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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2018
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.
N. Ron-Harel, Notarangelo, G., Ghergurovich, J. M., Paulo, J. A., Sage, P. T., Santos, D., F Satterstrom, K., Gygi, S. P., Rabinowitz, J. D., Sharpe, A. H., and Haigis, M. C., Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice., Proc Natl Acad Sci U S A, vol. 115, no. 52, pp. 13347-13352, 2018.
D. Guan, Xiong, Y., Borck, P. C., Jang, C., Doulias, P. - T., Papazyan, R., Fang, B., Jiang, C., Zhang, Y., Briggs, E. R., Hu, W., Steger, D., Ischiropoulos, H., Rabinowitz, J. D., and Lazar, M. A., Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes., Cell, vol. 174, no. 4, pp. 831-842.e12, 2018.
Y. -suk Lee, Wong, A. K., Tadych, A., Hartmann, B. M., Park, C. Y., DeJesus, V. A., Ramos, I., Zaslavsky, E., Sealfon, S. C., and Troyanskaya, O. G., Interpretation of an individual functional genomics experiment guided by massive public data., Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
R. J. Morscher, Ducker, G. S., Li, S. Hsin- Jung, Mayer, J. A., Gitai, Z., Sperl, W., and Rabinowitz, J. D., Mitochondrial translation requires folate-dependent tRNA methylation., Nature, vol. 554, no. 7690, pp. 128-132, 2018.
2013
N. Slavov and Botstein, D., Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression., Mol Biol Cell, vol. 24, no. 2, pp. 157-68, 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.
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.
L. S. Cheung, Simakov, D. S. A., Fuchs, A., Pyrowolakis, G., and Shvartsman, S. Y., Dynamic model for the coordination of two enhancers of broad by EGFR signaling., Proc Natl Acad Sci U S A, vol. 110, no. 44, pp. 17939-44, 2013.
J. Fan, Kamphorst, J. J., Mathew, R., Chung, M. K., White, E., Shlomi, T., and Rabinowitz, J. D., Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia., Mol Syst Biol, vol. 9, p. 712, 2013.
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.
A. A. Caudy, Guan, Y., Jia, Y., Hansen, C., DeSevo, C., Hayes, A. P., Agee, J., Alvarez-Dominguez, J. R., Arellano, H., Barrett, D., Bauerle, C., Bisaria, N., Bradley, P. H., J Breunig, S., Bush, E., Cappel, D., Capra, E., Chen, W., Clore, J., Combs, P. A., Doucette, C., Demuren, O., Fellowes, P., Freeman, S., Frenkel, E., Gadala-Maria, D., Gawande, R., Glass, D., Grossberg, S., Gupta, A., Hammonds-Odie, L., Hoisos, A., Hsi, J., Hsu, Y. - H. Huang, Inukai, S., Karczewski, K. J., Ke, X., Kojima, M., Leachman, S., Lieber, D., Liebowitz, A., Liu, J., Liu, Y., Martin, T., Mena, J., Mendoza, R., Myhrvold, C., Millian, C., Pfau, S., Raj, S., Rich, M., Rokicki, J., Rounds, W., Salazar, M., Salesi, M., Sharma, R., Silverman, S., Singer, C., Sinha, S., Staller, M., Stern, P., Tang, H., Weeks, S., Weidmann, M., Wolf, A., Young, C., Yuan, J., Crutchfield, C., McClean, M., Murphy, C. T., Llinás, M., Botstein, D., Troyanskaya, O. G., and Dunham, M. J., A new system for comparative functional genomics of Saccharomyces yeasts., Genetics, vol. 195, no. 1, pp. 275-87, 2013.
Y. -suk Lee, Krishnan, A., Zhu, Q., and Troyanskaya, O. G., Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies., Bioinformatics, vol. 29, no. 23, pp. 3036-44, 2013.
Y. -suk Lee, Krishnan, A., Zhu, Q., and Troyanskaya, O. G., Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies., Bioinformatics, vol. 29, no. 23, pp. 3036-44, 2013.
T. Pilizota and Shaevitz, J. W., Plasmolysis and cell shape depend on solute outer-membrane permeability during hyperosmotic shock in E. coli., Biophys J, vol. 104, no. 12, pp. 2733-42, 2013.
