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

Filters: First Letter Of Last Name is V  [Clear All Filters]
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Mice
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. 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. L. Olszewski, Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., “Host-parasite interactions revealed by Plasmodium falciparum metabolomics.”, Cell Host Microbe, vol. 5, no. 2, pp. 191-9, 2009.
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
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.
J. Vacher and Tilghman, S. M., “Dominant negative regulation of the mouse alpha-fetoprotein gene in adult liver.”, Science, vol. 250, no. 4988, pp. 1732-5, 1990.
C. D. van Raamsdonk and Tilghman, S. M., “Optimizing the detection of nascent transcripts by RNA fluorescence in situ hybridization.”, Nucleic Acids Res, vol. 29, no. 8, pp. E42-2, 2001.
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.
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.
K. K. Benson, Hu, W., Weller, A. H., Bennett, A. H., Chen, E. R., Khetarpal, S. A., Yoshino, S., Bone, W. P., Wang, L., Rabinowitz, J. D., Voight, B. F., and Soccio, R. E., “Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene.”, Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 2019.
Mice, Inbred C3H
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.
Mice, Inbred C57BL
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.
Mice, Inbred Strains
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.
Mice, Mutant Strains
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.
Mice, Transgenic
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.
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.
Microbiota
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.
Microfilament Proteins
B. Haarer, Viggiano, S., Hibbs, M. A., Troyanskaya, O. G., and Amberg, D. C., “Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.”, Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
Microscopy, Fluorescence
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
H. Y. Chang, Chi, J. - T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., and Brown, P. O., “Diversity, topographic differentiation, and positional memory in human fibroblasts.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12877-82, 2002.
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.
Middle Aged
S. C. Linn, West, R. B., Pollack, J. R., Zhu, S., Hernandez-Boussard, T., Nielsen, T. O., Rubin, B. P., Patel, iv, R., Goldblum, J. R., Siegmund, D., Botstein, D., Brown, P. O., C Gilks, B., and van de Rijn, M., “Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.”, Am J Pathol, vol. 163, no. 6, pp. 2383-95, 2003.
Mitotic Index
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.
Models, Animal
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
Models, Biological
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.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
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.
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.
Models, Chemical
C. L. Vizcarra, Zhang, N., Marshall, S. A., Wingreen, N. S., Zeng, C., and Mayo, S. L., “An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design.”, J Comput Chem, vol. 29, no. 7, pp. 1153-62, 2008.
J. D. Rabinowitz and Vastag, L., “Teaching the design principles of metabolism.”, Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 2012.
Models, Genetic
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.
Models, Neurological
I. Nemenman, Lewen, G. D., Bialek, W., and van Steveninck, R. R. de Ruyte, “Neural coding of natural stimuli: information at sub-millisecond resolution.”, PLoS Comput Biol, vol. 4, no. 3, p. e1000025, 2008.
Models, Statistical
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.
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.
Models, Theoretical
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.
Molecular Sequence Data
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.
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.
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.
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.
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
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.
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
Morphogenesis
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
Motion Perception
I. Nemenman, Lewen, G. D., Bialek, W., and van Steveninck, R. R. de Ruyte, “Neural coding of natural stimuli: information at sub-millisecond resolution.”, PLoS Comput Biol, vol. 4, no. 3, p. e1000025, 2008.
Movement
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.
Mucin-1
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
Multifactorial Inheritance
B. Haarer, Viggiano, S., Hibbs, M. A., Troyanskaya, O. G., and Amberg, D. C., “Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.”, Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
Multigene Family
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
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.
N. Slavov, Airoldi, E. M., van Oudenaarden, A., and Botstein, D., “A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.”, Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
Muscle Cells
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
Mushroom Bodies
L. Zwarts, Broeck, L. Vanden, Cappuyns, E., Ayroles, J. F., Magwire, M. M., Vulsteke, V., Clements, J., Mackay, T. F. C., and Callaerts, P., “The genetic basis of natural variation in mushroom body size in Drosophila melanogaster.”, Nat Commun, vol. 6, p. 10115, 2015.
Mutation
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.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., “The genetic landscape of a cell.”, Science, vol. 327, no. 5964, pp. 425-31, 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.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., “The genetic landscape of a cell.”, Science, vol. 327, no. 5964, pp. 425-31, 2010.
P. A. Gibney, Schieler, A., Chen, J. C., Bacha-Hummel, J. M., Botstein, M., Volpe, M., Silverman, S. J., Xu, Y., Bennett, B. D., Rabinowitz, J. D., and Botstein, D., “Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast.”, Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 2018.
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.
