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

Journal Article
P. Koivunen, Fell, S. M., Lu, W., Rabinowitz, J. D., Kung, A. L., and Schlisio, S., “The 2-oxoglutarate analog 3-oxoglutarate decreases normoxic hypoxia-inducible factor-1α in cancer cells, induces cell death, and reduces tumor xenograft growth.”, Hypoxia (Auckl), vol. 4, pp. 15-27, 2016.
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.
M. Louis Reaves, Sinha, S., Rabinowitz, J. D., Kruglyak, L., and Redfield, R. J., “Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells.”, Science, vol. 337, no. 6093, pp. 470-3, 2012.
A. L. Webber and Tilghman, S. M., “The absence of enhancer competition between Igf2 and H19 following transfer into differentiated cells.”, Mol Cell Biol, vol. 18, no. 4, pp. 1903-10, 1998.
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.
B. D. Bennett, Yuan, J., Kimball, E. H., and Rabinowitz, J. D., “Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach.”, Nat Protoc, vol. 3, no. 8, pp. 1299-311, 2008.
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.
R. G. Endres and Wingreen, N. S., “Accuracy of direct gradient sensing by cell-surface receptors.”, Prog Biophys Mol Biol, vol. 100, no. 1-3, pp. 33-9, 2009.
R. G. Endres and Wingreen, N. S., “Accuracy of direct gradient sensing by single cells.”, Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
C. L. Myers, Dunham, M. J., Kung, S. Y., and Troyanskaya, O. G., “Accurate detection of aneuploidies in array CGH and gene expression microarray data.”, Bioinformatics, vol. 20, no. 18, pp. 3533-43, 2004.
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. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
J. O. Dubuis, Samanta, R., and Gregor, T., “Accurate measurements of dynamics and reproducibility in small genetic networks.”, Mol Syst Biol, vol. 9, p. 639, 2013.
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.
M. D. Chikina and Troyanskaya, O. G., “Accurate quantification of functional analogy among close homologs.”, PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
S. Goyal, Yuan, J., Chen, T., Rabinowitz, J. D., and Wingreen, N. S., “Achieving optimal growth through product feedback inhibition in metabolism.”, PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
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.
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. Mignot and Shaevitz, J. W., “Active and passive mechanisms of intracellular transport and localization in bacteria.”, Curr Opin Microbiol, vol. 11, no. 6, pp. 580-5, 2008.
D. Swanson and Wingreen, N. S., “Active biopolymers confer fast reorganization kinetics.”, Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
S. - W. Teng, Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi.”, Mol Syst Biol, vol. 7, p. 491, 2011.
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.
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
C. T. Murphy, “Aging: miRacles of longevity?”, Curr Biol, vol. 20, no. 24, pp. R1076-8, 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.
K. Pfeifer and Tilghman, S. M., “Allele-specific gene expression in mammals: the curious case of the imprinted RNAs.”, Genes Dev, vol. 8, no. 16, pp. 1867-74, 1994.
M. J. O'Neill, Ingram, R. S., Vrana, P. B., and Tilghman, S. M., “Allelic expression of IGF2 in marsupials and birds.”, Dev Genes Evol, vol. 210, no. 1, pp. 18-20, 2000.
D. C. Hess, Lu, W., Rabinowitz, J. D., and Botstein, D., “Ammonium toxicity and potassium limitation in yeast.”, PLoS Biol, vol. 4, no. 11, p. e351, 2006.
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.
A. Chi, Huttenhower, C., Geer, L. Y., Coon, J. J., Syka, J. E. P., Bai, D. L., Shabanowitz, J., Burke, D. J., Troyanskaya, O. G., and Hunt, D. F., “Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.”, Proc Natl Acad Sci U S A, vol. 104, no. 7, pp. 2193-8, 2007.