T. Pilizota and Shaevitz, J. W., Plasmolysis and cell shape depend on solute outer-membrane permeability during hyperosmotic shock in E. coli., Biophys J, vol. 104, no. 12, pp. 2733-42, 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
N. Slavov, Airoldi, E. M., van Oudenaarden, A., and Botstein, D., A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes., Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
N. Slavov, Airoldi, E. M., van Oudenaarden, A., and Botstein, D., A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes., Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
T. Pilizota and Shaevitz, J. W., Fast, multiphase volume adaptation to hyperosmotic shock by Escherichia coli., PLoS One, vol. 7, no. 4, p. e35205, 2012.
S. Wang, Furchtgott, L., Huang, K. Casey, and Shaevitz, J. W., Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall., Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 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.
K. M. Doherty, Pride, L. D., Lukose, J., Snydsman, B. E., Charles, R., Pramanik, A., Muller, E. G., Botstein, D., and Moore, C. Wood, Loss of a 20S proteasome activator in Saccharomyces cerevisiae downregulates genes important for genomic integrity, increases DNA damage, and selectively sensitizes cells to agents with diverse mechanisms of action., G3 (Bethesda), vol. 2, no. 8, pp. 943-59, 2012.
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., Parallel molecular evolution in an herbivore community., Science, vol. 337, no. 6102, pp. 1634-7, 2012.
J. A. Drocco, Wieschaus, E. F., and Tank, D. W., The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs., Phys Biol, vol. 9, no. 5, p. 055004, 2012.
Y. Guan, Gorenshteyn, D., Burmeister, M., Wong, A. K., Schimenti, J. C., Handel, M. Ann, Bult, C. J., Hibbs, M. A., and Troyanskaya, O. G., Tissue-specific functional networks for prioritizing phenotype and disease genes., PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
A. Fuchs, Cheung, L. S., Charbonnier, E., Shvartsman, S. Y., and Pyrowolakis, G., Transcriptional interpretation of the EGF receptor signaling gradient., Proc Natl Acad Sci U S A, vol. 109, no. 5, pp. 1572-7, 2012.
M. A. Gelbart, He, B., Martin, A. C., Thiberge, S. Y., Wieschaus, E. F., and Kaschube, M., Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis., Proc Natl Acad Sci U S A, vol. 109, no. 47, pp. 19298-303, 2012.
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.
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.
N. Slavov and Botstein, D., Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast., Mol Biol Cell, vol. 22, no. 12, pp. 1997-2009, 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. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks., Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
J. A. Drocco, Grimm, O., Tank, D. W., and Wieschaus, E., Measurement and perturbation of morphogen lifetime: effects on gradient shape., Biophys J, vol. 101, no. 8, pp. 1807-15, 2011.
N. Slavov, Macinskas, J., Caudy, A., and Botstein, D., Metabolic cycling without cell division cycling in respiring yeast., Proc Natl Acad Sci U S A, vol. 108, no. 47, pp. 19090-5, 2011.
L. S. Cheung, Schüpbach, T., and Shvartsman, S. Y., Pattern formation by receptor tyrosine kinases: analysis of the Gurken gradient in Drosophila oogenesis., Curr Opin Genet Dev, vol. 21, no. 6, pp. 719-25, 2011.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., A population genetics-phylogenetics approach to inferring natural selection in coding sequences., PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
A. A. Petti, Crutchfield, C. A., Rabinowitz, J. D., and Botstein, D., Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function., Proc Natl Acad Sci U S A, vol. 108, no. 45, pp. E1089-98, 2011.
M. M. Klosinska, Crutchfield, C. A., Bradley, P. H., Rabinowitz, J. D., and Broach, J. R., Yeast cells can access distinct quiescent states., Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
2010
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria., Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 2010.
D. Gresham, Usaite, R., Germann, S. Manuela, Lisby, M., Botstein, D., and Regenberg, B., Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus., Proc Natl Acad Sci U S A, vol. 107, no. 43, pp. 18551-6, 2010.
M. E. Kavousanakis, Kanodia, J. S., Kim, Y., Kevrekidis, I. G., and Shvartsman, S. Y., A compartmental model for the bicoid gradient., Dev Biol, vol. 345, no. 1, pp. 12-7, 2010.
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.
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.
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees., PLoS One, vol. 5, no. 2, p. e9116, 2010.
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees., PLoS One, vol. 5, no. 2, p. e9116, 2010.
J. N. Landis and Murphy, C. T., Integration of diverse inputs in the regulation of Caenorhabditis elegans DAF-16/FOXO., Dev Dyn, vol. 239, no. 5, pp. 1405-12, 2010.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., Measuring the bending stiffness of bacterial cells using an optical trap., J Vis Exp, no. 38, 2010.
