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
L. Wang, Xing, X., Zeng, X., S Jackson, R. E., TeSlaa, T., Al-Dalahmah, O., Samarah, L. Z., Goodwin, K., Yang, L., McReynolds, M. R., Li, X., Wolff, J. J., Rabinowitz, J. D., and Davidson, S. M., “Spatially resolved isotope tracing reveals tissue metabolic activity.”, Nat Methods, vol. 19, no. 2, pp. 223-230, 2022.
2019
P. S. Minhas, Liu, L., Moon, P. K., Joshi, A. U., Dove, C., Mhatre, S., Contrepois, K., Wang, Q., Lee, B. A., Coronado, M., Bernstein, D., Snyder, M. P., Migaud, M., Majeti, R., Mochly-Rosen, D., Rabinowitz, J. D., and Andreasson, K. I., “Macrophage de novo NAD synthesis specifies immune function in aging and inflammation.”, Nat Immunol, vol. 20, no. 1, pp. 50-63, 2019.
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.
2015
V. Lakhina and Murphy, C. T., “Genome Sequencing Fishes out Longevity Genes.”, Cell, vol. 163, no. 6, pp. 1312-3, 2015.
2014
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
D. Krotov, Dubuis, J. O., Gregor, T., and Bialek, W., “Morphogenesis at criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
2013
J. O. Dubuis, Samanta, R., and Gregor, T., “Accurate measurements of dynamics and reproducibility in small genetic networks.”, Mol Syst Biol, vol. 9, p. 639, 2013.
S. Wang and Wingreen, N. S., “Cell shape can mediate the spatial organization of the bacterial cytoskeleton.”, Biophys J, vol. 104, no. 3, pp. 541-52, 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.
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.
J. Song and Singh, M., “From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization.”, PLoS Comput Biol, vol. 9, no. 2, p. e1002910, 2013.
A. M. Berezhkovskii and Shvartsman, S. Y., “Kinetics of receptor occupancy during morphogen gradient formation.”, J Chem Phys, vol. 138, no. 24, p. 244105, 2013.
P. V. Gordon, Muratov, C. B., and Shvartsman, S. Y., “Local accumulation times for source, diffusion, and degradation models in two and three dimensions.”, J Chem Phys, vol. 138, no. 10, p. 104121, 2013.
2011
D. Swanson and Wingreen, N. S., “Active biopolymers confer fast reorganization kinetics.”, Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
G. Liu, Rogers, J., Murphy, C. T., and Rongo, C., “EGF signalling activates the ubiquitin proteasome system to modulate C. elegans lifespan.”, EMBO J, vol. 30, no. 15, pp. 2990-3003, 2011.
M. Sun, Wartel, M., Cascales, E., Shaevitz, J. W., and Mignot, T., “Motor-driven intracellular transport powers bacterial gliding motility.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7559-64, 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.
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.
C. D. Doucette, Schwab, D. J., Wingreen, N. S., and Rabinowitz, J. D., “α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition.”, Nat Chem Biol, vol. 7, no. 12, pp. 894-901, 2011.
2010
O. Grimm and Wieschaus, E., “The Bicoid gradient is shaped independently of nuclei.”, Development, vol. 137, no. 17, pp. 2857-62, 2010.
A. M. Berezhkovskii, Sample, C., and Shvartsman, S. Y., “How long does it take to establish a morphogen gradient?”, Biophys J, vol. 99, no. 8, pp. L59-61, 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.
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.
W. Lu, Clasquin, M. F., Melamud, E., Amador-Noguez, D., Caudy, A. A., and Rabinowitz, J. D., “Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer.”, Anal Chem, vol. 82, no. 8, pp. 3212-21, 2010.
C. Sample and Shvartsman, S. Y., “Multiscale modeling of diffusion in the early Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 107, no. 22, pp. 10092-6, 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.
W. - L. Ng, Wei, Y., Perez, L. J., Cong, J., Long, T., Koch, M., Semmelhack, M. F., Wingreen, N. S., and Bassler, B. L., “Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules.”, Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5575-80, 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.
2009
J. Yuan, Doucette, C. D., Fowler, W. U., Feng, X. - J., Piazza, M., Rabitz, H. A., Wingreen, N. S., and Rabinowitz, J. D., “Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.”, Mol Syst Biol, vol. 5, p. 302, 2009.