J. F. Ayroles and Gibson, G., “Analysis of variance of microarray data.”, Methods Enzymol, vol. 411, pp. 214-33, 2006.
W. Lu, Bennett, B. D., and Rabinowitz, J. D., “Analytical strategies for LC-MS-based targeted metabolomics.”, J Chromatogr B Analyt Technol Biomed Life Sci, vol. 871, no. 2, pp. 236-42, 2008.
A. Di Gregorio and Levine, M., “Analyzing gene regulation in ascidian embryos: new tools for new perspectives.”, Differentiation, vol. 70, no. 4-5, pp. 132-9, 2002.
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.
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.
Y. Kyung Kwon, Higgins, M. B., and Rabinowitz, J. D., “Antifolate-induced depletion of intracellular glycine and purines inhibits thymineless death in E. coli.”, ACS Chem Biol, vol. 5, no. 8, pp. 787-95, 2010.
B. He, Doubrovinski, K., Polyakov, O., and Wieschaus, E., “Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation.”, Nature, vol. 508, no. 7496, pp. 392-6, 2014.
P. Mehta and Gregor, T., “Approaching the molecular origins of collective dynamics in oscillating cell populations.”, Curr Opin Genet Dev, vol. 20, no. 6, pp. 574-80, 2010.
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.
K. Thornton and Andolfatto, P., “Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.”, Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
S. L. Grady, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., “Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection.”, Proc Natl Acad Sci U S A, vol. 110, no. 51, pp. E5006-15, 2013.
D. E. Klein, Nappi, V. M., Reeves, G. T., Shvartsman, S. Y., and Lemmon, M. A., “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
H. A. Müller and Wieschaus, E., “armadillo, bazooka, and stardust are critical for early stages in formation of the zonula adherens and maintenance of the polarized blastoderm epithelium in Drosophila.”, J Cell Biol, vol. 134, no. 1, pp. 149-63, 1996.
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.
N. N. Pavlova, Hui, S., Ghergurovich, J. M., Fan, J., Intlekofer, A. M., White, R. M., Rabinowitz, J. D., Thompson, C. B., and Zhang, J., “As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid.”, Cell Metab, vol. 27, no. 2, pp. 428-438.e5, 2018.
J. Zhang, Fan, J., Venneti, S., Cross, J. R., Takagi, T., Bhinder, B., Djaballah, H., Kanai, M., Cheng, E. H., Judkins, A. R., Pawel, B., Baggs, J., Cherry, S., Rabinowitz, J. D., and Thompson, C. B., “Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion.”, Mol Cell, vol. 56, no. 2, pp. 205-18, 2014.
C. Huttenhower and Troyanskaya, O. G., “Assessing the functional structure of genomic data.”, Bioinformatics, vol. 24, no. 13, pp. i330-8, 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. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
K. Dolinski and Botstein, D., “Automating the construction of gene ontologies.”, Nat Biotechnol, vol. 31, no. 1, pp. 34-5, 2013.
E. Wieschaus and Riggleman, R., “Autonomous requirements for the segment polarity gene armadillo during Drosophila embryogenesis.”, Cell, vol. 49, no. 2, pp. 177-84, 1987.
J. D. Rabinowitz and White, E., “Autophagy and metabolism.”, Science, vol. 330, no. 6009, pp. 1344-8, 2010.
G. Karsli-Uzunbas, Guo, J. Yanxiang, Price, S., Teng, X., Laddha, S. V., Khor, S., Kalaany, N. Y., Jacks, T., Chan, C. S., Rabinowitz, J. D., and White, E., “Autophagy is required for glucose homeostasis and lung tumor maintenance.”, Cancer Discov, vol. 4, no. 8, pp. 914-27, 2014.
L. Poillet-Perez, Xie, X., Zhan, L., Yang, Y., Sharp, D. W., Hu, Z. Sherrie, Su, X., Maganti, A., Jiang, C., Lu, W., Zheng, H., Bosenberg, M. W., Mehnert, J. M., Guo, J. Yanxiang, Lattime, E., Rabinowitz, J. D., and White, E., “Autophagy maintains tumour growth through circulating arginine.”, Nature, vol. 563, no. 7732, pp. 569-573, 2018.
