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3' Flanking Region
E. Semenova, Wang, X. F., Jablonski, M. M., Levorse, J., and Tilghman, S. M., “An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina.”, Hum Mol Genet, vol. 12, no. 11, pp. 1301-12, 2003.
3' Untranslated Regions
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.
V. Hilgers, Lemke, S. B., and Levine, M., “ELAV mediates 3' UTR extension in the Drosophila nervous system.”, Genes Dev, vol. 26, no. 20, pp. 2259-64, 2012.
3',5'-Cyclic-AMP Phosphodiesterases
T. Gregor, Fujimoto, K., Masaki, N., and Sawai, S., “The onset of collective behavior in social amoebae.”, Science, vol. 328, no. 5981, pp. 1021-5, 2010.
3T3 Cells
S. M. Tilghman, “DNA methylation: a phoenix rises.”, Proc Natl Acad Sci U S A, vol. 90, no. 19, pp. 8761-2, 1993.
4-Butyrolactone
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.
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.
K. C. Mok, Wingreen, N. S., and Bassler, B. L., “Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression.”, EMBO J, vol. 22, no. 4, pp. 870-81, 2003.
5' Flanking Region
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.
5' Untranslated Regions
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase
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.
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.
Abdomen
J. Mohler and Wieschaus, E. F., “Dominant maternal-effect mutations of Drosophila melanogaster causing the production of double-abdomen embryos.”, Genetics, vol. 112, no. 4, pp. 803-22, 1986.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
E. Wieschaus, Nusslein-Volhard, C., and Kluding, H., “Krüppel, a gene whose activity is required early in the zygotic genome for normal embryonic segmentation.”, Dev Biol, vol. 104, no. 1, pp. 172-86, 1984.
H. M. Frydman, Li, J. M., Robson, D. N., and Wieschaus, E., “Somatic stem cell niche tropism in Wolbachia.”, Nature, vol. 441, no. 7092, pp. 509-12, 2006.
E. Wieschaus, “Cell lineage relationships in the Drosophila embryo.”, Results Probl Cell Differ, vol. 9, pp. 97-118, 1978.
E. Wieschaus and Gehring, W., “Clonal analysis of primordial disc cells in the early embryo of Drosophila melanogaster.”, Dev Biol, vol. 50, no. 2, pp. 249-63, 1976.
Abnormalities, Multiple
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.
Absorption
J. D. Rabinowitz, Lloyd, P. M., Munzar, P., Myers, D. J., Cross, S., Damani, R., Quintana, R., Spyker, D. A., Soni, P., and Cassella, J. V., “Ultra-fast absorption of amorphous pure drug aerosols via deep lung inhalation.”, J Pharm Sci, vol. 95, no. 11, pp. 2438-51, 2006.
Abstracting and Indexing as Topic
E. I. Boyle, Weng, S., Gollub, J., Jin, H., Botstein, D., J Cherry, M., and Sherlock, G., “GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.”, Bioinformatics, vol. 20, no. 18, pp. 3710-5, 2004.
Access to Information
D. Botstein, “It's the data!”, Mol Biol Cell, vol. 21, no. 1, pp. 4-6, 2010.
Acetates
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
B. D. Bennett, Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., and Rabinowitz, J. D., “Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.”, Nat Chem Biol, vol. 5, no. 8, pp. 593-9, 2009.
Acetolactate Synthase
M. Louis Reaves and Rabinowitz, J. D., “Characteristic phenotypes associated with ptsN-null mutants in Escherichia coli K-12 are absent in strains with functional ilvG.”, J Bacteriol, vol. 193, no. 18, pp. 4576-81, 2011.
Acetone
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
Acetonitriles
J. D. Rabinowitz and Kimball, E., “Acidic acetonitrile for cellular metabolome extraction from Escherichia coli.”, Anal Chem, vol. 79, no. 16, pp. 6167-73, 2007.
Acetyl Coenzyme A
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.
Acetylation
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.
W. Bailis, Shyer, J. A., Zhao, J., Canaveras, J. Carlos Gar, Khazal, F. J. Al, Qu, R., Steach, H. R., Bielecki, P., Khan, O., Jackson, R., Kluger, Y., Maher, L. J., Rabinowitz, J., Craft, J., and Flavell, R. A., “Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function.”, Nature, vol. 571, no. 7765, pp. 403-407, 2019.
