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beta-Galactosidase
K. C. Mok, Wingreen, N. S., and Bassler, B. L., “Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression.”, EMBO J, vol. 22, no. 4, pp. 870-81, 2003.
A. Di Gregorio, Harland, R. M., Levine, M., and Casey, E. Silva, “Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle.”, Dev Biol, vol. 244, no. 2, pp. 385-95, 2002.
beta-Transducin Repeat-Containing Proteins
D. Ghersi and Singh, M., “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
Bias (Epidemiology)
C. S. Greene and Troyanskaya, O. G., “Accurate evaluation and analysis of functional genomics data and methods.”, Ann N Y Acad Sci, vol. 1260, pp. 95-100, 2012.
Bibliometrics
D. Botstein, “It's the data!”, Mol Biol Cell, vol. 21, no. 1, pp. 4-6, 2010.
Binding Sites
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.
W. Bialek and Setayeshgar, S., “Cooperativity, sensitivity, and noise in biochemical signaling.”, Phys Rev Lett, vol. 100, no. 25, p. 258101, 2008.
A. V. Persikov and Singh, M., “De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins.”, Nucleic Acids Res, vol. 42, no. 1, pp. 97-108, 2014.
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.
M. L. Skoge, Endres, R. G., and Wingreen, N. S., “Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters.”, Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
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.
J. L. Wetzel and Singh, M., “Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination.”, Nucleic Acids Res, vol. 48, no. 2, p. e9, 2020.
B. D. Bennett, Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., and Rabinowitz, J. D., “Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.”, Nat Chem Biol, vol. 5, no. 8, pp. 593-9, 2009.
W. Ndifon, Wingreen, N. S., and Levin, S. A., “Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines.”, Proc Natl Acad Sci U S A, vol. 106, no. 21, pp. 8701-6, 2009.
P. Jiang and Singh, M., “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
S. R McIsaac, Petti, A. A., Bussemaker, H. J., and Botstein, D., “Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 2993-3007, 2012.
J. W. Shaevitz, Abbondanzieri, E. A., Landick, R., and Block, S. M., “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.”, Nature, vol. 426, no. 6967, pp. 684-7, 2003.
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.
R. G. Endres and Wingreen, N. S., “Weight matrices for protein-DNA binding sites from a single co-crystal structure.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 73, no. 6 Pt 1, p. 061921, 2006.
B. P. Berman, Nibu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M., and Eisen, M. B., “Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.”, Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 757-62, 2002.
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.
A. Chi, Huttenhower, C., Geer, L. Y., Coon, J. J., Syka, J. E. P., Bai, D. L., Shabanowitz, J., Burke, D. J., Troyanskaya, O. G., and Hunt, D. F., “Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.”, Proc Natl Acad Sci U S A, vol. 104, no. 7, pp. 2193-8, 2007.
D. Papatsenko and Levine, M., “Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 102, no. 14, pp. 4966-71, 2005.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
D. J. Katz, Beer, M. A., Levorse, J. M., and Tilghman, S. M., “Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region.”, Mol Cell Biol, vol. 25, no. 10, pp. 3855-63, 2005.
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.
D. Ghersi and Singh, M., “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
A. V. Persikov, Rowland, E. F., Oakes, B. L., Singh, M., and Noyes, M. B., “Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.”, Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
R. Osada, Zaslavsky, E., and Singh, M., “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
E. K. Farley, Olson, K. M., Zhang, W., Brandt, A. J., Rokhsar, D. S., and Levine, M. S., “Suboptimization of developmental enhancers.”, Science, vol. 350, no. 6258, pp. 325-8, 2015.
A. J. Pompeani, Irgon, J. J., Berger, M. F., Bulyk, M. L., Wingreen, N. S., and Bassler, B. L., “The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters.”, Mol Microbiol, vol. 70, no. 1, pp. 76-88, 2008.
