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Bacterial Physiological Phenomena
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.
Bacterial Proteins
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.
C. H. Hansen, Endres, R. G., and Wingreen, N. S., “Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation.”, PLoS Comput Biol, vol. 4, no. 1, p. e1, 2008.
T. Mora, Yu, H., Sowa, Y., and Wingreen, N. S., “Steps in the bacterial flagellar motor.”, PLoS Comput Biol, vol. 5, no. 10, p. e1000540, 2009.
R. G. Endres, Oleksiuk, O., Hansen, C. H., Meir, Y., Sourjik, V., and Wingreen, N. S., “Variable sizes of Escherichia coli chemoreceptor signaling teams.”, Mol Syst Biol, vol. 4, p. 211, 2008.
D. Greenfield, McEvoy, A. L., Shroff, H., Crooks, G. E., Wingreen, N. S., Betzig, E., and Liphardt, J., “Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy.”, PLoS Biol, vol. 7, no. 6, p. e1000137, 2009.
L. R. Swem, Swem, D. L., Wingreen, N. S., and Bassler, B. L., “Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi.”, Cell, vol. 134, no. 3, pp. 461-73, 2008.
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.
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.
T. Mignot and Shaevitz, J. W., “Active and passive mechanisms of intracellular transport and localization in bacteria.”, Curr Opin Microbiol, vol. 11, no. 6, pp. 580-5, 2008.
T. M. Bartlett, Bratton, B. P., Duvshani, A., Miguel, A., Sheng, Y., Martin, N. R., Nguyen, J. P., Persat, A., Desmarais, S. M., VanNieuwenhze, M. S., Huang, K. Casey, Zhu, J., Shaevitz, J. W., and Gitai, Z., “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
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.
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.
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.
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.
R. G. Endres and Wingreen, N. S., “Precise adaptation in bacterial chemotaxis through "assistance neighborhoods".”, Proc Natl Acad Sci U S A, vol. 103, no. 35, pp. 13040-4, 2006.
K. Casey Huang and Wingreen, N. S., “Min-protein oscillations in round bacteria.”, Phys Biol, vol. 1, no. 3-4, pp. 229-35, 2004.
E. Emberly and Wingreen, N. S., “Hourglass model for a protein-based circadian oscillator.”, Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
K. Jim, Parmar, K., Singh, M., and Tavazoie, S., “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
T. Mignot, Shaevitz, J. W., Hartzell, P. L., and Zusman, D. R., “Evidence that focal adhesion complexes power bacterial gliding motility.”, Science, vol. 315, no. 5813, pp. 853-6, 2007.
D. E. Coulter and Wieschaus, E., “Gene activities and segmental patterning in Drosophila: analysis of odd-skipped and pair-rule double mutants.”, Genes Dev, vol. 2, no. 12B, pp. 1812-23, 1988.
T. Long, Tu, K. C., Wang, Y., Mehta, P., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Quantifying the integration of quorum-sensing signals with single-cell resolution.”, PLoS Biol, vol. 7, no. 3, p. e68, 2009.
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.
Z. Khan, Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., and Tavazoie, S., “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
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.
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.
R. G. Endres, Falke, J. J., and Wingreen, N. S., “Chemotaxis receptor complexes: from signaling to assembly.”, PLoS Comput Biol, vol. 3, no. 7, p. e150, 2007.
E. J. Banigan, Gelbart, M. A., Gitai, Z., Wingreen, N. S., and Liu, A. J., “Filament depolymerization can explain chromosome pulling during bacterial mitosis.”, PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
C. N. Peterson, Levchenko, I., Rabinowitz, J. D., Baker, T. A., and Silhavy, T. J., “RpoS proteolysis is controlled directly by ATP levels in Escherichia coli.”, Genes Dev, vol. 26, no. 6, pp. 548-53, 2012.
S. van Teeffelen, Shaevitz, J. W., and Gitai, Z., “Image analysis in fluorescence microscopy: bacterial dynamics as a case study.”, Bioessays, vol. 34, no. 5, pp. 427-36, 2012.
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.
T. Mora, Bai, F., Che, Y. - S., Minamino, T., Namba, K., and Wingreen, N. S., “Non-genetic individuality in Escherichia coli motor switching.”, Phys Biol, vol. 8, no. 2, p. 024001, 2011.
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.