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.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., “The genetic landscape of a cell.”, Science, vol. 327, no. 5964, pp. 425-31, 2010.
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.
Myocardium
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
Myocytes, Cardiac
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
NAD
S. L. Grady, Hwang, J., Vastag, L., Rabinowitz, J. D., and Shenk, T., “Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase.”, J Virol, vol. 86, no. 15, pp. 8259-68, 2012.
National Institutes of Health (U.S.)
W. R. Uhlmann, Bennett, R., Botkin, J. R., Botstein, D., Boughman, J. A., Chakravarti, A., Clayton, E. Wright, Kahn, J., Koenig, B., Murray, T. H., Olson, M. V., Rowley, J., Terry, S., and Valle, D., “Planning the genome institute's future.”, Science, vol. 299, no. 5612, p. 1515; author reply 1515, 2003.
Neoplasm Invasiveness
V. N. Kristensen, Vaske, C. J., Ursini-Siegel, J., Van Loo, P., Nordgard, S. H., Sachidanandam, R., Sørlie, T., Wärnberg, F., Haakensen, V. D., Helland, Å., Naume, B., Perou, C. M., Haussler, D., Troyanskaya, O. G., and Børresen-Dale, A. - L., “Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
V. N. Kristensen, Vaske, C. J., Ursini-Siegel, J., Van Loo, P., Nordgard, S. H., Sachidanandam, R., Sørlie, T., Wärnberg, F., Haakensen, V. D., Helland, Å., Naume, B., Perou, C. M., Haussler, D., Troyanskaya, O. G., and Børresen-Dale, A. - L., “Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
H. Y. Chang, Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J. - T., van de Rijn, M., Botstein, D., and Brown, P. O., “Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds.”, PLoS Biol, vol. 2, no. 2, p. E7, 2004.
Neoplasm Proteins
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Neoplasm Staging
M. van de Rijn, Perou, C. M., Tibshirani, R., Haas, P., Kallioniemi, O., Kononen, J., Torhorst, J., Sauter, G., Zuber, M., Köchli, O. R., Mross, F., Dieterich, H., Seitz, R., Ross, D., Botstein, D., and Brown, P., “Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome.”, Am J Pathol, vol. 161, no. 6, pp. 1991-6, 2002.
Neoplasms
J. D. Rabinowitz and Vastag, L., “Teaching the design principles of metabolism.”, Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 2012.
H. Y. Chang, Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J. - T., van de Rijn, M., Botstein, D., and Brown, P. O., “Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds.”, PLoS Biol, vol. 2, no. 2, p. E7, 2004.
J. R. Pollack, van de Rijn, M., and Botstein, D., “Challenges in developing a molecular characterization of cancer.”, Semin Oncol, vol. 29, no. 3, pp. 280-5, 2002.
Neurons
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.
Nuclear Proteins
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. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
J. Vacher and Tilghman, S. M., “Dominant negative regulation of the mouse alpha-fetoprotein gene in adult liver.”, Science, vol. 250, no. 4988, pp. 1732-5, 1990.
Nucleic Acid Conformation
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.
Nucleic Acid Hybridization
S. C. Linn, West, R. B., Pollack, J. R., Zhu, S., Hernandez-Boussard, T., Nielsen, T. O., Rubin, B. P., Patel, iv, R., Goldblum, J. R., Siegmund, D., Botstein, D., Brown, P. O., C Gilks, B., and van de Rijn, M., “Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.”, Am J Pathol, vol. 163, no. 6, pp. 2383-95, 2003.
Nucleotides
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
Obesity
K. K. Benson, Hu, W., Weller, A. H., Bennett, A. H., Chen, E. R., Khetarpal, S. A., Yoshino, S., Bone, W. P., Wang, L., Rabinowitz, J. D., Voight, B. F., and Soccio, R. E., “Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene.”, Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 2019.
Oligonucleotide Array Sequence Analysis
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
M. van de Rijn, Perou, C. M., Tibshirani, R., Haas, P., Kallioniemi, O., Kononen, J., Torhorst, J., Sauter, G., Zuber, M., Köchli, O. R., Mross, F., Dieterich, H., Seitz, R., Ross, D., Botstein, D., and Brown, P., “Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome.”, Am J Pathol, vol. 161, no. 6, pp. 1991-6, 2002.
X. Chen, Cheung, S. Tim, So, S., Fan, S. Tat, Barry, C., Higgins, J., Lai, K. - M., Ji, J., Dudoit, S., Ng, I. O. L., van de Rijn, M., Botstein, D., and Brown, P. O., “Gene expression patterns in human liver cancers.”, Mol Biol Cell, vol. 13, no. 6, pp. 1929-39, 2002.
