Journal Article
L. H. Rodan, Qi, W., Ducker, G. S., Demirbas, D., Laine, R., Yang, E., Walker, M. A., Eichler, F., Rabinowitz, J. D., Anselm, I., and Berry, G. T.,
“5,10-methenyltetrahydrofolate synthetase deficiency causes a neurometabolic disorder associated with microcephaly, epilepsy, and cerebral hypomyelination.”,
Mol Genet Metab, vol. 125, no. 1-2, pp. 118-126, 2018.
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.
Z. Khan, Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., and Tavazoie, S.,
“Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”,
Genome Biol, vol. 12, no. 12, p. R122, 2011.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W.,
“Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria.”,
Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 2010.
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.
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.
S. R. Browning, Browning, B. L., Zhou, Y., Tucci, S., and Akey, J. M.,
“Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.”,
Cell, vol. 173, no. 1, pp. 53-61.e9, 2018.
Z. Barutcuoglu, Airoldi, E. M., Dumeaux, V., Schapire, R. E., and Troyanskaya, O. G.,
“Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.”,
Bioinformatics, vol. 25, no. 10, pp. 1307-13, 2009.
J. D. Jensen, Thornton, K. R., and Andolfatto, P.,
“An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”,
PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
M. J. Lang, Asbury, C. L., Shaevitz, J. W., and Block, S. M.,
“An automated two-dimensional optical force clamp for single molecule studies.”,
Biophys J, vol. 83, no. 1, pp. 491-501, 2002.
J. W. Shaevitz, Abbondanzieri, E. A., Landick, R., and Block, S. M.,
“Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.”,
Nature, vol. 426, no. 6967, pp. 684-7, 2003.
O. G. Troyanskaya, Dolinski, K., Owen, A. B., Altman, R. B., and Botstein, D.,
“A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).”,
Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8348-53, 2003.
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.
J. F. Ayroles, Buchanan, S. M., O'Leary, C., Skutt-Kakaria, K., Grenier, J. K., Clark, A. G., Hartl, D. L., and de Bivort, B. L.,
“Behavioral idiosyncrasy reveals genetic control of phenotypic variability.”,
Proc Natl Acad Sci U S A, vol. 112, no. 21, pp. 6706-11, 2015.
C. Jang, Oh, S. F., Wada, S., Rowe, G. C., Liu, L., Chan, M. Chun, Rhee, J., Hoshino, A., Kim, B., Ibrahim, A., Baca, L. G., Kim, E., Ghosh, C. C., Parikh, S. M., Jiang, A., Chu, Q., Forman, D. E., Lecker, S. H., Krishnaiah, S., Rabinowitz, J. D., Weljie, A. M., Baur, J. A., Kasper, D. L., and Arany, Z.,
“A branched-chain amino acid metabolite drives vascular fatty acid transport and causes insulin resistance.”,
Nat Med, vol. 22, no. 4, pp. 421-6, 2016.
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.
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.
W. M. Shaw, Luo, S., Landis, J., Ashraf, J., and Murphy, C. T.,
“The C. elegans TGF-beta Dauer pathway regulates longevity via insulin signaling.”,
Curr Biol, vol. 17, no. 19, pp. 1635-45, 2007.
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.
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.
J. Wang, Kaletsky, R., Silva, M., Williams, A., Haas, L. A., Androwski, R. J., Landis, J. N., Patrick, C., Rashid, A., Santiago-Martinez, D., Gravato-Nobre, M., Hodgkin, J., Hall, D. H., Murphy, C. T., and Barr, M. M.,
“Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis.”,
Curr Biol, vol. 25, no. 24, pp. 3232-8, 2015.
M. J. Dunham, Badrane, H., Ferea, T., Adams, J., Brown, P. O., Rosenzweig, F., and Botstein, D.,
“Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.”,
Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16144-9, 2002.
E. Wieschaus, Audit, C., and Masson, M.,
“A clonal analysis of the roles of somatic cells and germ line during oogenesis in Drosophila.”,
Dev Biol, vol. 88, no. 1, pp. 92-103, 1981.
T. Reguly, Breitkreutz, A., Boucher, L., Breitkreutz, B. - J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N., and Tyers, M.,
“Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.”,
J Biol, vol. 5, no. 4, p. 11, 2006.
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.
R. P. Oliveira, Abate, J. Porter, Dilks, K., Landis, J., Ashraf, J., Murphy, C. T., and T Blackwell, K.,
“Condition-adapted stress and longevity gene regulation by Caenorhabditis elegans SKN-1/Nrf.”,
Aging Cell, vol. 8, no. 5, pp. 524-41, 2009.
R. P. Oliveira, Abate, J. Porter, Dilks, K., Landis, J., Ashraf, J., Murphy, C. T., and T Blackwell, K.,
“Condition-adapted stress and longevity gene regulation by Caenorhabditis elegans SKN-1/Nrf.”,
Aging Cell, vol. 8, no. 5, pp. 524-41, 2009.
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.
M. J. Brauer, Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G., and Botstein, D.,
“Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.”,
Mol Biol Cell, vol. 19, no. 1, pp. 352-67, 2008.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C.,
“Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”,
Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I.,
“Correlated evolution of nearby residues in Drosophilid proteins.”,
PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
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.
E. A. Abbondanzieri, Greenleaf, W. J., Shaevitz, J. W., Landick, R., and Block, S. M.,
“Direct observation of base-pair stepping by RNA polymerase.”,
Nature, vol. 438, no. 7067, pp. 460-5, 2005.
