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. H. Rodan, Qi, W., Ducker, G. S., Demirbas, D., Laine, R., Yang, E., Walker, M. A., Eichler, F., Rabinowitz, J. D., Anselm, I., and Berry, G. T., 5,10-methenyltetrahydrofolate synthetase deficiency causes a neurometabolic disorder associated with microcephaly, epilepsy, and cerebral hypomyelination., Mol Genet Metab, vol. 125, no. 1-2, pp. 118-126, 2018.
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. 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.
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.
A. V. Rangan, McGrouther, C. C., Kelsoe, J., Schork, N., Stahl, E., Zhu, Q., Krishnan, A., Yao, V., Troyanskaya, O., Bilaloglu, S., Raghavan, P., Bergen, S., Jureus, A., and Landen, M., A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data., PLoS Comput Biol, vol. 14, no. 5, p. e1006105, 2018.
C. Jang, Chen, L., and Rabinowitz, J. D., Metabolomics and Isotope Tracing., Cell, vol. 173, no. 4, pp. 822-837, 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.
A. Davila, Liu, L., Chellappa, K., Redpath, P., Nakamaru-Ogiso, E., Paolella, L. M., Zhang, Z., Migaud, M. E., Rabinowitz, J. D., and Baur, J. A., Nicotinamide adenine dinucleotide is transported into mammalian mitochondria., Elife, vol. 7, 2018.
M. Nofal and Rabinowitz, J. D., Ribosomes on the night shift., Science, vol. 360, no. 6390, pp. 710-711, 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.
R. A. Miller, Shi, Y., Lu, W., Pirman, D. A., Jatkar, A., Blatnik, M., Wu, H., Cárdenas, C., Wan, M., J Foskett, K., Park, J. O., Zhang, Y., Holland, W. L., Rabinowitz, J. D., and Birnbaum, M. J., Targeting hepatic glutaminase activity to ameliorate hyperglycemia., Nat Med, vol. 24, no. 4, pp. 518-524, 2018.
D. Munro, Ghersi, D., and Singh, M., Two critical positions in zinc finger domains are heavily mutated in three human cancer types., PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 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.
P. F. Przytycki and Singh, M., Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes., Genome Med, vol. 9, no. 1, p. 79, 2017.
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J., Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy., Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
H. In Kim, Raffler, J., Lu, W., Lee, J. - J., Abbey, D., Saleheen, D., Rabinowitz, J. D., Bennett, M. J., Hand, N. J., Brown, C., and Rader, D. J., Fine Mapping and Functional Analysis Reveal a Role of SLC22A1 in Acylcarnitine Transport., Am J Hum Genet, vol. 101, no. 4, pp. 489-502, 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.
W. Lu, Su, X., Klein, M. S., Lewis, I. A., Fiehn, O., and Rabinowitz, J. D., Metabolite Measurement: Pitfalls to Avoid and Practices to Follow., Annu Rev Biochem, vol. 86, pp. 277-304, 2017.
2013
S. L. Grady, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection., Proc Natl Acad Sci U S A, vol. 110, no. 51, pp. E5006-15, 2013.
P. Jiang, Singh, M., and Coller, H. A., Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay., PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
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.
D. Ghersi and Singh, M., Disentangling function from topology to infer the network properties of disease genes., BMC Syst Biol, vol. 7, p. 5, 2013.
A. S. Futran, A Link, J., Seger, R., and Shvartsman, S. Y., ERK as a model for systems biology of enzyme kinetics in cells., Curr Biol, vol. 23, no. 21, pp. R972-9, 2013.
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.
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.
B. Lim, Samper, N., Lu, H., Rushlow, C., Jiménez, G., and Shvartsman, S. Y., Kinetics of gene derepression by ERK signaling., Proc Natl Acad Sci U S A, vol. 110, no. 25, pp. 10330-5, 2013.
Y. -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.
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.
E. Koyuncu, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., Saturated very long chain fatty acids are required for the production of infectious human cytomegalovirus progeny., PLoS Pathog, vol. 9, no. 5, p. e1003333, 2013.
Y. Pritykin and Singh, M., Simple topological features reflect dynamics and modularity in protein interaction networks., PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 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.
