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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2022
K. Olszewski, Barsotti, A., Feng, X. - J., Momcilovic, M., Liu, K. G., Kim, J. - I., Morris, K., Lamarque, C., Gaffney, J., Yu, X., Patel, J. P., Rabinowitz, J. D., Shackelford, D. B., and Poyurovsky, M. V., “Inhibition of glucose transport synergizes with chemical or genetic disruption of mitochondrial metabolism and suppresses TCA cycle-deficient tumors.”, Cell Chem Biol, vol. 29, no. 3, pp. 423-435.e10, 2022.
L. Yang, TeSlaa, T., Ng, S., Nofal, M., Wang, L., Lan, T., Zeng, X., Cowan, A., McBride, M., Lu, W., Davidson, S., Liang, G., Oh, T. Gyu, Downes, M., Evans, R., Von Hoff, D., Guo, J. Yanxiang, Han, H., and Rabinowitz, J. D., “Ketogenic diet and chemotherapy combine to disrupt pancreatic cancer metabolism and growth.”, Med (N Y), vol. 3, no. 2, pp. 119-136, 2022.
2020
D. Hermans, Gautam, S., García-Cañaveras, J. C., Gromer, D., Mitra, S., Spolski, R., Li, P., Christensen, S., Nguyen, R., Lin, J. - X., Oh, J., Du, N., Veenbergen, S., Fioravanti, J., Ebina-Shibuya, R., Bleck, C., Neckers, L. M., Rabinowitz, J. D., Gattinoni, L., and Leonard, W. J., “Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8 T cell stemness and antitumor immunity.”, Proc Natl Acad Sci U S A, vol. 117, no. 11, pp. 6047-6055, 2020.
R. Menon, Otto, E. A., Hoover, P., Eddy, S., Mariani, L., Godfrey, B., Berthier, C. C., Eichinger, F., Subramanian, L., Harder, J., Ju, W., Nair, V., Larkina, M., Naik, A. S., Luo, J., Jain, S., Sealfon, R., Troyanskaya, O., Hacohen, N., Hodgin, J. B., Kretzler, M., and Kpmp, K. Precision, “Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker.”, JCI Insight, vol. 5, no. 6, 2020.
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.
C. Jang, Hui, S., Zeng, X., Cowan, A. J., Wang, L., Chen, L., Morscher, R. J., Reyes, J., Frezza, C., Hwang, H. Y., Imai, A., Saito, Y., Okamoto, K., Vaspoli, C., Kasprenski, L., Zsido, G. A. 2nd, Gorman, J. H. 3rd, Gorman, R. C., and Rabinowitz, J. D., “Metabolite exchange between mammalian organs quantified in pigs.”, Cell Metab., vol. 30, no. 3, pp. 594-606, 2019.
C. Jang, Hui, S., Zeng, X., Cowan, A. J., Wang, L., Chen, L., Morscher, R. J., Reyes, J., Frezza, C., Hwang, H. Young, Imai, A., Saito, Y., Okamoto, K., Vaspoli, C., Kasprenski, L., Zsido, G. A., Gorman, J. H., Gorman, R. C., and Rabinowitz, J. D., “Metabolite Exchange between Mammalian Organs Quantified in Pigs.”, Cell Metab, vol. 30, no. 3, pp. 594-606.e3, 2019.
A. S. Dekhne, Shah, K., Ducker, G. S., Katinas, J. M., Wong-Roushar, J., Nayeen, M. Junayed, Doshi, A., Ning, C., Bao, X., Frühauf, J., Liu, J., Wallace-Povirk, A., O'Connor, C., Dzinic, S. H., White, K., Kushner, J., Kim, S., Hüttemann, M., Polin, L., Rabinowitz, J. D., Li, J., Hou, Z., Dann, C. E., Gangjee, A., and Matherly, L. H., “Novel pyrrolo[3,2-d]pyrimidine compounds target mitochondrial and cytosolic one-carbon metabolism with broad-spectrum antitumor efficacy.”, Mol Cancer Ther, 2019.
