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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A
A. L. Webber and Tilghman, S. M., The absence of enhancer competition between Igf2 and H19 following transfer into differentiated cells., Mol Cell Biol, vol. 18, no. 4, pp. 1903-10, 1998.
C. L. Myers, Dunham, M. J., Kung, S. Y., and Troyanskaya, O. G., Accurate detection of aneuploidies in array CGH and gene expression microarray data., Bioinformatics, vol. 20, no. 18, pp. 3533-43, 2004.
C. S. Greene and Troyanskaya, O. G., Accurate evaluation and analysis of functional genomics data and methods., Ann N Y Acad Sci, vol. 1260, pp. 95-100, 2012.
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.
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.
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.
Z. Khan, Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., and Tavazoie, S., Accurate proteome-wide protein quantification from high-resolution 15N mass spectra., Genome Biol, vol. 12, no. 12, p. R122, 2011.
M. D. Chikina and Troyanskaya, O. G., Accurate quantification of functional analogy among close homologs., PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
S. - W. Teng, Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S., Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi., Mol Syst Biol, vol. 7, p. 491, 2011.
S. - W. Teng, Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S., Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi., Mol Syst Biol, vol. 7, p. 491, 2011.
K. Pfeifer and Tilghman, S. M., Allele-specific gene expression in mammals: the curious case of the imprinted RNAs., Genes Dev, vol. 8, no. 16, pp. 1867-74, 1994.
M. J. O'Neill, Ingram, R. S., Vrana, P. B., and Tilghman, S. M., Allelic expression of IGF2 in marsupials and birds., Dev Genes Evol, vol. 210, no. 1, pp. 18-20, 2000.
S. R. Browning, Browning, B. L., Zhou, Y., Tucci, S., and Akey, J. M., Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture., Cell, vol. 173, no. 1, pp. 53-61.e9, 2018.
A. Chi, Huttenhower, C., Geer, L. Y., Coon, J. J., Syka, J. E. P., Bai, D. L., Shabanowitz, J., Burke, D. J., Troyanskaya, O. G., and Hunt, D. F., Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry., Proc Natl Acad Sci U S A, vol. 104, no. 7, pp. 2193-8, 2007.
Z. Barutcuoglu, Airoldi, E. M., Dumeaux, V., Schapire, R. E., and Troyanskaya, O. G., Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields., Bioinformatics, vol. 25, no. 10, pp. 1307-13, 2009.
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.
K. Thornton and Andolfatto, P., Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster., Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
N. S. Tolwinski and Wieschaus, E., Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan., Development, vol. 128, no. 11, pp. 2107-17, 2001.
N. N. Pavlova, Hui, S., Ghergurovich, J. M., Fan, J., Intlekofer, A. M., White, R. M., Rabinowitz, J. D., Thompson, C. B., and Zhang, J., As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid., Cell Metab, vol. 27, no. 2, pp. 428-438.e5, 2018.
J. Zhang, Fan, J., Venneti, S., Cross, J. R., Takagi, T., Bhinder, B., Djaballah, H., Kanai, M., Cheng, E. H., Judkins, A. R., Pawel, B., Baggs, J., Cherry, S., Rabinowitz, J. D., and Thompson, C. B., Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion., Mol Cell, vol. 56, no. 2, pp. 205-18, 2014.
J. Zhang, Fan, J., Venneti, S., Cross, J. R., Takagi, T., Bhinder, B., Djaballah, H., Kanai, M., Cheng, E. H., Judkins, A. R., Pawel, B., Baggs, J., Cherry, S., Rabinowitz, J. D., and Thompson, C. B., Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion., Mol Cell, vol. 56, no. 2, pp. 205-18, 2014.
C. Huttenhower and Troyanskaya, O. G., Assessing the functional structure of genomic data., Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
G. Karsli-Uzunbas, Guo, J. Yanxiang, Price, S., Teng, X., Laddha, S. V., Khor, S., Kalaany, N. Y., Jacks, T., Chan, C. S., Rabinowitz, J. D., and White, E., Autophagy is required for glucose homeostasis and lung tumor maintenance., Cancer Discov, vol. 4, no. 8, pp. 914-27, 2014.
J. Yanxiang Guo, Teng, X., Laddha, S. V., Ma, S., Van Nostrand, S. C., Yang, Y., Khor, S., Chan, C. S., Rabinowitz, J. D., and White, E., Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells., Genes Dev, vol. 30, no. 15, pp. 1704-17, 2016.
