List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

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Algorithms
A. V. Rangan, McGrouther, C. C., Kelsoe, J., Schork, N., Stahl, E., Zhu, Q., Krishnan, A., Yao, V., Troyanskaya, O., Bilaloglu, S., Raghavan, P., Bergen, S., Jureus, A., and Landen, M., A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data., PLoS Comput Biol, vol. 14, no. 5, p. e1006105, 2018.
D. Gorenshteyn, Zaslavsky, E., Fribourg, M., Park, C. Y., Wong, A. K., Tadych, A., Hartmann, B. M., Albrecht, R. A., García-Sastre, A., Kleinstein, S. H., Troyanskaya, O. G., and Sealfon, S. C., Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases., Immunity, vol. 43, no. 3, pp. 605-14, 2015.
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development., PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
L. Peña-Castillo, Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W. Kyu, Krumpelman, C., Tian, W., Obozinski, G., Qi, Y., Mostafavi, S., Lin, G. Ning, Berriz, G. F., Gibbons, F. D., Lanckriet, G., Qiu, J., Grant, C., Barutcuoglu, Z., Hill, D. P., Warde-Farley, D., Grouios, C., Ray, D., Blake, J. A., Deng, M., Jordan, M. I., Noble, W. S., Morris, Q., Klein-Seetharaman, J., Bar-Joseph, iv, Z., Chen, T., Sun, F., Troyanskaya, O. G., Marcotte, E. M., Xu, D., Hughes, T. R., and Roth, F. P., A critical assessment of Mus musculus gene function prediction using integrated genomic evidence., Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
J. J. Zartman, Cheung, L. S., Niepielko, M. G., Bonini, C., Haley, B., Yakoby, N., and Shvartsman, S. Y., Pattern formation by a moving morphogen source., Phys Biol, vol. 8, no. 4, p. 045003, 2011.
J. Zhou and Troyanskaya, O. G., Global quantitative modeling of chromatin factor interactions., PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
K. M. Chen, Cofer, E. M., Zhou, J., and Troyanskaya, O. G., Selene: a PyTorch-based deep learning library for sequence data., Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
Y. -suk Lee, Wong, A. K., Tadych, A., Hartmann, B. M., Park, C. Y., DeJesus, V. A., Ramos, I., Zaslavsky, E., Sealfon, S. C., and Troyanskaya, O. G., Interpretation of an individual functional genomics experiment guided by massive public data., Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
J. Zhou, Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., and Troyanskaya, O. G., Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk., Nat Genet, vol. 50, no. 8, pp. 1171-1179, 2018.
R. Osada, Zaslavsky, E., and Singh, M., Comparative analysis of methods for representing and searching for transcription factor binding sites., Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk., Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
Alleles
S. M. Tilghman, Bartolomei, M. S., Webber, A. L., Brunkow, M. E., Saam, J., Leighton, P. A., Pfeifer, K., and Zemel, S., Parental imprinting of the H19 and Igf2 genes in the mouse., Cold Spring Harb Symp Quant Biol, vol. 58, pp. 287-95, 1993.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk., Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
S. B. Zusman, Sweeton, D., and Wieschaus, E. F., short gastrulation, a mutation causing delays in stage-specific cell shape changes during gastrulation in Drosophila melanogaster., Dev Biol, vol. 129, no. 2, pp. 417-27, 1988.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., The Drosophila melanogaster Genetic Reference Panel., Nature, vol. 482, no. 7384, pp. 173-8, 2012.
R. B. Corbett-Detig, Zhou, J., Clark, A. G., Hartl, D. L., and Ayroles, J. F., Genetic incompatibilities are widespread within species., Nature, vol. 504, no. 7478, pp. 135-7, 2013.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., The Drosophila melanogaster Genetic Reference Panel., Nature, vol. 482, no. 7384, pp. 173-8, 2012.
Amino-Acid N-Acetyltransferase
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
Animals
L. Peña-Castillo, Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W. Kyu, Krumpelman, C., Tian, W., Obozinski, G., Qi, Y., Mostafavi, S., Lin, G. Ning, Berriz, G. F., Gibbons, F. D., Lanckriet, G., Qiu, J., Grant, C., Barutcuoglu, Z., Hill, D. P., Warde-Farley, D., Grouios, C., Ray, D., Blake, J. A., Deng, M., Jordan, M. I., Noble, W. S., Morris, Q., Klein-Seetharaman, J., Bar-Joseph, iv, Z., Chen, T., Sun, F., Troyanskaya, O. G., Marcotte, E. M., Xu, D., Hughes, T. R., and Roth, F. P., A critical assessment of Mus musculus gene function prediction using integrated genomic evidence., Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
T. J. Vasicek, Zeng, L., Guan, X. J., Zhang, T., Costantini, F., and Tilghman, S. M., Two dominant mutations in the mouse fused gene are the result of transposon insertions., Genetics, vol. 147, no. 2, pp. 777-86, 1997.
