-Manuel de Villena

Genetics June 2017 206: 537-556; https://doi.org/10.1534/genetics.116.198838
Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross

John R. Shorter, Fanny Odet, David L. Aylor, Wenqi Pan, Chia-Yu Kao, Chen-Ping Fu, Andrew P. Morgan, Seth Greenstein, Timothy A. Bell, Alicia M. Stevans, Ryan W. Feathers, Sunny Patel, Sarah E. Cates, Ginger D. Shaw, Darla R. Miller, Elissa J. Chesler, Leonard McMillian, Deborah A. O’Brien, Fernando Pardo-Manuel de Villena

Genetics June 2017 206: 557-572; https://doi.org/10.1534/genetics.116.199596
Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice
Lisa E. Gralinski, Vineet D. Menachery, Andrew P. Morgan, Allison L. Totura, Anne Beall, Jacob Kocher, Jessica Plante, D. Corinne Harrison-Shostak, Alexandra Schäfer, Fernando Pardo-Manuel de Villena, Martin T. Ferris, Ralph S. Baric

G3: Genes, Genomes, Genetics June 2017 7: 1653-1663; https://doi.org/10.1534/g3.117.041434
Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross
Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Duncan M. Hendrick, Kathleen Voss, Renee C. Ireton, Michael Mooney, Jennifer T. Go, Gabrielle Choonoo, Sophia Jeng, Fernando Pardo-Manuel de Villena, Martin T. Ferris, Shannon McWeeney, Michael Gale

G3: Genes, Genomes, Genetics June 2017 7: 1665-1682; https://doi.org/10.1534/g3.117.041624
Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders
Daniel Oreper, Yanwei Cai, Lisa M. Tarantino, Fernando Pardo- Manuel de Villena, William Valdar

G3: Genes, Genomes, Genetics June 2017 7: 1623-1630; https://doi.org/10.1534/g3.117.041491
The Evolutionary Fates of a Large Segmental Duplication in Mouse

Andrew P. Morgan, J. Matthew Holt, Rachel C. McMullan, Timothy A. Bell, Amelia M.-F. Clayshulte, John P. Didion, Liran Yadgary, David Thybert, Duncan T. Odom, Paul Flicek, Leonard McMillan, Fernando Pardo-Manuel de Villena

Genetics September 2016 204: 267-285; https://doi.org/10.1534/genetics.116.191007
Plethysmography Phenotype QTL in Mice Before and After Allergen Sensitization and Challenge
Samir N. P. Kelada

G3: Genes, Genomes, Genetics September 2016 6: 2857-2865; https://doi.org/10.1534/g3.116.032912
The Founder Strains of the Collaborative Cross Express a Complex Combination of Advantageous and Deleterious Traits for Male Reproduction
Fanny Odet, Wenqi Pan, Timothy A. Bell, Summer G. Goodson, Alicia M. Stevans, Zianing Yun, David L. Aylor, Chia-Yu Kao, Leonard McMillan, Fernando Pardo-Manuel de Villena, Deborah A. O’Brien

G3: Genes, Genomes, Genetics December 2015 5: 2671-2683; https://doi.org/10.1534/g3.115.020172
Linkage Disequilibrium with Linkage Analysis of Multiline Crosses Reveals Different Multiallelic QTL for Hybrid Performance in the Flint and Dent Heterotic Groups of Maize

Héloïse Giraud, Christina Lehermeier, Eva Bauer, Matthieu Falque, Vincent Segura, Cyril Bauland, Christian Camisan, Laura Campo, Nina Meyer, Nicolas Ranc, Wolfgang Schipprack, Pascal Flament, Albrecht E. Melchinger, Monica Menz, Jesús Moreno-González, Milena Ouzunova, Alain Charcosset, Chris-Carolin Schön, Laurence Moreau

Genetics December 2014 198: 1717-1734; https://doi.org/10.1534/genetics.114.169367
RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations
Open Access

Steven C. Munger, Narayanan Raghupathy, Kwangbom Choi, Allen K. Simons, Daniel M. Gatti, Douglas A. Hinerfeld, Karen L. Svenson, Mark P. Keller, Alan D. Attie, Matthew A. Hibbs, Joel H. Graber, Elissa J. Chesler, Gary A. Churchill