J. Yanxiang Guo, Teng, X., Laddha, S. V., Ma, S., Van Nostrand, S. C., Yang, Y., Khor, S., Chan, C. S., Rabinowitz, J. D., and White, E., “Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells.”, Genes Dev, vol. 30, no. 15, pp. 1704-17, 2016.
Y. - F. Xu, Lu, W., and Rabinowitz, J. D., “Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics.”, Anal Chem, vol. 87, no. 4, pp. 2273-81, 2015.
N. Wingreen and Botstein, D., “Back to the future: education for systems-level biologists.”, Nat Rev Mol Cell Biol, vol. 7, no. 11, pp. 829-32, 2006.
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.
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.
C. Huttenhower and Troyanskaya, O. G., “Bayesian data integration: a functional perspective.”, Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
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.
A. Ochoa, Storey, J. D., Llinás, M., and Singh, M., “Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.”, PLoS Comput Biol, vol. 11, no. 11, p. e1004509, 2015.
J. Mohler and Wieschaus, E. F., “Bicaudal mutations of Drosophila melanogaster: alteration of blastoderm cell fate.”, Cold Spring Harb Symp Quant Biol, vol. 50, pp. 105-11, 1985.
P. A. DiMaggio, McAllister, S. R., Floudas, C. A., Feng, X. - J., Rabinowitz, J. D., and Rabitz, H. A., “Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.”, BMC Bioinformatics, vol. 9, p. 458, 2008.
O. Grimm and Wieschaus, E., “The Bicoid gradient is shaped independently of nuclei.”, Development, vol. 137, no. 17, pp. 2857-62, 2010.
A. Munivenkatappa, Devi, B. Indira, Gregor, T. Issac, Bhat, D. I., Kumarsamy, A. Deepika, and Shukla, D. P., “Bicycle accident-related head injuries in India.”, J Neurosci Rural Pract, vol. 4, no. 3, pp. 262-6, 2013.
T. Clancy, Dannenfelser, R., Troyanskaya, O. G., Malmberg, K. Johan, Hovig, E., and Kristensen, V., “Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery.”, Curr Pharm Des, 2017.
J. P. Nguyen, Bratton, B. P., and Shaevitz, J. W., “Biophysical Measurements of Bacterial Cell Shape.”, Methods Mol Biol, vol. 1440, pp. 227-45, 2016.
R. C. Oslund, Su, X., Haugbro, M., Kee, J. - M., Esposito, M., David, Y., Wang, B., Ge, E., Perlman, D. H., Kang, Y., Muir, T. W., and Rabinowitz, J. D., “Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate.”, Nat Chem Biol, vol. 13, no. 10, pp. 1081-1087, 2017.
L. Qiao, Nachbar, R. B., Kevrekidis, I. G., and Shvartsman, S. Y., “Bistability and oscillations in the Huang-Ferrell model of MAPK signaling.”, PLoS Comput Biol, vol. 3, no. 9, pp. 1819-26, 2007.
S. - J. Yan, Zartman, J. J., Zhang, M., Scott, A., Shvartsman, S. Y., and Li, W. X., “Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation.”, Mol Syst Biol, vol. 5, p. 278, 2009.
K. S. Smith, Chanda, S. K., Lingbeek, M., Ross, D. T., Botstein, D., van Lohuizen, M., and Cleary, M. L., “Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1.”, Mol Cell, vol. 12, no. 2, pp. 393-400, 2003.
L. Christiaen, Stolfi, A., and Levine, M., “BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development.”, Dev Biol, vol. 340, no. 2, pp. 179-87, 2010.
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.
A. M. Berezhkovskii, Makhnovskii, Y. A., Monine, M. I., Zitserman, V. Yu, and Shvartsman, S. Y., “Boundary homogenization for trapping by patchy surfaces.”, J Chem Phys, vol. 121, no. 22, pp. 11390-4, 2004.
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.