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.
R. Shyamsundar, Kim, Y. H., Higgins, J. P., Montgomery, K., Jorden, M., Sethuraman, A., van de Rijn, M., Botstein, D., Brown, P. O., and Pollack, J. R., “A DNA microarray survey of gene expression in normal human tissues.”, Genome Biol, vol. 6, no. 3, p. R22, 2005.
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
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.
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
T. O. Nielsen, West, R. B., Linn, S. C., Alter, O., Knowling, M. A., O'Connell, J. X., Zhu, S., Fero, M., Sherlock, G., Pollack, J. R., Brown, P. O., Botstein, D., and van de Rijn, M., “Molecular characterisation of soft tissue tumours: a gene expression study.”, Lancet, vol. 359, no. 9314, pp. 1301-7, 2002.
H. Y. Chang, Chi, J. - T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., and Brown, P. O., “Diversity, topographic differentiation, and positional memory in human fibroblasts.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12877-82, 2002.
S. C. Linn, West, R. B., Pollack, J. R., Zhu, S., Hernandez-Boussard, T., Nielsen, T. O., Rubin, B. P., Patel, iv, R., Goldblum, J. R., Siegmund, D., Botstein, D., Brown, P. O., C Gilks, B., and van de Rijn, M., “Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.”, Am J Pathol, vol. 163, no. 6, pp. 2383-95, 2003.
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.
N. Slavov, Airoldi, E. M., van Oudenaarden, A., and Botstein, D., “A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.”, Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
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.
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.
J. R. Pollack, van de Rijn, M., and Botstein, D., “Challenges in developing a molecular characterization of cancer.”, Semin Oncol, vol. 29, no. 3, pp. 280-5, 2002.
Oligonucleotides, Antisense
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
Oncogene Proteins, Fusion
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.
Opossums
M. J. O'Neill, Ingram, R. S., Vrana, P. B., and Tilghman, S. M., “Allelic expression of IGF2 in marsupials and birds.”, Dev Genes Evol, vol. 210, no. 1, pp. 18-20, 2000.
Ornithine
K. L. Olszewski, Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., “Host-parasite interactions revealed by Plasmodium falciparum metabolomics.”, Cell Host Microbe, vol. 5, no. 2, pp. 191-9, 2009.
Oscillometry
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.
Ovarian Neoplasms
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Ovum
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.
Oxygen Consumption
N. Slavov, Airoldi, E. M., van Oudenaarden, A., and Botstein, D., “A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.”, Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
Paired Box Transcription Factors
C. D. van Raamsdonk and Tilghman, S. M., “Optimizing the detection of nascent transcripts by RNA fluorescence in situ hybridization.”, Nucleic Acids Res, vol. 29, no. 8, pp. E42-2, 2001.
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.
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Pan troglodytes
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
Paraffin Embedding
S. C. Linn, West, R. B., Pollack, J. R., Zhu, S., Hernandez-Boussard, T., Nielsen, T. O., Rubin, B. P., Patel, iv, R., Goldblum, J. R., Siegmund, D., Botstein, D., Brown, P. O., C Gilks, B., and van de Rijn, M., “Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.”, Am J Pathol, vol. 163, no. 6, pp. 2383-95, 2003.
Peptides
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
Peptidoglycan
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.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
Periplasm
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.
Peromyscus
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.
P. B. Vrana, Fossella, J. A., Matteson, P., del Rio, T., O'Neill, M. J., and Tilghman, S. M., “Genetic and epigenetic incompatibilities underlie hybrid dysgenesis in Peromyscus.”, Nat Genet, vol. 25, no. 1, pp. 120-4, 2000.
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
Phenotype
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.
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.
H. Y. Chang, Chi, J. - T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., and Brown, P. O., “Diversity, topographic differentiation, and positional memory in human fibroblasts.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12877-82, 2002.
B. Haarer, Viggiano, S., Hibbs, M. A., Troyanskaya, O. G., and Amberg, D. C., “Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.”, Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
K. K. Benson, Hu, W., Weller, A. H., Bennett, A. H., Chen, E. R., Khetarpal, S. A., Yoshino, S., Bone, W. P., Wang, L., Rabinowitz, J. D., Voight, B. F., and Soccio, R. E., “Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene.”, Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 2019.
Phosphoric Monoester Hydrolases
O. Oleksiuk, Jakovljevic, V., Vladimirov, N., Carvalho, R., Paster, E., Ryu, W. S., Meir, Y., Wingreen, N. S., Kollmann, M., and Sourjik, V., “Thermal robustness of signaling in bacterial chemotaxis.”, Cell, vol. 145, no. 2, pp. 312-21, 2011.