J. L. Harder, Menon, R., Otto, E. A., Zhou, J., Eddy, S., Wys, N. L., O'Connor, C., Luo, J., Nair, V., Cebrián, C., Spence, J. R., Bitzer, M., Troyanskaya, O. G., Hodgin, J. B., Wiggins, R. C., Freedman, B. S., and Kretzler, M., “Organoid single cell profiling identifies a transcriptional signature of glomerular disease.”, JCI Insight, vol. 4, no. 1, 2019.
J. L. Harder, Menon, R., Otto, E. A., Zhou, J., Eddy, S., Wys, N. L., O'Connor, C., Luo, J., Nair, V., Cebrián, C., Spence, J. R., Bitzer, M., Troyanskaya, O. G., Hodgin, J. B., Wiggins, R. C., Freedman, B. S., and Kretzler, M., “Organoid single cell profiling identifies a transcriptional signature of glomerular disease.”, JCI Insight, vol. 4, no. 1, 2019.
W. Wang, Ishibashi, J., Trefely, S., Shao, M., Cowan, A. J., Sakers, A., Lim, H. - W., O'Connor, S., Doan, M. T., Cohen, P., Baur, J. A., M King, T., Veech, R. L., Won, K. - J., Rabinowitz, J. D., Snyder, N. W., Gupta, R. K., and Seale, P., “A PRDM16-Driven Metabolic Signal from Adipocytes Regulates Precursor Cell Fate.”, Cell Metab, vol. 30, no. 1, pp. 174-189.e5, 2019.
2018
M. A. Lanaspa, Andres-Hernando, A., Orlicky, D. J., Cicerchi, C., Jang, C., Li, N., Milagres, T., Kuwabara, M., Wempe, M. F., Rabinowitz, J. D., Johnson, R. J., and Tolan, D. R., “Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice.”, J Clin Invest, vol. 128, no. 6, pp. 2226-2238, 2018.
R. Menon, Otto, E. A., Kokoruda, A., Zhou, J., Zhang, Z., Yoon, E., Chen, Y. - C., Troyanskaya, O., Spence, J. R., Kretzler, M., and Cebrián, C., “Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.”, Development, vol. 145, no. 16, 2018.
2017
R. C. Oslund, Su, X., Haugbro, M., Kee, J. - M., Esposito, M., David, Y., Wang, B., Ge, E., Perlman, D. H., Kang, Y., Muir, T. W., and Rabinowitz, J. D., “Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate.”, Nat Chem Biol, vol. 13, no. 10, pp. 1081-1087, 2017.
A. Ochoa and Singh, M., “Domain prediction with probabilistic directional context.”, Bioinformatics, vol. 33, no. 16, pp. 2471-2478, 2017.
A. L. Wooldridge, Bischof, R. J., Liu, H., Heinemann, G. K., Hunter, D. S., Giles, L. C., Simmons, R. A., Lien, Y. - C., Lu, W., Rabinowitz, J. D., Kind, K. L., Owens, J. A., Clifton, V. L., and Gatford, K. L., “Late gestation maternal dietary methyl donor and cofactor supplementation in sheep partially reverses protection against allergic sensitization by IUGR.”, Am J Physiol Regul Integr Comp Physiol, p. ajpregu.00549.2016, 2017.
J. Choi, Rajagopal, A., Xu, Y. - F., Rabinowitz, J. D., and O'Shea, E. K., “A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae.”, PLoS One, vol. 12, no. 5, p. e0176085, 2017.
2016
C. Jang, Oh, S. F., Wada, S., Rowe, G. C., Liu, L., Chan, M. Chun, Rhee, J., Hoshino, A., Kim, B., Ibrahim, A., Baca, L. G., Kim, E., Ghosh, C. C., Parikh, S. M., Jiang, A., Chu, Q., Forman, D. E., Lecker, S. H., Krishnaiah, S., Rabinowitz, J. D., Weljie, A. M., Baur, J. A., Kasper, D. L., and Arany, Z., “A branched-chain amino acid metabolite drives vascular fatty acid transport and causes insulin resistance.”, Nat Med, vol. 22, no. 4, pp. 421-6, 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.
E. Watson, Olin-Sandoval, V., Hoy, M. J., Li, C. - H., Louisse, T., Yao, V., Mori, A., Holdorf, A. D., Troyanskaya, O. G., Ralser, M., and Walhout, A. Jm, “Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.”, Elife, vol. 5, 2016.