F. Markowetz, Mulder, K. W., Airoldi, E. M., Lemischka, I. R., and Troyanskaya, O. G., “Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells.”, PLoS Comput Biol, vol. 6, no. 12, p. e1001034, 2010.
Acids
H. Goodarzi, Bennett, B. D., Amini, S., Reaves, M. L., Hottes, A. K., Rabinowitz, J. D., and Tavazoie, S., “Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli.”, Mol Syst Biol, vol. 6, p. 378, 2010.
Acoustic Stimulation
T. Sharpee, Rust, N. C., and Bialek, W., “Analyzing neural responses to natural signals: maximally informative dimensions.”, Neural Comput, vol. 16, no. 2, pp. 223-50, 2004.
Actin Cytoskeleton
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.
M. A. Postner and Wieschaus, E. F., “The nullo protein is a component of the actin-myosin network that mediates cellularization in Drosophila melanogaster embryos.”, J Cell Sci, vol. 107 ( Pt 7), pp. 1863-73, 1994.
J. H. Thomas and Wieschaus, E., “src64 and tec29 are required for microfilament contraction during Drosophila cellularization.”, Development, vol. 131, no. 4, pp. 863-71, 2004.
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.
Actin Depolymerizing Factors
M. A. Postner, Miller, K. G., and Wieschaus, E. F., “Maternal effect mutations of the sponge locus affect actin cytoskeletal rearrangements in Drosophila melanogaster embryos.”, J Cell Biol, vol. 119, no. 5, pp. 1205-18, 1992.
Actin-Related Protein 2
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.
Actin-Related Protein 3
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.
Actins
C. Hunter, Sung, P., Schejter, E. D., and Wieschaus, E., “Conserved domains of the Nullo protein required for cell-surface localization and formation of adherens junctions.”, Mol Biol Cell, vol. 13, no. 1, pp. 146-57, 2002.
A. Marie Sokac and Wieschaus, E., “Zygotically controlled F-actin establishes cortical compartments to stabilize furrows during Drosophila cellularization.”, J Cell Sci, vol. 121, no. Pt 11, pp. 1815-24, 2008.
A. C. Martin, Kaschube, M., and Wieschaus, E. F., “Pulsed contractions of an actin-myosin network drive apical constriction.”, Nature, vol. 457, no. 7228, pp. 495-9, 2009.
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.
M. A. Postner and Wieschaus, E. F., “The nullo protein is a component of the actin-myosin network that mediates cellularization in Drosophila melanogaster embryos.”, J Cell Sci, vol. 107 ( Pt 7), pp. 1863-73, 1994.
J. W. Shaevitz and Fletcher, D. A., “Curvature and torsion in growing actin networks.”, Phys Biol, vol. 5, no. 2, p. 026006, 2008.
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.
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.
E. D. Schejter, Rose, L. S., Postner, M. A., and Wieschaus, E., “Role of the zygotic genome in the restructuring of the actin cytoskeleton at the cycle-14 transition during Drosophila embryogenesis.”, Cold Spring Harb Symp Quant Biol, vol. 57, pp. 653-9, 1992.
A. Marie Sokac and Wieschaus, E., “Local actin-dependent endocytosis is zygotically controlled to initiate Drosophila cellularization.”, Dev Cell, vol. 14, no. 5, pp. 775-86, 2008.
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.
M. J. Rosenbluth, Crow, A., Shaevitz, J. W., and Fletcher, D. A., “Slow stress propagation in adherent cells.”, Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
L. Simpson and Wieschaus, E., “Zygotic activity of the nullo locus is required to stabilize the actin-myosin network during cellularization in Drosophila.”, Development, vol. 110, no. 3, pp. 851-63, 1990.
J. H. Thomas and Wieschaus, E., “src64 and tec29 are required for microfilament contraction during Drosophila cellularization.”, Development, vol. 131, no. 4, pp. 863-71, 2004.