S. J. Silverman, Petti, A. A., Slavov, N., Parsons, L., Briehof, R., Thiberge, S. Y., Zenklusen, D., Gandhi, S. J., Larson, D. R., Singer, R. H., and Botstein, D., Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate., Proc Natl Acad Sci U S A, vol. 107, no. 15, pp. 6946-51, 2010.
D. Gresham, Curry, B., Ward, A., D Gordon, B., Brizuela, L., Kruglyak, L., and Botstein, D., Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes., Proc Natl Acad Sci U S A, vol. 107, no. 4, pp. 1482-7, 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.
R. Kaletsky and Murphy, C. T., The role of insulin/IGF-like signaling in C. elegans longevity and aging., Dis Model Mech, vol. 3, no. 7-8, pp. 415-9, 2010.
Y. Guan, Dunham, M., Caudy, A., and Troyanskaya, O., Systematic planning of genome-scale experiments in poorly studied species., PLoS Comput Biol, vol. 6, no. 3, p. e1000698, 2010.
S. Luo, Kleemann, G. A., Ashraf, J. M., Shaw, W. M., and Murphy, C. T., TGF-β and insulin signaling regulate reproductive aging via oocyte and germline quality maintenance., Cell, vol. 143, no. 2, pp. 299-312, 2010.
2009
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.
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.
J. Cande, Goltsev, Y., and Levine, M. S., Conservation of enhancer location in divergent insects., Proc Natl Acad Sci U S A, vol. 106, no. 34, pp. 14414-9, 2009.
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.
Y. Goltsev, Rezende, G. L., Vranizan, K., Lanzaro, G., Valle, D., and Levine, M., Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo., Dev Biol, vol. 330, no. 2, pp. 462-70, 2009.
J. J. Zartman, Kanodia, J. S., Yakoby, N., Schafer, X., Watson, C., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Expression patterns of cadherin genes in Drosophila oogenesis., Gene Expr Patterns, vol. 9, no. 1, pp. 31-6, 2009.
J. J. Zartman, Kanodia, J. S., Yakoby, N., Schafer, X., Watson, C., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Expression patterns of cadherin genes in Drosophila oogenesis., Gene Expr Patterns, vol. 9, no. 1, pp. 31-6, 2009.
J. J. Zartman, Kanodia, J. S., Cheung, L. S., and Shvartsman, S. Y., Feedback control of the EGFR signaling gradient: superposition of domain-splitting events in Drosophila oogenesis., Development, vol. 136, no. 17, pp. 2903-11, 2009.
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.
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.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Isolation of sea squirt (Ciona) gametes, fertilization, dechorionation, and development., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5344, 2009.
J. S. Bloom, Khan, Z., Kruglyak, L., Singh, M., and Caudy, A. A., Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays., BMC Genomics, vol. 10, p. 221, 2009.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Microinjection of morpholino oligos and RNAs in sea squirt (Ciona) embryos., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5347, 2009.
C. Hei Ho, Magtanong, L., Barker, S. L., Gresham, D., Nishimura, S., Natarajan, P., L Y Koh, J., Porter, J., Gray, C. A., Andersen, R. J., Giaever, G., Nislow, C., Andrews, B., Botstein, D., Graham, T. R., Yoshida, M., and Boone, C., A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds., Nat Biotechnol, vol. 27, no. 4, pp. 369-77, 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.
S. Luo, Shaw, W. M., Ashraf, J., and Murphy, C. T., TGF-beta Sma/Mab signaling mutations uncouple reproductive aging from somatic aging., PLoS Genet, vol. 5, no. 12, p. e1000789, 2009.
2008
P. A. DiMaggio, McAllister, S. R., Floudas, C. A., Feng, X. - J., Rabinowitz, J. D., and Rabitz, H. A., Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies., BMC Bioinformatics, vol. 9, p. 458, 2008.
J. J. Zartman, Yakoby, N., Bristow, C. A., Zhou, X., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis., Dev Biol, vol. 322, no. 2, pp. 289-301, 2008.
J. J. Zartman, Yakoby, N., Bristow, C. A., Zhou, X., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis., Dev Biol, vol. 322, no. 2, pp. 289-301, 2008.