R. G. Endres, Schulthess, T. C., and Wingreen, N. S., “Toward an atomistic model for predicting transcription-factor binding sites.”, Proteins, vol. 57, no. 2, pp. 262-8, 2004.
K. Senger, Armstrong, G. W., Rowell, W. J., Kwan, J. M., Markstein, M., and Levine, M., “Immunity regulatory DNAs share common organizational features in Drosophila.”, Mol Cell, vol. 13, no. 1, pp. 19-32, 2004.
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.
M. Markstein, Markstein, P., Markstein, V., and Levine, M. S., “Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 763-8, 2002.
J. J. Zartman and Shvartsman, S. Y., “Enhancer organization: transistor with a twist or something in a different vein?”, Curr Biol, vol. 17, no. 24, pp. R1048-50, 2007.
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.
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. E. Klein, Nappi, V. M., Reeves, G. T., Shvartsman, S. Y., and Lemmon, M. A., “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
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.
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.
A. T. Hark and Tilghman, S. M., “Chromatin conformation of the H19 epigenetic mark.”, Hum Mol Genet, vol. 7, no. 12, pp. 1979-85, 1998.
R. V. Kulkarni, Huang, K. Casey, Kloster, M., and Wingreen, N. S., “Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules.”, Phys Rev Lett, vol. 93, no. 22, p. 228103, 2004.
D. Papatsenko, Goltsev, Y., and Levine, M., “Organization of developmental enhancers in the Drosophila embryo.”, Nucleic Acids Res, vol. 37, no. 17, pp. 5665-77, 2009.
J. A. Capra, Laskowski, R. A., Thornton, J. M., Singh, M., and Funkhouser, T. A., “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
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.
M. Markstein and Levine, M., “Decoding cis-regulatory DNAs in the Drosophila genome.”, Curr Opin Genet Dev, vol. 12, no. 5, pp. 601-6, 2002.
S. Nadimpalli Kobren and Singh, M., “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
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.
E. S. Click, Stearns, T., and Botstein, D., “Systematic structure-function analysis of the small GTPase Arf1 in yeast.”, Mol Biol Cell, vol. 13, no. 5, pp. 1652-64, 2002.
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.
Biocatalysis
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.
Biochemical Phenomena
J. L. Wetzel and Singh, M., “Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination.”, Nucleic Acids Res, vol. 48, no. 2, p. e9, 2020.
Biochemical Processes
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.
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.
Biochemistry
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.
J. D. Rabinowitz, Hsiao, J. J., Gryncel, K. R., Kantrowitz, E. R., Feng, X. - J., Li, G., and Rabitz, H., “Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase.”, Biochemistry, vol. 47, no. 21, pp. 5881-8, 2008.
Biofilms
C. M. Waters, Lu, W., Rabinowitz, J. D., and Bassler, B. L., “Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT.”, J Bacteriol, vol. 190, no. 7, pp. 2527-36, 2008.
K. Drescher, Nadell, C. D., Stone, H. A., Wingreen, N. S., and Bassler, B. L., “Solutions to the public goods dilemma in bacterial biofilms.”, Curr Biol, vol. 24, no. 1, pp. 50-5, 2014.
Biological Clocks
S. E. Cole, Levorse, J. M., Tilghman, S. M., and Vogt, T. F., “Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis.”, Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
L. Qiao, Nachbar, R. B., Kevrekidis, I. G., and Shvartsman, S. Y., “Bistability and oscillations in the Huang-Ferrell model of MAPK signaling.”, PLoS Comput Biol, vol. 3, no. 9, pp. 1819-26, 2007.
E. Emberly and Wingreen, N. S., “Hourglass model for a protein-based circadian oscillator.”, Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
Biological Evolution
M. Peifer and Wieschaus, E., “The segment polarity gene armadillo encodes a functionally modular protein that is the Drosophila homolog of human plakoglobin.”, Cell, vol. 63, no. 6, pp. 1167-76, 1990.