Phosphotransferases
O. Oleksiuk, Jakovljevic, V., Vladimirov, N., Carvalho, R., Paster, E., Ryu, W. S., Meir, Y., Wingreen, N. S., Kollmann, M., and Sourjik, V., “Thermal robustness of signaling in bacterial chemotaxis.”, Cell, vol. 145, no. 2, pp. 312-21, 2011.
Photic Stimulation
I. Nemenman, Lewen, G. D., Bialek, W., and van Steveninck, R. R. de Ruyte, “Neural coding of natural stimuli: information at sub-millisecond resolution.”, PLoS Comput Biol, vol. 4, no. 3, p. e1000025, 2008.
Photoreceptor Cells
I. Nemenman, Lewen, G. D., Bialek, W., and van Steveninck, R. R. de Ruyte, “Neural coding of natural stimuli: information at sub-millisecond resolution.”, PLoS Comput Biol, vol. 4, no. 3, p. e1000025, 2008.
Phylogeny
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.
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
Placenta
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
Placental Lactogen
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
Plasmodium berghei
K. L. Olszewski, Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., “Host-parasite interactions revealed by Plasmodium falciparum metabolomics.”, Cell Host Microbe, vol. 5, no. 2, pp. 191-9, 2009.
Plasmodium falciparum
K. L. Olszewski, Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., “Host-parasite interactions revealed by Plasmodium falciparum metabolomics.”, Cell Host Microbe, vol. 5, no. 2, pp. 191-9, 2009.
K. L. Olszewski, Mather, M. W., Morrisey, J. M., Garcia, B. A., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., “Branched tricarboxylic acid metabolism in Plasmodium falciparum.”, Nature, vol. 466, no. 7307, pp. 774-8, 2010.
Poisson Distribution
C. L. Vizcarra, Zhang, N., Marshall, S. A., Wingreen, N. S., Zeng, C., and Mayo, S. L., “An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design.”, J Comput Chem, vol. 29, no. 7, pp. 1153-62, 2008.
Pollination
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
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.
Poly(ADP-ribose) Polymerases
S. L. Grady, Hwang, J., Vastag, L., Rabinowitz, J. D., and Shenk, T., “Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase.”, J Virol, vol. 86, no. 15, pp. 8259-68, 2012.
Polycomb Repressive Complex 1
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.
Polymorphism, Single Nucleotide
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
Pongo
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
PPAR gamma
K. K. Benson, Hu, W., Weller, A. H., Bennett, A. H., Chen, E. R., Khetarpal, S. A., Yoshino, S., Bone, W. P., Wang, L., Rabinowitz, J. D., Voight, B. F., and Soccio, R. E., “Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene.”, Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 2019.
Pregnancy
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. 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.
Primary Cell Culture
N. Slavov, Airoldi, E. M., van Oudenaarden, A., and Botstein, D., “A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.”, Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
Prognosis
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
M. van de Rijn, Perou, C. M., Tibshirani, R., Haas, P., Kallioniemi, O., Kononen, J., Torhorst, J., Sauter, G., Zuber, M., Köchli, O. R., Mross, F., Dieterich, H., Seitz, R., Ross, D., Botstein, D., and Brown, P., “Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome.”, Am J Pathol, vol. 161, no. 6, pp. 1991-6, 2002.
V. N. Kristensen, Vaske, C. J., Ursini-Siegel, J., Van Loo, P., Nordgard, S. H., Sachidanandam, R., Sørlie, T., Wärnberg, F., Haakensen, V. D., Helland, Å., Naume, B., Perou, C. M., Haussler, D., Troyanskaya, O. G., and Børresen-Dale, A. - L., “Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
H. Y. Chang, Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J. - T., van de Rijn, M., Botstein, D., and Brown, P. O., “Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds.”, PLoS Biol, vol. 2, no. 2, p. E7, 2004.
V. N. Kristensen, Vaske, C. J., Ursini-Siegel, J., Van Loo, P., Nordgard, S. H., Sachidanandam, R., Sørlie, T., Wärnberg, F., Haakensen, V. D., Helland, Å., Naume, B., Perou, C. M., Haussler, D., Troyanskaya, O. G., and Børresen-Dale, A. - L., “Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
Prostatic Neoplasms
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
Protein Interaction Mapping
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., “The genetic landscape of a cell.”, Science, vol. 327, no. 5964, pp. 425-31, 2010.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., “The genetic landscape of a cell.”, Science, vol. 327, no. 5964, pp. 425-31, 2010.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., “The genetic landscape of a cell.”, Science, vol. 327, no. 5964, pp. 425-31, 2010.