R. E. Dawes-Hoang, Parmar, K. M., Christiansen, A. E., Phelps, C. B., Brand, A. H., and Wieschaus, E. F., “folded gastrulation, cell shape change and the control of myosin localization.”, Development, vol. 132, no. 18, pp. 4165-78, 2005.
Y. - C. Wang, Khan, Z., and Wieschaus, E. F., “Distinct Rap1 activity states control the extent of epithelial invagination via α-catenin.”, Dev Cell, vol. 25, no. 3, pp. 299-309, 2013.
W. Shi, Peyrot, S. M., Munro, E., and Levine, M., “FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole.”, Development, vol. 136, no. 1, pp. 23-8, 2009.
J. W. Shaevitz and Gitai, Z., “The structure and function of bacterial actin homologs.”, Cold Spring Harb Perspect Biol, vol. 2, no. 9, p. a000364, 2010.
J. W. Shaevitz and Fletcher, D. A., “Load fluctuations drive actin network growth.”, Proc Natl Acad Sci U S A, vol. 104, no. 40, pp. 15688-92, 2007.
Action Potentials
T. Sharpee, Rust, N. C., and Bialek, W., “Analyzing neural responses to natural signals: maximally informative dimensions.”, Neural Comput, vol. 16, no. 2, pp. 223-50, 2004.
E. Schneidman, Puchalla, J. L., Segev, R., Harris, R. A., Bialek, W., and Berry, M. J., “Synergy from silence in a combinatorial neural code.”, J Neurosci, vol. 31, no. 44, pp. 15732-41, 2011.
T. L. Adelman, Bialek, W., and Olberg, R. M., “The information content of receptive fields.”, Neuron, vol. 40, no. 4, pp. 823-33, 2003.
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.
E. Schneidman, Berry, M. J., Segev, R., and Bialek, W., “Weak pairwise correlations imply strongly correlated network states in a neural population.”, Nature, vol. 440, no. 7087, pp. 1007-12, 2006.
G. Tkačik, Marre, O., Amodei, D., Schneidman, E., Bialek, W., and Berry, M. J., “Searching for collective behavior in a large network of sensory neurons.”, PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
L. C. Osborne, Bialek, W., and Lisberger, S. G., “Time course of information about motion direction in visual area MT of macaque monkeys.”, J Neurosci, vol. 24, no. 13, pp. 3210-22, 2004.
E. Schneidman, Bialek, W., and Berry, M. J., “Synergy, redundancy, and independence in population codes.”, J Neurosci, vol. 23, no. 37, pp. 11539-53, 2003.
B. Agüera y Arcas, Fairhall, A. L., and Bialek, W., “Computation in a single neuron: Hodgkin and Huxley revisited.”, Neural Comput, vol. 15, no. 8, pp. 1715-49, 2003.
Active Transport, Cell Nucleus
N. S. Tolwinski, Wehrli, M., Rives, A., Erdeniz, N., DiNardo, S., and Wieschaus, E., “Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity.”, Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
N. S. Tolwinski and Wieschaus, E., “Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan.”, Development, vol. 128, no. 11, pp. 2107-17, 2001.
C. Sample and Shvartsman, S. Y., “Multiscale modeling of diffusion in the early Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 107, no. 22, pp. 10092-6, 2010.
O. Grimm and Wieschaus, E., “The Bicoid gradient is shaped independently of nuclei.”, Development, vol. 137, no. 17, pp. 2857-62, 2010.
N. S. Tolwinski and Wieschaus, E., “A nuclear escort for beta-catenin.”, Nat Cell Biol, vol. 6, no. 7, pp. 579-80, 2004.
Actomyosin
A. C. Martin, Gelbart, M., Fernandez-Gonzalez, R., Kaschube, M., and Wieschaus, E. F., “Integration of contractile forces during tissue invagination.”, J Cell Biol, vol. 188, no. 5, pp. 735-49, 2010.
A. C. Martin and Wieschaus, E. F., “Tensions divide.”, Nat Cell Biol, vol. 12, no. 1, pp. 5-7, 2010.
Acyl-Butyrolactones
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.
Adaptation, Biological
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. B. Wolf and Akey, J. M., “Outstanding questions in the study of archaic hominin admixture.”, PLoS Genet, vol. 14, no. 5, p. e1007349, 2018.