A. S. Putnam, J Scriber, M., and Andolfatto, P.,
“Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”,
Evolution, vol. 61, no. 4, pp. 912-27, 2007.
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.
Y. Ahmed, Nouri, A., and Wieschaus, E.,
“Drosophila Apc1 and Apc2 regulate Wingless transduction throughout development.”,
Development, vol. 129, no. 7, pp. 1751-62, 2002.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A.,
“The Drosophila melanogaster Genetic Reference Panel.”,
Nature, vol. 482, no. 7384, pp. 173-8, 2012.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A.,
“The Drosophila melanogaster Genetic Reference Panel.”,
Nature, vol. 482, no. 7384, pp. 173-8, 2012.
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.
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.
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.
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J.,
“Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy.”,
Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
N. Haupaix, Abitua, P. B., Sirour, C., Yasuo, H., Levine, M., and Hudson, C.,
“Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS.”,
Dev Biol, vol. 394, no. 1, pp. 170-80, 2014.
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C.,
“Epistasis dominates the genetic architecture of Drosophila quantitative traits.”,
Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C.,
“Epistasis dominates the genetic architecture of Drosophila quantitative traits.”,
Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
M. Schumer, Cui, R., Boussau, B., Walter, R., Rosenthal, G., and Andolfatto, P.,
“An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.”,
Evolution, vol. 67, no. 4, pp. 1155-68, 2013.
M. L. Aardema, Zhen, Y., and Andolfatto, P.,
“The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”,
Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
M. L. Aardema, Zhen, Y., and Andolfatto, P.,
“The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”,
Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
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.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N.,
“Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.”,
PLoS One, vol. 7, no. 8, p. e43888, 2012.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B.,
“Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.”,
Cell, vol. 139, no. 6, pp. 1189-96, 2009.
S. Tucci, Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., Nelson, B. J., Fu, W., Purnomo, G. A., Sudoyo, H., Eichler, E. E., Barbujani, G., Visscher, P. M., Akey, J. M., and Green, R. E.,
“Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia.”,
Science, vol. 361, no. 6401, pp. 511-516, 2018.
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P.,
“Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.”,
Evolution, vol. 60, no. 2, pp. 292-302, 2006.
H. In Kim, Raffler, J., Lu, W., Lee, J. - J., Abbey, D., Saleheen, D., Rabinowitz, J. D., Bennett, M. J., Hand, N. J., Brown, C., and Rader, D. J.,
“Fine Mapping and Functional Analysis Reveal a Role of SLC22A1 in Acylcarnitine Transport.”,
Am J Hum Genet, vol. 101, no. 4, pp. 489-502, 2017.
L. Abouchar, Petkova, M. D., Steinhardt, C. R., and Gregor, T.,
“Fly wing vein patterns have spatial reproducibility of a single cell.”,
J R Soc Interface, vol. 11, no. 97, p. 20140443, 2014.
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C.,
“Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”,
Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 2011.
Y. Guan, Ackert-Bicknell, C. L., Kell, B., Troyanskaya, O. G., and Hibbs, M. A.,
“Functional genomics complements quantitative genetics in identifying disease-gene associations.”,
PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
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.
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.
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.
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
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.
Y. Kim, Andreu, M. José, Lim, B., Chung, K., Terayama, M., Jiménez, G., Berg, C. A., Lu, H., and Shvartsman, S. Y.,
“Gene regulation by MAPK substrate competition.”,
Dev Cell, vol. 20, no. 6, pp. 880-7, 2011.
O. Alter, Brown, P. O., and Botstein, D.,
“Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.”,
Proc Natl Acad Sci U S A, vol. 100, no. 6, pp. 3351-6, 2003.
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.
T. Slotte, Hazzouri, K. M., Stern, D., Andolfatto, P., and Wright, S. I.,
“Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”,
Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
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.
R. B. Corbett-Detig, Zhou, J., Clark, A. G., Hartl, D. L., and Ayroles, J. F.,
“Genetic incompatibilities are widespread within species.”,
Nature, vol. 504, no. 7478, pp. 135-7, 2013.
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.
T. F. C. Mackay, Stone, E. A., and Ayroles, J. F.,
“The genetics of quantitative traits: challenges and prospects.”,
Nat Rev Genet, vol. 10, no. 8, pp. 565-77, 2009.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C.,
“Genome sequencing reveals complex speciation in the Drosophila simulans clade.”,
Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
J. E. Hirschman, Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hong, E. L., Livstone, M. S., Nash, R., Park, J., Oughtred, R., Skrzypek, M., Starr, B., Theesfeld, C. L., Williams, J., Andrada, R., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Thanawala, M. K., Weng, S., Dolinski, K., Botstein, D., and J Cherry, M.,
“Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.”,
Nucleic Acids Res, vol. 34, no. Database issue, pp. D442-5, 2006.
J. F. Ayroles, Hughes, K. A., Rowe, K. C., Reedy, M. M., Rodriguez-Zas, S. L., Drnevich, J. M., Cáceres, C. E., and Paige, K. N.,
“A genomewide assessment of inbreeding depression: gene number, function, and mode of action.”,
Conserv Biol, vol. 23, no. 4, pp. 920-30, 2009.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T.,
“Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.”,
Neuron, vol. 85, no. 2, pp. 330-45, 2015.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T.,
“Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.”,
Neuron, vol. 85, no. 2, pp. 330-45, 2015.