S. - W. Teng, Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi.”, Mol Syst Biol, vol. 7, p. 491, 2011.
K. C. Tu, Long, T., Svenningsen, S. L., Wingreen, N. S., and Bassler, B. L., “Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response.”, Mol Cell, vol. 37, no. 4, pp. 567-79, 2010.
Bacterial Toxins
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.
Bacteriological Techniques
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Measuring the bending stiffness of bacterial cells using an optical trap.”, J Vis Exp, no. 38, 2010.
Bacteriophage lambda
D. Botstein, “Ira Herskowitz: 1946-2003.”, Genetics, vol. 166, no. 2, pp. 653-60, 2004.
Bacteriophages
J. S. Weitz, Benfey, P. N., and Wingreen, N. S., “Evolution, interactions, and biological networks.”, PLoS Biol, vol. 5, no. 1, p. e11, 2007.
Base Composition
D. A. Hendrix, Hong, J. - W., Zeitlinger, J., Rokhsar, D. S., and Levine, M. S., “Promoter elements associated with RNA Pol II stalling in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 105, no. 22, pp. 7762-7, 2008.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “Statistical mechanics of RNA folding: importance of alphabet size.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 68, no. 4 Pt 1, p. 041904, 2003.
Base Pair Mismatch
J. Akiko Heck, Gresham, D., Botstein, D., and Alani, E., “Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements.”, Genetics, vol. 174, no. 1, pp. 519-23, 2006.
Base Pairing
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.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
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.
Base Sequence
M. H. Feuerman, Godbout, R., Ingram, R. S., and Tilghman, S. M., “Tissue-specific transcription of the mouse alpha-fetoprotein gene promoter is dependent on HNF-1.”, Mol Cell Biol, vol. 9, no. 10, pp. 4204-12, 1989.
A. Pane, Jiang, P., Zhao, D. Yanling, Singh, M., and Schüpbach, T., “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
C. Huttenhower and Troyanskaya, O. G., “Assessing the functional structure of genomic data.”, Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
Y. Kim, Iagovitina, A., Ishihara, K., Fitzgerald, K. M., Deplancke, B., Papatsenko, D., and Shvartsman, S. Y., “Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.”, Chaos, vol. 23, no. 2, p. 025105, 2013.
C. Rauskolb, Peifer, M., and Wieschaus, E., “extradenticle, a regulator of homeotic gene activity, is a homolog of the homeobox-containing human proto-oncogene pbx1.”, Cell, vol. 74, no. 6, pp. 1101-12, 1993.
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
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.
A. S. Putnam, J Scriber, M., and Andolfatto, P., “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
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, Zinzen, R., Markstein, P., Yee, K. - P., Erives, A., Stathopoulos, A., and Levine, M., “A regulatory code for neurogenic gene expression in the Drosophila embryo.”, Development, vol. 131, no. 10, pp. 2387-94, 2004.
L. J. Kurihara, Semenova, E., Levorse, J. M., and Tilghman, S. M., “Expression and functional analysis of Uch-L3 during mouse development.”, Mol Cell Biol, vol. 20, no. 7, pp. 2498-504, 2000.
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. 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.
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.
R. Papazyan, Sun, Z., Kim, Y. Hoon, Titchenell, P. M., Hill, D. A., Lu, W., Damle, M., Wan, M., Zhang, Y., Briggs, E. R., Rabinowitz, J. D., and Lazar, M. A., “Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP.”, Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
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.
V. Pachnis, Brannan, C. I., and Tilghman, S. M., “The structure and expression of a novel gene activated in early mouse embryogenesis.”, EMBO J, vol. 7, no. 3, pp. 673-81, 1988.
A. V. Persikov, Osada, R., and Singh, M., “Predicting DNA recognition by Cys2His2 zinc finger proteins.”, Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
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.
R. Godbout, Ingram, R. S., and Tilghman, S. M., “Fine-structure mapping of the three mouse alpha-fetoprotein gene enhancers.”, Mol Cell Biol, vol. 8, no. 3, pp. 1169-78, 1988.
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.
P. A. Leighton, Ingram, R. S., Eggenschwiler, J., Efstratiadis, A., and Tilghman, S. M., “Disruption of imprinting caused by deletion of the H19 gene region in mice.”, Nature, vol. 375, no. 6526, pp. 34-9, 1995.
S. De Renzis, Elemento, O., Tavazoie, S., and Wieschaus, E. F., “Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo.”, PLoS Biol, vol. 5, no. 5, p. e117, 2007.