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., “Parallel molecular evolution in an herbivore community.”, Science, vol. 337, no. 6102, pp. 1634-7, 2012.
G. I. Lang, Botstein, D., and Desai, M. M., “Genetic variation and the fate of beneficial mutations in asexual populations.”, Genetics, vol. 188, no. 3, pp. 647-61, 2011.
Adaptation, Physiological
H. Goodarzi, Bennett, B. D., Amini, S., Reaves, M. L., Hottes, A. K., Rabinowitz, J. D., and Tavazoie, S., “Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli.”, Mol Syst Biol, vol. 6, p. 378, 2010.
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
S. Neumann, Vladimirov, N., Krembel, A. K., Wingreen, N. S., and Sourjik, V., “Imprecision of adaptation in Escherichia coli chemotaxis.”, PLoS One, vol. 9, no. 1, p. e84904, 2014.
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.
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
D. Gresham, Desai, M. M., Tucker, C. M., Jenq, H. T., Pai, D. A., Ward, A., DeSevo, C. G., Botstein, D., and Dunham, M. J., “The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.”, PLoS Genet, vol. 4, no. 12, p. e1000303, 2008.
A. Z. Welch, Gibney, P. A., Botstein, D., and Koshland, D. E., “TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 24, no. 2, pp. 115-28, 2013.
T. Pilizota and Shaevitz, J. W., “Fast, multiphase volume adaptation to hyperosmotic shock by Escherichia coli.”, PLoS One, vol. 7, no. 4, p. e35205, 2012.
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.
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.
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.
G. I. Lang, Rice, D. P., Hickman, M. J., Sodergren, E., Weinstock, G. M., Botstein, D., and Desai, M. M., “Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.”, Nature, vol. 500, no. 7464, pp. 571-4, 2013.
Adaptor Protein Complex 3
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.
Adaptor Protein Complex beta Subunits
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.
Adaptor Proteins, Signal Transducing
W. Shi, Peyrot, S. M., Munro, E., and Levine, M., “FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole.”, Development, vol. 136, no. 1, pp. 23-8, 2009.
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.
N. S. Tolwinski, Wehrli, M., Rives, A., Erdeniz, N., DiNardo, S., and Wieschaus, E., “Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity.”, Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
N. S. Tolwinski and Wieschaus, E., “Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan.”, Development, vol. 128, no. 11, pp. 2107-17, 2001.
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Adenine Nucleotides
Q. Bao, Lu, W., Rabinowitz, J. D., and Shi, Y., “Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1.”, Mol Cell, vol. 25, no. 2, pp. 181-92, 2007.
Adenocarcinoma
J. Isaac Murray, Whitfield, M. L., Trinklein, N. D., Myers, R. M., Brown, P. O., and Botstein, D., “Diverse and specific gene expression responses to stresses in cultured human cells.”, Mol Biol Cell, vol. 15, no. 5, pp. 2361-74, 2004.
S. Y. Leung, Chen, X., Chu, K. M., Yuen, S. T., Mathy, J., Ji, J., S Y Chan, A., Li, R., Law, S., Troyanskaya, O. G., Tu, I. - P., Wong, J., So, S., Botstein, D., and Brown, P. O., “Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.”, Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16203-8, 2002.
H. Zhao, Whitfield, M. L., Xu, T., Botstein, D., and Brooks, J. D., “Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells.”, Mol Biol Cell, vol. 15, no. 2, pp. 506-19, 2004.
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.
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.
M. E. Garber, Troyanskaya, O. G., Schluens, K., Petersen, S., Thaesler, Z., Pacyna-Gengelbach, M., van de Rijn, M., Rosen, G. D., Perou, C. M., Whyte, R. I., Altman, R. B., Brown, P. O., Botstein, D., and Petersen, I., “Diversity of gene expression in adenocarcinoma of the lung.”, Proc Natl Acad Sci U S A, vol. 98, no. 24, pp. 13784-9, 2001.
Adenocarcinoma, Clear Cell
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.
Adenomatous Polyposis Coli
D. Munro, Ghersi, D., and Singh, M., “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
Adenomatous Polyposis Coli Protein
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.
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.