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. E. Dawes-Hoang, Zallen, J. A., and Wieschaus, E. F., “Bringing classical embryology to C elegans gastrulation.”, Dev Cell, vol. 4, no. 1, pp. 6-8, 2003.
B. VanderSluis, Hess, D. C., Pesyna, C., Krumholz, E. W., Syed, T., Szappanos, B., Nislow, C., Papp, B., Troyanskaya, O. G., Myers, C. L., and Caudy, A. A., “Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection.”, Genome Biol, vol. 15, no. 4, p. R64, 2014.
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.
J. - H. Hahm, Kim, S., DiLoreto, R., Shi, C., Lee, S. - J. V., Murphy, C. T., and Nam, H. Gil, “C. elegans maximum velocity correlates with healthspan and is maintained in worms with an insulin receptor mutation.”, Nat Commun, vol. 6, p. 8919, 2015.
G. M. Stein and Murphy, C. T., “C. elegans positive olfactory associative memory is a molecularly conserved behavioral paradigm.”, Neurobiol Learn Mem, vol. 115, pp. 86-94, 2014.
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.
J. J. Zartman, Yakoby, N., Bristow, C. A., Zhou, X., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., “Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis.”, Dev Biol, vol. 322, no. 2, pp. 289-301, 2008.
S. Luo and Murphy, C. T., “Caenorhabditis elegans reproductive aging: Regulation and underlying mechanisms.”, Genesis, vol. 49, no. 2, pp. 53-65, 2011.
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.
L. Jo Kurihara, Semenova, E., Miller, W., Ingram, R. S., Guan, X. - J., and Tilghman, S. M., “Candidate genes required for embryonic development: a comparative analysis of distal mouse chromosome 14 and human chromosome 13q22.”, Genomics, vol. 79, no. 2, pp. 154-61, 2002.
G. Jiménez, Shvartsman, S. Y., and Paroush, Z. 'ev, “The Capicua repressor--a general sensor of RTK signaling in development and disease.”, J Cell Sci, vol. 125, no. Pt 6, pp. 1383-91, 2012.
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
P. Jiang and Singh, M., “CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.”, Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
R. E. Dawes-Hoang and Wieschaus, E. F., “Cell and developmental biology--a shared past, an intertwined future.”, Dev Cell, vol. 1, no. 1, pp. 27-36, 2001.
R. DiLoreto and Murphy, C. T., “The cell biology of aging.”, Mol Biol Cell, vol. 26, no. 25, pp. 4524-31, 2015.
X. Lu, Drocco, J., and Wieschaus, E. F., “Cell cycle regulation via inter-nuclear communication during the early embryonic development of Drosophila melanogaster.”, Cell Cycle, vol. 9, no. 14, pp. 2908-10, 2010.
K. D. Irvine and Wieschaus, E., “Cell intercalation during Drosophila germband extension and its regulation by pair-rule segmentation genes.”, Development, vol. 120, no. 4, pp. 827-41, 1994.
J. Szabad, Schupbach, T., and Wieschaus, E., “Cell lineage and development in the larval epidermis of Drosophila melanogaster.”, Dev Biol, vol. 73, no. 2, pp. 256-71, 1979.
E. Wieschaus, “Cell lineage relationships in the Drosophila embryo.”, Results Probl Cell Differ, vol. 9, pp. 97-118, 1978.
S. B. Zusman and Wieschaus, E., “A cell marker system and mosaic patterns during early embryonic development in Drosophila melanogaster.”, Genetics, vol. 115, no. 4, pp. 725-36, 1987.
K. Casey Huang, Mukhopadhyay, R., Wen, B., Gitai, Z., and Wingreen, N. S., “Cell shape and cell-wall organization in Gram-negative bacteria.”, Proc Natl Acad Sci U S A, vol. 105, no. 49, pp. 19282-7, 2008.
S. Wang and Wingreen, N. S., “Cell shape can mediate the spatial organization of the bacterial cytoskeleton.”, Biophys J, vol. 104, no. 3, pp. 541-52, 2013.
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.
