Atropos: specific, sensitive, and speedy trimming of sequencing reads von Didion, John P, Martin, Marcel, Collins, Francis S

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Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle von Taylor, D. Leland, Jackson, Anne U., Narisu, Narisu, Hemani, Gibran, Erdos, Michael R., Chines, Peter S., Swift, Amy, Idol, Jackie, Didion, John P., Welch, Ryan P., Kinnunen, Leena, Saramies, Jouko, Lakka, Timo A., Laakso, Markku, Tuomilehto, Jaakko, Parker, Stephen C. J., Koistinen, Heikki A., Smith, George Davey, Boehnke, Michael, Scott, Laura J., Birney, Ewan, Collins, Francis S.

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Genetic regulatory signatures underlying islet gene expression and type 2 diabetes von Varshney, Arushi, Scott, Laura J., Welch, Ryan P., Erdos, Michael R., Chines, Peter S., Narisu, Narisu, Albanus, Ricardo D’O., Orchard, Peter, Wolford, Brooke N., Kursawe, Romy, Vadlamudi, Swarooparani, Cannon, Maren E., Didion, John P., Hensley, John, Kirilusha, Anthony, Bonnycastle, Lori L., Taylor, D. Leland, Watanabe, Richard, Mohlke, Karen L., Boehnke, Michael, Collins, Francis S., Parker, Stephen C. J., Stitzel, Michael L.

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The Mouse Universal Genotyping Array: From Substrains to Subspecies von Morgan, Andrew P, Fu, Chen-Ping, Kao, Chia-Yu, Welsh, Catherine E, Didion, John P, Yadgary, Liran, Hyacinth, Leeanna, Ferris, Martin T, Bell, Timothy A, Miller, Darla R, Giusti-Rodriguez, Paola, Nonneman, Randal J, Cook, Kevin D, Whitmire, Jason K, Gralinski, Lisa E, Keller, Mark, Attie, Alan D, Churchill, Gary A, Petkov, Petko, Sullivan, Patrick F, Brennan, Jennifer R, McMillan, Leonard, Pardo-Manuel de Villena, Fernando

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Subspecific origin and haplotype diversity in the laboratory mouse von Churchill, Gary A, de Villena, Fernando Pardo-Manuel, Yang, Hyuna, Wang, Jeremy R, Didion, John P, Buus, Ryan J, Bell, Timothy A, Welsh, Catherine E, Bonhomme, François, Yu, Alex Hon-Tsen, Nachman, Michael W, Pialek, Jaroslav, Tucker, Priscilla, Boursot, Pierre, McMillan, Leonard

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Coexistent ARID1A–PIK3CA mutations promote ovarian clear-cell tumorigenesis through pro-tumorigenic inflammatory cytokine signalling von Chandler, Ronald L., Damrauer, Jeffrey S., Raab, Jesse R., Schisler, Jonathan C., Wilkerson, Matthew D., Didion, John P., Starmer, Joshua, Serber, Daniel, Yee, Della, Xiong, Jessie, Darr, David B., de Villena, Fernando Pardo-Manuel, Kim, William Y., Magnuson, Terry

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Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures von Rai, Vivek, Quang, Daniel X., Erdos, Michael R., Cusanovich, Darren A., Daza, Riza M., Narisu, Narisu, Zou, Luli S., Didion, John P., Guan, Yuanfang, Shendure, Jay, Parker, Stephen C.J., Collins, Francis S.

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Genetic architecture of skewed X inactivation in the laboratory mouse von Calaway, John D, Lenarcic, Alan B, Didion, John P, Wang, Jeremy R, Searle, Jeremy B, McMillan, Leonard, Valdar, William, Pardo-Manuel de Villena, Fernando

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Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance von Crowley, James J, Zhabotynsky, Vasyl, Sun, Wei, Huang, Shunping, Pakatci, Isa Kemal, Kim, Yunjung, Wang, Jeremy R, Morgan, Andrew P, Calaway, John D, Aylor, David L, Yun, Zaining, Bell, Timothy A, Buus, Ryan J, Calaway, Mark E, Didion, John P, Gooch, Terry J, Hansen, Stephanie D, Robinson, Nashiya N, Shaw, Ginger D, Spence, Jason S, Quackenbush, Corey R, Barrick, Cordelia J, Nonneman, Randal J, Kim, Kyungsu, Xenakis, James, Xie, Yuying, Valdar, William, Lenarcic, Alan B, Wang, Wei, Welsh, Catherine E, Fu, Chen-Ping, Zhang, Zhaojun, Holt, James, Guo, Zhishan, Threadgill, David W, Tarantino, Lisa M, Miller, Darla R, Zou, Fei, McMillan, Leonard, Sullivan, Patrick F, Pardo-Manuel de Villena, Fernando

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BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues von Zou, Luli S, Erdos, Michael R, Taylor, D Leland, Chines, Peter S, Varshney, Arushi, Parker, Stephen C J, Collins, Francis S, Didion, John P