C
L. Jo Kurihara, Semenova, E., Miller, W., Ingram, R. S., Guan, X. - J., and Tilghman, S. M., Candidate genes required for embryonic development: a comparative analysis of distal mouse chromosome 14 and human chromosome 13q22., Genomics, vol. 79, no. 2, pp. 154-61, 2002.
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.
C. S. Greene and Troyanskaya, O. G., Chapter 2: Data-driven view of disease biology., PLoS Comput Biol, vol. 8, no. 12, p. e1002816, 2012.
J. I. Kliegman, Fiedler, D., Ryan, C. J., Xu, Y. - F., Su, X. - Y., Thomas, D., Caccese, M. C., Cheng, A., Shales, M., Rabinowitz, J. D., Krogan, N. J., and Shokat, K. M., Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae., Cell Rep, vol. 5, no. 6, pp. 1725-36, 2013.
A. T. Hark and Tilghman, S. M., Chromatin conformation of the H19 epigenetic mark., Hum Mol Genet, vol. 7, no. 12, pp. 1979-85, 1998.
S. E. Cole, Levorse, J. M., Tilghman, S. M., and Vogt, T. F., Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis., Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
Y. Guan, Dunham, M. J., Troyanskaya, O. G., and Caudy, A. A., Comparative gene expression between two yeast species., BMC Genomics, vol. 14, p. 33, 2013.
T. P. O'Brien, Metallinos, D. L., Chen, H., Shin, M. K., and Tilghman, S. M., Complementation mapping of skeletal and central nervous system abnormalities in mice of the piebald deletion complex., Genetics, vol. 143, no. 1, pp. 447-61, 1996.
T. Reguly, Breitkreutz, A., Boucher, L., Breitkreutz, B. - J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N., and Tyers, M., Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae., J Biol, vol. 5, no. 4, p. 11, 2006.
T. Reguly, Breitkreutz, A., Boucher, L., Breitkreutz, B. - J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N., and Tyers, M., Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae., J Biol, vol. 5, no. 4, p. 11, 2006.
T. Reguly, Breitkreutz, A., Boucher, L., Breitkreutz, B. - J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N., and Tyers, M., Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae., J Biol, vol. 5, no. 4, p. 11, 2006.
C. Huttenhower, Myers, C. L., Hibbs, M. A., and Troyanskaya, O. G., Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data., Methods Mol Biol, vol. 548, pp. 273-93, 2009.
Y. -suk Lee, Krishnan, A., Oughtred, R., Rust, J., Chang, C. S., Ryu, J., Kristensen, V. N., Dolinski, K., Theesfeld, C. L., and Troyanskaya, O. G., A Computational Framework for Genome-wide Characterization of the Human Disease Landscape., Cell Syst, vol. 8, no. 2, pp. 152-162.e6, 2019.
Y. -suk Lee, Krishnan, A., Oughtred, R., Rust, J., Chang, C. S., Ryu, J., Kristensen, V. N., Dolinski, K., Theesfeld, C. L., and Troyanskaya, O. G., A Computational Framework for Genome-wide Characterization of the Human Disease Landscape., Cell Syst, vol. 8, no. 2, pp. 152-162.e6, 2019.
F. Markowetz and Troyanskaya, O. G., Computational identification of cellular networks and pathways., Mol Biosyst, vol. 3, no. 7, pp. 478-82, 2007.
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., A computational statistics approach for estimating the spatial range of morphogen gradients., Development, vol. 138, no. 22, pp. 4867-74, 2011.
D. C. Hess, Myers, C. L., Huttenhower, C., Hibbs, M. A., Hayes, A. P., Paw, J., Clore, J. J., Mendoza, R. M., San Luis, B., Nislow, C., Giaever, G., Costanzo, M., Troyanskaya, O. G., and Caudy, A. A., Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis., PLoS Genet, vol. 5, no. 3, p. e1000407, 2009.
R. Godbout and Tilghman, S. M., Configuration of the alpha-fetoprotein regulatory domain during development., Genes Dev, vol. 2, no. 8, pp. 949-56, 1988.
C. L. Myers and Troyanskaya, O. G., Context-sensitive data integration and prediction of biological networks., Bioinformatics, vol. 23, no. 17, pp. 2322-30, 2007.
P. H. Bradley, Brauer, M. J., Rabinowitz, J. D., and Troyanskaya, O. G., Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae., PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
M. J. Brauer, Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G., and Botstein, D., Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast., Mol Biol Cell, vol. 19, no. 1, pp. 352-67, 2008.