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B.,
“Genomic variation and its impact on gene expression in Drosophila melanogaster.”,
PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B.,
“Genomic variation and its impact on gene expression in Drosophila melanogaster.”,
PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C.,
“A global genetic interaction network maps a wiring diagram of cellular function.”,
Science, vol. 353, no. 6306, 2016.
A. Bren, Park, J. O., Towbin, B. D., Dekel, E., Rabinowitz, J. D., and Alon, U.,
“Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP.”,
Sci Rep, vol. 6, p. 24834, 2016.
M. Schumer, Cui, R., Powell, D. L., Dresner, R., Rosenthal, G. G., and Andolfatto, P.,
“High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species.”,
Elife, vol. 3, 2014.
M. Schumer, Rosenthal, G. G., and Andolfatto, P.,
“How common is homoploid hybrid speciation?”,
Evolution, vol. 68, no. 6, pp. 1553-60, 2014.
P. Barron Abitua, Wagner, E., Navarrete, I. A., and Levine, M.,
“Identification of a rudimentary neural crest in a non-vertebrate chordate.”,
Nature, vol. 492, no. 7427, pp. 104-7, 2012.
M. L. Whitfield, Sherlock, G., Saldanha, A. J., Murray, J. I., Ball, C. A., Alexander, K. E., Matese, J. C., Perou, C. M., Hurt, M. M., Brown, P. O., and Botstein, D.,
“Identification of genes periodically expressed in the human cell cycle and their expression in tumors.”,
Mol Biol Cell, vol. 13, no. 6, pp. 1977-2000, 2002.
L. Chen, Wolf, A. B., Fu, W., Li, L., and Akey, J. M.,
“Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals.”,
Cell, vol. 180, no. 4, pp. 677-687.e16, 2020.
C. J. Nirschl, Suárez-Fariñas, M., Izar, B., Prakadan, S., Dannenfelser, R., Tirosh, I., Liu, Y., Zhu, Q., K Devi, S. P., Carroll, S. L., Chau, D., Rezaee, M., Kim, T. - G., Huang, R., Fuentes-Duculan, J., Song-Zhao, G. X., Gulati, N., Lowes, M. A., King, S. L., Quintana, F. J., Lee, Y. -suk, Krueger, J. G., Sarin, K. Y., Yoon, C. H., Garraway, L., Regev, iv, A., Shalek, A. K., Troyanskaya, O. G., and Anandasabapathy, N.,
“IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.”,
Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
K. Senger, Armstrong, G. W., Rowell, W. J., Kwan, J. M., Markstein, M., and Levine, M.,
“Immunity regulatory DNAs share common organizational features in Drosophila.”,
Mol Cell, vol. 13, no. 1, pp. 19-32, 2004.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N.,
“Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors.”,
Genome Biol, vol. 14, no. 11, p. R126, 2013.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N.,
“Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors.”,
Genome Biol, vol. 14, no. 11, p. R126, 2013.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N.,
“Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors.”,
Genome Biol, vol. 14, no. 11, p. R126, 2013.
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M.,
“Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees.”,
PLoS One, vol. 5, no. 2, p. e9116, 2010.
V. M. Boer, Amini, S., and Botstein, D.,
“Influence of genotype and nutrition on survival and metabolism of starving yeast.”,
Proc Natl Acad Sci U S A, vol. 105, no. 19, pp. 6930-5, 2008.
T. L. Adelman, Bialek, W., and Olberg, R. M.,
“The information content of receptive fields.”,
Neuron, vol. 40, no. 4, pp. 823-33, 2003.
N. Slonim, Atwal, G. Singh, Tkačik, G., and Bialek, W.,
“Information-based clustering.”,
Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18297-302, 2005.
A. Dejean, Solano, P. Jean, Ayroles, J., Corbara, B., and Orivel, J.,
“Insect behaviour: arboreal ants build traps to capture prey.”,
Nature, vol. 434, no. 7036, p. 973, 2005.
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.
D. Andrea Fer de Abreu, Caballero, A., Fardel, P., Stroustrup, N., Chen, Z., Lee, K., Keyes, W. D., Nash, Z. M., López-Moyado, I. F., Vaggi, F., Cornils, A., Regenass, M., Neagu, A., Ostojic, I., Liu, C., Cho, Y., Sifoglu, D., Shen, Y., Fontana, W., Lu, H., Csikasz-Nagy, A., Murphy, C. T., Antebi, A., Blanc, E., Apfeld, J., Zhang, Y., Alcedo, J., and Ch'ng, Q.,
“An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology.”,
PLoS Genet, vol. 10, no. 3, p. e1004225, 2014.
D. Andrea Fer de Abreu, Caballero, A., Fardel, P., Stroustrup, N., Chen, Z., Lee, K., Keyes, W. D., Nash, Z. M., López-Moyado, I. F., Vaggi, F., Cornils, A., Regenass, M., Neagu, A., Ostojic, I., Liu, C., Cho, Y., Sifoglu, D., Shen, Y., Fontana, W., Lu, H., Csikasz-Nagy, A., Murphy, C. T., Antebi, A., Blanc, E., Apfeld, J., Zhang, Y., Alcedo, J., and Ch'ng, Q.,
“An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology.”,
PLoS Genet, vol. 10, no. 3, p. e1004225, 2014.