S. B. Zusman, Sweeton, D., and Wieschaus, E. F., short gastrulation, a mutation causing delays in stage-specific cell shape changes during gastrulation in Drosophila melanogaster., Dev Biol, vol. 129, no. 2, pp. 417-27, 1988.
J. Zhou and Troyanskaya, O. G., Global quantitative modeling of chromatin factor interactions., PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
S. B. Zusman and Wieschaus, E. F., Requirements for zygotic gene activity during gastrulation in Drosophila melanogaster., Dev Biol, vol. 111, no. 2, pp. 359-71, 1985.
S. E. McKee, Zhang, S., Chen, L., Rabinowitz, J. D., and Reyes, T. M., Perinatal high fat diet and early life methyl donor supplementation alter one carbon metabolism and DNA methylation in the brain., J Neurochem, vol. 145, no. 5, pp. 362-373, 2018.
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., Parallel molecular evolution in an herbivore community., Science, vol. 337, no. 6102, pp. 1634-7, 2012.
C. J. Nirschl, Suárez-Fariñas, M., Izar, B., Prakadan, S., Dannenfelser, R., Tirosh, I., Liu, Y., Zhu, Q., K Devi, S. P., Carroll, S. L., Chau, D., Rezaee, M., Kim, T. - G., Huang, R., Fuentes-Duculan, J., Song-Zhao, G. X., Gulati, N., Lowes, M. A., King, S. L., Quintana, F. J., Lee, Y. -suk, Krueger, J. G., Sarin, K. Y., Yoon, C. H., Garraway, L., Regev, iv, A., Shalek, A. K., Troyanskaya, O. G., and Anandasabapathy, N., IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment., Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
M. Nofal, Zhang, K., Han, S., and Rabinowitz, J. D., mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein., Mol Cell, vol. 67, no. 6, pp. 936-946.e5, 2017.
S. B. Zusman and Wieschaus, E., A cell marker system and mosaic patterns during early embryonic development in Drosophila melanogaster., Genetics, vol. 115, no. 4, pp. 725-36, 1987.
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., Comparing genomic expression patterns across species identifies shared transcriptional profile in aging., Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
J. J. Zartman, Yakoby, N., Bristow, C. A., Zhou, X., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis., Dev Biol, vol. 322, no. 2, pp. 289-301, 2008.
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J., Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy., Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
S. - J. Yan, Zartman, J. J., Zhang, M., Scott, A., Shvartsman, S. Y., and Li, W. X., Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation., Mol Syst Biol, vol. 5, p. 278, 2009.
M. van de Rijn, Perou, C. M., Tibshirani, R., Haas, P., Kallioniemi, O., Kononen, J., Torhorst, J., Sauter, G., Zuber, M., Köchli, O. R., Mross, F., Dieterich, H., Seitz, R., Ross, D., Botstein, D., and Brown, P., Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome., Am J Pathol, vol. 161, no. 6, pp. 1991-6, 2002.
J. Miller, Zeng, C., Wingreen, N. S., and Tang, C., Emergence of highly designable protein-backbone conformations in an off-lattice model., Proteins, vol. 47, no. 4, pp. 506-12, 2002.
J. A. Zallen, Cohen, Y., Hudson, A. M., Cooley, L., Wieschaus, E., and Schejter, E. D., SCAR is a primary regulator of Arp2/3-dependent morphological events in Drosophila., J Cell Biol, vol. 156, no. 4, pp. 689-701, 2002.
D. A. Hendrix, Hong, J. - W., Zeitlinger, J., Rokhsar, D. S., and Levine, M. S., Promoter elements associated with RNA Pol II stalling in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 105, no. 22, pp. 7762-7, 2008.
M. A. Cleary, van Raamsdonk, C. D., Levorse, J., Zheng, B., Bradley, A., and Tilghman, S. M., Disruption of an imprinted gene cluster by a targeted chromosomal translocation in mice., Nat Genet, vol. 29, no. 1, pp. 78-82, 2001.
