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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3' Flanking Region
E. Semenova, Wang, X. F., Jablonski, M. M., Levorse, J., and Tilghman, S. M., “An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina.”, Hum Mol Genet, vol. 12, no. 11, pp. 1301-12, 2003.
Abdomen
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
Abstracting and Indexing as Topic
E. I. Boyle, Weng, S., Gollub, J., Jin, H., Botstein, D., J Cherry, M., and Sherlock, G., “GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.”, Bioinformatics, vol. 20, no. 18, pp. 3710-5, 2004.
Acetylation
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.
Adaptation, Physiological
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
O. Oleksiuk, Jakovljevic, V., Vladimirov, N., Carvalho, R., Paster, E., Ryu, W. S., Meir, Y., Wingreen, N. S., Kollmann, M., and Sourjik, V., “Thermal robustness of signaling in bacterial chemotaxis.”, Cell, vol. 145, no. 2, pp. 312-21, 2011.
Y. Meir, Jakovljevic, V., Oleksiuk, O., Sourjik, V., and Wingreen, N. S., “Precision and kinetics of adaptation in bacterial chemotaxis.”, Biophys J, vol. 99, no. 9, pp. 2766-74, 2010.
D. Gresham, Desai, M. M., Tucker, C. M., Jenq, H. T., Pai, D. A., Ward, A., DeSevo, C. G., Botstein, D., and Dunham, M. J., “The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.”, PLoS Genet, vol. 4, no. 12, p. e1000303, 2008.
Adenocarcinoma
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
S. Y. Leung, Chen, X., Chu, K. M., Yuen, S. T., Mathy, J., Ji, J., S Y Chan, A., Li, R., Law, S., Troyanskaya, O. G., Tu, I. - P., Wong, J., So, S., Botstein, D., and Brown, P. O., “Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.”, Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16203-8, 2002.
X. Chen, Leung, S. Y., Yuen, S. T., Chu, K. - M., Ji, J., Li, R., S Y Chan, A., Law, S., Troyanskaya, O. G., Wong, J., So, S., Botstein, D., and Brown, P. O., “Variation in gene expression patterns in human gastric cancers.”, Mol Biol Cell, vol. 14, no. 8, pp. 3208-15, 2003.
Adenocarcinoma, Clear Cell
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Africa
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
Age Factors
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
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.
Aging
P. S. Minhas, Liu, L., Moon, P. K., Joshi, A. U., Dove, C., Mhatre, S., Contrepois, K., Wang, Q., Lee, B. A., Coronado, M., Bernstein, D., Snyder, M. P., Migaud, M., Majeti, R., Mochly-Rosen, D., Rabinowitz, J. D., and Andreasson, K. I., “Macrophage de novo NAD synthesis specifies immune function in aging and inflammation.”, Nat Immunol, vol. 20, no. 1, pp. 50-63, 2019.
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.
Albumins
S. M. Davidson, Jonas, O., Keibler, M. A., Hou, H. Wei, Luengo, A., Mayers, J. R., Wyckoff, J., Del Rosario, A. M., Whitman, M., Chin, C. R., Condon, K. J., Lammers, A., Kellersberger, K. A., Stall, B. K., Stephanopoulos, G., Bar-Sagi, D., Han, J., Rabinowitz, J. D., Cima, M. J., Langer, R., and Heiden, M. G. Vander, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
Alcohol Drinking
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
Algorithms
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.
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
P. Jiang and Singh, M., “SPICi: a fast clustering algorithm for large biological networks.”, Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
E. Nabieva, Jim, K., Agarwal, A., Chazelle, B., and Singh, M., “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
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.
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.
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Alleles
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.
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.
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.
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.
Allelic Imbalance
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
Allografts
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.
Amines
R. C. Kelly, Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. - L., Jeffrey, P. D., Rabinowitz, J. D., Semmelhack, M. F., Hughson, F. M., and Bassler, B. L., “The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA.”, Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
Amino Acid Motifs
P. Jiang, Singh, M., and Coller, H. A., “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
Amino Acid Sequence
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
Amino Acids
S. M. Davidson, Jonas, O., Keibler, M. A., Hou, H. Wei, Luengo, A., Mayers, J. R., Wyckoff, J., Del Rosario, A. M., Whitman, M., Chin, C. R., Condon, K. J., Lammers, A., Kellersberger, K. A., Stall, B. K., Stephanopoulos, G., Bar-Sagi, D., Han, J., Rabinowitz, J. D., Cima, M. J., Langer, R., and Heiden, M. G. Vander, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
Amino Acids, Branched-Chain
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.