J. D. Rabinowitz, “Cellular metabolomics of Escherchia coli.”, Expert Rev Proteomics, vol. 4, no. 2, pp. 187-98, 2007.
J. R. Pollack, van de Rijn, M., and Botstein, D., “Challenges in developing a molecular characterization of cancer.”, Semin Oncol, vol. 29, no. 3, pp. 280-5, 2002.
K. Dolinski and Botstein, D., “Changing perspectives in yeast research nearly a decade after the genome sequence.”, Genome Res, vol. 15, no. 12, pp. 1611-9, 2005.
C. S. Greene and Troyanskaya, O. G., “Chapter 2: Data-driven view of disease biology.”, PLoS Comput Biol, vol. 8, no. 12, p. e1002816, 2012.
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.
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.
J. A. Capra and Singh, M., “Characterization and prediction of residues determining protein functional specificity.”, Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
E. Bae, Calhoun, V. C., Levine, M., Lewis, E. B., and Drewell, R. A., “Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16847-52, 2002.
P. A. Gibney, Schieler, A., Chen, J. C., Rabinowitz, J. D., and Botstein, D., “Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter.”, Proc Natl Acad Sci U S A, 2015.
Z. Zhang, Chen, L., Liu, L., Su, X., and Rabinowitz, J. D., “Chemical Basis for Deuterium Labeling of Fat and NADPH.”, J Am Chem Soc, vol. 139, no. 41, pp. 14368-14371, 2017.
J. I. Kliegman, Fiedler, D., Ryan, C. J., Xu, Y. - F., Su, X. - Y., Thomas, D., Caccese, M. C., Cheng, A., Shales, M., Rabinowitz, J. D., Krogan, N. J., and Shokat, K. M., “Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae.”, Cell Rep, vol. 5, no. 6, pp. 1725-36, 2013.
M. Skoge, Naqvi, S., Meir, Y., and Wingreen, N. S., “Chemical sensing by nonequilibrium cooperative receptors.”, Phys Rev Lett, vol. 110, no. 24, p. 248102, 2013.
M. Skoge, Naqvi, S., Meir, Y., and Wingreen, N. S., “Chemical Sensing by Nonequilibrium Cooperative Receptors.”, Phys Rev Lett, vol. 110, no. 24, 2013.
J. E. Keymer, Endres, R. G., Skoge, M., Meir, Y., and Wingreen, N. S., “Chemosensing in Escherichia coli: two regimes of two-state receptors.”, Proc Natl Acad Sci U S A, vol. 103, no. 6, pp. 1786-91, 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.
R. G. Endres, Falke, J. J., and Wingreen, N. S., “Chemotaxis receptor complexes: from signaling to assembly.”, PLoS Comput Biol, vol. 3, no. 7, p. e150, 2007.
A. T. Hark and Tilghman, S. M., “Chromatin conformation of the H19 epigenetic mark.”, Hum Mol Genet, vol. 7, no. 12, pp. 1979-85, 1998.
M. Stadlmeier, Runtsch, L. Simon, Streshnev, F., Wühr, M., and Carell, T., “A Click-chemistry based enrichable cross-linker for structural and protein interaction analysis by mass spectrometry.”, Chembiochem, 2019.
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.
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.
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.
D. Papatsenko, Levine, M., and Goltsev, Y., “Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles.”, PLoS Biol, vol. 9, no. 1, p. e1000584, 2011.
N. Yakoby, Bristow, C. A., Gong, D., Schafer, X., Lembong, J., Zartman, J. J., Halfon, M. S., Schüpbach, T., and Shvartsman, S. Y., “A combinatorial code for pattern formation in Drosophila oogenesis.”, Dev Cell, vol. 15, no. 5, pp. 725-37, 2008.
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.
E. Zaslavsky and Singh, M., “A combinatorial optimization approach for diverse motif finding applications.”, Algorithms Mol Biol, vol. 1, p. 13, 2006.