X. Lu, Li, J. M., Elemento, O., Tavazoie, S., and Wieschaus, E. F., Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition., Development, vol. 136, no. 12, pp. 2101-10, 2009.
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.
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.
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.
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.
A. T. Hark, Schoenherr, C. J., Katz, D. J., Ingram, R. S., Levorse, J. M., and Tilghman, S. M., CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus., Nature, vol. 405, no. 6785, pp. 486-9, 2000.
D
R. G. Tepper, Murphy, C. T., and Bussemaker, H. J., DAF-16 and PQM-1: partners in longevity., Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 2014.
R. Dannenfelser, Nome, M., Tahiri, A., Ursini-Siegel, J., Vollan, H. Kristian M., Haakensen, V. D., Helland, Å., Naume, B., Caldas, C., Børresen-Dale, A. - L., Kristensen, V. N., and Troyanskaya, O. G., Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity., Oncotarget, vol. 8, no. 34, pp. 57121-57133, 2017.
R. Dannenfelser, Nome, M., Tahiri, A., Ursini-Siegel, J., Vollan, H. Kristian M., Haakensen, V. D., Helland, Å., Naume, B., Caldas, C., Børresen-Dale, A. - L., Kristensen, V. N., and Troyanskaya, O. G., Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity., Oncotarget, vol. 8, no. 34, pp. 57121-57133, 2017.
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.
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.
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.
B. K. Jones, Levorse, J., and Tilghman, S. M., Deletion of a nuclease-sensitive region between the Igf2 and H19 genes leads to Igf2 misregulation and increased adiposity., Hum Mol Genet, vol. 10, no. 8, pp. 807-14, 2001.
E. G. Emberly, Wingreen, N. S., and Tang, C., Designability of alpha-helical proteins., Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 2002.
H. Li, Tang, C., and Wingreen, N. S., Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix., Proteins, vol. 49, no. 3, pp. 403-12, 2002.
C. Huttenhower, K Mutungu, T., Indik, N., Yang, W., Schroeder, M., Forman, J. J., Troyanskaya, O. G., and Coller, H. A., Detailing regulatory networks through large scale data integration., Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
S. Zhao, Jang, C., Liu, J., Uehara, K., Gilbert, M., Izzo, L., Zeng, X., Trefely, S., Fernandez, S., Carrer, A., Miller, K. D., Schug, Z. T., Snyder, N. W., Gade, T. P., Titchenell, P. M., Rabinowitz, J. D., and Wellen, K. E., Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate., Nature, vol. 579, no. 7800, pp. 586-591, 2020.
S. Zhao, Jang, C., Liu, J., Uehara, K., Gilbert, M., Izzo, L., Zeng, X., Trefely, S., Fernandez, S., Carrer, A., Miller, K. D., Schug, Z. T., Snyder, N. W., Gade, T. P., Titchenell, P. M., Rabinowitz, J. D., and Wellen, K. E., Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate., Nature, vol. 579, no. 7800, pp. 586-591, 2020.
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.
D. Mancini-Dinardo, Steele, S. J. S., Ingram, R. S., and Tilghman, S. M., A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer., Hum Mol Genet, vol. 12, no. 3, pp. 283-94, 2003.
T. Gregor, Bialek, W., van Steveninck, R. R. de Ruyte, Tank, D. W., and Wieschaus, E. F., Diffusion and scaling during early embryonic pattern formation., Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18403-7, 2005.
G. Tkačik and Bialek, W., Diffusion, dimensionality, and noise in transcriptional regulation., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 79, no. 5 Pt 1, p. 051901, 2009.
P. M. Titchenell, Quinn, W. J., Lu, M., Chu, Q., Lu, W., Li, C., Chen, H., Monks, B. R., Chen, J., Rabinowitz, J. D., and Birnbaum, M. J., Direct Hepatocyte Insulin Signaling Is Required for Lipogenesis but Is Dispensable for the Suppression of Glucose Production., Cell Metab, 2016.
M. A. Hibbs, Myers, C. L., Huttenhower, C., Hess, D. C., Li, K., Caudy, A. A., and Troyanskaya, O. G., Directing experimental biology: a case study in mitochondrial biogenesis., PLoS Comput Biol, vol. 5, no. 3, p. e1000322, 2009.
S. Thutupalli, Sun, M., Bunyak, F., Palaniappan, K., and Shaevitz, J. W., Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation., J R Soc Interface, vol. 12, no. 109, p. 20150049, 2015.
C. L. Myers, Chiriac, C., and Troyanskaya, O. G., Discovering biological networks from diverse functional genomic data., Methods Mol Biol, vol. 563, pp. 157-75, 2009.