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.
AMP Deaminase
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.
Animals
P. Jiang and Singh, M., “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
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.
B. K. Jones, Levorse, J. M., and Tilghman, S. M., “Igf2 imprinting does not require its own DNA methylation or H19 RNA.”, Genes Dev, vol. 12, no. 14, pp. 2200-7, 1998.
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.
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
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.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., “Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.”, Cell, vol. 139, no. 6, pp. 1189-96, 2009.
D. Straile, Eckmann, R., Jüngling, T., Thomas, G., and Löffler, H., “Influence of climate variability on whitefish (Coregonus lavaretus) year-class strength in a deep, warm monomictic lake.”, Oecologia, vol. 151, no. 3, pp. 521-9, 2007.
P. Jumbo-Lucioni, Ayroles, J. F., Chambers, M. Moses, Jordan, K. W., Leips, J., Mackay, T. Fc, and De Luca, M., “Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster.”, BMC Genomics, vol. 11, p. 297, 2010.
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Animals, Genetically Modified
A. Helman, Lim, B., Andreu, M. José, Kim, Y., Shestkin, T., Lu, H., Jiménez, G., Shvartsman, S. Y., and Paroush, Z. 'ev, “RTK signaling modulates the Dorsal gradient.”, Development, vol. 139, no. 16, pp. 3032-9, 2012.
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Animals, Inbred Strains
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
Animals, Newborn
E. Semenova, Wang, X. F., Jablonski, M. M., Levorse, J., and Tilghman, S. M., “An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina.”, Hum Mol Genet, vol. 12, no. 11, pp. 1301-12, 2003.
Antigens, Neoplasm
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A., “SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”, Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
Apoptosis
J. M. S. Lemons, Feng, X. - J., Bennett, B. D., Legesse-Miller, A., Johnson, E. L., Raitman, I., Pollina, E. A., Rabitz, H. A., Rabinowitz, J. D., and Coller, H. A., “Quiescent fibroblasts exhibit high metabolic activity.”, PLoS Biol, vol. 8, no. 10, p. e1000514, 2010.
Arabidopsis
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
Arginase
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.
Arginine
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.
Artificial Intelligence
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.
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.
Asian Continental Ancestry Group
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
Aspartic Acid
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.
Autistic Disorder
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
Autocrine Communication
M. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
Autophagy
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.
Autophagy-Related Protein 5
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.
Autophagy-Related Protein 7
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.
Bacterial Proteins
Y. Meir, Jakovljevic, V., Oleksiuk, O., Sourjik, V., and Wingreen, N. S., “Precision and kinetics of adaptation in bacterial chemotaxis.”, Biophys J, vol. 99, no. 9, pp. 2766-74, 2010.
K. Jim, Parmar, K., Singh, M., and Tavazoie, S., “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
Base Sequence
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. V. Schmidt, Matteson, P. G., Jones, B. K., Guan, X. J., and Tilghman, S. M., “The Dlk1 and Gtl2 genes are linked and reciprocally imprinted.”, Genes Dev, vol. 14, no. 16, pp. 1997-2002, 2000.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
X. Chen, Leung, S. Y., Yuen, S. T., Chu, K. - M., Ji, J., Li, R., S Y Chan, A., Law, S., Troyanskaya, O. G., Wong, J., So, S., Botstein, D., and Brown, P. O., “Variation in gene expression patterns in human gastric cancers.”, Mol Biol Cell, vol. 14, no. 8, pp. 3208-15, 2003.
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.
Basic Helix-Loop-Helix Transcription Factors
A. Helman, Lim, B., Andreu, M. José, Kim, Y., Shestkin, T., Lu, H., Jiménez, G., Shvartsman, S. Y., and Paroush, Z. 'ev, “RTK signaling modulates the Dorsal gradient.”, Development, vol. 139, no. 16, pp. 3032-9, 2012.