E. Wieschaus, “A combined genetic and mosaic approach to the study of oogenesis in Drosophila.”, Basic Life Sci, vol. 16, pp. 85-94, 1980.
J. W. Shaevitz, “Combining modeling and experiment to understand bacterial growth.”, Biophys J, vol. 104, no. 12, p. 2573, 2013.
P. A. Gibney, Schieler, A., Chen, J. C., Bacha-Hummel, J. M., Botstein, M., Volpe, M., Silverman, S. J., Xu, Y., Bennett, B. D., Rabinowitz, J. D., and Botstein, D., “Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast.”, Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 2018.
R. Osada, Zaslavsky, E., and Singh, M., “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
Y. Guan, Dunham, M. J., Troyanskaya, O. G., and Caudy, A. A., “Comparative gene expression between two yeast species.”, BMC Genomics, vol. 14, p. 33, 2013.
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.
D. Gresham, Dunham, M. J., and Botstein, D., “Comparing whole genomes using DNA microarrays.”, Nat Rev Genet, vol. 9, no. 4, pp. 291-302, 2008.
M. E. Kavousanakis, Kanodia, J. S., Kim, Y., Kevrekidis, I. G., and Shvartsman, S. Y., “A compartmental model for the bicoid gradient.”, Dev Biol, vol. 345, no. 1, pp. 12-7, 2010.
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.
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.
H. V. Dinh, Suthers, P. F., Chan, S. Hung Joshu, Shen, Y., Xiao, T., Deewan, A., Jagtap, S. S., Zhao, H., Rao, C. V., Rabinowitz, J. D., and Maranas, C. D., “A comprehensive genome-scale model for IFO0880 accounting for functional genomics and phenotypic data.”, Metab Eng Commun, vol. 9, p. e00101, 2019.
F. Biemar, Nix, D. A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., J Manak, R., and Levine, M. S., “Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.”, Proc Natl Acad Sci U S A, vol. 103, no. 34, pp. 12763-8, 2006.
C. Cao, Lemaire, L. A., Wang, W., Yoon, P. H., Choi, Y. A., Parsons, L. R., Matese, J. C., Wang, W., Levine, M., and Chen, K., “Comprehensive single-cell transcriptome lineages of a proto-vertebrate.”, Nature, vol. 571, no. 7765, pp. 349-354, 2019.
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.
G. T. Reeves, Kalifa, R., Klein, D. E., Lemmon, M. A., and Shvartsman, S. Y., “Computational analysis of EGFR inhibition by Argos.”, Dev Biol, vol. 284, no. 2, pp. 523-35, 2005.
C. Huttenhower, Myers, C. L., Hibbs, M. A., and Troyanskaya, O. G., “Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.”, Methods Mol Biol, vol. 548, pp. 273-93, 2009.
X. X. Du, Osterfield, M., and Shvartsman, S. Y., “Computational analysis of three-dimensional epithelial morphogenesis using vertex models.”, Phys Biol, vol. 11, no. 6, p. 066007, 2014.
P. Jiang, Singh, M., and Coller, H. A., “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
Y. -suk Lee, Krishnan, A., Oughtred, R., Rust, J., Chang, C. S., Ryu, J., Kristensen, V. N., Dolinski, K., Theesfeld, C. L., and Troyanskaya, O. G., “A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.”, Cell Syst, vol. 8, no. 2, pp. 152-162.e6, 2019.
F. Markowetz and Troyanskaya, O. G., “Computational identification of cellular networks and pathways.”, Mol Biosyst, vol. 3, no. 7, pp. 478-82, 2007.
D. Papatsenko and Levine, M., “Computational identification of regulatory DNAs underlying animal development.”, Nat Methods, vol. 2, no. 7, pp. 529-34, 2005.
S. H Wiley, Shvartsman, S. Y., and Lauffenburger, D. A., “Computational modeling of the EGF-receptor system: a paradigm for systems biology.”, Trends Cell Biol, vol. 13, no. 1, pp. 43-50, 2003.