N. Ouzounov, Nguyen, J. P., Bratton, B. P., Jacobowitz, D., Gitai, Z., and Shaevitz, J. W., “MreB Orientation Correlates with Cell Diameter in Escherichia coli.”, Biophys J, vol. 111, no. 5, pp. 1035-43, 2016.
E. K. Farley, Olson, K. M., Zhang, W., Rokhsar, D. S., and Levine, M. S., “Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers.”, Proc Natl Acad Sci U S A, vol. 113, no. 23, pp. 6508-13, 2016.
2015
J. F. Ayroles, Buchanan, S. M., O'Leary, C., Skutt-Kakaria, K., Grenier, J. K., Clark, A. G., Hartl, D. L., and de Bivort, B. L., “Behavioral idiosyncrasy reveals genetic control of phenotypic variability.”, Proc Natl Acad Sci U S A, vol. 112, no. 21, pp. 6706-11, 2015.
A. Ochoa, Storey, J. D., Llinás, M., and Singh, M., “Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.”, PLoS Comput Biol, vol. 11, no. 11, p. e1004509, 2015.
K. Oktaba, Zhang, W., Lotz, T. Sabrina, Jun, D. Jayhyun, Lemke, S. Beatrice, Ng, S. Pak, Esposito, E., Levine, M., and Hilgers, V., “ELAV Links Paused Pol II to Alternative Polyadenylation in the Drosophila Nervous System.”, Mol Cell, vol. 57, no. 2, pp. 341-8, 2015.
R. M. Morgenstein, Bratton, B. P., Nguyen, J. P., Ouzounov, N., Shaevitz, J. W., and Gitai, Z., “RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis.”, Proc Natl Acad Sci U S A, vol. 112, no. 40, pp. 12510-5, 2015.
E. K. Farley, Olson, K. M., Zhang, W., Brandt, A. J., Rokhsar, D. S., and Levine, M. S., “Suboptimization of developmental enhancers.”, Science, vol. 350, no. 6258, pp. 325-8, 2015.
A. V. Persikov, Wetzel, J. L., Rowland, E. F., Oakes, B. L., Xu, D. J., Singh, M., and Noyes, M. B., “A systematic survey of the Cys2His2 zinc finger DNA-binding landscape.”, Nucleic Acids Res, vol. 43, no. 3, pp. 1965-84, 2015.
2014
X. X. Du, Osterfield, M., and Shvartsman, S. Y., “Computational analysis of three-dimensional epithelial morphogenesis using vertex models.”, Phys Biol, vol. 11, no. 6, p. 066007, 2014.
A. V. Persikov, Rowland, E. F., Oakes, B. L., Singh, M., and Noyes, M. B., “Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.”, Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
D. Andrea Fer de Abreu, Caballero, A., Fardel, P., Stroustrup, N., Chen, Z., Lee, K., Keyes, W. D., Nash, Z. M., López-Moyado, I. F., Vaggi, F., Cornils, A., Regenass, M., Neagu, A., Ostojic, I., Liu, C., Cho, Y., Sifoglu, D., Shen, Y., Fontana, W., Lu, H., Csikasz-Nagy, A., Murphy, C. T., Antebi, A., Blanc, E., Apfeld, J., Zhang, Y., Alcedo, J., and Ch'ng, Q., “An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology.”, PLoS Genet, vol. 10, no. 3, p. e1004225, 2014.
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, “Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.”, Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
A. G. Fletcher, Osterfield, M., Baker, R. E., and Shvartsman, S. Y., “Vertex models of epithelial morphogenesis.”, Biophys J, vol. 106, no. 11, pp. 2291-304, 2014.
S. Melody Foo, Sun, Y., Lim, B., Ziukaite, R., O'Brien, K., Nien, C. - Y., Kirov, N., Shvartsman, S. Y., and Rushlow, C. A., “Zelda potentiates morphogen activity by increasing chromatin accessibility.”, Curr Biol, vol. 24, no. 12, pp. 1341-6, 2014.
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.