Y. Kim, Paroush, Z. 'ev, Nairz, K., Hafen, E., Jiménez, G., and Shvartsman, S. Y., “Substrate-dependent control of MAPK phosphorylation in vivo.”, Mol Syst Biol, vol. 7, p. 467, 2011.
Bayes Theorem
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
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.
Behavior, Animal
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “Dimensionality and dynamics in the behavior of C. elegans.”, PLoS Comput Biol, vol. 4, no. 4, p. e1000028, 2008.
Binding Sites
P. Jiang and Singh, M., “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
R. C. Kelly, Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. - L., Jeffrey, P. D., Rabinowitz, J. D., Semmelhack, M. F., Hughson, F. M., and Bassler, B. L., “The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA.”, Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Biological Evolution
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
Biological Transport
M. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
Biophysical Phenomena
Y. Meir, Jakovljevic, V., Oleksiuk, O., Sourjik, V., and Wingreen, N. S., “Precision and kinetics of adaptation in bacterial chemotaxis.”, Biophys J, vol. 99, no. 9, pp. 2766-74, 2010.
Biophysics
M. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
Biopsy
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.
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.
Bipolar Disorder
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.
Blastula
L. Vastag, Jorgensen, P., Peshkin, L., Wei, R., Rabinowitz, J. D., and Kirschner, M. W., “Remodeling of the metabolome during early frog development.”, PLoS One, vol. 6, no. 2, p. e16881, 2011.
Blood Pressure
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
Blotting, Western
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.
Body Composition
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.
Body Mass Index
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
Body Patterning
A. Helman, Lim, B., Andreu, M. José, Kim, Y., Shestkin, T., Lu, H., Jiménez, G., Shvartsman, S. Y., and Paroush, Z. 'ev, “RTK signaling modulates the Dorsal gradient.”, Development, vol. 139, no. 16, pp. 3032-9, 2012.
B. Lim, Samper, N., Lu, H., Rushlow, C., Jiménez, G., and Shvartsman, S. Y., “Kinetics of gene derepression by ERK signaling.”, Proc Natl Acad Sci U S A, vol. 110, no. 25, pp. 10330-5, 2013.
Y. Kim, Coppey, M., Grossman, R., Ajuria, L., Jiménez, G., Paroush, Z. 'ev, and Shvartsman, S. Y., “MAPK substrate competition integrates patterning signals in the Drosophila embryo.”, Curr Biol, vol. 20, no. 5, pp. 446-51, 2010.
Body Weight
P. Jumbo-Lucioni, Ayroles, J. F., Chambers, M. Moses, Jordan, K. W., Leips, J., Mackay, T. Fc, and De Luca, M., “Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster.”, BMC Genomics, vol. 11, p. 297, 2010.
P. Jumbo-Lucioni, Ayroles, J. F., Chambers, M. Moses, Jordan, K. W., Leips, J., Mackay, T. Fc, and De Luca, M., “Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster.”, BMC Genomics, vol. 11, p. 297, 2010.
Bone Morphogenetic Protein Receptors, Type I
A. Jaźwińska, Kirov, N., Wieschaus, E., Roth, S., and Rushlow, C., “The Drosophila gene brinker reveals a novel mechanism of Dpp target gene regulation.”, Cell, vol. 96, no. 4, pp. 563-73, 1999.
Breast
M. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
Breast Neoplasms
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
H. Zhao, Langerød, A., Ji, Y., Nowels, K. W., Nesland, J. M., Tibshirani, R., Bukholm, I. K., Kåresen, R., Botstein, D., Børresen-Dale, A. - L., and Jeffrey, S. S., “Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.”, Mol Biol Cell, vol. 15, no. 6, pp. 2523-36, 2004.
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.
S. S. Jeffrey, Fero, M. J., Børresen-Dale, A. - L., and Botstein, D., “Expression array technology in the diagnosis and treatment of breast cancer.”, Mol Interv, vol. 2, no. 2, pp. 101-9, 2002.
J. R. Pollack, Sørlie, T., Perou, C. M., Rees, C. A., Jeffrey, S. S., Lonning, P. E., Tibshirani, R., Botstein, D., Børresen-Dale, A. - L., and Brown, P. O., “Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12963-8, 2002.
