Ashbrook, D. G., Arends, D., Prins, P., Mulligan, M. K., Roy, S., Williams, E., Lutz, C. M., Valenzuela, A., Bohl, C. J., Ingels, J. F., McCarty, M. S., Centeno, A. G., Hager, R., Auwerx, J., Lu, L., & Williams, R. W. (2021). A platform for experimental precision medicine: The extended BXD mouse family. Cell systems, 12(3), 235-247.e9.
Čuklina, J., Lee, C. H., Williams, E., Sajic, T., Collins, B. C., Rodríguez Martínez, M., Sharma, V. S., Wendt, F., Goetze, S., Keele, G. R., Wollscheid, B., Aebersold, R., & Pedrioli, P. G. A. (2021). Diagnostics and correction of batch effects in large-scale proteomic studies: a tutorial. Molecular systems biology, 17(8), 10240.
Pfister, N., Williams, E., Peters, J., Aebersold, R., & Bühlmann, P. (2021). Stabilizing variable selection and regression. Annals of Applied Statistics, 15(3).
Roy, S., Bou Sleiman, M., Jha, P., Ingels, J., Chapman, C., McCarty, M., Ziebarth, J., Hook, M., Sun, A., Zhao, W., Huang, J., Neuner, S., Wilmott, L., Shapaker, T., Centeno, A., Ashbrook, D., Mulligan, M., Kaczorowski, C., Makowski, L., Cui, Y., Read, R., Miller, R., Mozhui, K., Williams, E., Sen, S., Lu, L., Auwerx, J., & Williams, R. (2021). Gene-by-environment modulation of lifespan and weight gain in the murine BXD family. Nature Metabolism.
van der Kolk, B. W., Saari, S., Lovric, A., Arif, M., Alvarez, M., Ko, A., Miao, Z., Sahebekhtiari, N., Muniandy, M., Heinonen, S., Oghabian, A., Jokinen, R., Jukarainen, S., Hakkarainen, A., Lundbom, J., Kuula, J., Groop, P.-H., Tukiainen, T., Lundbom, N., Rissanen, A., Kaprio, J., Williams, E., Zamboni, N., Mardinoglu, A., Pajukanta, P., & Pietiläinen, K. H. (2021). Molecular pathways behind acquired obesity: Adipose tissue and skeletal muscle multiomics in monozygotic twin pairs discordant for BMI. Cell Reports Medicine, 2(4), 100226.
Williams, E., Pfister, N., Roy, S., Statzer, C., Haverty, J., Ingels, J., Bohl, C., Hasan, M., Cuklina, J., Bühlmann, P., Zamboni, N., Lu, L., Ewald, C., Williams, R., & Aebersold, R. (2021). Multiomic profiling of the liver across diets and age in a diverse mouse population. Cell Systems.


Liu, Y. J., McIntyre, R. L., Janssens, G. E., Williams, E., Lan, J., van Weeghel, M., Schomakers, B., van der Veen, H., van der Wel, N. N., Yao, P., Mair, W. B., Aebersold, R., MacInnes, A. W., & Houtkooper, R. H. (2020). Mitochondrial translation and dynamics synergistically extend lifespan in C. elegans through HLH-30. The Journal of cell biology, 219(6).
Molenaars, M., Janssens, G. E., Williams, E., Jongejan, A., Lan, J., Rabot, S., Joly, F., Moerland, P. D., Schomakers, B. V., Lezzerini, M., Liu, Y. J., McCormick, M. A., Kennedy, B. K., van Weeghel, M., van Kampen, A. H. C., Aebersold, R., MacInnes, A. W., & Houtkooper, R. H. (2020). A Conserved Mito-Cytosolic Translational Balance Links Two Longevity Pathways. Cell metabolism, 31(3), 549-563.e7.
Rosenberger, G., Heusel, M., Bludau, I., Collins, B. C., Martelli, C., Williams, E., Xue, P., Liu, Y., Aebersold, R., & Califano, A. (2020). SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell systems, 11(6), 589-607.e8.
Sandoval-Sierra, J. V., Helbing, A. H. B., Williams, E., Ashbrook, D. G., Roy, S., Williams, R. W., & Mozhui, K. (2020). Body weight and high-fat diet are associated with epigenetic aging in female members of the BXD murine family. Aging cell, 19(9), 13207.