D. Botstein, “Genome-sequencing anniversary. Fruits of genome sequences for biology.”, Science, vol. 331, no. 6020, p. 1025, 2011.
N. Haupaix, Abitua, P. B., Sirour, C., Yasuo, H., Levine, M., and Hudson, C., “Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS.”, Dev Biol, vol. 394, no. 1, pp. 170-80, 2014.
S. M. Tilghman, “The sins of the fathers and mothers: genomic imprinting in mammalian development.”, Cell, vol. 96, no. 2, pp. 185-93, 1999.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
D. Botstein, “Lasker∼Koshland to genetics pioneer.”, Cell, vol. 158, no. 6, pp. 1230-2, 2014.
K. Pfeifer and Tilghman, S. M., “Allele-specific gene expression in mammals: the curious case of the imprinted RNAs.”, Genes Dev, vol. 8, no. 16, pp. 1867-74, 1994.
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.
P. Engel, Kwong, W. K., McFrederick, Q., Anderson, K. E., Barribeau, S. Michael, Chandler, J. Angus, R Cornman, S., Dainat, J., de Miranda, J. R., Doublet, V., Emery, O., Evans, J. D., Farinelli, L., Flenniken, M. L., Granberg, F., Grasis, J. A., Gauthier, L., Hayer, J., Koch, H., Kocher, S., Martinson, V. G., Moran, N., Munoz-Torres, M., Newton, I., Paxton, R. J., Powell, E., Sadd, B. M., Schmid-Hempel, P., Schmid-Hempel, R., Song, S. Jin, Schwarz, R. S., vanEngelsdorp, D., and Dainat, B., “The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.”, MBio, vol. 7, no. 2, pp. e02164-15, 2016.
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.
C. Cao, Lemaire, L. A., Wang, W., Yoon, P. H., Choi, Y. A., Parsons, L. R., Matese, J. C., Wang, W., Levine, M., and Chen, K., “Comprehensive single-cell transcriptome lineages of a proto-vertebrate.”, Nature, vol. 571, no. 7765, pp. 349-354, 2019.
R. Cui, Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., and Rosenthal, G. G., “Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.”, Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
M. L. Aardema, Zhen, Y., and Andolfatto, P., “The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”, Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
B. Davidson and Levine, M., “Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis.”, Proc Natl Acad Sci U S A, vol. 100, no. 20, pp. 11469-73, 2003.
S. Tucci and Akey, J. M., “The long walk to African genomics.”, Genome Biol, vol. 20, no. 1, p. 130, 2019.
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., “Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.”, Evolution, vol. 60, no. 2, pp. 292-302, 2006.
K. Dolinski and Botstein, D., “Orthology and functional conservation in eukaryotes.”, Annu Rev Genet, vol. 41, pp. 465-507, 2007.
C. Shi and Murphy, C. T., “Mating induces shrinking and death in Caenorhabditis mothers.”, Science, vol. 343, no. 6170, pp. 536-40, 2014.
V. Lakhina and Murphy, C. T., “Genome Sequencing Fishes out Longevity Genes.”, Cell, vol. 163, no. 6, pp. 1312-3, 2015.
S. Goyal and Wingreen, N. S., “Growth-induced instability in metabolic networks.”, Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
T. Slotte, Hazzouri, K. M., Stern, D., Andolfatto, P., and Wright, S. I., “Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”, Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
A. Stolfi, T Gainous, B., Young, J. J., Mori, A., Levine, M., and Christiaen, L., “Early chordate origins of the vertebrate second heart field.”, Science, vol. 329, no. 5991, pp. 565-8, 2010.
Biological Factors
D. Bruce Borenstein, Meir, Y., Shaevitz, J. W., and Wingreen, N. S., “Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model.”, PLoS One, vol. 8, no. 5, p. e63304, 2013.
Biological Markers
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.