Genetics September 2014 198: 59-73; https://doi.org/10.1534/genetics.114.165886
Rapid Identification of Major-Effect Genes Using the Collaborative Cross
Open Access

Ramesh Ram, Munish Mehta, Lois Balmer, Daniel M. Gatti, Grant Morahan

Genetics September 2014 198: 75-86; https://doi.org/10.1534/genetics.114.163014
High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized Distribution of Crossovers in Male Germline
Open Access

Eric Yi Liu, Andrew P. Morgan, Elissa J. Chesler, Wei Wang, Gary A. Churchill, Fernando Pardo-Manuel de Villena

Genetics May 2014 197: 91-106; https://doi.org/10.1534/genetics.114.161653
Genetics of Adverse Reactions to Haloperidol in a Mouse Diallel: A Drug–Placebo Experiment and Bayesian Causal Analysis
Open Access

James J. Crowley, Yunjung Kim, Alan B. Lenarcic, Corey R. Quackenbush, Cordelia J. Barrick, Daniel E. Adkins, Ginger S. Shaw, Darla R. Miller, Fernando Pardo-Manuel de Villena, Patrick F. Sullivan, William Valdar

Genetics January 2014 196: 321-347; https://doi.org/10.1534/genetics.113.156901
Ten Years of the Collaborative Cross

David W. Threadgill, Gary A. Churchill

Genetics February 2012 190: 291-294; https://doi.org/10.1534/genetics.111.138032
Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines
Open Access

Karl W. Broman

Genetics February 2012 190: 403-412; https://doi.org/10.1534/genetics.111.132647
The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population
Open Access

Collaborative Cross Consortium

Genetics February 2012 190: 389-401; https://doi.org/10.1534/genetics.111.132639
Varying Coefficient Models for Mapping Quantitative Trait Loci Using Recombinant Inbred Intercrosses

Yi Gong, Fei Zou

Genetics February 2012 190: 475-486; https://doi.org/10.1534/genetics.111.132522
Expression Quantitative Trait Loci for Extreme Host Response to Influenza A in Pre-Collaborative Cross Mice
Daniel Bottomly, Martin T. Ferris, Lauri D. Aicher, Elizabeth Rosenzweig, Alan Whitmore, David L. Aylor, Bart L. Haagmans, Lisa E. Gralinski, Birgit G. Bradel-Tretheway, Janine T. Bryan, David W. Threadgill, Fernando Pardo-Manuel de Villena, Ralph S. Baric, Michael G. Katze, Mark Heise, Shannon K. McWeeney

G3: Genes, Genomes, Genetics February 2012 2: 213-221; https://doi.org/10.1534/g3.111.001800
Genetic Analysis of Hematological Parameters in Incipient Lines of the Collaborative Cross
Samir N. P. Kelada, David L. Aylor, Bailey C. E. Peck, Joseph F. Ryan, Urraca Tavarez, Ryan J. Buus, Darla R. Miller, Elissa J. Chesler, David W. Threadgill, Gary A. Churchill, Fernando Pardo-Manuel de Villena, Francis S. Collins

G3: Genes, Genomes, Genetics February 2012 2: 157-165; https://doi.org/10.1534/g3.111.001776
Simulating the Collaborative Cross: Power of Quantitative Trait Loci Detection and Mapping Resolution in Large Sets of Recombinant Inbred Strains of Mice

William Valdar, Jonathan Flint, Richard Mott

Genetics March 2006 172: 1783-1797; https://doi.org/10.1534/genetics.104.039313

Diversity Outbred

Testing Pleiotropy vs. Separate QTL in Multiparental Populations
Frederick J. Boehm, Elissa J. Chesler, Brian S. Yandell, Karl W. Broman

G3: Genes, Genomes, Genetics July 2019 9: 2317-2324; https://doi.org/10.1534/g3.119.400098
Cleaning Genotype Data from Diversity Outbred Mice
Karl W. Broman, Daniel M. Gatti, Karen L. Svenson, Śaunak Sen, Gary A. Churchill

