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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Active Transport, Cell Nucleus
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.
Algorithms
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.
O. Troyanskaya, Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., and Altman, R. B., Missing value estimation methods for DNA microarrays., Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
M. Coppey, Berezhkovskii, A. M., Kim, Y., Boettiger, A. N., and Shvartsman, S. Y., Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein., Dev Biol, vol. 312, no. 2, pp. 623-30, 2007.
R. G. Endres and Wingreen, N. S., Maximum likelihood and the single receptor., Phys Rev Lett, vol. 103, no. 15, p. 158101, 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.
S. Li, Stone, H. A., and Murphy, C. T., A microfluidic device and automatic counting system for the study of C. elegans reproductive aging., Lab Chip, vol. 15, no. 2, pp. 524-31, 2015.
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.
Animals
S. Y. Shvartsman and Baker, R. E., Mathematical models of morphogen gradients and their effects on gene expression., Wiley Interdiscip Rev Dev Biol, vol. 1, no. 5, pp. 715-30, 2012.
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.
S. Y. Shvartsman, Coppey, M., and Berezhkovskii, A. M., MAPK signaling in equations and embryos., Fly (Austin), vol. 3, no. 1, pp. 62-7, 2009.
M. K. Shin, Russell, L. B., and Tilghman, S. M., Molecular characterization of four induced alleles at the Ednrb locus., Proc Natl Acad Sci U S A, vol. 94, no. 24, pp. 13105-10, 1997.
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.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P., Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations., Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
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.
M. Peifer and Wieschaus, E., Mutations in the Drosophila gene extradenticle affect the way specific homeo domain proteins regulate segmental identity., Genes Dev, vol. 4, no. 7, pp. 1209-23, 1990.
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.
Y. Zhen and Andolfatto, P., Methods to detect selection on noncoding DNA., Methods Mol Biol, vol. 856, pp. 141-59, 2012.
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.
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.
T. Mora, Walczak, A. M., Bialek, W., and Callan, C. G., Maximum entropy models for antibody diversity., Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5405-10, 2010.
M. A. Postner, Miller, K. G., and Wieschaus, E. F., Maternal effect mutations of the sponge locus affect actin cytoskeletal rearrangements in Drosophila melanogaster embryos., J Cell Biol, vol. 119, no. 5, pp. 1205-18, 1992.
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.
B. Riggleman, Wieschaus, E., and Schedl, P., Molecular analysis of the armadillo locus: uniformly distributed transcripts and a protein with novel internal repeats are associated with a Drosophila segment polarity gene., Genes Dev, vol. 3, no. 1, pp. 96-113, 1989.
O. Grimm, Coppey, M., and Wieschaus, E., Modelling the Bicoid gradient., Development, vol. 137, no. 14, pp. 2253-64, 2010.
F. Markowetz, Mulder, K. W., Airoldi, E. M., Lemischka, I. R., and Troyanskaya, O. G., Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells., PLoS Comput Biol, vol. 6, no. 12, p. e1001034, 2010.
S. Li, Stone, H. A., and Murphy, C. T., A microfluidic device and automatic counting system for the study of C. elegans reproductive aging., Lab Chip, vol. 15, no. 2, pp. 524-31, 2015.
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.
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.
D. T. Burke, Rossi, J. M., Leung, J., Koos, D. S., and Tilghman, S. M., A mouse genomic library of yeast artificial chromosome clones., Mamm Genome, vol. 1, no. 1, p. 65, 1991.
C. Nusslein-Volhard and Wieschaus, E., Mutations affecting segment number and polarity in Drosophila., Nature, vol. 287, no. 5785, pp. 795-801, 1980.
T. J. Levario, Zhan, M., Lim, B., Shvartsman, S. Y., and Lu, H., Microfluidic trap array for massively parallel imaging of Drosophila embryos., Nat Protoc, vol. 8, no. 4, pp. 721-36, 2013.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., Multiplexed shotgun genotyping for rapid and efficient genetic mapping., Genome Res, vol. 21, no. 4, pp. 610-7, 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.
J. P. Bothma, Levine, M., and Boettiger, A., Morphogen gradients: limits to signaling or limits to measurement?, Curr Biol, vol. 20, no. 5, pp. R232-4, 2010.
C. Shi and Murphy, C. T., Mating induces shrinking and death in Caenorhabditis mothers., Science, vol. 343, no. 6170, pp. 536-40, 2014.
J. H. Millonig, Emerson, J. A., Levorse, J. M., and Tilghman, S. M., Molecular analysis of the distal enhancer of the mouse alpha-fetoprotein gene., Mol Cell Biol, vol. 15, no. 7, pp. 3848-56, 1995.
M. Nofal, Zhang, K., Han, S., and Rabinowitz, J. D., mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein., Mol Cell, vol. 67, no. 6, pp. 936-946.e5, 2017.
K. C. Rowe, Singhal, S., Macmanes, M. D., Ayroles, J. F., Morelli, T. Lyn, Rubidge, E. M., Bi, K., and Moritz, C. C., Museum genomics: low-cost and high-accuracy genetic data from historical specimens., Mol Ecol Resour, vol. 11, no. 6, pp. 1082-92, 2011.
D. Hendrix, Levine, M., and Shi, W., miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data., Genome Biol, vol. 11, no. 4, p. R39, 2010.