A. C. Martin, Gelbart, M., Fernandez-Gonzalez, R., Kaschube, M., and Wieschaus, E. F., “Integration of contractile forces during tissue invagination.”, J Cell Biol, vol. 188, no. 5, pp. 735-49, 2010.
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.
A. Stolfi and Levine, M., “Neuronal subtype specification in the spinal cord of a protovertebrate.”, Development, vol. 138, no. 5, pp. 995-1004, 2011.
Biological Processes
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.
Biological Science Disciplines
W. Bialek and Botstein, D., “Introductory science and mathematics education for 21st-Century biologists.”, Science, vol. 303, no. 5659, pp. 788-90, 2004.
J. D. Rabinowitz and Vastag, L., “Teaching the design principles of metabolism.”, Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 2012.
O. G. Vukmirovic and Tilghman, S. M., “Exploring genome space.”, Nature, vol. 405, no. 6788, pp. 820-2, 2000.
Biological Transport
J. Yuan and Rabinowitz, J. D., “Differentiating metabolites formed from de novo synthesis versus macromolecule decomposition.”, J Am Chem Soc, vol. 129, no. 30, pp. 9294-5, 2007.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., “Long-range signal transmission in autocrine relays.”, Biophys J, vol. 84, no. 2 Pt 1, pp. 883-96, 2003.
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.
S. P. Gross, Welte, M. A., Block, S. M., and Wieschaus, E. F., “Dynein-mediated cargo transport in vivo. A switch controls travel distance.”, J Cell Biol, vol. 148, no. 5, pp. 945-56, 2000.
A. Bejsovec and Wieschaus, E., “Signaling activities of the Drosophila wingless gene are separately mutable and appear to be transduced at the cell surface.”, Genetics, vol. 139, no. 1, pp. 309-20, 1995.
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.
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.
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.
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.
R. G. Endres and Wingreen, N. S., “Accuracy of direct gradient sensing by single cells.”, Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
Biological Transport, Active
C. B. Muratov and Shvartsman, S. Y., “Signal propagation and failure in discrete autocrine relays.”, Phys Rev Lett, vol. 93, no. 11, p. 118101, 2004.
Biology
M. A. Hibbs, Myers, C. L., Huttenhower, C., Hess, D. C., Li, K., Caudy, A. A., and Troyanskaya, O. G., “Directing experimental biology: a case study in mitochondrial biogenesis.”, PLoS Comput Biol, vol. 5, no. 3, p. e1000322, 2009.
N. Wingreen and Botstein, D., “Back to the future: education for systems-level biologists.”, Nat Rev Mol Cell Biol, vol. 7, no. 11, pp. 829-32, 2006.
D. Botstein, “Why we need more basic biology research, not less.”, Mol Biol Cell, vol. 23, no. 21, pp. 4160-1, 2012.
O. G. Troyanskaya, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
Biomass
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.
S. Goyal, Yuan, J., Chen, T., Rabinowitz, J. D., and Wingreen, N. S., “Achieving optimal growth through product feedback inhibition in metabolism.”, PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
Biomechanical Phenomena
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.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Silvestri, E., Viale, M., and Walczak, A. M., “Statistical mechanics for natural flocks of birds.”, Proc Natl Acad Sci U S A, vol. 109, no. 13, pp. 4786-91, 2012.
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.
Biomedical Research
O. Troyanskaya, “"Getting started in..": a series not to miss.”, PLoS Comput Biol, vol. 3, no. 10, p. 1841, 2007.
W. Bialek and Botstein, D., “Introductory science and mathematics education for 21st-Century biologists.”, Science, vol. 303, no. 5659, pp. 788-90, 2004.
Biophysical Phenomena
J. L. Wetzel and Singh, M., “Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination.”, Nucleic Acids Res, vol. 48, no. 2, p. e9, 2020.