D. Andrea Fer de Abreu, Caballero, A., Fardel, P., Stroustrup, N., Chen, Z., Lee, K., Keyes, W. D., Nash, Z. M., López-Moyado, I. F., Vaggi, F., Cornils, A., Regenass, M., Neagu, A., Ostojic, I., Liu, C., Cho, Y., Sifoglu, D., Shen, Y., Fontana, W., Lu, H., Csikasz-Nagy, A., Murphy, C. T., Antebi, A., Blanc, E., Apfeld, J., Zhang, Y., Alcedo, J., and Ch'ng, Q.,
“An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology.”,
PLoS Genet, vol. 10, no. 3, p. e1004225, 2014.
D. Gorenshteyn, Zaslavsky, E., Fribourg, M., Park, C. Y., Wong, A. K., Tadych, A., Hartmann, B. M., Albrecht, R. A., García-Sastre, A., Kleinstein, S. H., Troyanskaya, O. G., and Sealfon, S. C.,
“Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”,
Immunity, vol. 43, no. 3, pp. 605-14, 2015.
M. A. Lanaspa, Andres-Hernando, A., Orlicky, D. J., Cicerchi, C., Jang, C., Li, N., Milagres, T., Kuwabara, M., Wempe, M. F., Rabinowitz, J. D., Johnson, R. J., and Tolan, D. R.,
“Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice.”,
J Clin Invest, vol. 128, no. 6, pp. 2226-2238, 2018.
R. L. Rogers, Cridland, J. M., Shao, L., Hu, T. T., Andolfatto, P., and Thornton, K. R.,
“Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans.”,
Mol Biol Evol, vol. 31, no. 7, pp. 1750-66, 2014.
X. J. Guan, Arhin, G., Leung, J., and Tilghman, S. M.,
“Linkage between vitamin D-binding protein and alpha-fetoprotein in the mouse.”,
Mamm Genome, vol. 7, no. 2, pp. 103-6, 1996.
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.
Y. Kim, Coppey, M., Grossman, R., Ajuria, L., Jiménez, G., Paroush, Z. 'ev, and Shvartsman, S. Y.,
“MAPK substrate competition integrates patterning signals in the Drosophila embryo.”,
Curr Biol, vol. 20, no. 5, pp. 446-51, 2010.
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.
M. O. Press, McCoy, R. C., Hall, A. N., Akey, J. M., and Queitsch, C.,
“Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana.”,
Genome Res, vol. 28, no. 8, pp. 1169-1178, 2018.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W.,
“Measuring the bending stiffness of bacterial cells using an optical trap.”,
J Vis Exp, no. 38, 2010.
J. O. Park, Rubin, S. A., Xu, Y. - F., Amador-Noguez, D., Fan, J., Shlomi, T., and Rabinowitz, J. D.,
“Metabolite concentrations, fluxes and free energies imply efficient enzyme usage.”,
Nat Chem Biol, 2016.
M. A. Estrella, Du, J., Chen, L., Rath, S., Prangley, E., Chitrakar, A., Aoki, T., Schedl, P., Rabinowitz, J., and Korennykh, A.,
“The metabolites NADP and NADPH are the targets of the circadian protein Nocturnin (Curled).”,
Nat Commun, vol. 10, no. 1, p. 2367, 2019.
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.
W. Lu, Clasquin, M. F., Melamud, E., Amador-Noguez, D., Caudy, A. A., and Rabinowitz, J. D.,
“Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer.”,
Anal Chem, vol. 82, no. 8, pp. 3212-21, 2010.
O. Troyanskaya, Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., and Altman, R. B.,
“Missing value estimation methods for DNA microarrays.”,
Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
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.
C. Hei Ho, Magtanong, L., Barker, S. L., Gresham, D., Nishimura, S., Natarajan, P., L Y Koh, J., Porter, J., Gray, C. A., Andersen, R. J., Giaever, G., Nislow, C., Andrews, B., Botstein, D., Graham, T. R., Yoshida, M., and Boone, C.,
“A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.”,
Nat Biotechnol, vol. 27, no. 4, pp. 369-77, 2009.
C. Hei Ho, Magtanong, L., Barker, S. L., Gresham, D., Nishimura, S., Natarajan, P., L Y Koh, J., Porter, J., Gray, C. A., Andersen, R. J., Giaever, G., Nislow, C., Andrews, B., Botstein, D., Graham, T. R., Yoshida, M., and Boone, C.,
“A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.”,
Nat Biotechnol, vol. 27, no. 4, pp. 369-77, 2009.
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.
J. G. Moloughney, Kim, P. K., Vega-Cotto, N. M., Wu, C. - C., Zhang, S., Adlam, M., Lynch, T., Chou, P. - C., Rabinowitz, J. D., Werlen, G., and Jacinto, E.,
“mTORC2 Responds to Glutamine Catabolite Levels to Modulate the Hexosamine Biosynthesis Enzyme GFAT1.”,
Mol Cell, vol. 63, no. 5, pp. 811-26, 2016.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P.,
“Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations.”,
Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L.,
“Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”,
Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
K. C. Rowe, Singhal, S., Macmanes, M. D., Ayroles, J. F., Morelli, T. Lyn, Rubidge, E. M., Bi, K., and Moritz, C. C.,
“Museum genomics: low-cost and high-accuracy genetic data from historical specimens.”,
Mol Ecol Resour, vol. 11, no. 6, pp. 1082-92, 2011.