R. C. Kelly, Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. - L., Jeffrey, P. D., Rabinowitz, J. D., Semmelhack, M. F., Hughson, F. M., and Bassler, B. L., “The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA.”, Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
2008
W. Bialek and Setayeshgar, S., “Cooperativity, sensitivity, and noise in biochemical signaling.”, Phys Rev Lett, vol. 100, no. 25, p. 258101, 2008.
D. Papatsenko and Levine, M. S., “Dual regulation by the Hunchback gradient in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 105, no. 8, pp. 2901-6, 2008.
J. Yuan, Bennett, B. D., and Rabinowitz, J. D., “Kinetic flux profiling for quantitation of cellular metabolic fluxes.”, Nat Protoc, vol. 3, no. 8, pp. 1328-40, 2008.
2007
S. Goyal and Wingreen, N. S., “Growth-induced instability in metabolic networks.”, Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
A. R. Ureta, Endres, R. G., Wingreen, N. S., and Silhavy, T. J., “Kinetic analysis of the assembly of the outer membrane protein LamB in Escherichia coli mutants each lacking a secretion or targeting factor in a different cellular compartment.”, J Bacteriol, vol. 189, no. 2, pp. 446-54, 2007.
J. W. Shaevitz and Fletcher, D. A., “Load fluctuations drive actin network growth.”, Proc Natl Acad Sci U S A, vol. 104, no. 40, pp. 15688-92, 2007.
2006
J. Yuan, Fowler, W. U., Kimball, E., Lu, W., and Rabinowitz, J. D., “Kinetic flux profiling of nitrogen assimilation in Escherichia coli.”, Nat Chem Biol, vol. 2, no. 10, pp. 529-30, 2006.
2005
G. T. Reeves, Kalifa, R., Klein, D. E., Lemmon, M. A., and Shvartsman, S. Y., “Computational analysis of EGFR inhibition by Argos.”, Dev Biol, vol. 284, no. 2, pp. 523-35, 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.
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. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
J. W. Shaevitz, Block, S. M., and Schnitzer, M. J., “Statistical kinetics of macromolecular dynamics.”, Biophys J, vol. 89, no. 4, pp. 2277-85, 2005.
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.
2003
Y. Nibu, Senger, K., and Levine, M., “CtBP-independent repression in the Drosophila embryo.”, Mol Cell Biol, vol. 23, no. 11, pp. 3990-9, 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. 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.
S. M. Block, Asbury, C. L., Shaevitz, J. W., and Lang, M. J., “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
S. M. Block, Asbury, C. L., Shaevitz, J. W., and Lang, M. J., “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
2002
M. J. Lang, Asbury, C. L., Shaevitz, J. W., and Block, S. M., “An automated two-dimensional optical force clamp for single molecule studies.”, Biophys J, vol. 83, no. 1, pp. 491-501, 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.
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.
1999
T. Caspary, Cleary, M. A., Perlman, E. J., Zhang, P., Elledge, S. J., and Tilghman, S. M., “Oppositely imprinted genes p57(Kip2) and igf2 interact in a mouse model for Beckwith-Wiedemann syndrome.”, Genes Dev, vol. 13, no. 23, pp. 3115-24, 1999.
1998
M. A. Welte, Gross, S. P., Postner, M., Block, S. M., and Wieschaus, E. F., “Developmental regulation of vesicle transport in Drosophila embryos: forces and kinetics.”, Cell, vol. 92, no. 4, pp. 547-57, 1998.
M. A. Welte, Gross, S. P., Postner, M., Block, S. M., and Wieschaus, E. F., “Developmental regulation of vesicle transport in Drosophila embryos: forces and kinetics.”, Cell, vol. 92, no. 4, pp. 547-57, 1998.
A. L. Webber, Ingram, R. S., Levorse, J. M., and Tilghman, S. M., “Location of enhancers is essential for the imprinting of H19 and Igf2 genes.”, Nature, vol. 391, no. 6668, pp. 711-5, 1998.
T. Caspary, Cleary, M. A., Baker, C. C., Guan, X. J., and Tilghman, S. M., “Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster.”, Mol Cell Biol, vol. 18, no. 6, pp. 3466-74, 1998.
T. Caspary, Cleary, M. A., Baker, C. C., Guan, X. J., and Tilghman, S. M., “Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster.”, Mol Cell Biol, vol. 18, no. 6, pp. 3466-74, 1998.