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.
P. A. Leighton, Saam, J. R., Ingram, R. S., Stewart, C. L., and Tilghman, S. M., “An enhancer deletion affects both H19 and Igf2 expression.”, Genes Dev, vol. 9, no. 17, pp. 2079-89, 1995.
C. I. Brannan, Dees, E. C., Ingram, R. S., and Tilghman, S. M., “The product of the H19 gene may function as an RNA.”, Mol Cell Biol, vol. 10, no. 1, pp. 28-36, 1990.
M. Shakoury-Elizeh, Tiedeman, J., Rashford, J., Ferea, T., Demeter, J., Garcia, E., Rolfes, R., Brown, P. O., Botstein, D., and Philpott, C. C., “Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
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.
J. M. Rossi, Chen, H., and Tilghman, S. M., “Genetic map of the fused locus on mouse chromosome 17.”, Genomics, vol. 23, no. 1, pp. 178-84, 1994.
M. D. Chikina, Huttenhower, C., Murphy, C. T., and Troyanskaya, O. G., “Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.”, PLoS Comput Biol, vol. 5, no. 6, p. e1000417, 2009.
A. Fuchs, Cheung, L. S., Charbonnier, E., Shvartsman, S. Y., and Pyrowolakis, G., “Transcriptional interpretation of the EGF receptor signaling gradient.”, Proc Natl Acad Sci U S A, vol. 109, no. 5, pp. 1572-7, 2012.
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.
S. Parks and Wieschaus, E., “The Drosophila gastrulation gene concertina encodes a G alpha-like protein.”, Cell, vol. 64, no. 2, pp. 447-58, 1991.
O. G. Troyanskaya, Arbell, O., Koren, Y., Landau, G. M., and Bolshoy, A., “Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.”, Bioinformatics, vol. 18, no. 5, pp. 679-88, 2002.
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.
P. Andolfatto, J Scriber, M., and Charlesworth, B., “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
T. J. Vasicek, Zeng, L., Guan, X. J., Zhang, T., Costantini, F., and Tilghman, S. M., “Two dominant mutations in the mouse fused gene are the result of transposon insertions.”, Genetics, vol. 147, no. 2, pp. 777-86, 1997.
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.
L. Christiaen, Stolfi, A., Davidson, B., and Levine, M., “Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp.”, Dev Biol, vol. 328, no. 2, pp. 552-60, 2009.
P. Armand, Knapp, A. C., Hirsch, A. J., Wieschaus, E. F., and Cole, M. D., “A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis.”, Mol Cell Biol, vol. 14, no. 6, pp. 4145-54, 1994.
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.
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. V. Schmidt, Matteson, P. G., Jones, B. K., Guan, X. J., and Tilghman, S. M., “The Dlk1 and Gtl2 genes are linked and reciprocally imprinted.”, Genes Dev, vol. 14, no. 16, pp. 1997-2002, 2000.
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.
V. Hilgers, Perry, M. W., Hendrix, D., Stark, A., Levine, M., and Haley, B., “Neural-specific elongation of 3' UTRs during Drosophila development.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15864-9, 2011.
H. Yoo-Warren, Pachnis, V., Ingram, R. S., and Tilghman, S. M., “Two regulatory domains flank the mouse H19 gene.”, Mol Cell Biol, vol. 8, no. 11, pp. 4707-15, 1988.
D. Papatsenko, Kislyuk, A., Levine, M., and Dubchak, I., “Conservation patterns in different functional sequence categories of divergent Drosophila species.”, Genomics, vol. 88, no. 4, pp. 431-42, 2006.
P. B. Vrana, Guan, X. J., Ingram, R. S., and Tilghman, S. M., “Genomic imprinting is disrupted in interspecific Peromyscus hybrids.”, Nat Genet, vol. 20, no. 4, pp. 362-5, 1998.
S. M. Tilghman, “Lessons learned, promises kept: a biologist's eye view of the Genome Project.”, Genome Res, vol. 6, no. 9, pp. 773-80, 1996.
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.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., “Genome sequencing reveals complex speciation in the Drosophila simulans clade.”, Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
X. J. Guan, Arhin, G., Leung, J., and Tilghman, S. M., “Linkage between vitamin D-binding protein and alpha-fetoprotein in the mouse.”, Mamm Genome, vol. 7, no. 2, pp. 103-6, 1996.