R. B. Corbett-Detig, Zhou, J., Clark, A. G., Hartl, D. L., and Ayroles, J. F., Genetic incompatibilities are widespread within species., Nature, vol. 504, no. 7478, pp. 135-7, 2013.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster., PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
M. S. Bartolomei, Zemel, S., and Tilghman, S. M., Parental imprinting of the mouse H19 gene., Nature, vol. 351, no. 6322, pp. 153-5, 1991.
W. Bailis, Shyer, J. A., Zhao, J., Canaveras, J. Carlos Gar, Khazal, F. J. Al, Qu, R., Steach, H. R., Bielecki, P., Khan, O., Jackson, R., Kluger, Y., Maher, L. J., Rabinowitz, J., Craft, J., and Flavell, R. A., Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function., Nature, vol. 571, no. 7765, pp. 403-407, 2019.
M. Markstein, Zinzen, R., Markstein, P., Yee, K. - P., Erives, A., Stathopoulos, A., and Levine, M., A regulatory code for neurogenic gene expression in the Drosophila embryo., Development, vol. 131, no. 10, pp. 2387-94, 2004.
T. J. Levario, Zhan, M., Lim, B., Shvartsman, S. Y., and Lu, H., Microfluidic trap array for massively parallel imaging of Drosophila embryos., Nat Protoc, vol. 8, no. 4, pp. 721-36, 2013.
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C., Epistasis dominates the genetic architecture of Drosophila quantitative traits., Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
T. M. Bartlett, Bratton, B. P., Duvshani, A., Miguel, A., Sheng, Y., Martin, N. R., Nguyen, J. P., Persat, A., Desmarais, S. M., VanNieuwenhze, M. S., Huang, K. Casey, Zhu, J., Shaevitz, J. W., and Gitai, Z., A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis., Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
S. De Renzis, Yu, J., Zinzen, R., and Wieschaus, E., Dorsal-ventral pattern of Delta trafficking is established by a Snail-Tom-Neuralized pathway., Dev Cell, vol. 10, no. 2, pp. 257-64, 2006.
D. Guan, Xiong, Y., Borck, P. C., Jang, C., Doulias, P. - T., Papazyan, R., Fang, B., Jiang, C., Zhang, Y., Briggs, E. R., Hu, W., Steger, D., Ischiropoulos, H., Rabinowitz, J. D., and Lazar, M. A., Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes., Cell, vol. 174, no. 4, pp. 831-842.e12, 2018.
M. Lagha, Bothma, J. P., Esposito, E., Ng, S., Stefanik, L., Tsui, C., Johnston, J., Chen, K., Gilmour, D. S., Zeitlinger, J., and Levine, M. S., Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo., Cell, vol. 153, no. 5, pp. 976-87, 2013.
L. Poillet-Perez, Xie, X., Zhan, L., Yang, Y., Sharp, D. W., Hu, Z. Sherrie, Su, X., Maganti, A., Jiang, C., Lu, W., Zheng, H., Bosenberg, M. W., Mehnert, J. M., Guo, J. Yanxiang, Lattime, E., Rabinowitz, J. D., and White, E., Autophagy maintains tumour growth through circulating arginine., Nature, vol. 563, no. 7732, pp. 569-573, 2018.
R. Papazyan, Sun, Z., Kim, Y. Hoon, Titchenell, P. M., Hill, D. A., Lu, W., Damle, M., Wan, M., Zhang, Y., Briggs, E. R., Rabinowitz, J. D., and Lazar, M. A., Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP., Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., The Drosophila melanogaster Genetic Reference Panel., Nature, vol. 482, no. 7384, pp. 173-8, 2012.
S. Hong, Zhou, W., Fang, B., Lu, W., Loro, E., Damle, M., Ding, G., Jager, J., Zhang, S., Zhang, Y., Feng, D., Chu, Q., Dill, B. D., Molina, H., Khurana, T. S., Rabinowitz, J. D., Lazar, M. A., and Sun, Z., Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion., Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
T. J. Vasicek, Zeng, L., Guan, X. J., Zhang, T., Costantini, F., and Tilghman, S. M., Two dominant mutations in the mouse fused gene are the result of transposon insertions., Genetics, vol. 147, no. 2, pp. 777-86, 1997.
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J., Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy., Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
J. J. Zartman, Yakoby, N., Bristow, C. A., Zhou, X., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis., Dev Biol, vol. 322, no. 2, pp. 289-301, 2008.