W. Bialek and Setayeshgar, S., “Physical limits to biochemical signaling.”, Proc Natl Acad Sci U S A, vol. 102, no. 29, pp. 10040-5, 2005.
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.
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. Coppey, Berezhkovskii, A. M., Sealfon, S. C., and Shvartsman, S. Y., “Time and length scales of autocrine signals in three dimensions.”, Biophys J, vol. 93, no. 6, pp. 1917-22, 2007.
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.
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.
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.
Biophysics
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.
W. Bialek and Setayeshgar, S., “Physical limits to biochemical signaling.”, Proc Natl Acad Sci U S A, vol. 102, no. 29, pp. 10040-5, 2005.
J. W. Shaevitz, “Super-resolution for a 3D world.”, Nat Methods, vol. 5, no. 6, pp. 471-2, 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.
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. 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.
M. Coppey, Berezhkovskii, A. M., Sealfon, S. C., and Shvartsman, S. Y., “Time and length scales of autocrine signals in three dimensions.”, Biophys J, vol. 93, no. 6, pp. 1917-22, 2007.
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, “Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.”, Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
L. Batsilas, Berezhkovskii, A. M., and Shvartsman, S. Y., “Stochastic model of autocrine and paracrine signals in cell culture assays.”, Biophys J, vol. 85, no. 6, pp. 3659-65, 2003.
K. Casey Huang, Mukhopadhyay, R., Wen, B., Gitai, Z., and Wingreen, N. S., “Cell shape and cell-wall organization in Gram-negative bacteria.”, Proc Natl Acad Sci U S A, vol. 105, no. 49, pp. 19282-7, 2008.
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.
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.
W. Bialek, “QnAs with William Bialek.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, p. 16288, 2013.
Biopolymers
D. Swanson and Wingreen, N. S., “Active biopolymers confer fast reorganization kinetics.”, Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
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.
Biopsy
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.
Biostatistics
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.
Biosynthetic Pathways
P. H. Bradley, Brauer, M. J., Rabinowitz, J. D., and Troyanskaya, O. G., “Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
M. F. Clasquin, Melamud, E., Singer, A., Gooding, J. R., Xu, X., Dong, A., Cui, H., Campagna, S. R., Savchenko, A., Yakunin, A. F., Rabinowitz, J. D., and Caudy, A. A., “Riboneogenesis in yeast.”, Cell, vol. 145, no. 6, pp. 969-80, 2011.
Biotechnology
D. Botstein, “Why we need more basic biology research, not less.”, Mol Biol Cell, vol. 23, no. 21, pp. 4160-1, 2012.
O. G. Vukmirovic and Tilghman, S. M., “Exploring genome space.”, Nature, vol. 405, no. 6788, pp. 820-2, 2000.
Bipolar Disorder
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.
Blastoderm
T. Schupbach and Wieschaus, E., “Female sterile mutations on the second chromosome of Drosophila melanogaster. I. Maternal effect mutations.”, Genetics, vol. 121, no. 1, pp. 101-17, 1989.
J. H. Thomas and Wieschaus, E., “src64 and tec29 are required for microfilament contraction during Drosophila cellularization.”, Development, vol. 131, no. 4, pp. 863-71, 2004.
L. S. Rose and Wieschaus, E., “The Drosophila cellularization gene nullo produces a blastoderm-specific transcript whose levels respond to the nucleocytoplasmic ratio.”, Genes Dev, vol. 6, no. 7, pp. 1255-68, 1992.
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.
K. D. Irvine and Wieschaus, E., “Cell intercalation during Drosophila germband extension and its regulation by pair-rule segmentation genes.”, Development, vol. 120, no. 4, pp. 827-41, 1994.
S. B. Zusman and Wieschaus, E., “A cell marker system and mosaic patterns during early embryonic development in Drosophila melanogaster.”, Genetics, vol. 115, no. 4, pp. 725-36, 1987.