L. Chen, Zhang, Z., Hoshino, A., Zheng, H. D., Morley, M., Arany, Z., and Rabinowitz, J. D.,
“NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism.”,
Nat Metab, vol. 1, pp. 404-415, 2019.
J. O. Park, Tanner, L. B., Wei, M. H., Khana, D. B., Jacobson, T. B., Zhang, Z., Rubin, S. A., Li, S. Hsin- Jung, Higgins, M. B., Stevenson, D. M., Amador-Noguez, D., and Rabinowitz, J. D.,
“Near-equilibrium glycolysis supports metabolic homeostasis and energy yield.”,
Nat Chem Biol, vol. 15, no. 10, pp. 1001-1008, 2019.
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.
A. A. Caudy, Guan, Y., Jia, Y., Hansen, C., DeSevo, C., Hayes, A. P., Agee, J., Alvarez-Dominguez, J. R., Arellano, H., Barrett, D., Bauerle, C., Bisaria, N., Bradley, P. H., J Breunig, S., Bush, E., Cappel, D., Capra, E., Chen, W., Clore, J., Combs, P. A., Doucette, C., Demuren, O., Fellowes, P., Freeman, S., Frenkel, E., Gadala-Maria, D., Gawande, R., Glass, D., Grossberg, S., Gupta, A., Hammonds-Odie, L., Hoisos, A., Hsi, J., Hsu, Y. - H. Huang, Inukai, S., Karczewski, K. J., Ke, X., Kojima, M., Leachman, S., Lieber, D., Liebowitz, A., Liu, J., Liu, Y., Martin, T., Mena, J., Mendoza, R., Myhrvold, C., Millian, C., Pfau, S., Raj, S., Rich, M., Rokicki, J., Rounds, W., Salazar, M., Salesi, M., Sharma, R., Silverman, S., Singer, C., Sinha, S., Staller, M., Stern, P., Tang, H., Weeks, S., Weidmann, M., Wolf, A., Young, C., Yuan, J., Crutchfield, C., McClean, M., Murphy, C. T., Llinás, M., Botstein, D., Troyanskaya, O. G., and Dunham, M. J.,
“A new system for comparative functional genomics of Saccharomyces yeasts.”,
Genetics, vol. 195, no. 1, pp. 275-87, 2013.
A. A. Caudy, Guan, Y., Jia, Y., Hansen, C., DeSevo, C., Hayes, A. P., Agee, J., Alvarez-Dominguez, J. R., Arellano, H., Barrett, D., Bauerle, C., Bisaria, N., Bradley, P. H., J Breunig, S., Bush, E., Cappel, D., Capra, E., Chen, W., Clore, J., Combs, P. A., Doucette, C., Demuren, O., Fellowes, P., Freeman, S., Frenkel, E., Gadala-Maria, D., Gawande, R., Glass, D., Grossberg, S., Gupta, A., Hammonds-Odie, L., Hoisos, A., Hsi, J., Hsu, Y. - H. Huang, Inukai, S., Karczewski, K. J., Ke, X., Kojima, M., Leachman, S., Lieber, D., Liebowitz, A., Liu, J., Liu, Y., Martin, T., Mena, J., Mendoza, R., Myhrvold, C., Millian, C., Pfau, S., Raj, S., Rich, M., Rokicki, J., Rounds, W., Salazar, M., Salesi, M., Sharma, R., Silverman, S., Singer, C., Sinha, S., Staller, M., Stern, P., Tang, H., Weeks, S., Weidmann, M., Wolf, A., Young, C., Yuan, J., Crutchfield, C., McClean, M., Murphy, C. T., Llinás, M., Botstein, D., Troyanskaya, O. G., and Dunham, M. J.,
“A new system for comparative functional genomics of Saccharomyces yeasts.”,
Genetics, vol. 195, no. 1, pp. 275-87, 2013.
A. A. Caudy, Guan, Y., Jia, Y., Hansen, C., DeSevo, C., Hayes, A. P., Agee, J., Alvarez-Dominguez, J. R., Arellano, H., Barrett, D., Bauerle, C., Bisaria, N., Bradley, P. H., J Breunig, S., Bush, E., Cappel, D., Capra, E., Chen, W., Clore, J., Combs, P. A., Doucette, C., Demuren, O., Fellowes, P., Freeman, S., Frenkel, E., Gadala-Maria, D., Gawande, R., Glass, D., Grossberg, S., Gupta, A., Hammonds-Odie, L., Hoisos, A., Hsi, J., Hsu, Y. - H. Huang, Inukai, S., Karczewski, K. J., Ke, X., Kojima, M., Leachman, S., Lieber, D., Liebowitz, A., Liu, J., Liu, Y., Martin, T., Mena, J., Mendoza, R., Myhrvold, C., Millian, C., Pfau, S., Raj, S., Rich, M., Rokicki, J., Rounds, W., Salazar, M., Salesi, M., Sharma, R., Silverman, S., Singer, C., Sinha, S., Staller, M., Stern, P., Tang, H., Weeks, S., Weidmann, M., Wolf, A., Young, C., Yuan, J., Crutchfield, C., McClean, M., Murphy, C. T., Llinás, M., Botstein, D., Troyanskaya, O. G., and Dunham, M. J.,
“A new system for comparative functional genomics of Saccharomyces yeasts.”,
Genetics, vol. 195, no. 1, pp. 275-87, 2013.