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Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias von Didion, John P, Yang, Hyuna, Sheppard, Keith, Fu, Chen-Ping, McMillan, Leonard, de Villena, Fernando Pardo-Manuel, Churchill, Gary A

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Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse von Didion, John P, de Villena, Fernando Pardo-Manuel

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Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales von Morgan, Andrew P, Hughes, Jonathan J, Didion, John P, Jolley, Wesley J, Campbell, Karl J, Threadgill, David W, Bonhomme, Francois, Searle, Jeremy B, de Villena, Fernando Pardo-Manuel

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A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2 von Didion, John P, Morgan, Andrew P, Clayshulte, Amelia M-F, Mcmullan, Rachel C, Yadgary, Liran, Petkov, Petko M, Bell, Timothy A, Gatti, Daniel M, Crowley, James J, Hua, Kunjie, Aylor, David L, Bai, Ling, Calaway, Mark, Chesler, Elissa J, French, John E, Geiger, Thomas R, Gooch, Terry J, Garland, Jr, Theodore, Harrill, Alison H, Hunter, Kent, McMillan, Leonard, Holt, Matt, Miller, Darla R, O'Brien, Deborah A, Paigen, Kenneth, Pan, Wenqi, Rowe, Lucy B, Shaw, Ginger D, Simecek, Petr, Sullivan, Patrick F, Svenson, Karen L, Weinstock, George M, Threadgill, David W, Pomp, Daniel, Churchill, Gary A, Pardo-Manuel de Villena, Fernando

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R2d2 Drives Selfish Sweeps in the House Mouse von Didion, John P, Morgan, Andrew P, Yadgary, Liran, Bell, Timothy A, McMullan, Rachel C, Ortiz de Solorzano, Lydia, Britton-Davidian, Janice, Bult, Carol J, Campbell, Karl J, Castiglia, Riccardo, Ching, Yung-Hao, Chunco, Amanda J, Crowley, James J, Chesler, Elissa J, Förster, Daniel W, French, John E, Gabriel, Sofia I, Gatti, Daniel M, Garland, Jr, Theodore, Giagia-Athanasopoulou, Eva B, Giménez, Mabel D, Grize, Sofia A, Gündüz, İslam, Holmes, Andrew, Hauffe, Heidi C, Herman, Jeremy S, Holt, James M, Hua, Kunjie, Jolley, Wesley J, Lindholm, Anna K, López-Fuster, María J, Mitsainas, George, da Luz Mathias, Maria, McMillan, Leonard, Ramalhinho, Maria da Graça Morgado, Rehermann, Barbara, Rosshart, Stephan P, Searle, Jeremy B, Shiao, Meng-Shin, Solano, Emanuela, Svenson, Karen L, Thomas-Laemont, Patricia, Threadgill, David W, Ventura, Jacint, Weinstock, George M, Pomp, Daniel, Churchill, Gary A, Pardo-Manuel de Villena, Fernando

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The genetic regulatory signature of type 2 diabetes in human skeletal muscle von Scott, Laura J., Erdos, Michael R., Huyghe, Jeroen R., Welch, Ryan P., Beck, Andrew T., Wolford, Brooke N., Chines, Peter S., Didion, John P., Narisu, Narisu, Stringham, Heather M., Taylor, D. Leland, Jackson, Anne U., Vadlamudi, Swarooparani, Bonnycastle, Lori L., Kinnunen, Leena, Saramies, Jouko, Sundvall, Jouko, Albanus, Ricardo D'Oliveira, Kiseleva, Anna, Hensley, John, Crawford, Gregory E., Jiang, Hui, Wen, Xiaoquan, Watanabe, Richard M., Lakka, Timo A., Mohlke, Karen L., Laakso, Markku, Tuomilehto, Jaakko, Koistinen, Heikki A., Boehnke, Michael, Collins, Francis S., Parker, Stephen C. J.

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Targeted Quantitative Analysis of Streptococcus pyogenes Virulence Factors by Multiple Reaction Monitoring von Lange, Vinzenz, Malmström, Johan A., Didion, John, King, Nichole L., Johansson, Björn P., Schäfer, Juliane, Rameseder, Jonathan, Wong, Chee-Hong, Deutsch, Eric W., Brusniak, Mi-Youn, Buühlmann, Peter, Björck, Lars, Domon, Bruno, Aebersold, Ruedi

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The Evolutionary Fates of a Large Segmental Duplication in Mouse von Morgan, Andrew P, Holt, J Matthew, McMullan, Rachel C, Bell, Timothy A, Clayshulte, Amelia M-F, Didion, John P, Yadgary, Liran, Thybert, David, Odom, Duncan T, Flicek, Paul, McMillan, Leonard, de Villena, Fernando Pardo-Manuel

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SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy von Didion, John P, Buus, Ryan J, Naghashfar, Zohreh, Threadgill, David W, Morse, 3rd, Herbert C, de Villena, Fernando Pardo-Manuel

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Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers von Morgan, Andrew P, Didion, John P, Doran, Anthony G, Holt, James M, McMillan, Leonard, Keane, Thomas M, de Villena, Fernando Pardo-Manuel

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