Protein Kinase Inhibitors
L. J. Terry, Vastag, L., Rabinowitz, J. D., and Shenk, T., “Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 3071-6, 2012.
Protein Structure, Tertiary
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.
Proteins
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
C. L. Vizcarra, Zhang, N., Marshall, S. A., Wingreen, N. S., Zeng, C., and Mayo, S. L., “An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design.”, J Comput Chem, vol. 29, no. 7, pp. 1153-62, 2008.
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.
Proteolysis
S. L. Grady, Hwang, J., Vastag, L., Rabinowitz, J. D., and Shenk, T., “Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase.”, J Virol, vol. 86, no. 15, pp. 8259-68, 2012.
Proteomics
L. J. Terry, Vastag, L., Rabinowitz, J. D., and Shenk, T., “Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 3071-6, 2012.
Proto-Oncogene Proteins
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. 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.
Proto-Oncogene Proteins c-raf
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.
Protozoan Proteins
K. L. Olszewski, Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., “Host-parasite interactions revealed by Plasmodium falciparum metabolomics.”, Cell Host Microbe, vol. 5, no. 2, pp. 191-9, 2009.
Pyrimidines
L. Vastag, Koyuncu, E., Grady, S. L., Shenk, T. E., and Rabinowitz, J. D., “Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism.”, PLoS Pathog, vol. 7, no. 7, p. e1002124, 2011.
Pyruvate Carboxylase
L. Vastag, Koyuncu, E., Grady, S. L., Shenk, T. E., and Rabinowitz, J. D., “Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism.”, PLoS Pathog, vol. 7, no. 7, p. e1002124, 2011.
Pyruvate Kinase
J. D. Rabinowitz and Vastag, L., “Teaching the design principles of metabolism.”, Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 2012.
Receptor Protein-Tyrosine Kinases
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.
Receptor, Epidermal Growth Factor
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.
Receptors, Estrogen
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Recombination, Genetic
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
Recurrence
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
Repressor Proteins
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.
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.
C. D. van Raamsdonk and Tilghman, S. M., “Optimizing the detection of nascent transcripts by RNA fluorescence in situ hybridization.”, Nucleic Acids Res, vol. 29, no. 8, pp. E42-2, 2001.
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.
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.
Reproducibility of Results
V. N. Kristensen, Vaske, C. J., Ursini-Siegel, J., Van Loo, P., Nordgard, S. H., Sachidanandam, R., Sørlie, T., Wärnberg, F., Haakensen, V. D., Helland, Å., Naume, B., Perou, C. M., Haussler, D., Troyanskaya, O. G., and Børresen-Dale, A. - L., “Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
C. L. Vizcarra, Zhang, N., Marshall, S. A., Wingreen, N. S., Zeng, C., and Mayo, S. L., “An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design.”, J Comput Chem, vol. 29, no. 7, pp. 1153-62, 2008.
V. N. Kristensen, Vaske, C. J., Ursini-Siegel, J., Van Loo, P., Nordgard, S. H., Sachidanandam, R., Sørlie, T., Wärnberg, F., Haakensen, V. D., Helland, Å., Naume, B., Perou, C. M., Haussler, D., Troyanskaya, O. G., and Børresen-Dale, A. - L., “Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
Research
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
Research Design
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
Research Personnel
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
Retinal Ganglion Cells
C. D. van Raamsdonk and Tilghman, S. M., “Optimizing the detection of nascent transcripts by RNA fluorescence in situ hybridization.”, Nucleic Acids Res, vol. 29, no. 8, pp. E42-2, 2001.
Retroelements
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.
Retroviridae
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.
Ribosomes
B. Haarer, Viggiano, S., Hibbs, M. A., Troyanskaya, O. G., and Amberg, D. C., “Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.”, Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
Risk Factors
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
RNA
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.
RNA Interference
L. Zwarts, Broeck, L. Vanden, Cappuyns, E., Ayroles, J. F., Magwire, M. M., Vulsteke, V., Clements, J., Mackay, T. F. C., and Callaerts, P., “The genetic basis of natural variation in mushroom body size in Drosophila melanogaster.”, Nat Commun, vol. 6, p. 10115, 2015.
RNA Processing, Post-Transcriptional
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.
RNA, Messenger
R. Shyamsundar, Kim, Y. H., Higgins, J. P., Montgomery, K., Jorden, M., Sethuraman, A., van de Rijn, M., Botstein, D., Brown, P. O., and Pollack, J. R., “A DNA microarray survey of gene expression in normal human tissues.”, Genome Biol, vol. 6, no. 3, p. R22, 2005.

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