S. R McIsaac, Oakes, B. L., Botstein, D., and Noyes, M. B., “Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters.”, J Vis Exp, no. 81, p. e51153, 2013.
S. R McIsaac, Oakes, B. L., Wang, X., Dummit, K. A., Botstein, D., and Noyes, M. B., “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
M. Osterfield, Du, X. X., Schüpbach, T., Wieschaus, E., and Shvartsman, S. Y., “Three-dimensional epithelial morphogenesis in the developing Drosophila egg.”, Dev Cell, vol. 24, no. 4, pp. 400-10, 2013.
2012
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.
V. D. Nair, Ge, Y., Balasubramaniyan, N., Kim, J., Okawa, Y., Chikina, M., Troyanskaya, O., and Sealfon, S. C., “Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells.”, Mol Cell Biol, vol. 32, no. 23, pp. 4861-76, 2012.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
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.
Y. Wang, Tu, K. C., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit.”, Biophys J, vol. 100, no. 12, pp. 3045-53, 2011.
G. J. Stephens, Osborne, L. C., and Bialek, W., “Searching for simplicity in the analysis of neurons and behavior.”, Proc Natl Acad Sci U S A, vol. 108 Suppl 3, pp. 15565-71, 2011.
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.
A. Ochoa, Llinás, M., and Singh, M., “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
2010
K. L. Olszewski, Mather, M. W., Morrisey, J. M., Garcia, B. A., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., “Branched tricarboxylic acid metabolism in Plasmodium falciparum.”, Nature, vol. 466, no. 7307, pp. 774-8, 2010.
S. - W. Teng, Wang, Y., Tu, K. C., Long, T., Mehta, P., Wingreen, N. S., Bassler, B. L., and Ong, N. P., “Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell.”, Biophys J, vol. 98, no. 9, pp. 2024-31, 2010.
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.
A. Baryshnikova, Costanzo, M., Kim, Y., Ding, H., Koh, J., Toufighi, K., Youn, J. - Y., Ou, J., San Luis, B. - J., Bandyopadhyay, S., Hibbs, M., Hess, D., Gingras, A. - C., Bader, G. D., Troyanskaya, O. G., Brown, G. W., Andrews, B., Boone, C., and Myers, C. L., “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”, Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
S. R. Engel, Balakrishnan, R., Binkley, G., Christie, K. R., Costanzo, M. C., Dwight, S. S., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Hong, E. L., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R., Oughtred, R., Park, J., Skrzypek, M. S., Weng, S., Wong, E. D., Dolinski, K., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database provides mutant phenotype data.”, Nucleic Acids Res, vol. 38, no. Database issue, pp. D433-6, 2010.
2009
B. D. Bennett, Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., and Rabinowitz, J. D., “Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.”, Nat Chem Biol, vol. 5, no. 8, pp. 593-9, 2009.
R. P. Oliveira, Abate, J. Porter, Dilks, K., Landis, J., Ashraf, J., Murphy, C. T., and T Blackwell, K., “Condition-adapted stress and longevity gene regulation by Caenorhabditis elegans SKN-1/Nrf.”, Aging Cell, vol. 8, no. 5, pp. 524-41, 2009.
K. L. Olszewski, Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., “Host-parasite interactions revealed by Plasmodium falciparum metabolomics.”, Cell Host Microbe, vol. 5, no. 2, pp. 191-9, 2009.
A. V. Persikov, Osada, R., and Singh, M., “Predicting DNA recognition by Cys2His2 zinc finger proteins.”, Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
T. Long, Tu, K. C., Wang, Y., Mehta, P., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Quantifying the integration of quorum-sensing signals with single-cell resolution.”, PLoS Biol, vol. 7, no. 3, p. e68, 2009.
L. Salwinski, Licata, L., Winter, A., Thorneycroft, D., Khadake, J., Ceol, A., Aryamontri, A. Chatr, Oughtred, R., Livstone, M., Boucher, L., Botstein, D., Dolinski, K., Berardini, T., Huala, E., Tyers, M., Eisenberg, D., Cesareni, G., and Hermjakob, H., “Recurated protein interaction datasets.”, Nat Methods, vol. 6, no. 12, pp. 860-1, 2009.
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.