H. A. Müller and Wieschaus, E., “armadillo, bazooka, and stardust are critical for early stages in formation of the zonula adherens and maintenance of the polarized blastoderm epithelium in Drosophila.”, J Cell Biol, vol. 134, no. 1, pp. 149-63, 1996.
W. J. Gehring, Wieschaus, E., and Holliger, M., “The use of 'normal' and 'transformed' gynandromorphs in mapping the primordial germ cells and the gonadal mesoderm in Drosophila.”, J Embryol Exp Morphol, vol. 35, no. 3, pp. 607-16, 1976.
E. D. Schejter and Wieschaus, E., “Functional elements of the cytoskeleton in the early Drosophila embryo.”, Annu Rev Cell Biol, vol. 9, pp. 67-99, 1993.
E. D. Schejter, Rose, L. S., Postner, M. A., and Wieschaus, E., “Role of the zygotic genome in the restructuring of the actin cytoskeleton at the cycle-14 transition during Drosophila embryogenesis.”, Cold Spring Harb Symp Quant Biol, vol. 57, pp. 653-9, 1992.
M. A. Postner and Wieschaus, E. F., “The nullo protein is a component of the actin-myosin network that mediates cellularization in Drosophila melanogaster embryos.”, J Cell Sci, vol. 107 ( Pt 7), pp. 1863-73, 1994.
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.
A. Vincent, Blankenship, J. T., and Wieschaus, E., “Integration of the head and trunk segmentation systems controls cephalic furrow formation in Drosophila.”, Development, vol. 124, no. 19, pp. 3747-54, 1997.
J. Mohler and Wieschaus, E. F., “Bicaudal mutations of Drosophila melanogaster: alteration of blastoderm cell fate.”, Cold Spring Harb Symp Quant Biol, vol. 50, pp. 105-11, 1985.
E. D. Schejter and Wieschaus, E., “bottleneck acts as a regulator of the microfilament network governing cellularization of the Drosophila embryo.”, Cell, vol. 75, no. 2, pp. 373-85, 1993.
J. L. Marsh, van Deusen, E. B., Wieschaus, E., and Gehring, W. J., “Germ line dependence of the deep orange maternal effect in Drosophila.”, Dev Biol, vol. 56, no. 1, pp. 195-9, 1977.
Blastula
L. Vastag, Jorgensen, P., Peshkin, L., Wei, R., Rabinowitz, J. D., and Kirschner, M. W., “Remodeling of the metabolome during early frog development.”, PLoS One, vol. 6, no. 2, p. e16881, 2011.
N. Haupaix, Abitua, P. B., Sirour, C., Yasuo, H., Levine, M., and Hudson, C., “Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS.”, Dev Biol, vol. 394, no. 1, pp. 170-80, 2014.
X. Lu, Li, J. M., Elemento, O., Tavazoie, S., and Wieschaus, E. F., “Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition.”, Development, vol. 136, no. 12, pp. 2101-10, 2009.
Blood Pressure
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.
Blotting, Northern
L. S. Rose and Wieschaus, E., “The Drosophila cellularization gene nullo produces a blastoderm-specific transcript whose levels respond to the nucleocytoplasmic ratio.”, Genes Dev, vol. 6, no. 7, pp. 1255-68, 1992.
L. J. Kurihara, Kikuchi, T., Wada, K., and Tilghman, S. M., “Loss of Uch-L1 and Uch-L3 leads to neurodegeneration, posterior paralysis and dysphagia.”, Hum Mol Genet, vol. 10, no. 18, pp. 1963-70, 2001.
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.
J. Vacher, Camper, S. A., Krumlauf, R., Compton, R. S., and Tilghman, S. M., “raf regulates the postnatal repression of the mouse alpha-fetoprotein gene at the posttranscriptional level.”, Mol Cell Biol, vol. 12, no. 2, pp. 856-64, 1992.
Blotting, Southern
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.
Blotting, Western
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.