Y. Kim, Coppey, M., Grossman, R., Ajuria, L., Jiménez, G., Paroush, Z. 'ev, and Shvartsman, S. Y., MAPK substrate competition integrates patterning signals in the Drosophila embryo., Curr Biol, vol. 20, no. 5, pp. 446-51, 2010.
K. Chung, Kim, Y., Kanodia, J. S., Gong, E., Shvartsman, S. Y., and Lu, H., A microfluidic array for large-scale ordering and orientation of embryos., Nat Methods, vol. 8, no. 2, pp. 171-6, 2011.
B. He, Caudy, A., Parsons, L., Rosebrock, A., Pane, A., Raj, S., and Wieschaus, E., Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster., Genome Res, vol. 22, no. 12, pp. 2507-19, 2012.
M. Coppey, Berezhkovskii, A. M., Kim, Y., Boettiger, A. N., and Shvartsman, S. Y., Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein., Dev Biol, vol. 312, no. 2, pp. 623-30, 2007.
M. W. Perry, Boettiger, A. N., and Levine, M., Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 108, no. 33, pp. 13570-5, 2011.
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.
D. E. Coulter, Swaykus, E. A., Beran-Koehn, M. A., Goldberg, D., Wieschaus, E., and Schedl, P., Molecular analysis of odd-skipped, a zinc finger encoding segmentation gene with a novel pair-rule expression pattern., EMBO J, vol. 9, no. 11, pp. 3795-804, 1990.
Antibody Diversity
T. Mora, Walczak, A. M., Bialek, W., and Callan, C. G., Maximum entropy models for antibody diversity., Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5405-10, 2010.
Antineoplastic Agents
D. Ghersi and Singh, M., molBLOCKS: decomposing small molecule sets and uncovering enriched fragments., Bioinformatics, vol. 30, no. 14, pp. 2081-3, 2014.
Bacteria
M. Louis Reaves and Rabinowitz, J. D., Metabolomics in systems microbiology., Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
S. Wang and Shaevitz, J. W., The mechanics of shape in prokaryotes., Front Biosci (Schol Ed), vol. 5, pp. 564-74, 2013.
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., The molecular origins of chiral growth in walled cells., Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
Bacterial Physiological Phenomena
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., The molecular origins of chiral growth in walled cells., Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
Bacterial Proteins
K. Casey Huang and Wingreen, N. S., Min-protein oscillations in round bacteria., Phys Biol, vol. 1, no. 3-4, pp. 229-35, 2004.
Base Sequence
D. E. Coulter, Swaykus, E. A., Beran-Koehn, M. A., Goldberg, D., Wieschaus, E., and Schedl, P., Molecular analysis of odd-skipped, a zinc finger encoding segmentation gene with a novel pair-rule expression pattern., EMBO J, vol. 9, no. 11, pp. 3795-804, 1990.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P., Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations., Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
T. Mora, Walczak, A. M., Bialek, W., and Callan, C. G., Maximum entropy models for antibody diversity., Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5405-10, 2010.
B. Riggleman, Wieschaus, E., and Schedl, P., Molecular analysis of the armadillo locus: uniformly distributed transcripts and a protein with novel internal repeats are associated with a Drosophila segment polarity gene., Genes Dev, vol. 3, no. 1, pp. 96-113, 1989.
J. H. Millonig, Emerson, J. A., Levorse, J. M., and Tilghman, S. M., Molecular analysis of the distal enhancer of the mouse alpha-fetoprotein gene., Mol Cell Biol, vol. 15, no. 7, pp. 3848-56, 1995.
D. Hendrix, Levine, M., and Shi, W., miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data., Genome Biol, vol. 11, no. 4, p. R39, 2010.
K. C. Rowe, Singhal, S., Macmanes, M. D., Ayroles, J. F., Morelli, T. Lyn, Rubidge, E. M., Bi, K., and Moritz, C. C., Museum genomics: low-cost and high-accuracy genetic data from historical specimens., Mol Ecol Resour, vol. 11, no. 6, pp. 1082-92, 2011.
Biological Evolution
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.
C. Shi and Murphy, C. T., Mating induces shrinking and death in Caenorhabditis mothers., Science, vol. 343, no. 6170, pp. 536-40, 2014.
Biophysical Phenomena
T. Mora, Walczak, A. M., Bialek, W., and Callan, C. G., Maximum entropy models for antibody diversity., Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5405-10, 2010.
Biophysical Processes
S. Y. Shvartsman, Coppey, M., and Berezhkovskii, A. M., MAPK signaling in equations and embryos., Fly (Austin), vol. 3, no. 1, pp. 62-7, 2009.
Blotting, Western
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.
Carbon Cycle
M. Louis Reaves and Rabinowitz, J. D., Metabolomics in systems microbiology., Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Carbon Radioisotopes
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.
Cell Shape
S. Wang and Shaevitz, J. W., The mechanics of shape in prokaryotes., Front Biosci (Schol Ed), vol. 5, pp. 564-74, 2013.
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., The molecular origins of chiral growth in walled cells., Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
Cells
R. G. Endres and Wingreen, N. S., Maximum likelihood and the single receptor., Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
Cytochrome P-450 Enzyme System
C. Shi and Murphy, C. T., Mating induces shrinking and death in Caenorhabditis mothers., Science, vol. 343, no. 6170, pp. 536-40, 2014.

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