Adenosine Triphosphatases
R. V. Kulkarni, Huang, K. Casey, Kloster, M., and Wingreen, N. S., “Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules.”, Phys Rev Lett, vol. 93, no. 22, p. 228103, 2004.
K. Casey Huang, Meir, Y., and Wingreen, N. S., “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”, Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
Adenosine Triphosphate
M. Sun, Wartel, M., Cascales, E., Shaevitz, J. W., and Mignot, T., “Motor-driven intracellular transport powers bacterial gliding motility.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7559-64, 2011.
K. Casey Huang, Meir, Y., and Wingreen, N. S., “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”, Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
J. D. Rabinowitz, Hsiao, J. J., Gryncel, K. R., Kantrowitz, E. R., Feng, X. - J., Li, G., and Rabitz, H., “Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase.”, Biochemistry, vol. 47, no. 21, pp. 5881-8, 2008.
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. M. Block, Asbury, C. L., Shaevitz, J. W., and Lang, M. J., “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
J. Fan, Kamphorst, J. J., Mathew, R., Chung, M. K., White, E., Shlomi, T., and Rabinowitz, J. D., “Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia.”, Mol Syst Biol, vol. 9, p. 712, 2013.
W. Lu, Su, X., Klein, M. S., Lewis, I. A., Fiehn, O., and Rabinowitz, J. D., “Metabolite Measurement: Pitfalls to Avoid and Practices to Follow.”, Annu Rev Biochem, vol. 86, pp. 277-304, 2017.
Adenylate Cyclase
T. Gregor, Fujimoto, K., Masaki, N., and Sawai, S., “The onset of collective behavior in social amoebae.”, Science, vol. 328, no. 5981, pp. 1021-5, 2010.
Adherens Junctions
R. E. Dawes-Hoang, Parmar, K. M., Christiansen, A. E., Phelps, C. B., Brand, A. H., and Wieschaus, E. F., “folded gastrulation, cell shape change and the control of myosin localization.”, Development, vol. 132, no. 18, pp. 4165-78, 2005.
A. C. Martin, Gelbart, M., Fernandez-Gonzalez, R., Kaschube, M., and Wieschaus, E. F., “Integration of contractile forces during tissue invagination.”, J Cell Biol, vol. 188, no. 5, pp. 735-49, 2010.
A. C. Martin, Kaschube, M., and Wieschaus, E. F., “Pulsed contractions of an actin-myosin network drive apical constriction.”, Nature, vol. 457, no. 7228, pp. 495-9, 2009.
C. Hunter, Sung, P., Schejter, E. D., and Wieschaus, E., “Conserved domains of the Nullo protein required for cell-surface localization and formation of adherens junctions.”, Mol Biol Cell, vol. 13, no. 1, pp. 146-57, 2002.
Y. - C. Wang, Khan, Z., Kaschube, M., and Wieschaus, E. F., “Differential positioning of adherens junctions is associated with initiation of epithelial folding.”, Nature, vol. 484, no. 7394, pp. 390-3, 2012.
Adipocytes
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.
Adipose Tissue
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.
S. Hui and Rabinowitz, J. D., “An unexpected trigger for calorie burning in brown fat.”, Nature, vol. 560, no. 7716, pp. 38-39, 2018.
Adipose Tissue, Brown
S. Hui and Rabinowitz, J. D., “An unexpected trigger for calorie burning in brown fat.”, Nature, vol. 560, no. 7716, pp. 38-39, 2018.
Administration, Inhalation
J. D. Rabinowitz, Lloyd, P. M., Munzar, P., Myers, D. J., Cross, S., Damani, R., Quintana, R., Spyker, D. A., Soni, P., and Cassella, J. V., “Ultra-fast absorption of amorphous pure drug aerosols via deep lung inhalation.”, J Pharm Sci, vol. 95, no. 11, pp. 2438-51, 2006.
Adolescent
I. S. Lossos, Czerwinski, D. K., Alizadeh, A. A., Wechser, M. A., Tibshirani, R., Botstein, D., and Levy, R., “Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes.”, N Engl J Med, vol. 350, no. 18, pp. 1828-37, 2004.