N. Yakoby, Bristow, C. A., Gong, D., Schafer, X., Lembong, J., Zartman, J. J., Halfon, M. S., Schüpbach, T., and Shvartsman, S. Y., A combinatorial code for pattern formation in Drosophila oogenesis., Dev Cell, vol. 15, no. 5, pp. 725-37, 2008.
N. Yakoby, Bristow, C. A., Gong, D., Schafer, X., Lembong, J., Zartman, J. J., Halfon, M. S., Schüpbach, T., and Shvartsman, S. Y., A combinatorial code for pattern formation in Drosophila oogenesis., Dev Cell, vol. 15, no. 5, pp. 725-37, 2008.
D. Gresham, Dunham, M. J., and Botstein, D., Comparing whole genomes using DNA microarrays., Nat Rev Genet, vol. 9, no. 4, pp. 291-302, 2008.
N. Yakoby, Lembong, J., Schüpbach, T., and Shvartsman, S. Y., Drosophila eggshell is patterned by sequential action of feedforward and feedback loops., Development, vol. 135, no. 2, pp. 343-51, 2008.
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.
J. - W. Hong, Hendrix, D. A., and Levine, M. S., Shadow enhancers as a source of evolutionary novelty., Science, vol. 321, no. 5894, p. 1314, 2008.
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., The transcription/migration interface in heart precursors of Ciona intestinalis., Science, vol. 320, no. 5881, pp. 1349-52, 2008.
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., The transcription/migration interface in heart precursors of Ciona intestinalis., Science, vol. 320, no. 5881, pp. 1349-52, 2008.
2006
D. C. Hess, Lu, W., Rabinowitz, J. D., and Botstein, D., Ammonium toxicity and potassium limitation in yeast., PLoS Biol, vol. 4, no. 11, p. e351, 2006.
J. F. Ayroles and Gibson, G., Analysis of variance of microarray data., Methods Enzymol, vol. 411, pp. 214-33, 2006.
F. Biemar, Nix, D. A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., J Manak, R., and Levine, M. S., Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array., Proc Natl Acad Sci U S A, vol. 103, no. 34, pp. 12763-8, 2006.
T. Sørlie, Perou, C. M., Fan, C., Geisler, S., Aas, T., Nobel, A., Anker, G., Akslen, L. A., Botstein, D., Børresen-Dale, A. - L., and Lønning, P. Eystein, Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer., Mol Cancer Ther, vol. 5, no. 11, pp. 2914-8, 2006.
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O., Genome-scale identification of membrane-associated human mRNAs., PLoS Genet, vol. 2, no. 1, p. e11, 2006.
D. Gresham, Ruderfer, D. M., Pratt, S. C., Schacherer, J., Dunham, M. J., Botstein, D., and Kruglyak, L., Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray., Science, vol. 311, no. 5769, pp. 1932-6, 2006.
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.
L. A. Goentoro, Reeves, G. T., Kowal, C. P., Martinelli, L., Schüpbach, T., and Shvartsman, S. Y., Quantifying the Gurken morphogen gradient in Drosophila oogenesis., Dev Cell, vol. 11, no. 2, pp. 263-72, 2006.
L. A. Goentoro, Yakoby, N., Goodhouse, J., Schüpbach, T., and Shvartsman, S. Y., Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis., Genesis, vol. 44, no. 2, pp. 66-74, 2006.
D. G. Fisk, Ball, C. A., Dolinski, K., Engel, S. R., Hong, E. L., Issel-Tarver, L., Schwartz, K., Sethuraman, A., Botstein, D., and J Cherry, M., Saccharomyces cerevisiae S288C genome annotation: a working hypothesis., Yeast, vol. 23, no. 12, pp. 857-65, 2006.
K. A. Hughes, Ayroles, J. F., Reedy, M. M., Drnevich, J. M., Rowe, K. C., Ruedi, E. A., Cáceres, C. E., and Paige, K. N., Segregating variation in the transcriptome: cis regulation and additivity of effects., Genetics, vol. 173, no. 3, pp. 1347-55, 2006.
H. M. Frydman, Li, J. M., Robson, D. N., and Wieschaus, E., Somatic stem cell niche tropism in Wolbachia., Nature, vol. 441, no. 7092, pp. 509-12, 2006.
2005
E. A. Abbondanzieri, Greenleaf, W. J., Shaevitz, J. W., Landick, R., and Block, S. M., Direct observation of base-pair stepping by RNA polymerase., Nature, vol. 438, no. 7067, pp. 460-5, 2005.
