List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

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A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
Abdomen
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.
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.
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.
Acetylation
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.
Actins
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.
Action Potentials
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.
T. L. Adelman, Bialek, W., and Olberg, R. M., “The information content of receptive fields.”, Neuron, vol. 40, no. 4, pp. 823-33, 2003.
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.
Adaptation, Biological
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.
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.
Adaptation, Physiological
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
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.
Adaptor Proteins, Signal Transducing
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
J. 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.
Adenocarcinoma
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.
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.
Adenosine Triphosphate
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.
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.
Adult
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.
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.
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.
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.
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.
Aged
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.
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.
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.
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.
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.
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.
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
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. 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.
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. 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.
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.
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.
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.
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.
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.
Alcohol Drinking
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.
Algorithms
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.
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.
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.
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.
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.
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.
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.
G. Wallace, Anshus, O. J., Bi, P., Chen, H., Chen, Y., Clark, D., Cook, P., Finkelstein, A., Funkhouser, T., Gupta, A., Hibbs, M., Li, K., Liu, Z., Samanta, R., Sukthankar, R., and Troyanskaya, O., “Tools and applications for large-scale display walls.”, IEEE Comput Graph Appl, vol. 25, no. 4, pp. 24-33, 2005.
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.
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.
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.
E. Nabieva, Jim, K., Agarwal, A., Chazelle, B., and Singh, M., “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
J. P. Huelsenbeck and Andolfatto, P., “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
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.
Alleles
J. P. Huelsenbeck and Andolfatto, P., “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
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.
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.
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.
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.
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.
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.
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.
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.
Allelic Imbalance
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.
Allosteric Regulation
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.
Y. - F. Xu, Amador-Noguez, D., Reaves, M. Louis, Feng, X. - J., and Rabinowitz, J. D., “Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase.”, Nat Chem Biol, vol. 8, no. 6, pp. 562-8, 2012.
Allosteric Site
Y. - F. Xu, Amador-Noguez, D., Reaves, M. Louis, Feng, X. - J., and Rabinowitz, J. D., “Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase.”, Nat Chem Biol, vol. 8, no. 6, pp. 562-8, 2012.
alpha-Fetoproteins
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.
Alternative Splicing
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.
Amino Acid Motifs
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.
Amino Acid Sequence
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.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
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