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., “A computational statistics approach for estimating the spatial range of morphogen gradients.”, Development, vol. 138, no. 22, pp. 4867-74, 2011.
D. C. Hess, Myers, C. L., Huttenhower, C., Hibbs, M. A., Hayes, A. P., Paw, J., Clore, J. J., Mendoza, R. M., San Luis, B., Nislow, C., Giaever, G., Costanzo, M., Troyanskaya, O. G., and Caudy, A. A., “Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.”, PLoS Genet, vol. 5, no. 3, p. e1000407, 2009.
M. Levine, “Computing away the magic?”, Elife, vol. 2, p. e01135, 2013.
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
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. Godbout and Tilghman, S. M., “Configuration of the alpha-fetoprotein regulatory domain during development.”, Genes Dev, vol. 2, no. 8, pp. 949-56, 1988.
J. Cande, Goltsev, Y., and Levine, M. S., “Conservation of enhancer location in divergent insects.”, Proc Natl Acad Sci U S A, vol. 106, no. 34, pp. 14414-9, 2009.
M. J. Brauer, Yuan, J., Bennett, B. D., Lu, W., Kimball, E., Botstein, D., and Rabinowitz, J. D., “Conservation of the metabolomic response to starvation across two divergent microbes.”, Proc Natl Acad Sci U S A, vol. 103, no. 51, pp. 19302-7, 2006.
D. Papatsenko, Kislyuk, A., Levine, M., and Dubchak, I., “Conservation patterns in different functional sequence categories of divergent Drosophila species.”, Genomics, vol. 88, no. 4, pp. 431-42, 2006.
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.
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.
R. N. Arey and Murphy, C. T., “Conserved regulators of cognitive aging: From worms to humans.”, Behav Brain Res, vol. 322, no. Pt B, pp. 299-310, 2017.
Y. Kim, Iagovitina, A., Ishihara, K., Fitzgerald, K. M., Deplancke, B., Papatsenko, D., and Shvartsman, S. Y., “Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.”, Chaos, vol. 23, no. 2, p. 025105, 2013.
C. L. Myers and Troyanskaya, O. G., “Context-sensitive data integration and prediction of biological networks.”, Bioinformatics, vol. 23, no. 17, pp. 2322-30, 2007.
M. Levine, “The contraction of time and space in remote chromosomal interactions.”, Cell, vol. 158, no. 2, pp. 243-4, 2014.
J. Grosshans, H Müller, A. J., and Wieschaus, E., “Control of cleavage cycles in Drosophila embryos by frühstart.”, Dev Cell, vol. 5, no. 2, pp. 285-94, 2003.
D. N. Keys, Levine, M., Harland, R. M., and Wallingford, J. B., “Control of intercalation is cell-autonomous in the notochord of Ciona intestinalis.”, Dev Biol, vol. 246, no. 2, pp. 329-40, 2002.
P. Andolfatto, “Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA.”, Genetics, vol. 180, no. 3, pp. 1767-71, 2008.
N. S. Wingreen and Levin, S. A., “Cooperation among microorganisms.”, PLoS Biol, vol. 4, no. 9, p. e299, 2006.
W. Bialek and Setayeshgar, S., “Cooperativity, sensitivity, and noise in biochemical signaling.”, Phys Rev Lett, vol. 100, no. 25, p. 258101, 2008.
A. Erives and Levine, M., “Coordinate enhancers share common organizational features in the Drosophila genome.”, Proc Natl Acad Sci U S A, vol. 101, no. 11, pp. 3851-6, 2004.
V. C. Calhoun and Levine, M., “Coordinate regulation of an extended chromosome domain.”, Cell, vol. 113, no. 3, pp. 278-80, 2003.
C. Rauskolb and Wieschaus, E., “Coordinate regulation of downstream genes by extradenticle and the homeotic selector proteins.”, EMBO J, vol. 13, no. 15, pp. 3561-9, 1994.