R. Shyamsundar, Kim, Y. H., Higgins, J. P., Montgomery, K., Jorden, M., Sethuraman, A., van de Rijn, M., Botstein, D., Brown, P. O., and Pollack, J. R., A DNA microarray survey of gene expression in normal human tissues., Genome Biol, vol. 6, no. 3, p. R22, 2005.
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A., Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme., Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
M. J. Brauer, Saldanha, A. J., Dolinski, K., and Botstein, D., Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures., Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
M. J. Brauer, Saldanha, A. J., Dolinski, K., and Botstein, D., Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures., Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
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.
A. Stathopoulos and Levine, M., Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo., Dev Biol, vol. 280, no. 2, pp. 482-93, 2005.
J. M. Goodliffe, Wieschaus, E., and Cole, M. D., Polycomb mediates Myc autorepression and its transcriptional control of many loci in Drosophila., Genes Dev, vol. 19, no. 24, pp. 2941-6, 2005.
O. G. Troyanskaya, Putting microarrays in a context: integrated analysis of diverse biological data., Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
M. A. Hibbs, Dirksen, N. C., Li, K., and Troyanskaya, O. G., Visualization methods for statistical analysis of microarray clusters., BMC Bioinformatics, vol. 6, p. 115, 2005.
C. L. Myers, Chen, X., and Troyanskaya, O. G., Visualization-based discovery and analysis of genomic aberrations in microarray data., BMC Bioinformatics, vol. 6, p. 146, 2005.
P. M. Ferree, Frydman, H. M., Li, J. M., Cao, J., Wieschaus, E., and Sullivan, W., Wolbachia utilizes host microtubules and Dynein for anterior localization in the Drosophila oocyte., PLoS Pathog, vol. 1, no. 2, p. e14, 2005.
P. M. Ferree, Frydman, H. M., Li, J. M., Cao, J., Wieschaus, E., and Sullivan, W., Wolbachia utilizes host microtubules and Dynein for anterior localization in the Drosophila oocyte., PLoS Pathog, vol. 1, no. 2, p. e14, 2005.
2004
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.
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.
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.
M. Shapira, Segal, E., and Botstein, D., Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress., Mol Biol Cell, vol. 15, no. 12, pp. 5659-69, 2004.
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.
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.
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.
H. Zhao, Whitfield, M. L., Xu, T., Botstein, D., and Brooks, J. D., Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells., Mol Biol Cell, vol. 15, no. 2, pp. 506-19, 2004.
H. Zhao, Whitfield, M. L., Xu, T., Botstein, D., and Brooks, J. D., Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells., Mol Biol Cell, vol. 15, no. 2, pp. 506-19, 2004.
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.
C. A. Rees, Demeter, J., Matese, J. C., Botstein, D., and Sherlock, G., GeneXplorer: an interactive web application for microarray data visualization and analysis., BMC Bioinformatics, vol. 5, p. 141, 2004.
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.
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J., A method for detecting and correcting feature misidentification on expression microarrays., BMC Genomics, vol. 5, p. 64, 2004.
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J., A method for detecting and correcting feature misidentification on expression microarrays., BMC Genomics, vol. 5, p. 64, 2004.
A. J. Saldanha, Brauer, M. J., and Botstein, D., Nutritional homeostasis in batch and steady-state culture of yeast., Mol Biol Cell, vol. 15, no. 9, pp. 4089-104, 2004.
I. S. Lossos, Czerwinski, D. K., Alizadeh, A. A., Wechser, M. A., Tibshirani, R., Botstein, D., and Levy, R., Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes., N Engl J Med, vol. 350, no. 18, pp. 1828-37, 2004.
M. Shakoury-Elizeh, Tiedeman, J., Rashford, J., Ferea, T., Demeter, J., Garcia, E., Rolfes, R., Brown, P. O., Botstein, D., and Philpott, C. C., Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae., Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
N. Novoradovskaya, Whitfield, M. L., Basehore, L. S., Novoradovsky, A., Pesich, R., Usary, J., Karaca, M., Wong, W. K., Aprelikova, O., Fero, M., Perou, C. M., Botstein, D., and Braman, J., Universal Reference RNA as a standard for microarray experiments., BMC Genomics, vol. 5, no. 1, p. 20, 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.
K. S. Smith, Chanda, S. K., Lingbeek, M., Ross, D. T., Botstein, D., van Lohuizen, M., and Cleary, M. L., Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1., Mol Cell, vol. 12, no. 2, pp. 393-400, 2003.