P. Andolfatto, J Scriber, M., and Charlesworth, B.,
“No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”,
Evolution, vol. 57, no. 2, pp. 305-16, 2003.
K. J. Arrow, Axelrod, J., Benacerraf, B., Berg, P., Bishop, J. M., Bloembergen, N., Brown, H. C., Cibelli, J., Cohen, S., Cooper, L. N., Corey, E. J., Cronin, J. W., Curl, R., Dulbecco, R., Fischer, E. H., Fitch, V. L., Fogel, R., Friedman, J. I., Furchgott, R. F., Gell-Mann, M., Gilbert, W., Gilman, A., Glaser, D., Glashow, S. L., Green, R. M., Greengard, P., Guillemin, R., Hayflick, L., Hauptman, H. A., Heckman, J. J., Heeger, A., Herschbach, D., Hubel, D. H., Hulse, R., Kandel, E., Karle, J., Klein, L. R., Kohn, W., Kornberg, A., Krebs, E. G., Lanza, R. P., Laughlin, R., Lederman, L., Lee, D. M., Lewis, E., Lipscomb, W., Marcus, R. A., McFadden, D., Merrifield, R. B., Merton, R., Modigliani, F., Molina, M. J., Murad, F., Nirenberg, M. W., North, D. C., Olah, G. A., Osheroff, D., Palade, G. E., Perl, M., Ramsey, N. F., Richter, B., Roberts, R. J., Samuelson, P. A., Schwartz, M., Sharp, P. A., Smalley, R. E., Smith, H. O., Solow, R. M., Stormer, H., Taube, H., Taylor, R., Thomas, E. D., Tobin, J., Tonegawa, S., Townes, C., Watson, J. D., Weinberg, S., Weller, T. H., West, M. D., Wieschaus, E. F., Wiesel, T. N., and Wilson, R. W.,
“Nobel laureates' letter to President Bush.”,
Washington Post, p. A02, 2001.
K. J. Arrow, Axelrod, J., Benacerraf, B., Berg, P., Bishop, J. M., Bloembergen, N., Brown, H. C., Cibelli, J., Cohen, S., Cooper, L. N., Corey, E. J., Cronin, J. W., Curl, R., Dulbecco, R., Fischer, E. H., Fitch, V. L., Fogel, R., Friedman, J. I., Furchgott, R. F., Gell-Mann, M., Gilbert, W., Gilman, A., Glaser, D., Glashow, S. L., Green, R. M., Greengard, P., Guillemin, R., Hayflick, L., Hauptman, H. A., Heckman, J. J., Heeger, A., Herschbach, D., Hubel, D. H., Hulse, R., Kandel, E., Karle, J., Klein, L. R., Kohn, W., Kornberg, A., Krebs, E. G., Lanza, R. P., Laughlin, R., Lederman, L., Lee, D. M., Lewis, E., Lipscomb, W., Marcus, R. A., McFadden, D., Merrifield, R. B., Merton, R., Modigliani, F., Molina, M. J., Murad, F., Nirenberg, M. W., North, D. C., Olah, G. A., Osheroff, D., Palade, G. E., Perl, M., Ramsey, N. F., Richter, B., Roberts, R. J., Samuelson, P. A., Schwartz, M., Sharp, P. A., Smalley, R. E., Smith, H. O., Solow, R. M., Stormer, H., Taube, H., Taylor, R., Thomas, E. D., Tobin, J., Tonegawa, S., Townes, C., Watson, J. D., Weinberg, S., Weller, T. H., West, M. D., Wieschaus, E. F., Wiesel, T. N., and Wilson, R. W.,
“Nobel laureates' letter to President Bush.”,
Washington Post, p. A02, 2001.
O. G. Troyanskaya, Garber, M. E., Brown, P. O., Botstein, D., and Altman, R. B.,
“Nonparametric methods for identifying differentially expressed genes in microarray data.”,
Bioinformatics, vol. 18, no. 11, pp. 1454-61, 2002.
P. Armand, Knapp, A. C., Hirsch, A. J., Wieschaus, E. F., and Cole, M. D.,
“A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis.”,
Mol Cell Biol, vol. 14, no. 6, pp. 4145-54, 1994.
Y. - F. Xu, Létisse, F., Absalan, F., Lu, W., Kuznetsova, E., Brown, G., Caudy, A. A., Yakunin, A. F., Broach, J. R., and Rabinowitz, J. D.,
“Nucleotide degradation and ribose salvage in yeast.”,
Mol Syst Biol, vol. 9, p. 665, 2013.
M. Anna Carbone, Ayroles, J. F., Yamamoto, A., Morozova, T. V., West, S. A., Magwire, M. M., Mackay, T. F. C., and Anholt, R. R. H.,
“Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma.”,
PLoS One, vol. 4, no. 1, p. e4216, 2009.
M. Anna Carbone, Ayroles, J. F., Yamamoto, A., Morozova, T. V., West, S. A., Magwire, M. M., Mackay, T. F. C., and Anholt, R. R. H.,
“Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma.”,
PLoS One, vol. 4, no. 1, p. e4216, 2009.
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.
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.
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.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D.,
“Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.”,
Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P.,
“Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”,
Genome Biol, vol. 6, no. 8, p. R67, 2005.