P. H. Bradley, Brauer, M. J., Rabinowitz, J. D., and Troyanskaya, O. G., “Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
J. M. Goodliffe, Cole, M. D., and Wieschaus, E., “Coordinated regulation of Myc trans-activation targets by Polycomb and the Trithorax group protein Ash1.”, BMC Mol Biol, vol. 8, p. 40, 2007.
M. J. Hickman, Petti, A. A., Ho-Shing, O., Silverman, S. J., R McIsaac, S., Lee, T. A., and Botstein, D., “Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.”, Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
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. P. Gross, Welte, M. A., Block, S. M., and Wieschaus, E. F., “Coordination of opposite-polarity microtubule motors.”, J Cell Biol, vol. 156, no. 4, pp. 715-24, 2002.
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.
G. I. Lang, Murray, A. W., and Botstein, D., “The cost of gene expression underlies a fitness trade-off in yeast.”, Proc Natl Acad Sci U S A, vol. 106, no. 14, pp. 5755-60, 2009.
N. Slavov and Botstein, D., “Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast.”, Mol Biol Cell, vol. 22, no. 12, pp. 1997-2009, 2011.
X. Lu, Li, J. M., Elemento, O., Tavazoie, S., and Wieschaus, E. F., “Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition.”, Development, vol. 136, no. 12, pp. 2101-10, 2009.
L. Peña-Castillo, Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W. Kyu, Krumpelman, C., Tian, W., Obozinski, G., Qi, Y., Mostafavi, S., Lin, G. Ning, Berriz, G. F., Gibbons, F. D., Lanckriet, G., Qiu, J., Grant, C., Barutcuoglu, Z., Hill, D. P., Warde-Farley, D., Grouios, C., Ray, D., Blake, J. A., Deng, M., Jordan, M. I., Noble, W. S., Morris, Q., Klein-Seetharaman, J., Bar-Joseph, iv, Z., Chen, T., Sun, F., Troyanskaya, O. G., Marcotte, E. M., Xu, D., Hughes, T. R., and Roth, F. P., “A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.”, Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
K. Jim, Parmar, K., Singh, M., and Tavazoie, S., “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
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.
A. T. Hark, Schoenherr, C. J., Katz, D. J., Ingram, R. S., Levorse, J. M., and Tilghman, S. M., “CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus.”, Nature, vol. 405, no. 6785, pp. 486-9, 2000.
R. Mukhopadhyay and Wingreen, N. S., “Curvature and shape determination of growing bacteria.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 6 Pt 1, p. 062901, 2009.
J. W. Shaevitz and Fletcher, D. A., “Curvature and torsion in growing actin networks.”, Phys Biol, vol. 5, no. 2, p. 026006, 2008.
K. Casey Huang, Mukhopadhyay, R., and Wingreen, N. S., “A curvature-mediated mechanism for localization of lipids to bacterial poles.”, PLoS Comput Biol, vol. 2, no. 11, p. e151, 2006.
A. Pane, Jiang, P., Zhao, D. Yanling, Singh, M., and Schüpbach, T., “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
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.
R. Dannenfelser, Nome, M., Tahiri, A., Ursini-Siegel, J., Vollan, H. Kristian M., Haakensen, V. D., Helland, Å., Naume, B., Caldas, C., Børresen-Dale, A. - L., Kristensen, V. N., and Troyanskaya, O. G., “Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity.”, Oncotarget, vol. 8, no. 34, pp. 57121-57133, 2017.
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.
A. V. Persikov and Singh, M., “De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins.”, Nucleic Acids Res, vol. 42, no. 1, pp. 97-108, 2014.
M. Markstein and Levine, M., “Decoding cis-regulatory DNAs in the Drosophila genome.”, Curr Opin Genet Dev, vol. 12, no. 5, pp. 601-6, 2002.
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.
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.
J. Zhou, Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., and Troyanskaya, O. G., “Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.”, Nat Genet, vol. 50, no. 8, pp. 1171-1179, 2018.
A. V. Persikov, Rowland, E. F., Oakes, B. L., Singh, M., and Noyes, M. B., “Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.”, Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 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.

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