Leandro, J., Violante, S., Argmann, C. A., Hagen, J., Dodatko, T., Bender, A., Zhang, W., Williams, E., Bachmann, A. M., Auwerx, J., Yu, C., & Houten, S. M. (2019). Mild inborn errors of metabolism in commonly used inbred mouse strains. Molecular Genetics and Metabolism, 126(4), 388-396.
Liu, Y., Mi, Y., Mueller, T., Kreibich, S., Williams, E., Van Drogen, A., Borel, C., Frank, M., Germain, P.-L., Bludau, I., Mehnert, M., Seifert, M., Emmenlauer, M., Sorg, I., Bezrukov, F., Bena, F. S., Zhou, H., Dehio, C., Testa, G., Saez-Rodriguez, J., Antonarakis, S. E., Hardt, W.-D., & Aebersold, R. (2019). Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature biotechnology, 37(3), 314-322.
Perez-Munoz, M. E., McKnite, A. M., Williams, E., Auwerx, J., Williams, R. W., Peterson, D. A., & Ciobanu, D. C. (2019). Diet modulates cecum bacterial diversity and physiological phenotypes across the BXD mouse genetic reference population. PloS one, 14(10), 0224100.
Sajic, T., Ciuffa, R., Lemos, V., Xu, P., Leone, V., Li, C., Williams, E., Makris, G., Banaei-Esfahani, A., Heikenwalder, M., Schoonjans, K., & Aebersold, R. (2019). A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model. Scientific reports, 9(1), 6913.
Williams, E., & Stein, S. (2019). JCAD: from systems genetics identification to the experimental validation of a coronary artery disease risk locus. European heart journal, 40(29), 2409-2412.


Hook, M., Roy, S., Williams, E., Bou Sleiman, M., Mozhui, K., Nelson, J. F., Lu, L., Auwerx, J., & Williams, R. W. (2018). Genetic cartography of longevity in humans and mice: Current landscape and horizons. Biochimica et biophysica acta. Molecular basis of disease, 1864(9 Pt A), 2718-2732.
Jha, P., McDevitt, M. T., Gupta, R., Quiros, P. M., Williams, E., Gariani, K., Sleiman, M. B., Diserens, L., Jochem, A., Ulbrich, A., Coon, J. J., Auwerx, J., & Pagliarini, D. J. (2018). Systems Analyses Reveal Physiological Roles and Genetic Regulators of Liver Lipid Species. Cell systems, 6(6), 722-733.e6.
Jha, P., McDevitt, M. T., Halilbasic, E., Williams, E., Quiros, P. M., Gariani, K., Sleiman, M. B., Gupta, R., Ulbrich, A., Jochem, A., Coon, J. J., Trauner, M., Pagliarini, D. J., & Auwerx, J. (2018). Genetic Regulation of Plasma Lipid Species and Their Association with Metabolic Phenotypes. Cell systems, 6(6), 709-721.e6.
Sajic, T., Liu, Y., Arvaniti, E., Surinova, S., Williams, E., Schiess, R., Huttenhain, R., Sethi, A., Pan, S., Brentnall, T. A., Chen, R., Blattmann, P., Friedrich, B., Nimeus, E., Malander, S., Omlin, A., Gillessen, S., Claassen, M., & Aebersold, R. (2018). Similarities and Differences of Blood N-Glycoproteins in Five Solid Carcinomas at Localized Clinical Stage Analyzed by SWATH-MS. Cell reports, 23(9), 2819-2831.e5.
Williams, E., Wu, Y., Wolski, W., Kim, J. Y., Lan, J., Hasan, M., Halter, C., Jha, P., Ryu, D., Auwerx, J., & Aebersold, R. (2018). Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population. Molecular and Cellular Proteomics, 17(9), 1766-1777.


Liu, Y., Borel, C., Li, L., Muller, T., Williams, E., Germain, P.-L., Buljan, M., Sajic, T., Boersema, P. J., Shao, W., Faini, M., Testa, G., Beyer, A., Antonarakis, S. E., & Aebersold, R. (2017). Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nature communications, 8(1), 1212.
Williams, R. W., & Williams, E. (2017). Resources for Systems Genetics. Methods in Molecular Biology, 1488, 3-29.
Wu, Y., Williams, E., & Aebersold, R. (2017). Application of SWATH Proteomics to Mouse Biology. Current protocols in mouse biology, 7(2), 130-143.