Y. - F. Xu, Lu, W., Chen, J. C., Johnson, S. A., Gibney, P. A., Thomas, D. G., Brown, G., May, A. L., Campagna, S. R., Yakunin, A. F., Botstein, D., and Rabinowitz, J. D., Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase., ACS Chem Biol, vol. 13, no. 10, pp. 3011-3020, 2018.
C. L. Myers, Robson, D., Wible, A., Hibbs, M. A., Chiriac, C., Theesfeld, C. L., Dolinski, K., and Troyanskaya, O. G., Discovery of biological networks from diverse functional genomic data., Genome Biol, vol. 6, no. 13, p. R114, 2005.
C. L. Myers, Robson, D., Wible, A., Hibbs, M. A., Chiriac, C., Theesfeld, C. L., Dolinski, K., and Troyanskaya, O. G., Discovery of biological networks from diverse functional genomic data., Genome Biol, vol. 6, no. 13, p. R114, 2005.
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.
P. A. Leighton, Ingram, R. S., Eggenschwiler, J., Efstratiadis, A., and Tilghman, S. M., Disruption of imprinting caused by deletion of the H19 gene region in mice., Nature, vol. 375, no. 6526, pp. 34-9, 1995.
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study., PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study., PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
J. Isaac Murray, Whitfield, M. L., Trinklein, N. D., Myers, R. M., Brown, P. O., and Botstein, D., Diverse and specific gene expression responses to stresses in cultured human cells., Mol Biol Cell, vol. 15, no. 5, pp. 2361-74, 2004.
M. E. Garber, Troyanskaya, O. G., Schluens, K., Petersen, S., Thaesler, Z., Pacyna-Gengelbach, M., van de Rijn, M., Rosen, G. D., Perou, C. M., Whyte, R. I., Altman, R. B., Brown, P. O., Botstein, D., and Petersen, I., Diversity of gene expression in adenocarcinoma of the lung., Proc Natl Acad Sci U S A, vol. 98, no. 24, pp. 13784-9, 2001.
M. E. Garber, Troyanskaya, O. G., Schluens, K., Petersen, S., Thaesler, Z., Pacyna-Gengelbach, M., van de Rijn, M., Rosen, G. D., Perou, C. M., Whyte, R. I., Altman, R. B., Brown, P. O., Botstein, D., and Petersen, I., Diversity of gene expression in adenocarcinoma of the lung., Proc Natl Acad Sci U S A, vol. 98, no. 24, pp. 13784-9, 2001.
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.
S. M. Tilghman, DNA methylation: a phoenix rises., Proc Natl Acad Sci U S A, vol. 90, no. 19, pp. 8761-2, 1993.
J. Vacher and Tilghman, S. M., Dominant negative regulation of the mouse alpha-fetoprotein gene in adult liver., Science, vol. 250, no. 4988, pp. 1732-5, 1990.
C. D. van Raamsdonk and Tilghman, S. M., Dosage requirement and allelic expression of PAX6 during lens placode formation., Development, vol. 127, no. 24, pp. 5439-48, 2000.
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.
E
M. E. Brunkow and Tilghman, S. M., Ectopic expression of the H19 gene in mice causes prenatal lethality., Genes Dev, vol. 5, no. 6, pp. 1092-101, 1991.
M. D. Chikina and Troyanskaya, O. G., An effective statistical evaluation of ChIPseq dataset similarity., Bioinformatics, vol. 28, no. 5, pp. 607-13, 2012.
D. Mancini-Dinardo, Steele, S. J. S., Levorse, J. M., Ingram, R. S., and Tilghman, S. M., Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes., Genes Dev, vol. 20, no. 10, pp. 1268-82, 2006.
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.
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.
V. Yao, Wong, A. K., and Troyanskaya, O. G., Enabling Precision Medicine through Integrative Network Models., J Mol Biol, vol. 430, no. 18 Pt A, pp. 2913-2923, 2018.
J. - T. Chi, Chang, H. Y., Haraldsen, G., Jahnsen, F. L., Troyanskaya, O. G., Chang, D. S., Wang, Z., Rockson, S. G., van de Rijn, M., Botstein, D., and Brown, P. O., Endothelial cell diversity revealed by global expression profiling., Proc Natl Acad Sci U S A, vol. 100, no. 19, pp. 10623-8, 2003.
Y. Song, Park, J. O., Tanner, L., Nagano, Y., Rabinowitz, J. D., and Shvartsman, S. Y., Energy budget of Drosophila embryogenesis., Curr Biol, vol. 29, no. 12, pp. R566-R567, 2019.