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
ADP-Ribosylation Factor 1
E. S. Click, Stearns, T., and Botstein, D., “Systematic structure-function analysis of the small GTPase Arf1 in yeast.”, Mol Biol Cell, vol. 13, no. 5, pp. 1652-64, 2002.
ADP-Ribosylation Factors
E. S. Click, Stearns, T., and Botstein, D., “Systematic structure-function analysis of the small GTPase Arf1 in yeast.”, Mol Biol Cell, vol. 13, no. 5, pp. 1652-64, 2002.
Adult
S. P. Bohen, Troyanskaya, O. G., Alter, O., Warnke, R., Botstein, D., Brown, P. O., and Levy, R., “Variation in gene expression patterns in follicular lymphoma and the response to rituximab.”, Proc Natl Acad Sci U S A, vol. 100, no. 4, pp. 1926-30, 2003.
M. L. Whitfield, Finlay, D. R., Murray, J. Isaac, Troyanskaya, O. G., Chi, J. - T., Pergamenschikov, A., McCalmont, T. H., Brown, P. O., Botstein, D., and M Connolly, K., “Systemic and cell type-specific gene expression patterns in scleroderma skin.”, Proc Natl Acad Sci U S A, vol. 100, no. 21, pp. 12319-24, 2003.
I. S. Lossos, Czerwinski, D. K., Alizadeh, A. A., Wechser, M. A., Tibshirani, R., Botstein, D., and Levy, R., “Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes.”, N Engl J Med, vol. 350, no. 18, pp. 1828-37, 2004.
J. D. Rabinowitz, Lloyd, P. M., Munzar, P., Myers, D. J., Cross, S., Damani, R., Quintana, R., Spyker, D. A., Soni, P., and Cassella, J. V., “Ultra-fast absorption of amorphous pure drug aerosols via deep lung inhalation.”, J Pharm Sci, vol. 95, no. 11, pp. 2438-51, 2006.
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
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.
K. Ranade, Hinds, D., Hsiung, C. Agnes, Chuang, L. - M., Chang, M. - S., Chen, Y. - T., Pesich, R., Hebert, J., Chen, Y. - D. I., Dzau, V., Olshen, R., Curb, D., Botstein, D., Cox, D. R., and Risch, N., “A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins.”, Am J Hypertens, vol. 16, no. 2, pp. 158-62, 2003.
T. Sørlie, Perou, C. M., Fan, C., Geisler, S., Aas, T., Nobel, A., Anker, G., Akslen, L. A., Botstein, D., Børresen-Dale, A. - L., and Lønning, P. Eystein, “Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer.”, Mol Cancer Ther, vol. 5, no. 11, pp. 2914-8, 2006.
Aerobiosis
N. Slavov and Botstein, D., “Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression.”, Mol Biol Cell, vol. 24, no. 2, pp. 157-68, 2013.
C. Lu, Brauer, M. J., and Botstein, D., “Slow growth induces heat-shock resistance in normal and respiratory-deficient yeast.”, Mol Biol Cell, vol. 20, no. 3, pp. 891-903, 2009.
M. J. Brauer, Saldanha, A. J., Dolinski, K., and Botstein, D., “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
Aerosols
J. D. Rabinowitz, Lloyd, P. M., Munzar, P., Myers, D. J., Cross, S., Damani, R., Quintana, R., Spyker, D. A., Soni, P., and Cassella, J. V., “Ultra-fast absorption of amorphous pure drug aerosols via deep lung inhalation.”, J Pharm Sci, vol. 95, no. 11, pp. 2438-51, 2006.
Africa
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.
African Americans
S. Tucci and Akey, J. M., “The long walk to African genomics.”, Genome Biol, vol. 20, no. 1, p. 130, 2019.
Age Factors
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
R. G. Tepper, Murphy, C. T., and Bussemaker, H. J., “DAF-16 and PQM-1: partners in longevity.”, Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 2014.
N. Ron-Harel, Notarangelo, G., Ghergurovich, J. M., Paulo, J. A., Sage, P. T., Santos, D., F Satterstrom, K., Gygi, S. P., Rabinowitz, J. D., Sharpe, A. H., and Haigis, M. C., “Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice.”, Proc Natl Acad Sci U S A, vol. 115, no. 52, pp. 13347-13352, 2018.