Merkwirth, C., Jovaisaite, V., Durieux, J., Matilainen, O., Jordan, S. D., Quiros, P. M., Steffen, K. K., Williams, E., Mouchiroud, L., Tronnes, S. U., Murillo, V., Wolff, S. C., Shaw, R. J., Auwerx, J., & Dillin, A. (2016). Two Conserved Histone Demethylases Regulate Mitochondrial Stress-Induced Longevity. Cell, 165(5), 1209-1223.
Mouchiroud, L., Sorrentino, V., Williams, E., Cornaglia, M., Frochaux, M. V., Lin, T., Nicolet-Dit-Felix, A. A., Krishnamani, G., Ouhmad, T., Gijs, M. A. M., Deplancke, B., & Auwerx, J. (2016). The Movement Tracker: A Flexible System for Automated Movement Analysis in Invertebrate Model Organisms. Current protocols in neuroscience, 77, 8.37.1-8.37.21.
Ryu, D., Mouchiroud, L., Andreux, P. A., Katsyuba, E., Moullan, N., Nicolet-Dit-Felix, A. A., Williams, E., Jha, P., Lo Sasso, G., Huzard, D., Aebischer, P., Sandi, C., Rinsch, C., & Auwerx, J. (2016). Urolithin A induces mitophagy and prolongs lifespan in C. elegans and increases muscle function in rodents. Nature medicine, 22(8), 879-88.
Wang, X., Pandey, A. K., Mulligan, M. K., Williams, E., Mozhui, K., Li, Z., Jovaisaite, V., Quarles, L. D., Xiao, Z., Huang, J., Capra, J. A., Chen, Z., Taylor, W. L., Bastarache, L., Niu, X., Pollard, K. S., Ciobanu, D. C., Reznik, A. O., Tishkov, A. V., Zhulin, I. B., Peng, J., Nelson, S. F., Denny, J. C., Auwerx, J., Lu, L., & Williams, R. W. (2016). Joint mouse-human phenome-wide association to test gene function and disease risk. Nature communications, 7, 10464.
Williams, E., Wu, Y., Jha, P., Dubuis, S., Blattmann, P., Argmann, C. A., Houten, S. M., Amariuta, T., Wolski, W., Zamboni, N., Aebersold, R., & Auwerx, J. (2016). Systems proteomics of liver mitochondria function. Science (New York, N.Y.), 352(6291), 0189.


Moullan, N., Mouchiroud, L., Wang, X., Ryu, D., Williams, E., Mottis, A., Jovaisaite, V., Frochaux, M. V., Quiros, P. M., Deplancke, B., Houtkooper, R. H., & Auwerx, J. (2015). Tetracyclines Disturb Mitochondrial Function across Eukaryotic Models: A Call for Caution in Biomedical Research. Cell reports, 10(10), 1681-1691.
van de Weijer, T., Phielix, E., Bilet, L., Williams, E., Ropelle, E. R., Bierwagen, A., Livingstone, R., Nowotny, P., Sparks, L. M., Paglialunga, S., Szendroedi, J., Havekes, B., Moullan, N., Pirinen, E., Hwang, J.-H., Schrauwen-Hinderling, V. B., Hesselink, M. K. C., Auwerx, J., Roden, M., & Schrauwen, P. (2015). Evidence for a direct effect of the NAD+ precursor acipimox on muscle mitochondrial function in humans. Diabetes, 64(4), 1193-201.
Williams, E., & Auwerx, J. (2015). The Convergence of Systems and Reductionist Approaches in Complex Trait Analysis. Cell, 162(1), 23-32.


Hasenfuss, S. C., Bakiri, L., Thomsen, M. K., Williams, E., Auwerx, J., & Wagner, E. F. (2014). Regulation of steatohepatitis and PPARgamma signaling by distinct AP-1 dimers. Cell metabolism, 19(1), 84-95.
Pirinen, E., Canto, C., Jo, Y. S., Morato, L., Zhang, H., Menzies, K. J., Williams, E., Mouchiroud, L., Moullan, N., Hagberg, C., Li, W., Timmers, S., Imhof, R., Verbeek, J., Pujol, A., van Loon, B., Viscomi, C., Zeviani, M., Schrauwen, P., Sauve, A. A., Schoonjans, K., & Auwerx, J. (2014). Pharmacological Inhibition of poly(ADP-ribose) polymerases improves fitness and mitochondrial function in skeletal muscle. Cell metabolism, 19(6), 1034-41.
Williams, E., Mouchiroud, L., Frochaux, M., Pandey, A., Andreux, P. A., Deplancke, B., & Auwerx, J. (2014). An evolutionarily conserved role for the aryl hydrocarbon receptor in the regulation of movement. PLoS genetics, 10(9), 1004673.
Wu, Y., Williams, E., Dubuis, S., Mottis, A., Jovaisaite, V., Houten, S. M., Argmann, C. A., Faridi, P., Wolski, W., Kutalik, Z., Zamboni, N., Auwerx, J., & Aebersold, R. (2014). Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell, 158(6), 1415-1430.


Andreux, P. A., Williams, E., Koutnikova, H., Houtkooper, R. H., Champy, M.-F., Henry, H., Schoonjans, K., Williams, R. W., & Auwerx, J. (2012). Systems genetics of metabolism: the use of the BXD murine reference panel for multiscalar integration of traits. Cell, 150(6), 1287-99.
McKnite, A. M., Perez-Munoz, M. E., Lu, L., Williams, E., Brewer, S., Andreux, P. A., Bastiaansen, J. W. M., Wang, X., Kachman, S. D., Auwerx, J., Williams, R. W., Benson, A. K., Peterson, D. A., & Ciobanu, D. C. (2012). Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits. PloS one, 7(6), 39191.


Yamamoto, H., Williams, E., Mouchiroud, L., Canto, C., Fan, W., Downes, M., Heligon, C., Barish, G. D., Desvergne, B., Evans, R. M., Schoonjans, K., & Auwerx, J. (2011). NCoR1 is a conserved physiological modulator of muscle mass and oxidative function. Cell, 147(4), 827-39.