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J. J. Zartman, Kanodia, J. S., Cheung, L. S., and Shvartsman, S. Y., Feedback control of the EGFR signaling gradient: superposition of domain-splitting events in Drosophila oogenesis., Development, vol. 136, no. 17, pp. 2903-11, 2009.
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J. S. Kanodia, Liang, H. - L., Kim, Y., Lim, B., Zhan, M., Lu, H., Rushlow, C. A., and Shvartsman, S. Y., Pattern formation by graded and uniform signals in the early Drosophila embryo., Biophys J, vol. 102, no. 3, pp. 427-33, 2012.
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R. E. Dawes-Hoang, Zallen, J. A., and Wieschaus, E. F., Bringing classical embryology to C elegans gastrulation., Dev Cell, vol. 4, no. 1, pp. 6-8, 2003.
J. J. Zartman, Kanodia, J. S., Yakoby, N., Schafer, X., Watson, C., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Expression patterns of cadherin genes in Drosophila oogenesis., Gene Expr Patterns, vol. 9, no. 1, pp. 31-6, 2009.
J. A. Zallen and Wieschaus, E., Patterned gene expression directs bipolar planar polarity in Drosophila., Dev Cell, vol. 6, no. 3, pp. 343-55, 2004.
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J. J. Zartman and Shvartsman, S. Y., Unit operations of tissue development: epithelial folding., Annu Rev Chem Biomol Eng, vol. 1, pp. 231-46, 2010.
L. Zwarts, Broeck, L. Vanden, Cappuyns, E., Ayroles, J. F., Magwire, M. M., Vulsteke, V., Clements, J., Mackay, T. F. C., and Callaerts, P., The genetic basis of natural variation in mushroom body size in Drosophila melanogaster., Nat Commun, vol. 6, p. 10115, 2015.
O. Grimm, Zini, V. Sanchez, Kim, Y., Casanova, J., Shvartsman, S. Y., and Wieschaus, E., Torso RTK controls Capicua degradation by changing its subcellular localization., Development, vol. 139, no. 21, pp. 3962-8, 2012.
L. Poillet-Perez, Xie, X., Zhan, L., Yang, Y., Sharp, D. W., Hu, Z. Sherrie, Su, X., Maganti, A., Jiang, C., Lu, W., Zheng, H., Bosenberg, M. W., Mehnert, J. M., Guo, J. Yanxiang, Lattime, E., Rabinowitz, J. D., and White, E., Autophagy maintains tumour growth through circulating arginine., Nature, vol. 563, no. 7732, pp. 569-573, 2018.
S. - J. Yan, Zartman, J. J., Zhang, M., Scott, A., Shvartsman, S. Y., and Li, W. X., Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation., Mol Syst Biol, vol. 5, p. 278, 2009.
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development., PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., The Drosophila melanogaster Genetic Reference Panel., Nature, vol. 482, no. 7384, pp. 173-8, 2012.
N. Yakoby, Bristow, C. A., Gong, D., Schafer, X., Lembong, J., Zartman, J. J., Halfon, M. S., Schüpbach, T., and Shvartsman, S. Y., A combinatorial code for pattern formation in Drosophila oogenesis., Dev Cell, vol. 15, no. 5, pp. 725-37, 2008.
T. Caspary, Cleary, M. A., Perlman, E. J., Zhang, P., Elledge, S. J., and Tilghman, S. M., Oppositely imprinted genes p57(Kip2) and igf2 interact in a mouse model for Beckwith-Wiedemann syndrome., Genes Dev, vol. 13, no. 23, pp. 3115-24, 1999.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
W. Ju, Greene, C. S., Eichinger, F., Nair, V., Hodgin, J. B., Bitzer, M., Lee, Y. -suk, Zhu, Q., Kehata, M., Li, M., Jiang, S., Rastaldi, M. Pia, Cohen, C. D., Troyanskaya, O. G., and Kretzler, M., Defining cell-type specificity at the transcriptional level in human disease., Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
J. J. Zartman and Shvartsman, S. Y., Enhancer organization: transistor with a twist or something in a different vein?, Curr Biol, vol. 17, no. 24, pp. R1048-50, 2007.
R. Menon, Otto, E. A., Kokoruda, A., Zhou, J., Zhang, Z., Yoon, E., Chen, Y. - C., Troyanskaya, O., Spence, J. R., Kretzler, M., and Cebrián, C., Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney., Development, vol. 145, no. 16, 2018.