L. X. Liu, Rowe, G. C., Yang, S., Li, J., Damilano, F., Chan, M. Chun, Lu, W., Jang, C., Wada, S., Morley, M., Hesse, M., Fleischmann, B. K., Rabinowitz, J., Das, S., Rosenzweig, A., and Arany, Z.,
“PDK4 Inhibits Cardiac Pyruvate Oxidation in Late Pregnancy.”,
Circ Res, 2017.
Q. Liu, Johnson, E. M., Lam, R. K., Wang, Q., Ye, H. Bo, Wilson, E. N., Minhas, P. S., Liu, L., Swarovski, M. S., Tran, S., Wang, J., Mehta, S. S., Yang, X., Rabinowitz, J. D., Yang, S. S., Shamloo, M., Mueller, C., James, M. L., and Andreasson, K. I.,
“Peripheral TREM1 responses to brain and intestinal immunogens amplify stroke severity.”,
Nat Immunol, vol. 20, no. 8, pp. 1023-1034, 2019.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P.,
“Pervasive natural selection in the Drosophila genome?”,
PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
R. Cui, Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., and Rosenthal, G. G.,
“Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.”,
Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
E. A. Abbondanzieri, Shaevitz, J. W., and Block, S. M.,
“Picocalorimetry of transcription by RNA polymerase.”,
Biophys J, vol. 89, no. 6, pp. L61-3, 2005.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M.,
“A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”,
PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P.,
“Positive and negative selection on noncoding DNA in Drosophila simulans.”,
Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
R. G. Tepper, Ashraf, J., Kaletsky, R., Kleemann, G., Murphy, C. T., and Bussemaker, H. J.,
“PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity.”,
Cell, vol. 154, no. 3, pp. 676-90, 2013.
E. M. Airoldi, Huttenhower, C., Gresham, D., Lu, C., Caudy, A. A., Dunham, M. J., Broach, J. R., Botstein, D., and Troyanskaya, O. G.,
“Predicting cellular growth from gene expression signatures.”,
PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
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.
P. Barron Abitua, T Gainous, B., Kaczmarczyk, A. N., Winchell, C. J., Hudson, C., Kamata, K., Nakagawa, M., Tsuda, M., Kusakabe, T. G., and Levine, M.,
“The pre-vertebrate origins of neurogenic placodes.”,
Nature, vol. 524, no. 7566, pp. 462-5, 2015.
S. Heinicke, Livstone, M. S., Lu, C., Oughtred, R., Kang, F., Angiuoli, S. V., White, O., Botstein, D., and Dolinski, K.,
“The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.”,
PLoS One, vol. 2, no. 8, p. e766, 2007.
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.
A. Baryshnikova, Costanzo, M., Kim, Y., Ding, H., Koh, J., Toufighi, K., Youn, J. - Y., Ou, J., San Luis, B. - J., Bandyopadhyay, S., Hibbs, M., Hess, D., Gingras, A. - C., Bader, G. D., Troyanskaya, O. G., Brown, G. W., Andrews, B., Boone, C., and Myers, C. L.,
“Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”,
Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
M. D. Neinast, Jang, C., Hui, S., Murashige, D. S., Chu, Q., Morscher, R. J., Li, X., Zhan, L., White, E., Anthony, T. G., Rabinowitz, J. D., and Arany, Z.,
“Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids.”,
Cell Metab, vol. 29, no. 2, pp. 417-429.e4, 2019.
M. D. Neinast, Jang, C., Hui, S., Murashige, D. S., Chu, Q., Morscher, R. J., Li, X., Zhan, L., White, E., Anthony, T. G., Rabinowitz, J. D., and Arany, Z.,
“Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids.”,
Cell Metab, vol. 29, no. 2, pp. 417-429.e4, 2019.
Z. Khan, Bloom, J. S., Amini, S., Singh, M., Perlman, D. H., Caudy, A. A., and Kruglyak, L.,
“Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”,
Mol Syst Biol, vol. 8, p. 602, 2012.
L. Salwinski, Licata, L., Winter, A., Thorneycroft, D., Khadake, J., Ceol, A., Aryamontri, A. Chatr, Oughtred, R., Livstone, M., Boucher, L., Botstein, D., Dolinski, K., Berardini, T., Huala, E., Tyers, M., Eisenberg, D., Cesareni, G., and Hermjakob, H.,
“Recurated protein interaction datasets.”,
Nat Methods, vol. 6, no. 12, pp. 860-1, 2009.
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.
Y. - F. Xu, Zhao, X., Glass, D. S., Absalan, F., Perlman, D. H., Broach, J. R., and Rabinowitz, J. D.,
“Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation.”,
Mol Cell, vol. 48, no. 1, pp. 52-62, 2012.
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.
R. L. Rogers, Shao, L., Sanjak, J. S., Andolfatto, P., and Thornton, K. R.,
“Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group.”,
G3 (Bethesda), vol. 4, no. 12, pp. 2345-51, 2014.
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.
H. G. Son, Seo, M., Ham, S., Hwang, W., Lee, D., An, S. Woo A., Artan, M., Seo, K., Kaletsky, R., Arey, R. N., Ryu, Y., Ha, C. Man, Kim, Y. Ki, Murphy, C. T., Roh, T. - Y., Nam, H. Gil, and Lee, S. - J. V.,
“RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans.”,
Nat Commun, vol. 8, p. 14749, 2017.