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.
J. V. Schmidt, Levorse, J. M., and Tilghman, S. M., Enhancer competition between H19 and Igf2 does not mediate their imprinting., Proc Natl Acad Sci U S A, vol. 96, no. 17, pp. 9733-8, 1999.
P. A. Leighton, Saam, J. R., Ingram, R. S., Stewart, C. L., and Tilghman, S. M., An enhancer deletion affects both H19 and Igf2 expression., Genes Dev, vol. 9, no. 17, pp. 2079-89, 1995.
M. S. Bartolomei, Webber, A. L., Brunkow, M. E., and Tilghman, S. M., Epigenetic mechanisms underlying the imprinting of the mouse H19 gene., Genes Dev, vol. 7, no. 9, pp. 1663-73, 1993.
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.
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.
S. Tucci, Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., Nelson, B. J., Fu, W., Purnomo, G. A., Sudoyo, H., Eichler, E. E., Barbujani, G., Visscher, P. M., Akey, J. M., and Green, R. E., Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia., Science, vol. 361, no. 6401, pp. 511-516, 2018.
R. Nash, Weng, S., Hitz, B., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Livstone, M. S., Oughtred, R., Park, J., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Dolinski, K., Botstein, D., and J Cherry, M., Expanded protein information at SGD: new pages and proteome browser., Nucleic Acids Res, vol. 35, no. Database issue, pp. D468-71, 2007.
B. P. Berman, Nibu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M., and Eisen, M. B., Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome., Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 757-62, 2002.
O. G. Vukmirovic and Tilghman, S. M., Exploring genome space., Nature, vol. 405, no. 6788, pp. 820-2, 2000.
M. A. Hibbs, Hess, D. C., Myers, C. L., Huttenhower, C., Li, K., and Troyanskaya, O. G., Exploring the functional landscape of gene expression: directed search of large microarray compendia., Bioinformatics, vol. 23, no. 20, pp. 2692-9, 2007.
C. Huttenhower, Haley, E. M., Hibbs, M. A., Dumeaux, V., Barrett, D. R., Coller, H. A., and Troyanskaya, O. G., Exploring the human genome with functional maps., Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
L. J. Kurihara, Semenova, E., Levorse, J. M., and Tilghman, S. M., Expression and functional analysis of Uch-L3 during mouse development., Mol Cell Biol, vol. 20, no. 7, pp. 2498-504, 2000.
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.
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.
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group., Evolution, vol. 60, no. 2, pp. 292-302, 2006.
F
C. L. Myers, Barrett, D. R., Hibbs, M. A., Huttenhower, C., and Troyanskaya, O. G., Finding function: evaluation methods for functional genomic data., BMC Genomics, vol. 7, p. 187, 2006.
D. L. Metallinos, Oppenheimer, A. J., Rinchik, E. M., Russell, L. B., Dietrich, W., and Tilghman, S. M., Fine structure mapping and deletion analysis of the murine piebald locus., Genetics, vol. 136, no. 1, pp. 217-23, 1994.
R. Godbout, Ingram, R. S., and Tilghman, S. M., Fine-structure mapping of the three mouse alpha-fetoprotein gene enhancers., Mol Cell Biol, vol. 8, no. 3, pp. 1169-78, 1988.
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., Flexibility of alpha-helices: results of a statistical analysis of database protein structures., J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
E. G. Emberly, Mukhopadhyay, R., Tang, C., and Wingreen, N. S., Flexibility of beta-sheets: principal component analysis of database protein structures., Proteins, vol. 55, no. 1, pp. 91-8, 2004.
J. Goya, Wong, A. K., Yao, V., Krishnan, A., Homilius, M., and Troyanskaya, O. G., FNTM: a server for predicting functional networks of tissues in mouse., Nucleic Acids Res, 2015.
S. C. Little, Tkačik, G., Kneeland, T. B., Wieschaus, E. F., and Gregor, T., The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA., PLoS Biol, vol. 9, no. 3, p. e1000596, 2011.
L. Bahati Tanner, Goglia, A. G., Wei, M. H., Sehgal, T., Parsons, L. R., Park, J. O., White, E., Toettcher, J. E., and Rabinowitz, J. D., Four Key Steps Control Glycolytic Flux in Mammalian Cells., Cell Syst, vol. 7, no. 1, pp. 49-62.e8, 2018.