2012
G. Jiménez, Shvartsman, S. Y., and Paroush, Z. 'ev, The Capicua repressor--a general sensor of RTK signaling in development and disease., J Cell Sci, vol. 125, no. Pt 6, pp. 1383-91, 2012.
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.
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.
S. L. Grady, Hwang, J., Vastag, L., Rabinowitz, J. D., and Shenk, T., Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase., J Virol, vol. 86, no. 15, pp. 8259-68, 2012.
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.
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.
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.
M. Lagha, Bothma, J. P., and Levine, M., Mechanisms of transcriptional precision in animal development., Trends Genet, vol. 28, no. 8, pp. 409-16, 2012.
Y. Zhen and Andolfatto, P., Methods to detect selection on noncoding DNA., Methods Mol Biol, vol. 856, pp. 141-59, 2012.
G. Tkačik, Walczak, A. M., and Bialek, W., Optimizing information flow in small genetic networks. III. A self-interacting gene., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 85, no. 4 Pt 1, p. 041903, 2012.
Z. Khan, Bloom, J. S., Amini, S., Singh, M., Perlman, D. H., Caudy, A. A., and Kruglyak, L., Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS., Mol Syst Biol, vol. 8, p. 602, 2012.
J. D. Rabinowitz and Vastag, L., Teaching the design principles of metabolism., Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 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.
D. Botstein, Why we need more basic biology research, not less., Mol Biol Cell, vol. 23, no. 21, pp. 4160-1, 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.
S. Luo and Murphy, C. T., Caenorhabditis elegans reproductive aging: Regulation and underlying mechanisms., Genesis, vol. 49, no. 2, pp. 53-65, 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.
L. Vastag, Koyuncu, E., Grady, S. L., Shenk, T. E., and Rabinowitz, J. D., Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism., PLoS Pathog, vol. 7, no. 7, p. e1002124, 2011.
G. Rizki, Iwata, T. Naoko, Li, J., Riedel, C. G., Picard, C. Lafontaine, Jan, M., Murphy, C. T., and Lee, S. Sylvia, The evolutionarily conserved longevity determinants HCF-1 and SIR-2.1/SIRT1 collaborate to regulate DAF-16/FOXO., PLoS Genet, vol. 7, no. 9, p. e1002235, 2011.
A. V. Persikov and Singh, M., An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces., Phys Biol, vol. 8, no. 3, p. 035010, 2011.
D. Botstein, Genome-sequencing anniversary. Fruits of genome sequences for biology., Science, vol. 331, no. 6020, p. 1025, 2011.
M. Levine, Paused RNA polymerase II as a developmental checkpoint., Cell, vol. 145, no. 4, pp. 502-11, 2011.
C. S. Greene and Troyanskaya, O. G., PILGRM: an interactive data-driven discovery platform for expert biologists., Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 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.
S. T. H. Liu, Sharon-Friling, R., Ivanova, P., Milne, S. B., Myers, D. S., Rabinowitz, J. D., H Brown, A., and Shenk, T., Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress., Proc Natl Acad Sci U S A, vol. 108, no. 31, pp. 12869-74, 2011.
A. Ochoa, Llinás, M., and Singh, M., Using context to improve protein domain identification., BMC Bioinformatics, vol. 12, p. 90, 2011.
D. Botstein and Fink, G. R., Yeast: an experimental organism for 21st Century biology., Genetics, vol. 189, no. 3, pp. 695-704, 2011.
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.
C. T. Murphy, Aging: miRacles of longevity?, Curr Biol, vol. 20, no. 24, pp. R1076-8, 2010.
P. Mehta and Gregor, T., Approaching the molecular origins of collective dynamics in oscillating cell populations., Curr Opin Genet Dev, vol. 20, no. 6, pp. 574-80, 2010.
J. D. Rabinowitz and White, E., Autophagy and metabolism., Science, vol. 330, no. 6009, pp. 1344-8, 2010.
S. Neumann, Hansen, C. H., Wingreen, N. S., and Sourjik, V., Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis., EMBO J, vol. 29, no. 20, pp. 3484-95, 2010.