J. M. Rossi, Burke, D. T., Leung, J. C., Koos, D. S., Chen, H., and Tilghman, S. M., “Genomic analysis using a yeast artificial chromosome library with mouse DNA inserts.”, Proc Natl Acad Sci U S A, vol. 89, no. 6, pp. 2456-60, 1992.
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.
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.
J. A. Emerson, Vacher, J., Cirillo, L. A., Tilghman, S. M., and Tyner, A. L., “The zonal expression of alpha-fetoprotein transgenes in the livers of adult mice.”, Dev Dyn, vol. 195, no. 1, pp. 55-66, 1992.
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “Statistical mechanics of RNA folding: importance of alphabet size.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 68, no. 4 Pt 1, p. 041904, 2003.
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.
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. Lagha, Bothma, J. P., Esposito, E., Ng, S., Stefanik, L., Tsui, C., Johnston, J., Chen, K., Gilmour, D. S., Zeitlinger, J., and Levine, M. S., “Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.”, Cell, vol. 153, no. 5, pp. 976-87, 2013.
K. C. Tu, Long, T., Svenningsen, S. L., Wingreen, N. S., and Bassler, B. L., “Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response.”, Mol Cell, vol. 37, no. 4, pp. 567-79, 2010.
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.
L. L. Sandell, Guan, X. - J., Ingram, R., and Tilghman, S. M., “Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta.”, Proc Natl Acad Sci U S A, vol. 100, no. 8, pp. 4622-7, 2003.
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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.
M. Costa, Wilson, E. T., and Wieschaus, E., “A putative cell signal encoded by the folded gastrulation gene coordinates cell shape changes during Drosophila gastrulation.”, Cell, vol. 76, no. 6, pp. 1075-89, 1994.
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.
T. P. O'Brien, Metallinos, D. L., Chen, H., Shin, M. K., and Tilghman, S. M., “Complementation mapping of skeletal and central nervous system abnormalities in mice of the piebald deletion complex.”, Genetics, vol. 143, no. 1, pp. 447-61, 1996.
M. A. Cleary, van Raamsdonk, C. D., Levorse, J., Zheng, B., Bradley, A., and Tilghman, S. M., “Disruption of an imprinted gene cluster by a targeted chromosomal translocation in mice.”, Nat Genet, vol. 29, no. 1, pp. 78-82, 2001.
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.
M. Peifer and Wieschaus, E., “The product of the Drosophila melanogaster segment polarity gene armadillo is highly conserved in sequence and expression in the housefly Musca domestica.”, J Mol Evol, vol. 36, no. 3, pp. 224-33, 1993.
D. L. Metallinos, Oppenheimer, A. J., Rinchik, E. M., Russell, L. B., Dietrich, W., and Tilghman, S. M., “Fine structure mapping and deletion analysis of the murine piebald locus.”, Genetics, vol. 136, no. 1, pp. 217-23, 1994.
C. D. van Raamsdonk and Tilghman, S. M., “Dosage requirement and allelic expression of PAX6 during lens placode formation.”, Development, vol. 127, no. 24, pp. 5439-48, 2000.
J. A. Capra, Paeschke, K., Singh, M., and Zakian, V. A., “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
D. G. Fisk, Ball, C. A., Dolinski, K., Engel, S. R., Hong, E. L., Issel-Tarver, L., Schwartz, K., Sethuraman, A., Botstein, D., and J Cherry, M., “Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.”, Yeast, vol. 23, no. 12, pp. 857-65, 2006.
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.
D. A. Hendrix, Hong, J. - W., Zeitlinger, J., Rokhsar, D. S., and Levine, M. S., “Promoter elements associated with RNA Pol II stalling in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 105, no. 22, pp. 7762-7, 2008.
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.
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.
D. N. Keys, Levine, M., Harland, R. M., and Wallingford, J. B., “Control of intercalation is cell-autonomous in the notochord of Ciona intestinalis.”, Dev Biol, vol. 246, no. 2, pp. 329-40, 2002.
Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
A. A. Petti, R McIsaac, S., Ho-Shing, O., Bussemaker, H. J., and Botstein, D., “Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 3008-24, 2012.
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.
Basic Helix-Loop-Helix Transcription Factors
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.
B. Davidson, Shi, W., and Levine, M., “Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis.”, Development, vol. 132, no. 21, pp. 4811-8, 2005.