E. L. Hong, Balakrishnan, R., Dong, Q., Christie, K. R., Park, J., Binkley, G., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R. S., Oughtred, R., Skrzypek, M. S., Weng, S., Wong, E. D., Zhu, K. K., Dolinski, K., Botstein, D., and J Cherry, M., “Gene Ontology annotations at SGD: new data sources and annotation methods.”, Nucleic Acids Res, vol. 36, no. Database issue, pp. D577-81, 2008.
L. C. Osborne, Palmer, S. E., Lisberger, S. G., and Bialek, W., “The neural basis for combinatorial coding in a cortical population response.”, J Neurosci, vol. 28, no. 50, pp. 13522-31, 2008.
R. G. Endres, Oleksiuk, O., Hansen, C. H., Meir, Y., Sourjik, V., and Wingreen, N. S., “Variable sizes of Escherichia coli chemoreceptor signaling teams.”, Mol Syst Biol, vol. 4, p. 211, 2008.
2007
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.
C. Huttenhower, Flamholz, A. I., Landis, J. N., Sahi, S., Myers, C. L., Olszewski, K. L., Hibbs, M. A., Siemers, N. O., Troyanskaya, O. G., and Coller, H. A., “Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.”, BMC Bioinformatics, vol. 8, p. 250, 2007.
S. Heinicke, Livstone, M. S., Lu, C., Oughtred, R., Kang, F., Angiuoli, S. V., White, O., Botstein, D., and Dolinski, K., “The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.”, PLoS One, vol. 2, no. 8, p. e766, 2007.
L. C. Osborne, Hohl, S. S., Bialek, W., and Lisberger, S. G., “Time course of precision in smooth-pursuit eye movements of monkeys.”, J Neurosci, vol. 27, no. 11, pp. 2987-98, 2007.
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.
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.
2005
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.
A. Dejean, Solano, P. Jean, Ayroles, J., Corbara, B., and Orivel, J., “Insect behaviour: arboreal ants build traps to capture prey.”, Nature, vol. 434, no. 7036, p. 973, 2005.
L. C. Osborne, Lisberger, S. G., and Bialek, W., “A sensory source for motor variation.”, Nature, vol. 437, no. 7057, pp. 412-6, 2005.
2004
R. Osada, Zaslavsky, E., and Singh, M., “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
L. C. Osborne, Bialek, W., and Lisberger, S. G., “Time course of information about motion direction in visual area MT of macaque monkeys.”, J Neurosci, vol. 24, no. 13, pp. 3210-22, 2004.
2003
O. G. Troyanskaya, Dolinski, K., Owen, A. B., Altman, R. B., and Botstein, D., “A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8348-53, 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.
K. Ranade, Hinds, D., Hsiung, C. Agnes, Chuang, L. - M., Chang, M. - S., Chen, Y. - T., Pesich, R., Hebert, J., Chen, Y. - D. I., Dzau, V., Olshen, R., Curb, D., Botstein, D., Cox, D. R., and Risch, N., “A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins.”, Am J Hypertens, vol. 16, no. 2, pp. 158-62, 2003.
T. L. Adelman, Bialek, W., and Olberg, R. M., “The information content of receptive fields.”, Neuron, vol. 40, no. 4, pp. 823-33, 2003.
W. R. Uhlmann, Bennett, R., Botkin, J. R., Botstein, D., Boughman, J. A., Chakravarti, A., Clayton, E. Wright, Kahn, J., Koenig, B., Murray, T. H., Olson, M. V., Rowley, J., Terry, S., and Valle, D., “Planning the genome institute's future.”, Science, vol. 299, no. 5612, p. 1515; author reply 1515, 2003.
T. O. Nielsen, Hsu, F. D., O'Connell, J. X., C Gilks, B., Sorensen, P. H. B., Linn, S., West, R. B., Liu, C. Long, Botstein, D., Brown, P. O., and van de Rijn, M., “Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology.”, Am J Pathol, vol. 163, no. 4, pp. 1449-56, 2003.
2002
H. Yoshimoto, Saltsman, K., Gasch, A. P., Li, H. Xia, Ogawa, N., Botstein, D., Brown, P. O., and Cyert, M. S., “Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 34, pp. 31079-88, 2002.