The Gene Ontology in 2010: extensions and refinements., Nucleic Acids Res, vol. 38, no. Database issue, pp. D331-5, 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. M. Zee, Levin, R. S., Xu, B., LeRoy, G., Wingreen, N. S., and Garcia, B. A., In vivo residue-specific histone methylation dynamics., J Biol Chem, vol. 285, no. 5, pp. 3341-50, 2010.
A. L. Kauffman, Ashraf, J. M., M Corces-Zimmerman, R., Landis, J. N., and Murphy, C. T., Insulin signaling and dietary restriction differentially influence the decline of learning and memory with age., PLoS Biol, vol. 8, no. 5, p. e1000372, 2010.
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.
S. M. Tilghman, It's all about the talent., Mol Biol Cell, vol. 21, no. 22, p. 3823, 2010.
D. Botstein, It's the data!, Mol Biol Cell, vol. 21, no. 1, pp. 4-6, 2010.
E. Melamud, Vastag, L., and Rabinowitz, J. D., Metabolomic analysis and visualization engine for LC-MS data., Anal Chem, vol. 82, no. 23, pp. 9818-26, 2010.
J. M. S. Lemons, Feng, X. - J., Bennett, B. D., Legesse-Miller, A., Johnson, E. L., Raitman, I., Pollina, E. A., Rabitz, H. A., Rabinowitz, J. D., and Coller, H. A., Quiescent fibroblasts exhibit high metabolic activity., PLoS Biol, vol. 8, no. 10, p. e1000514, 2010.
D. Amador-Noguez, Feng, X. - J., Fan, J., Roquet, N., Rabitz, H., and Rabinowitz, J. D., Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum., J Bacteriol, vol. 192, no. 17, pp. 4452-61, 2010.
A. C. Martin and Wieschaus, E. F., Tensions divide., Nat Cell Biol, vol. 12, no. 1, pp. 5-7, 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.
J. J. Zartman and Shvartsman, S. Y., Unit operations of tissue development: epithelial folding., Annu Rev Chem Biomol Eng, vol. 1, pp. 231-46, 2010.
2009
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., Alcohol sensitivity in Drosophila: translational potential of systems genetics., Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
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.
T. F. C. Mackay, Stone, E. A., and Ayroles, J. F., The genetics of quantitative traits: challenges and prospects., Nat Rev Genet, vol. 10, no. 8, pp. 565-77, 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.
R. G. Endres and Wingreen, N. S., Maximum likelihood and the single receptor., Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
E. A. Stone and Ayroles, J. F., Modulated modularity clustering as an exploratory tool for functional genomic inference., PLoS Genet, vol. 5, no. 5, p. e1000479, 2009.
M. Anna Carbone, Ayroles, J. F., Yamamoto, A., Morozova, T. V., West, S. A., Magwire, M. M., Mackay, T. F. C., and Anholt, R. R. H., Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma., PLoS One, vol. 4, no. 1, p. e4216, 2009.
Z. Khan, Bloom, J. S., Garcia, B. A., Singh, M., and Kruglyak, L., Protein quantification across hundreds of experimental conditions., Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 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.
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.
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.
E. Banks, Nabieva, E., Peterson, R., and Singh, M., NetGrep: fast network schema searches in interactomes., Genome Biol, vol. 9, no. 9, p. R138, 2008.
E. Banks, Nabieva, E., Chazelle, B., and Singh, M., Organization of physical interactomes as uncovered by network schemas., PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
M. J. Rosenbluth, Crow, A., Shaevitz, J. W., and Fletcher, D. A., Slow stress propagation in adherent cells., Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
J. W. Shaevitz, Super-resolution for a 3D world., Nat Methods, vol. 5, no. 6, pp. 471-2, 2008.
J. Munger, Bennett, B. D., Parikh, A., Feng, X. - J., McArdle, J., Rabitz, H. A., Shenk, T., and Rabinowitz, J. D., Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy., Nat Biotechnol, vol. 26, no. 10, pp. 1179-86, 2008.
2006
J. F. Ayroles and Gibson, G., Analysis of variance of microarray data., Methods Enzymol, vol. 411, pp. 214-33, 2006.
J. Munger, Bajad, S. U., Coller, H. A., Shenk, T., and Rabinowitz, J. D., Dynamics of the cellular metabolome during human cytomegalovirus infection., PLoS Pathog, vol. 2, no. 12, p. e132, 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.