J. Cowden and Levine, M., “The Snail repressor positions Notch signaling in the Drosophila embryo.”, Development, vol. 129, no. 7, pp. 1785-93, 2002.
P. A. Leighton, Saam, J. R., Ingram, R. S., Stewart, C. L., and Tilghman, S. M., “An enhancer deletion affects both H19 and Igf2 expression.”, Genes Dev, vol. 9, no. 17, pp. 2079-89, 1995.
A. Helman, Lim, B., Andreu, M. José, Kim, Y., Shestkin, T., Lu, H., Jiménez, G., Shvartsman, S. Y., and Paroush, Z. 'ev, “RTK signaling modulates the Dorsal gradient.”, Development, vol. 139, no. 16, pp. 3032-9, 2012.
Y. Kim, Paroush, Z. 'ev, Nairz, K., Hafen, E., Jiménez, G., and Shvartsman, S. Y., “Substrate-dependent control of MAPK phosphorylation in vivo.”, Mol Syst Biol, vol. 7, p. 467, 2011.
L. Christiaen, Stolfi, A., Davidson, B., and Levine, M., “Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp.”, Dev Biol, vol. 328, no. 2, pp. 552-60, 2009.
P. Armand, Knapp, A. C., Hirsch, A. J., Wieschaus, E. F., and Cole, M. D., “A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis.”, Mol Cell Biol, vol. 14, no. 6, pp. 4145-54, 1994.
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.
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.
Basic-Leucine Zipper Transcription Factors
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.
M. J. Hickman, Petti, A. A., Ho-Shing, O., Silverman, S. J., R McIsaac, S., Lee, T. A., and Botstein, D., “Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.”, Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
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.
Bayes Theorem
Y. Guan, Dunham, M. J., and Troyanskaya, O. G., “Functional analysis of gene duplications in Saccharomyces cerevisiae.”, Genetics, vol. 175, no. 2, pp. 933-43, 2007.
Z. Barutcuoglu, Schapire, R. E., and Troyanskaya, O. G., “Hierarchical multi-label prediction of gene function.”, Bioinformatics, vol. 22, no. 7, pp. 830-6, 2006.
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.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
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.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
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.
A. Pop, Huttenhower, C., Iyer-Pascuzzi, A., Benfey, P. N., and Troyanskaya, O. G., “Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.”, BMC Syst Biol, vol. 4, p. 180, 2010.
C. L. Myers, Robson, D., Wible, A., Hibbs, M. A., Chiriac, C., Theesfeld, C. L., Dolinski, K., and Troyanskaya, O. G., “Discovery of biological networks from diverse functional genomic data.”, Genome Biol, vol. 6, no. 13, p. R114, 2005.
M. D. Chikina and Troyanskaya, O. G., “Accurate quantification of functional analogy among close homologs.”, PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
J. P. Huelsenbeck and Andolfatto, P., “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
A. S. Putnam, J Scriber, M., and Andolfatto, P., “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
Y. Deng, Coen, P., Sun, M., and Shaevitz, J. W., “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
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.
Y. Guan, Myers, C. L., Hess, D. C., Barutcuoglu, Z., Caudy, A. A., and Troyanskaya, O. G., “Predicting gene function in a hierarchical context with an ensemble of classifiers.”, Genome Biol, vol. 9 Suppl 1, p. S3, 2008.
D. Gorenshteyn, Zaslavsky, E., Fribourg, M., Park, C. Y., Wong, A. K., Tadych, A., Hartmann, B. M., Albrecht, R. A., García-Sastre, A., Kleinstein, S. H., Troyanskaya, O. G., and Sealfon, S. C., “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
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.
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.
C. Huttenhower, Hibbs, M., Myers, C., and Troyanskaya, O. G., “A scalable method for integration and functional analysis of multiple microarray datasets.”, Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
K. Thornton and Andolfatto, P., “Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.”, Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
Y. Guan, Ackert-Bicknell, C. L., Kell, B., Troyanskaya, O. G., and Hibbs, M. A., “Functional genomics complements quantitative genetics in identifying disease-gene associations.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
C. Y. Park, Hess, D. C., Huttenhower, C., and Troyanskaya, O. G., “Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.”, PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
C. Huttenhower and Troyanskaya, O. G., “Bayesian data integration: a functional perspective.”, Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
C. Huttenhower, K Mutungu, T., Indik, N., Yang, W., Schroeder, M., Forman, J. J., Troyanskaya, O. G., and Coller, H. A., “Detailing regulatory networks through large scale data integration.”, Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., “A genomewide functional network for the laboratory mouse.”, PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
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.
bcl-2 Homologous Antagonist-Killer Protein
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.
bcl-2-Associated X Protein
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.