L. Bahati Tanner, Goglia, A. G., Wei, M. H., Sehgal, T., Parsons, L. R., Park, J. O., White, E., Toettcher, J. E., and Rabinowitz, J. D., Four Key Steps Control Glycolytic Flux in Mammalian Cells., Cell Syst, vol. 7, no. 1, pp. 49-62.e8, 2018.
Y. Guan, Dunham, M. J., and Troyanskaya, O. G., Functional analysis of gene duplications in Saccharomyces cerevisiae., Genetics, vol. 175, no. 2, pp. 933-43, 2007.
D. J. Katz, Beer, M. A., Levorse, J. M., and Tilghman, S. M., Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region., Mol Cell Biol, vol. 25, no. 10, pp. 3855-63, 2005.
A. B. Bowman, Levorse, J. M., Ingram, R. S., and Tilghman, S. M., Functional characterization of a testis-specific DNA binding activity at the H19/Igf2 imprinting control region., Mol Cell Biol, vol. 23, no. 22, pp. 8345-51, 2003.
Y. Guan, Ackert-Bicknell, C. L., Kell, B., Troyanskaya, O. G., and Hibbs, M. A., Functional genomics complements quantitative genetics in identifying disease-gene associations., PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
C. Y. Park, Wong, A. K., Greene, C. S., Rowland, J., Guan, Y., Bongo, L. A., Burdine, R. D., and Troyanskaya, O. G., Functional knowledge transfer for high-accuracy prediction of under-studied biological processes., PLoS Comput Biol, vol. 9, no. 3, p. e1002957, 2013.
R. Balakrishnan, Christie, K. R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Nash, R., Oughtred, R., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Sethuraman, A., Weng, S., Botstein, D., and J Cherry, M., Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)., Nucleic Acids Res, vol. 33, no. Database issue, pp. D374-7, 2005.
G
L. L. Sandell, Guan, X. - J., Ingram, R., and Tilghman, S. M., Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta., Proc Natl Acad Sci U S A, vol. 100, no. 8, pp. 4622-7, 2003.
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.
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.
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.
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.
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., Gene expression profiling identifies clinically relevant subtypes of prostate cancer., Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
Y. Kim, Andreu, M. José, Lim, B., Chung, K., Terayama, M., Jiménez, G., Berg, C. A., Lu, H., and Shvartsman, S. Y., Gene regulation by MAPK substrate competition., Dev Cell, vol. 20, no. 6, pp. 880-7, 2011.
P. B. Vrana, Fossella, J. A., Matteson, P., del Rio, T., O'Neill, M. J., and Tilghman, S. M., Genetic and epigenetic incompatibilities underlie hybrid dysgenesis in Peromyscus., Nat Genet, vol. 25, no. 1, pp. 120-4, 2000.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., The genetic landscape of a cell., Science, vol. 327, no. 5964, pp. 425-31, 2010.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., The genetic landscape of a cell., Science, vol. 327, no. 5964, pp. 425-31, 2010.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., The genetic landscape of a cell., Science, vol. 327, no. 5964, pp. 425-31, 2010.
J. M. Rossi, Chen, H., and Tilghman, S. M., Genetic map of the fused locus on mouse chromosome 17., Genomics, vol. 23, no. 1, pp. 178-84, 1994.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., Genome sequencing reveals complex speciation in the Drosophila simulans clade., Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
J. E. Hirschman, Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hong, E. L., Livstone, M. S., Nash, R., Park, J., Oughtred, R., Skrzypek, M., Starr, B., Theesfeld, C. L., Williams, J., Andrada, R., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Thanawala, M. K., Weng, S., Dolinski, K., Botstein, D., and J Cherry, M., Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome., Nucleic Acids Res, vol. 34, no. Database issue, pp. D442-5, 2006.
J. E. Hirschman, Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hong, E. L., Livstone, M. S., Nash, R., Park, J., Oughtred, R., Skrzypek, M., Starr, B., Theesfeld, C. L., Williams, J., Andrada, R., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Thanawala, M. K., Weng, S., Dolinski, K., Botstein, D., and J Cherry, M., Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome., Nucleic Acids Res, vol. 34, no. Database issue, pp. D442-5, 2006.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., A genomewide functional network for the laboratory mouse., PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder., Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder., Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder., Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
H. D. Møller, Bojsen, R. K., Tachibana, C., Parsons, L., Botstein, D., and Regenberg, B., Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells., J Vis Exp, no. 110, p. e54239 |, 2016.
J. M. Rossi, Burke, D. T., Leung, J. C., Koos, D. S., Chen, H., and Tilghman, S. M., Genomic analysis using a yeast artificial chromosome library with mouse DNA inserts., Proc Natl Acad Sci U S A, vol. 89, no. 6, pp. 2456-60, 1992.