A. Davila, Liu, L., Chellappa, K., Redpath, P., Nakamaru-Ogiso, E., Paolella, L. M., Zhang, Z., Migaud, M. E., Rabinowitz, J. D., and Baur, J. A., Nicotinamide adenine dinucleotide is transported into mammalian mitochondria., Elife, vol. 7, 2018.
S. Hong, Zhou, W., Fang, B., Lu, W., Loro, E., Damle, M., Ding, G., Jager, J., Zhang, S., Zhang, Y., Feng, D., Chu, Q., Dill, B. D., Molina, H., Khurana, T. S., Rabinowitz, J. D., Lazar, M. A., and Sun, Z., Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion., Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
S. Zemel, Bartolomei, M. S., and Tilghman, S. M., Physical linkage of two mammalian imprinted genes, H19 and insulin-like growth factor 2., Nat Genet, vol. 2, no. 1, pp. 61-5, 1992.
J. J. Zartman, Cheung, L. S., Niepielko, M. G., Bonini, C., Haley, B., Yakoby, N., and Shvartsman, S. Y., Pattern formation by a moving morphogen source., Phys Biol, vol. 8, no. 4, p. 045003, 2011.
Animals, Genetically Modified
J. A. Zallen and Wieschaus, E., Patterned gene expression directs bipolar planar polarity in Drosophila., Dev Cell, vol. 6, no. 3, pp. 343-55, 2004.
Antigens, CD
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J., Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy., Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J., Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy., Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
J. A. Zallen and Wieschaus, E., Patterned gene expression directs bipolar planar polarity in Drosophila., Dev Cell, vol. 6, no. 3, pp. 343-55, 2004.
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J., Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy., Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
Base Sequence
T. J. Vasicek, Zeng, L., Guan, X. J., Zhang, T., Costantini, F., and Tilghman, S. M., Two dominant mutations in the mouse fused gene are the result of transposon insertions., Genetics, vol. 147, no. 2, pp. 777-86, 1997.
M. A. Cleary, van Raamsdonk, C. D., Levorse, J., Zheng, B., Bradley, A., and Tilghman, S. M., Disruption of an imprinted gene cluster by a targeted chromosomal translocation in mice., Nat Genet, vol. 29, no. 1, pp. 78-82, 2001.
D. A. Hendrix, Hong, J. - W., Zeitlinger, J., Rokhsar, D. S., and Levine, M. S., Promoter elements associated with RNA Pol II stalling in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 105, no. 22, pp. 7762-7, 2008.
J. A. Zallen, Cohen, Y., Hudson, A. M., Cooley, L., Wieschaus, E., and Schejter, E. D., SCAR is a primary regulator of Arp2/3-dependent morphological events in Drosophila., J Cell Biol, vol. 156, no. 4, pp. 689-701, 2002.
R. Papazyan, Sun, Z., Kim, Y. Hoon, Titchenell, P. M., Hill, D. A., Lu, W., Damle, M., Wan, M., Zhang, Y., Briggs, E. R., Rabinowitz, J. D., and Lazar, M. A., Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP., Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
M. Markstein, Zinzen, R., Markstein, P., Yee, K. - P., Erives, A., Stathopoulos, A., and Levine, M., A regulatory code for neurogenic gene expression in the Drosophila embryo., Development, vol. 131, no. 10, pp. 2387-94, 2004.
T. J. Vasicek, Zeng, L., Guan, X. J., Zhang, T., Costantini, F., and Tilghman, S. M., Two dominant mutations in the mouse fused gene are the result of transposon insertions., Genetics, vol. 147, no. 2, pp. 777-86, 1997.
M. Lagha, Bothma, J. P., Esposito, E., Ng, S., Stefanik, L., Tsui, C., Johnston, J., Chen, K., Gilmour, D. S., Zeitlinger, J., and Levine, M. S., Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo., Cell, vol. 153, no. 5, pp. 976-87, 2013.
E. K. Farley, Olson, K. M., Zhang, W., Brandt, A. J., Rokhsar, D. S., and Levine, M. S., Suboptimization of developmental enhancers., Science, vol. 350, no. 6258, pp. 325-8, 2015.
A. Pane, Jiang, P., Zhao, D. Yanling, Singh, M., and Schüpbach, T., The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline., EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
J. A. Capra, Paeschke, K., Singh, M., and Zakian, V. A., G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae., PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
Bees
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
Biomechanical Phenomena
J. J. Zartman and Shvartsman, S. Y., Unit operations of tissue development: epithelial folding., Annu Rev Chem Biomol Eng, vol. 1, pp. 231-46, 2010.

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