K. S. Smith, Chanda, S. K., Lingbeek, M., Ross, D. T., Botstein, D., van Lohuizen, M., and Cleary, M. L., Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1., Mol Cell, vol. 12, no. 2, pp. 393-400, 2003.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., Discrete models of autocrine cell communication in epithelial layers., Biophys J, vol. 84, no. 6, pp. 3624-35, 2003.
K. Casey Huang, Meir, Y., and Wingreen, N. S., Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones., Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
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.
S. C. Linn, West, R. B., Pollack, J. R., Zhu, S., Hernandez-Boussard, T., Nielsen, T. O., Rubin, B. P., Patel, iv, R., Goldblum, J. R., Siegmund, D., Botstein, D., Brown, P. O., C Gilks, B., and van de Rijn, M., Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans., Am J Pathol, vol. 163, no. 6, pp. 2383-95, 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.
O. Alter, Brown, P. O., and Botstein, D., Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms., Proc Natl Acad Sci U S A, vol. 100, no. 6, pp. 3351-6, 2003.
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans., Nature, vol. 424, no. 6946, pp. 277-83, 2003.
E. Segal, Shapira, M., Regev, iv, A., Pe'er, D., Botstein, D., Koller, D., and Friedman, N., Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data., Nat Genet, vol. 34, no. 2, pp. 166-76, 2003.
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.
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.
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.
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression., PLoS Biol, vol. 1, no. 2, p. E53, 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.
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.
2002
J. R. Pollack, van de Rijn, M., and Botstein, D., Challenges in developing a molecular characterization of cancer., Semin Oncol, vol. 29, no. 3, pp. 280-5, 2002.
M. J. Dunham, Badrane, H., Ferea, T., Adams, J., Brown, P. O., Rosenzweig, F., and Botstein, D., Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae., Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16144-9, 2002.
H. Y. Chang, Chi, J. - T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., and Brown, P. O., Diversity, topographic differentiation, and positional memory in human fibroblasts., Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12877-82, 2002.
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.
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.
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.
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.
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.
M. L. Whitfield, Sherlock, G., Saldanha, A. J., Murray, J. I., Ball, C. A., Alexander, K. E., Matese, J. C., Perou, C. M., Hurt, M. M., Brown, P. O., and Botstein, D., Identification of genes periodically expressed in the human cell cycle and their expression in tumors., Mol Biol Cell, vol. 13, no. 6, pp. 1977-2000, 2002.
J. Mulholland and Botstein, D., Immunoelectron microscopy of aldehyde-fixed yeast cells., Methods Enzymol, vol. 351, pp. 50-81, 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.
E. W. Trotter, Kao, C. M. - F., Berenfeld, L., Botstein, D., Petsko, G. A., and Gray, J. V., Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae., J Biol Chem, vol. 277, no. 47, pp. 44817-25, 2002.
S. Y. Shvartsman, Muratov, C. B., and Lauffenburger, D. A., Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis., Development, vol. 129, no. 11, pp. 2577-89, 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.
O. G. Troyanskaya, Garber, M. E., Brown, P. O., Botstein, D., and Altman, R. B., Nonparametric methods for identifying differentially expressed genes in microarray data., Bioinformatics, vol. 18, no. 11, pp. 1454-61, 2002.
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.
J. A. Zallen, Cohen, Y., Hudson, A. M., Cooley, L., Wieschaus, E., and Schejter, E. D., SCAR is a primary regulator of Arp2/3-dependent morphological events in Drosophila., J Cell Biol, vol. 156, no. 4, pp. 689-701, 2002.
J. A. Zallen, Cohen, Y., Hudson, A. M., Cooley, L., Wieschaus, E., and Schejter, E. D., SCAR is a primary regulator of Arp2/3-dependent morphological events in Drosophila., J Cell Biol, vol. 156, no. 4, pp. 689-701, 2002.
N. Brenner, Agam, O., Bialek, W., and van Steveninck, Rde Ruyter, Statistical properties of spike trains: universal and stimulus-dependent aspects., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 66, no. 3 Pt 1, p. 031907, 2002.
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A., Stereotyped and specific gene expression programs in human innate immune responses to bacteria., Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J., Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11., BMC Immunol, vol. 3, p. 5, 2002.
A. Stathopoulos, Van Drenth, M., Erives, A., Markstein, M., and Levine, M., Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo., Cell, vol. 111, no. 5, pp. 687-701, 2002.

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