P. A. Leighton, Saam, J. R., Ingram, R. S., and Tilghman, S. M., Genomic imprinting in mice: its function and mechanism., Biol Reprod, vol. 54, no. 2, pp. 273-8, 1996.
P. B. Vrana, Guan, X. J., Ingram, R. S., and Tilghman, S. M., Genomic imprinting is disrupted in interspecific Peromyscus hybrids., Nat Genet, vol. 20, no. 4, pp. 362-5, 1998.
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.
O. Troyanskaya, "Getting started in..": a series not to miss., PLoS Comput Biol, vol. 3, no. 10, p. 1841, 2007.
A. K. Wong, Krishnan, A., and Troyanskaya, O. G., GIANT 2.0: genome-scale integrated analysis of gene networks in tissues., Nucleic Acids Research, vol. 46, no. W1, pp. W65-W70, 2018.
A. M. Roberts, Wong, A. K., Fisk, I., and Troyanskaya, O. G., GIANT API: an application programming interface for functional genomics., Nucleic Acids Res, 2016.
E. Kruus, Thumfort, P., Tang, C., and Wingreen, N. S., Gibbs sampling and helix-cap motifs., Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
E. Kruus, Thumfort, P., Tang, C., and Wingreen, N. S., Gibbs sampling and helix-cap motifs., Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
J. A. Brown, Sherlock, G., Myers, C. L., Burrows, N. M., Deng, C., H Wu, I., McCann, K. E., Troyanskaya, O. G., and J Brown, M., Global analysis of gene function in yeast by quantitative phenotypic profiling., Mol Syst Biol, vol. 2, p. 2006.0001, 2006.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., A global genetic interaction network maps a wiring diagram of cellular function., Science, vol. 353, no. 6306, 2016.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., A global genetic interaction network maps a wiring diagram of cellular function., Science, vol. 353, no. 6306, 2016.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., A global genetic interaction network maps a wiring diagram of cellular function., Science, vol. 353, no. 6306, 2016.
M. D. Chikina, Huttenhower, C., Murphy, C. T., and Troyanskaya, O. G., Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans., PLoS Comput Biol, vol. 5, no. 6, p. e1000417, 2009.
J. Zhou and Troyanskaya, O. G., Global quantitative modeling of chromatin factor interactions., PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
A. Bren, Park, J. O., Towbin, B. D., Dekel, E., Rabinowitz, J. D., and Alon, U., Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP., Sci Rep, vol. 6, p. 24834, 2016.
S. Hui, Ghergurovich, J. M., Morscher, R. J., Jang, C., Teng, X., Lu, W., Esparza, L. A., Reya, T., Guo, J. Yanxiang, White, E., and Rabinowitz, J. D., Glucose feeds the TCA cycle via circulating lactate., Nature, vol. 551, no. 7678, pp. 115-118, 2017.
R. S. G. Sealfon, Hibbs, M. A., Huttenhower, C., Myers, C. L., and Troyanskaya, O. G., GOLEM: an interactive graph-based gene-ontology navigation and analysis tool., BMC Bioinformatics, vol. 7, p. 443, 2006.
C. Huttenhower, Mehmood, S. O., and Troyanskaya, O. G., Graphle: Interactive exploration of large, dense graphs., BMC Bioinformatics, vol. 10, p. 417, 2009.
H
Z. Barutcuoglu, Schapire, R. E., and Troyanskaya, O. G., Hierarchical multi-label prediction of gene function., Bioinformatics, vol. 22, no. 7, pp. 830-6, 2006.
P. L. Nara, Tobin, G. J., A Chaudhuri, R., Trujillo, J. D., Lin, G., Cho, M. W., Levin, S. A., Ndifon, W., and Wingreen, N. S., How can vaccines against influenza and other viral diseases be made more effective?, PLoS Biol, vol. 8, no. 12, p. e1000571, 2010.
P. L. Nara, Tobin, G. J., A Chaudhuri, R., Trujillo, J. D., Lin, G., Cho, M. W., Levin, S. A., Ndifon, W., and Wingreen, N. S., How can vaccines against influenza and other viral diseases be made more effective?, PLoS Biol, vol. 8, no. 12, p. e1000571, 2010.
B. K. Jones, Levorse, J., and Tilghman, S. M., A human H19 transgene exhibits impaired paternal-specific imprint acquisition and maintenance in mice., Hum Mol Genet, vol. 11, no. 4, pp. 411-8, 2002.