O. Grimm, Zini, V. Sanchez, Kim, Y., Casanova, J., Shvartsman, S. Y., and Wieschaus, E., “Torso RTK controls Capicua degradation by changing its subcellular localization.”, Development, vol. 139, no. 21, pp. 3962-8, 2012.
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.
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. 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.
S. Hong, Zhou, W., Fang, B., Lu, W., Loro, E., Damle, M., Ding, G., Jager, J., Zhang, S., Zhang, Y., Feng, D., Chu, Q., Dill, B. D., Molina, H., Khurana, T. S., Rabinowitz, J. D., Lazar, M. A., and Sun, Z., “Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion.”, Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
S. Di Talia and Wieschaus, E. F., “Short-term integration of Cdc25 dynamics controls mitotic entry during Drosophila gastrulation.”, Dev Cell, vol. 22, no. 4, pp. 763-74, 2012.
N. S. Tolwinski and Wieschaus, E., “A nuclear function for armadillo/beta-catenin.”, PLoS Biol, vol. 2, no. 4, p. E95, 2004.
M. Tipping, Kim, Y., Kyriakakis, P., Tong, M., Shvartsman, S. Y., and Veraksa, A., “β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.”, EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
Body Composition
S. Hong, Zhou, W., Fang, B., Lu, W., Loro, E., Damle, M., Ding, G., Jager, J., Zhang, S., Zhang, Y., Feng, D., Chu, Q., Dill, B. D., Molina, H., Khurana, T. S., Rabinowitz, J. D., Lazar, M. A., and Sun, Z., “Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion.”, Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
Body Mass Index
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.
Body Patterning
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.
P. Barron Abitua, T Gainous, B., Kaczmarczyk, A. N., Winchell, C. J., Hudson, C., Kamata, K., Nakagawa, M., Tsuda, M., Kusakabe, T. G., and Levine, M., “The pre-vertebrate origins of neurogenic placodes.”, Nature, vol. 524, no. 7566, pp. 462-5, 2015.
E. Farley and Levine, M., “HOT DNAs: a novel class of developmental enhancers.”, Genes Dev, vol. 26, no. 9, pp. 873-6, 2012.
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.
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.
N. Haupaix, Abitua, P. B., Sirour, C., Yasuo, H., Levine, M., and Hudson, C., “Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS.”, Dev Biol, vol. 394, no. 1, pp. 170-80, 2014.
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.
R. E. Dawes-Hoang, Parmar, K. M., Christiansen, A. E., Phelps, C. B., Brand, A. H., and Wieschaus, E. F., “folded gastrulation, cell shape change and the control of myosin localization.”, Development, vol. 132, no. 18, pp. 4165-78, 2005.
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.
V. S. Chopra, Hong, J. - W., and Levine, M., “Regulation of Hox gene activity by transcriptional elongation in Drosophila.”, Curr Biol, vol. 19, no. 8, pp. 688-93, 2009.
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.
T. Gregor, McGregor, A. P., and Wieschaus, E. F., “Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos.”, Dev Biol, vol. 316, no. 2, pp. 350-8, 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.
P. V. Gordon, Sample, C., Berezhkovskii, A. M., Muratov, C. B., and Shvartsman, S. Y., “Local kinetics of morphogen gradients.”, Proc Natl Acad Sci U S A, vol. 108, no. 15, pp. 6157-62, 2011.
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.
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.
F. Liu, Morrison, A. H., and Gregor, T., “Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network.”, Proc Natl Acad Sci U S A, vol. 110, no. 17, pp. 6724-9, 2013.
S. E. Cole, Levorse, J. M., Tilghman, S. M., and Vogt, T. F., “Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis.”, Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
J. A. Zallen and Wieschaus, E., “Patterned gene expression directs bipolar planar polarity in Drosophila.”, Dev Cell, vol. 6, no. 3, pp. 343-55, 2004.

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