H. Zhao, Langerød, A., Ji, Y., Nowels, K. W., Nesland, J. M., Tibshirani, R., Bukholm, I. K., Kåresen, R., Botstein, D., Børresen-Dale, A. - L., and Jeffrey, S. S., “Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.”, Mol Biol Cell, vol. 15, no. 6, pp. 2523-36, 2004.
T. Sorlie, Tibshirani, R., Parker, J., Hastie, T., Marron, J. S., Nobel, A., Deng, S., Johnsen, H., Pesich, R., Geisler, S., Demeter, J., Perou, C. M., Lønning, P. E., Brown, P. O., Børresen-Dale, A. - L., and Botstein, D., “Repeated observation of breast tumor subtypes in independent gene expression data sets.”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8418-23, 2003.
Caenorhabditis elegans
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “Dimensionality and dynamics in the behavior of C. elegans.”, PLoS Comput Biol, vol. 4, no. 4, p. e1000028, 2008.
G. Rizki, Iwata, T. Naoko, Li, J., Riedel, C. G., Picard, C. Lafontaine, Jan, M., Murphy, C. T., and Lee, S. Sylvia, “The evolutionarily conserved longevity determinants HCF-1 and SIR-2.1/SIRT1 collaborate to regulate DAF-16/FOXO.”, PLoS Genet, vol. 7, no. 9, p. e1002235, 2011.
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.
Caenorhabditis elegans Proteins
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
G. Rizki, Iwata, T. Naoko, Li, J., Riedel, C. G., Picard, C. Lafontaine, Jan, M., Murphy, C. T., and Lee, S. Sylvia, “The evolutionarily conserved longevity determinants HCF-1 and SIR-2.1/SIRT1 collaborate to regulate DAF-16/FOXO.”, PLoS Genet, vol. 7, no. 9, p. e1002235, 2011.
California
J. Gollub, Ball, C. A., Binkley, G., Demeter, J., Finkelstein, D. B., Hebert, J. M., Hernandez-Boussard, T., Jin, H., Kaloper, M., Matese, J. C., Schroeder, M., Brown, P. O., Botstein, D., and Sherlock, G., “The Stanford Microarray Database: data access and quality assessment tools.”, Nucleic Acids Res, vol. 31, no. 1, pp. 94-6, 2003.
Capsella
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
Carbon
J. M. S. Lemons, Feng, X. - J., Bennett, B. D., Legesse-Miller, A., Johnson, E. L., Raitman, I., Pollina, E. A., Rabitz, H. A., Rabinowitz, J. D., and Coller, H. A., “Quiescent fibroblasts exhibit high metabolic activity.”, PLoS Biol, vol. 8, no. 10, p. e1000514, 2010.
Carboxylic Acids
C. Jang, Hui, S., Lu, W., Cowan, A. J., Morscher, R. J., Lee, G., Liu, W., Tesz, G. J., Birnbaum, M. J., and Rabinowitz, J. D., “The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids.”, Cell Metab, vol. 27, no. 2, pp. 351-361.e3, 2018.
Carcinogenesis
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.
Carcinoma
T. Sorlie, Tibshirani, R., Parker, J., Hastie, T., Marron, J. S., Nobel, A., Deng, S., Johnsen, H., Pesich, R., Geisler, S., Demeter, J., Perou, C. M., Lønning, P. E., Brown, P. O., Børresen-Dale, A. - L., and Botstein, D., “Repeated observation of breast tumor subtypes in independent gene expression data sets.”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8418-23, 2003.
S. S. Jeffrey, Fero, M. J., Børresen-Dale, A. - L., and Botstein, D., “Expression array technology in the diagnosis and treatment of breast cancer.”, Mol Interv, vol. 2, no. 2, pp. 101-9, 2002.
Carcinoma, Ductal, Breast
H. Zhao, Langerød, A., Ji, Y., Nowels, K. W., Nesland, J. M., Tibshirani, R., Bukholm, I. K., Kåresen, R., Botstein, D., Børresen-Dale, A. - L., and Jeffrey, S. S., “Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.”, Mol Biol Cell, vol. 15, no. 6, pp. 2523-36, 2004.
H. Zhao, Langerød, A., Ji, Y., Nowels, K. W., Nesland, J. M., Tibshirani, R., Bukholm, I. K., Kåresen, R., Botstein, D., Børresen-Dale, A. - L., and Jeffrey, S. S., “Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.”, Mol Biol Cell, vol. 15, no. 6, pp. 2523-36, 2004.