L. J. Terry, Vastag, L., Rabinowitz, J. D., and Shenk, T., Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection., Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 3071-6, 2012.
J. J. Kamphorst, Nofal, M., Commisso, C., Hackett, S. R., Lu, W., Grabocka, E., Heiden, M. G. Vander, Miller, G., Drebin, J. A., Bar-Sagi, D., Thompson, C. B., and Rabinowitz, J. D., Human pancreatic cancer tumors are nutrient poor and tumor cells actively scavenge extracellular protein., Cancer Res, vol. 75, no. 3, pp. 544-53, 2015.
J. Fan, Teng, X., Liu, L., Mattaini, K. R., Looper, R. E., Heiden, M. G. Vander, and Rabinowitz, J. D., Human Phosphoglycerate Dehydrogenase Produces the Oncometabolite d-2-Hydroxyglutarate., ACS Chem Biol, 2014.
J. - L. Li, Car, R., Tang, C., and Wingreen, N. S., Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water., Proc Natl Acad Sci U S A, vol. 104, no. 8, pp. 2626-30, 2007.
J. J. Kamphorst, Cross, J. R., Fan, J., de Stanchina, E., Mathew, R., White, E. P., Thompson, C. B., and Rabinowitz, J. D., Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids., Proc Natl Acad Sci U S A, vol. 110, no. 22, pp. 8882-7, 2013.
I
E. G. Emberly, Miller, J., Zeng, C., Wingreen, N. S., and Tang, C., Identifying proteins of high designability via surface-exposure patterns., Proteins, vol. 47, no. 3, pp. 295-304, 2002.
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.
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.
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. K. Wong, Krishnan, A., Yao, V., Tadych, A., and Troyanskaya, O. G., IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks., Nucleic Acids Res, 2015.
A. K. Wong, Krishnan, A., Yao, V., Tadych, A., and Troyanskaya, O. G., IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks., Nucleic Acids Res, 2015.
A. K. Wong, Park, C. Y., Greene, C. S., Bongo, L. A., Guan, Y., and Troyanskaya, O. G., IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks., Nucleic Acids Res, vol. 40, no. Web Server issue, pp. W484-90, 2012.
C. Huttenhower, Hibbs, M. A., Myers, C. L., Caudy, A. A., Hess, D. C., and Troyanskaya, O. G., The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction., Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
K. Dolinski and Troyanskaya, O. G., Implications of Big Data for cell biology., Mol Biol Cell, vol. 26, no. 14, pp. 2575-8, 2015.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N., Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors., Genome Biol, vol. 14, no. 11, p. R126, 2013.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N., Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors., Genome Biol, vol. 14, no. 11, p. R126, 2013.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N., Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors., Genome Biol, vol. 14, no. 11, p. R126, 2013.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N., Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors., Genome Biol, vol. 14, no. 11, p. R126, 2013.
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.
G. Tkačik, Callan, C. G., and Bialek, W., Information capacity of genetic regulatory elements., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, no. 1 Pt 1, p. 011910, 2008.
G. Tkačik, Callan, C. G., and Bialek, W., Information flow and optimization in transcriptional regulation., Proc Natl Acad Sci U S A, vol. 105, no. 34, pp. 12265-70, 2008.
N. Slonim, Atwal, G. Singh, Tkačik, G., and Bialek, W., Information-based clustering., Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18297-302, 2005.
O. G. Troyanskaya, Integrated analysis of microarray results., Methods Mol Biol, vol. 382, pp. 429-37, 2007.
A. Pop, Huttenhower, C., Iyer-Pascuzzi, A., Benfey, P. N., and Troyanskaya, O. G., Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana., BMC Syst Biol, vol. 4, p. 180, 2010.
V. N. Kristensen, Vaske, C. J., Ursini-Siegel, J., Van Loo, P., Nordgard, S. H., Sachidanandam, R., Sørlie, T., Wärnberg, F., Haakensen, V. D., Helland, Å., Naume, B., Perou, C. M., Haussler, D., Troyanskaya, O. G., and Børresen-Dale, A. - L., Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling., Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
C. S. Greene and Troyanskaya, O. G., Integrative systems biology for data-driven knowledge discovery., Semin Nephrol, vol. 30, no. 5, pp. 443-54, 2010.
V. Yao, Kaletsky, R., Keyes, W., Mor, D. E., Wong, A. K., Sohrabi, S., Murphy, C. T., and Troyanskaya, O. G., An integrative tissue-network approach to identify and test human disease genes., Nat Biotechnol, 2018.

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