H. G. Son, Seo, M., Ham, S., Hwang, W., Lee, D., An, S. Woo A., Artan, M., Seo, K., Kaletsky, R., Arey, R. N., Ryu, Y., Ha, C. Man, Kim, Y. Ki, Murphy, C. T., Roh, T. - Y., Nam, H. Gil, and Lee, S. - J. V.,
“RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans.”,
Nat Commun, vol. 8, p. 14749, 2017.
H. G. Son, Seo, M., Ham, S., Hwang, W., Lee, D., An, S. Woo A., Artan, M., Seo, K., Kaletsky, R., Arey, R. N., Ryu, Y., Ha, C. Man, Kim, Y. Ki, Murphy, C. T., Roh, T. - Y., Nam, H. Gil, and Lee, S. - J. V.,
“RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans.”,
Nat Commun, vol. 8, p. 14749, 2017.
J. M. Buescher, Antoniewicz, M. R., Boros, L. G., Burgess, S. C., Brunengraber, H., Clish, C. B., DeBerardinis, R. J., Feron, O., Frezza, C., Ghesquiere, B., Gottlieb, E., Hiller, K., Jones, R. G., Kamphorst, J. J., Kibbey, R. G., Kimmelman, A. C., Locasale, J. W., Lunt, S. Y., Maddocks, O. Dk, Malloy, C., Metallo, C. M., Meuillet, E. J., Munger, J., Nöh, K., Rabinowitz, J. D., Ralser, M., Sauer, U., Stephanopoulos, G., St-Pierre, J., Tennant, D. A., Wittmann, C., Heiden, M. G. Vander, Vazquez, A., Vousden, K., Young, J. D., Zamboni, N., and Fendt, S. - M.,
“A roadmap for interpreting (13)C metabolite labeling patterns from cells.”,
Curr Opin Biotechnol, vol. 34, pp. 189-201, 2015.
A. Helman, Lim, B., Andreu, M. José, Kim, Y., Shestkin, T., Lu, H., Jiménez, G., Shvartsman, S. Y., and Paroush, Z. 'ev,
“RTK signaling modulates the Dorsal gradient.”,
Development, vol. 139, no. 16, pp. 3032-9, 2012.
L. Issel-Tarver, Christie, K. R., Dolinski, K., Andrada, R., Balakrishnan, R., Ball, C. A., Binkley, G., Dong, S., Dwight, S. S., Fisk, D. G., Harris, M., Schroeder, M., Sethuraman, A., Tse, K., Weng, S., Botstein, D., and J Cherry, M.,
“Saccharomyces Genome Database.”,
Methods Enzymol, vol. 350, pp. 329-46, 2002.
S. Weng, Dong, Q., Balakrishnan, R., Christie, K., Costanzo, M., Dolinski, K., Dwight, S. S., Engel, S., Fisk, D. G., Hong, E., Issel-Tarver, L., Sethuraman, A., Theesfeld, C., Andrada, R., Binkley, G., Lane, C., Schroeder, M., Botstein, D., and J Cherry, M.,
“Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 216-8, 2003.
K. R. Christie, Weng, S., Balakrishnan, R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J. E., Hong, E. L., Issel-Tarver, L., Nash, R., Sethuraman, A., Starr, B., Theesfeld, C. L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Botstein, D., and J Cherry, M.,
“Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.”,
Nucleic Acids Res, vol. 32, no. Database issue, pp. D311-4, 2004.
S. S. Dwight, Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dolinski, K., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J., Hong, E. L., Issel-Tarver, L., Nash, R. S., Sethuraman, A., Starr, B., Theesfeld, C. L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Weng, S., Botstein, D., and J Cherry, M.,
“Saccharomyces genome database: underlying principles and organisation.”,
Brief Bioinform, vol. 5, no. 1, pp. 9-22, 2004.
S. D. Kocher, Tsuruda, J. M., Gibson, J. D., Emore, C. M., Arechavaleta-Velasco, M. E., Queller, D. C., Strassmann, J. E., Grozinger, C. M., Gribskov, M. R., San Miguel, P., Westerman, R., and Hunt, G. J.,
“A Search for Parent-of-Origin Effects on Honey Bee Gene Expression.”,
G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
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.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P.,
“A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.”,
Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
K. A. Hughes, Ayroles, J. F., Reedy, M. M., Drnevich, J. M., Rowe, K. C., Ruedi, E. A., Cáceres, C. E., and Paige, K. N.,
“Segregating variation in the transcriptome: cis regulation and additivity of effects.”,
Genetics, vol. 173, no. 3, pp. 1347-55, 2006.
O. G. Troyanskaya, Arbell, O., Koren, Y., Landau, G. M., and Bolshoy, A.,
“Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.”,
Bioinformatics, vol. 18, no. 5, pp. 679-88, 2002.
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
L. Wang, Xing, X., Zeng, X., S Jackson, R. E., TeSlaa, T., Al-Dalahmah, O., Samarah, L. Z., Goodwin, K., Yang, L., McReynolds, M. R., Li, X., Wolff, J. J., Rabinowitz, J. D., and Davidson, S. M.,
“Spatially resolved isotope tracing reveals tissue metabolic activity.”,
Nat Methods, vol. 19, no. 2, pp. 223-230, 2022.
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.
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