T. O. Nielsen, West, R. B., Linn, S. C., Alter, O., Knowling, M. A., O'Connell, J. X., Zhu, S., Fero, M., Sherlock, G., Pollack, J. R., Brown, P. O., Botstein, D., and van de Rijn, M., “Molecular characterisation of soft tissue tumours: a gene expression study.”, Lancet, vol. 359, no. 9314, pp. 1301-7, 2002.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
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.
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R., “Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”, Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
2001
K. J. Arrow, Axelrod, J., Benacerraf, B., Berg, P., Bishop, J. M., Bloembergen, N., Brown, H. C., Cibelli, J., Cohen, S., Cooper, L. N., Corey, E. J., Cronin, J. W., Curl, R., Dulbecco, R., Fischer, E. H., Fitch, V. L., Fogel, R., Friedman, J. I., Furchgott, R. F., Gell-Mann, M., Gilbert, W., Gilman, A., Glaser, D., Glashow, S. L., Green, R. M., Greengard, P., Guillemin, R., Hayflick, L., Hauptman, H. A., Heckman, J. J., Heeger, A., Herschbach, D., Hubel, D. H., Hulse, R., Kandel, E., Karle, J., Klein, L. R., Kohn, W., Kornberg, A., Krebs, E. G., Lanza, R. P., Laughlin, R., Lederman, L., Lee, D. M., Lewis, E., Lipscomb, W., Marcus, R. A., McFadden, D., Merrifield, R. B., Merton, R., Modigliani, F., Molina, M. J., Murad, F., Nirenberg, M. W., North, D. C., Olah, G. A., Osheroff, D., Palade, G. E., Perl, M., Ramsey, N. F., Richter, B., Roberts, R. J., Samuelson, P. A., Schwartz, M., Sharp, P. A., Smalley, R. E., Smith, H. O., Solow, R. M., Stormer, H., Taube, H., Taylor, R., Thomas, E. D., Tobin, J., Tonegawa, S., Townes, C., Watson, J. D., Weinberg, S., Weller, T. H., West, M. D., Wieschaus, E. F., Wiesel, T. N., and Wilson, R. W., “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
K. J. Arrow, Axelrod, J., Benacerraf, B., Berg, P., Bishop, J. M., Bloembergen, N., Brown, H. C., Cibelli, J., Cohen, S., Cooper, L. N., Corey, E. J., Cronin, J. W., Curl, R., Dulbecco, R., Fischer, E. H., Fitch, V. L., Fogel, R., Friedman, J. I., Furchgott, R. F., Gell-Mann, M., Gilbert, W., Gilman, A., Glaser, D., Glashow, S. L., Green, R. M., Greengard, P., Guillemin, R., Hayflick, L., Hauptman, H. A., Heckman, J. J., Heeger, A., Herschbach, D., Hubel, D. H., Hulse, R., Kandel, E., Karle, J., Klein, L. R., Kohn, W., Kornberg, A., Krebs, E. G., Lanza, R. P., Laughlin, R., Lederman, L., Lee, D. M., Lewis, E., Lipscomb, W., Marcus, R. A., McFadden, D., Merrifield, R. B., Merton, R., Modigliani, F., Molina, M. J., Murad, F., Nirenberg, M. W., North, D. C., Olah, G. A., Osheroff, D., Palade, G. E., Perl, M., Ramsey, N. F., Richter, B., Roberts, R. J., Samuelson, P. A., Schwartz, M., Sharp, P. A., Smalley, R. E., Smith, H. O., Solow, R. M., Stormer, H., Taube, H., Taylor, R., Thomas, E. D., Tobin, J., Tonegawa, S., Townes, C., Watson, J. D., Weinberg, S., Weller, T. H., West, M. D., Wieschaus, E. F., Wiesel, T. N., and Wilson, R. W., “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
2000
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.
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.
1996
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.
1994
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.
1993
M. Peifer, Orsulic, S., Sweeton, D., and Wieschaus, E., “A role for the Drosophila segment polarity gene armadillo in cell adhesion and cytoskeletal integrity during oogenesis.”, Development, vol. 118, no. 4, pp. 1191-207, 1993.