Aged
S. P. Bohen, Troyanskaya, O. G., Alter, O., Warnke, R., Botstein, D., Brown, P. O., and Levy, R., “Variation in gene expression patterns in follicular lymphoma and the response to rituximab.”, Proc Natl Acad Sci U S A, vol. 100, no. 4, pp. 1926-30, 2003.
I. S. Lossos, Czerwinski, D. K., Alizadeh, A. A., Wechser, M. A., Tibshirani, R., Botstein, D., and Levy, R., “Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes.”, N Engl J Med, vol. 350, no. 18, pp. 1828-37, 2004.
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.
T. Sørlie, Perou, C. M., Fan, C., Geisler, S., Aas, T., Nobel, A., Anker, G., Akslen, L. A., Botstein, D., Børresen-Dale, A. - L., and Lønning, P. Eystein, “Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer.”, Mol Cancer Ther, vol. 5, no. 11, pp. 2914-8, 2006.
Aged, 80 and over
T. Sørlie, Perou, C. M., Fan, C., Geisler, S., Aas, T., Nobel, A., Anker, G., Akslen, L. A., Botstein, D., Børresen-Dale, A. - L., and Lønning, P. Eystein, “Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer.”, Mol Cancer Ther, vol. 5, no. 11, pp. 2914-8, 2006.
Aggression
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.
Aging
S. A. Camper and Tilghman, S. M., “Postnatal repression of the alpha-fetoprotein gene is enhancer independent.”, Genes Dev, vol. 3, no. 4, pp. 537-46, 1989.
R. Kaletsky, Lakhina, V., Arey, R., Williams, A., Landis, J., Ashraf, J., and Murphy, C. T., “The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators.”, Nature, vol. 529, no. 7584, pp. 92-6, 2016.
C. T. Murphy, “Aging: miRacles of longevity?”, Curr Biol, vol. 20, no. 24, pp. R1076-8, 2010.
S. Luo, Kleemann, G. A., Ashraf, J. M., Shaw, W. M., and Murphy, C. T., “TGF-β and insulin signaling regulate reproductive aging via oocyte and germline quality maintenance.”, Cell, vol. 143, no. 2, pp. 299-312, 2010.
C. T. Murphy, Lee, S. - J., and Kenyon, C., “Tissue entrainment by feedback regulation of insulin gene expression in the endoderm of Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 104, no. 48, pp. 19046-50, 2007.
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
C. T. Murphy, “The search for DAF-16/FOXO transcriptional targets: approaches and discoveries.”, Exp Gerontol, vol. 41, no. 10, pp. 910-21, 2006.
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
R. G. Tepper, Murphy, C. T., and Bussemaker, H. J., “DAF-16 and PQM-1: partners in longevity.”, Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 2014.
S. Luo, Shaw, W. M., Ashraf, J., and Murphy, C. T., “TGF-beta Sma/Mab signaling mutations uncouple reproductive aging from somatic aging.”, PLoS Genet, vol. 5, no. 12, p. e1000789, 2009.
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.
R. DiLoreto and Murphy, C. T., “The cell biology of aging.”, Mol Biol Cell, vol. 26, no. 25, pp. 4524-31, 2015.
G. Liu, Rogers, J., Murphy, C. T., and Rongo, C., “EGF signalling activates the ubiquitin proteasome system to modulate C. elegans lifespan.”, EMBO J, vol. 30, no. 15, pp. 2990-3003, 2011.
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.
A. - L. Hsu, Murphy, C. T., and Kenyon, C., “Regulation of aging and age-related disease by DAF-16 and heat-shock factor.”, Science, vol. 300, no. 5622, pp. 1142-5, 2003.
C. Y. Ewald, Landis, J. N., Abate, J. Porter, Murphy, C. T., and T Blackwell, K., “Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity.”, Nature, vol. 519, no. 7541, pp. 97-101, 2015.
L. - B. Li, Lei, H., Arey, R. N., Li, P., Liu, J., Murphy, C. T., Xu, X. Z. Shawn, and Shen, K., “The Neuronal Kinesin UNC-104/KIF1A Is a Key Regulator of Synaptic Aging and Insulin Signaling-Regulated Memory.”, Curr Biol, vol. 26, no. 5, pp. 605-15, 2016.