Carcinoma, Hepatocellular
X. Chen, Cheung, S. Tim, So, S., Fan, S. Tat, Barry, C., Higgins, J., Lai, K. - M., Ji, J., Dudoit, S., Ng, I. O. L., van de Rijn, M., Botstein, D., and Brown, P. O., “Gene expression patterns in human liver cancers.”, Mol Biol Cell, vol. 13, no. 6, pp. 1929-39, 2002.
Carcinoma, Lobular
H. Zhao, Langerød, A., Ji, Y., Nowels, K. W., Nesland, J. M., Tibshirani, R., Bukholm, I. K., Kåresen, R., Botstein, D., Børresen-Dale, A. - L., and Jeffrey, S. S., “Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.”, Mol Biol Cell, vol. 15, no. 6, pp. 2523-36, 2004.
H. Zhao, Langerød, A., Ji, Y., Nowels, K. W., Nesland, J. M., Tibshirani, R., Bukholm, I. K., Kåresen, R., Botstein, D., Børresen-Dale, A. - L., and Jeffrey, S. S., “Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.”, Mol Biol Cell, vol. 15, no. 6, pp. 2523-36, 2004.
Carcinoma, Pancreatic Ductal
S. M. Davidson, Jonas, O., Keibler, M. A., Hou, H. Wei, Luengo, A., Mayers, J. R., Wyckoff, J., Del Rosario, A. M., Whitman, M., Chin, C. R., Condon, K. J., Lammers, A., Kellersberger, K. A., Stall, B. K., Stephanopoulos, G., Bar-Sagi, D., Han, J., Rabinowitz, J. D., Cima, M. J., Langer, R., and Heiden, M. G. Vander, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
Carcinoma, Papillary
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Cation Transport Proteins
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Cell Culture Techniques
M. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
Cell Cycle
L. Vastag, Jorgensen, P., Peshkin, L., Wei, R., Rabinowitz, J. D., and Kirschner, M. W., “Remodeling of the metabolome during early frog development.”, PLoS One, vol. 6, no. 2, p. e16881, 2011.
J. M. S. Lemons, Feng, X. - J., Bennett, B. D., Legesse-Miller, A., Johnson, E. L., Raitman, I., Pollina, E. A., Rabitz, H. A., Rabinowitz, J. D., and Coller, H. A., “Quiescent fibroblasts exhibit high metabolic activity.”, PLoS Biol, vol. 8, no. 10, p. e1000514, 2010.
Cell Differentiation
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.
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.
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.
Cell Division
X. Chen, Cheung, S. Tim, So, S., Fan, S. Tat, Barry, C., Higgins, J., Lai, K. - M., Ji, J., Dudoit, S., Ng, I. O. L., van de Rijn, M., Botstein, D., and Brown, P. O., “Gene expression patterns in human liver cancers.”, Mol Biol Cell, vol. 13, no. 6, pp. 1929-39, 2002.
Cell Line
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.
Cell Line, Tumor
S. M. Davidson, Jonas, O., Keibler, M. A., Hou, H. Wei, Luengo, A., Mayers, J. R., Wyckoff, J., Del Rosario, A. M., Whitman, M., Chin, C. R., Condon, K. J., Lammers, A., Kellersberger, K. A., Stall, B. K., Stephanopoulos, G., Bar-Sagi, D., Han, J., Rabinowitz, J. D., Cima, M. J., Langer, R., and Heiden, M. G. Vander, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
Cell Lineage
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.
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.
Cell Nucleus
B. Lim, Samper, N., Lu, H., Rushlow, C., Jiménez, G., and Shvartsman, S. Y., “Kinetics of gene derepression by ERK signaling.”, Proc Natl Acad Sci U S A, vol. 110, no. 25, pp. 10330-5, 2013.
Cell Proliferation
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.
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.
J. M. S. Lemons, Feng, X. - J., Bennett, B. D., Legesse-Miller, A., Johnson, E. L., Raitman, I., Pollina, E. A., Rabitz, H. A., Rabinowitz, J. D., and Coller, H. A., “Quiescent fibroblasts exhibit high metabolic activity.”, PLoS Biol, vol. 8, no. 10, p. e1000514, 2010.
Cells, Cultured
M. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.

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