G3: Genes, Genomes, Genetics May 2019 9: 1571-1579; https://doi.org/10.1534/g3.119.400165
Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice
Open Access

Anna L. Tyler, Bo Ji, Daniel M. Gatti, Steven C. Munger, Gary A. Churchill, Karen L. Svenson, Gregory W. Carter

Genetics June 2017 206: 621-639; https://doi.org/10.1534/genetics.116.198051
Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection
Elissa J. Chesler, Daniel M. Gatti, Andrew P. Morgan, Marge Strobel, Laura Trepanier, Denesa Oberbeck, Shannon McWeeney, Robert Hitzemann, Martin Ferris, Rachel McMullan, Amelia Clayshultle, Timothy A. Bell, Fernando Pardo Manuel de Villena, Gary A. Churchill

G3: Genes, Genomes, Genetics December 2016 6: 3893-3902; https://doi.org/10.1534/g3.116.035527
Genetic Architectures of Quantitative Variation in RNA Editing Pathways

Tongjun Gu, Daniel M. Gatti, Anuj Srivastava, Elizabeth M. Snyder, Narayanan Raghupathy, Petr Simecek, Karen L. Svenson, Ivan Dotu, Jeffrey H. Chuang, Mark P. Keller, Alan D. Attie, Robert E. Braun, Gary A. Churchill

Genetics February 2016 202: 787-798; https://doi.org/10.1534/genetics.115.179481
High-Resolution Genetic Mapping in the Diversity Outbred Mouse Population Identifies Apobec1 as a Candidate Gene for Atherosclerosis
Tangi L. Smallwood, Daniel M. Gatti, Pamela Quizon, George M. Weinstock, Kuo-Chen Jung, Liyang Zhao, Kunjie Hua, Daniel Pomp, Brian J. Bennett

G3: Genes, Genomes, Genetics December 2014 4: 2353-2363; https://doi.org/10.1534/g3.114.014704
Quantitative Trait Locus Mapping Methods for Diversity Outbred Mice
Daniel M. Gatti, Karen L. Svenson, Andrey Shabalin, Long-Yang Wu, William Valdar, Petr Simecek, Neal Goodwin, Riyan Cheng, Daniel Pomp, Abraham Palmer, Elissa J. Chesler, Karl W. Broman, Gary A. Churchill

G3: Genes, Genomes, Genetics September 2014 4: 1623-1633; https://doi.org/10.1534/g3.114.013748
High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population

Karen L. Svenson, Daniel M. Gatti, William Valdar, Catherine E. Welsh, Riyan Cheng, Elissa J. Chesler, Abraham A. Palmer, Leonard McMillan, Gary A. Churchill

Genetics February 2012 190: 437-447; https://doi.org/10.1534/genetics.111.132597
Genome-Wide Association Mapping of Quantitative Traits in Outbred Mice
Weidong Zhang, Ron Korstanje, Jill Thaisz, Frank Staedtler, Nicole Harttman, Lingfei Xu, Minjie Feng, Liane Yanas, Hyuna Yang, William Valdar, Gary A. Churchill, Keith DiPetrillo

G3: Genes, Genomes, Genetics February 2012 2: 167-174; https://doi.org/10.1534/g3.111.001792

Genomes

The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population
Open Access

Collaborative Cross Consortium

Genetics February 2012 190: 389-401; https://doi.org/10.1534/genetics.111.132639
Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines
Open Access

Karl W. Broman

Genetics February 2012 190: 403-412; https://doi.org/10.1534/genetics.111.132647

Genotyping

High-Density Genotypes of Inbred Mouse Strains: Improved Power and Precision of Association Mapping
Christoph D. Rau, Brian Parks, Yibin Wang, Eleazar Eskin, Petr Simecek, Gary A. Churchill, Aldons J. Lusis

G3: Genes, Genomes, Genetics October 2015 5: 2021-2026; https://doi.org/10.1534/g3.115.020784
Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines
Open Access

Karl W. Broman

Genetics February 2012 190: 403-412; https://doi.org/10.1534/genetics.111.132647

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