P. S. Minhas, Liu, L., Moon, P. K., Joshi, A. U., Dove, C., Mhatre, S., Contrepois, K., Wang, Q., Lee, B. A., Coronado, M., Bernstein, D., Snyder, M. P., Migaud, M., Majeti, R., Mochly-Rosen, D., Rabinowitz, J. D., and Andreasson, K. I., “Macrophage de novo NAD synthesis specifies immune function in aging and inflammation.”, Nat Immunol, vol. 20, no. 1, pp. 50-63, 2019.
S. Luo and Murphy, C. T., “Caenorhabditis elegans reproductive aging: Regulation and underlying mechanisms.”, Genesis, vol. 49, no. 2, pp. 53-65, 2011.
A. L. Tyner, Godbout, R., Compton, R. S., and Tilghman, S. M., “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.
Albumins
S. A. Camper and Tilghman, S. M., “Postnatal repression of the alpha-fetoprotein gene is enhancer independent.”, Genes Dev, vol. 3, no. 4, pp. 537-46, 1989.
S. M. Davidson, Jonas, O., Keibler, M. A., Hou, H. Wei, Luengo, A., Mayers, J. R., Wyckoff, J., Del Rosario, A. M., Whitman, M., Chin, C. R., Condon, K. J., Lammers, A., Kellersberger, K. A., Stall, B. K., Stephanopoulos, G., Bar-Sagi, D., Han, J., Rabinowitz, J. D., Cima, M. J., Langer, R., and Heiden, M. G. Vander, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.”, Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
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.
Alcohol Drinking
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
Alcohol Oxidoreductases
Y. Nibu, Senger, K., and Levine, M., “CtBP-independent repression in the Drosophila embryo.”, Mol Cell Biol, vol. 23, no. 11, pp. 3990-9, 2003.
Aldehyde Oxidoreductases
J. L. Marsh and Wieschaus, E., “Germ-line dependence of the maroon-like maternal effect in Drosophila.”, Dev Biol, vol. 60, no. 2, pp. 396-403, 1977.
Aldehydes
J. Mulholland and Botstein, D., “Immunoelectron microscopy of aldehyde-fixed yeast cells.”, Methods Enzymol, vol. 351, pp. 50-81, 2002.
Algorithms
K. M. Chen, Cofer, E. M., Zhou, J., and Troyanskaya, O. G., “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
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.
C. L. Kingsford, Chazelle, B., and Singh, M., “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
L. S. Chen and Storey, J. D., “Eigen-R2 for dissecting variation in high-dimensional studies.”, Bioinformatics, vol. 24, no. 19, pp. 2260-2, 2008.
J. W. Shaevitz and Fletcher, D. A., “Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function.”, J Opt Soc Am A Opt Image Sci Vis, vol. 24, no. 9, pp. 2622-7, 2007.
C. Huttenhower, Flamholz, A. I., Landis, J. N., Sahi, S., Myers, C. L., Olszewski, K. L., Hibbs, M. A., Siemers, N. O., Troyanskaya, O. G., and Coller, H. A., “Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.”, BMC Bioinformatics, vol. 8, p. 250, 2007.
C. S. Greene and Troyanskaya, O. G., “Accurate evaluation and analysis of functional genomics data and methods.”, Ann N Y Acad Sci, vol. 1260, pp. 95-100, 2012.
J. Song and Singh, M., “How and when should interactome-derived clusters be used to predict functional modules and protein function?”, Bioinformatics, vol. 25, no. 23, pp. 3143-50, 2009.
T. Sharpee, Rust, N. C., and Bialek, W., “Analyzing neural responses to natural signals: maximally informative dimensions.”, Neural Comput, vol. 16, no. 2, pp. 223-50, 2004.
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
Y. -suk Lee, Wong, A. K., Tadych, A., Hartmann, B. M., Park, C. Y., DeJesus, V. A., Ramos, I., Zaslavsky, E., Sealfon, S. C., and Troyanskaya, O. G., “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
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.
Z. Khan, Bloom, J. S., Garcia, B. A., Singh, M., and Kruglyak, L., “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.

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