Beckwith-Wiedemann Syndrome
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.
Bees
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
D. A. Galbraith, Kocher, S. D., Glenn, T., Albert, I., Hunt, G. J., Strassmann, J. E., Queller, D. C., and Grozinger, C. M., “Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera).”, Proc Natl Acad Sci U S A, vol. 113, no. 4, pp. 1020-5, 2016.
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., “Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”, PLoS One, vol. 5, no. 2, p. e9116, 2010.
J. Doran Cande, Chopra, V. S., and Levine, M., “Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum.”, Development, vol. 136, no. 18, pp. 3153-60, 2009.
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.
S. D. Kocher, Tsuruda, J. M., Gibson, J. D., Emore, C. M., Arechavaleta-Velasco, M. E., Queller, D. C., Strassmann, J. E., Grozinger, C. M., Gribskov, M. R., San Miguel, P., Westerman, R., and Hunt, G. J., “A Search for Parent-of-Origin Effects on Honey Bee Gene Expression.”, G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
Behavior
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.
Behavior, Animal
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
J. P. Nguyen, Shipley, F. B., Linder, A. N., Plummer, G. S., Liu, M., Setru, S. U., Shaevitz, J. W., and Leifer, A. M., “Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. E1074-81, 2016.
Y. Deng, Coen, P., Sun, M., and Shaevitz, J. W., “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
G. J. Stephens, de Mesquita, M. Bueno, Ryu, W. S., and Bialek, W., “Emergence of long timescales and stereotyped behaviors in Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7286-9, 2011.
U. Klibaite, Berman, G. J., Cande, J., Stern, D. L., and Shaevitz, J. W., “An unsupervised method for quantifying the behavior of paired animals.”, Phys Biol, vol. 14, no. 1, p. 015006, 2017.
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “Dimensionality and dynamics in the behavior of C. elegans.”, PLoS Comput Biol, vol. 4, no. 4, p. e1000028, 2008.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Pohl, O., Silvestri, E., Viale, M., and Walczak, A. M., “Social interactions dominate speed control in poising natural flocks near criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 20, pp. 7212-7, 2014.
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.
Benchmarking
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.
Benzamides
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.
beta Catenin
S. Hayashi, Rubinfeld, B., Souza, B., Polakis, P., Wieschaus, E., and Levine, A. J., “A Drosophila homolog of the tumor suppressor gene adenomatous polyposis coli down-regulates beta-catenin but its zygotic expression is not essential for the regulation of Armadillo.”, Proc Natl Acad Sci U S A, vol. 94, no. 1, pp. 242-7, 1997.
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.
N. S. Tolwinski and Wieschaus, E., “A nuclear escort for beta-catenin.”, Nat Cell Biol, vol. 6, no. 7, pp. 579-80, 2004.
M. Peifer and Wieschaus, E., “The product of the Drosophila melanogaster segment polarity gene armadillo is highly conserved in sequence and expression in the housefly Musca domestica.”, J Mol Evol, vol. 36, no. 3, pp. 224-33, 1993.
Y. Ahmed, Hayashi, S., Levine, A., and Wieschaus, E., “Regulation of armadillo by a Drosophila APC inhibits neuronal apoptosis during retinal development.”, Cell, vol. 93, no. 7, pp. 1171-82, 1998.
L. Christiaen, Stolfi, A., Davidson, B., and Levine, M., “Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp.”, Dev Biol, vol. 328, no. 2, pp. 552-60, 2009.
N. S. Tolwinski and Wieschaus, E., “A nuclear function for armadillo/beta-catenin.”, PLoS Biol, vol. 2, no. 4, p. E95, 2004.
T. Schupbach and Wieschaus, E., “Probing for gene specificity in epithelial development.”, Int J Dev Biol, vol. 42, no. 3, pp. 249-55, 1998.
M. Peifer, McCrea, P. D., Green, K. J., Wieschaus, E., and Gumbiner, B. M., “The vertebrate adhesive junction proteins beta-catenin and plakoglobin and the Drosophila segment polarity gene armadillo form a multigene family with similar properties.”, J Cell Biol, vol. 118, no. 3, pp. 681-91, 1992.

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