R. J. Pelham, Rodgers, L., Hall, I., Lucito, R., Nguyen, K. C. Q., Navin, N., Hicks, J., Mu, D., Powers, S., Wigler, M., and Botstein, D., Identification of alterations in DNA copy number in host stromal cells during tumor progression., Proc Natl Acad Sci U S A, vol. 103, no. 52, pp. 19848-53, 2006.
J. D. Rabinowitz, Lloyd, P. M., Munzar, P., Myers, D. J., Cross, S., Damani, R., Quintana, R., Spyker, D. A., Soni, P., and Cassella, J. V., Ultra-fast absorption of amorphous pure drug aerosols via deep lung inhalation., J Pharm Sci, vol. 95, no. 11, pp. 2438-51, 2006.
D. Botstein, Willing to do the math: an interview with David Botstein. Interview by Jane Gitschier., PLoS Genet, vol. 2, no. 5, p. e79, 2006.
2004
T. Sharpee, Rust, N. C., and Bialek, W., Analyzing neural responses to natural signals: maximally informative dimensions., Neural Comput, vol. 16, no. 2, pp. 223-50, 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.
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.
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.
H. Y. Chang, Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J. - T., van de Rijn, M., Botstein, D., and Brown, P. O., Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds., PLoS Biol, vol. 2, no. 2, p. E7, 2004.
A. M. Berezhkovskii, Batsilas, L., and Shvartsman, S. Y., Ligand trapping in epithelial layers and cell cultures., Biophys Chem, vol. 107, no. 3, pp. 221-7, 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.
J. H. Fong, Keating, A. E., and Singh, M., Predicting specificity in bZIP coiled-coil protein interactions., Genome Biol, vol. 5, no. 2, p. R11, 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.
N. D. Trinklein, Murray, J. I., Hartman, S. J., Botstein, D., and Myers, R. M., The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response., Mol Biol Cell, vol. 15, no. 3, pp. 1254-61, 2004.
K. R. Christie, Weng, S., Balakrishnan, R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J. E., Hong, E. L., Issel-Tarver, L., Nash, R., Sethuraman, A., Starr, B., Theesfeld, C. L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Botstein, D., and J Cherry, M., Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms., Nucleic Acids Res, vol. 32, no. Database issue, pp. D311-4, 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
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.
S. H Wiley, Shvartsman, S. Y., and Lauffenburger, D. A., Computational modeling of the EGF-receptor system: a paradigm for systems biology., Trends Cell Biol, vol. 13, no. 1, pp. 43-50, 2003.
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.
D. Botstein and Risch, N., Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease., Nat Genet, vol. 33 Suppl, pp. 228-37, 2003.
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.
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.
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.
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.
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. 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.
M. L. Whitfield, Finlay, D. R., Murray, J. Isaac, Troyanskaya, O. G., Chi, J. - T., Pergamenschikov, A., McCalmont, T. H., Brown, P. O., Botstein, D., and M Connolly, K., Systemic and cell type-specific gene expression patterns in scleroderma skin., Proc Natl Acad Sci U S A, vol. 100, no. 21, pp. 12319-24, 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.
M. Levine and Tjian, R., Transcription regulation and animal diversity., Nature, vol. 424, no. 6945, pp. 147-51, 2003.
S. P. Bohen, Troyanskaya, O. G., Alter, O., Warnke, R., Botstein, D., Brown, P. O., and Levy, R., Variation in gene expression patterns in follicular lymphoma and the response to rituximab., Proc Natl Acad Sci U S A, vol. 100, no. 4, pp. 1926-30, 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
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.
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.
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.
Y. Ahmed, Nouri, A., and Wieschaus, E., Drosophila Apc1 and Apc2 regulate Wingless transduction throughout development., Development, vol. 129, no. 7, pp. 1751-62, 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.
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O., Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation., Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 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. 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.
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.
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.
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.
S. Y. Shvartsman, Shooting from the hip: spatial control of signal release by intracellular waves., Proc Natl Acad Sci U S A, vol. 99, no. 14, pp. 9087-9, 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.
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
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.
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.

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