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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Animals
D. L. Metallinos, Oppenheimer, A. J., Rinchik, E. M., Russell, L. B., Dietrich, W., and Tilghman, S. M., “Fine structure mapping and deletion analysis of the murine piebald locus.”, Genetics, vol. 136, no. 1, pp. 217-23, 1994.
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. Tipping, Kim, Y., Kyriakakis, P., Tong, M., Shvartsman, S. Y., and Veraksa, A., “β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.”, EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
H. Yoo-Warren, Pachnis, V., Ingram, R. S., and Tilghman, S. M., “Two regulatory domains flank the mouse H19 gene.”, Mol Cell Biol, vol. 8, no. 11, pp. 4707-15, 1988.
S. Zemel, Bartolomei, M. S., and Tilghman, S. M., “Physical linkage of two mammalian imprinted genes, H19 and insulin-like growth factor 2.”, Nat Genet, vol. 2, no. 1, pp. 61-5, 1992.
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.
M. S. Bartolomei, Zemel, S., and Tilghman, S. M., “Parental imprinting of the mouse H19 gene.”, Nature, vol. 351, no. 6322, pp. 153-5, 1991.
J. M. Rossi, Burke, D. T., Leung, J. C., Koos, D. S., Chen, H., and Tilghman, S. M., “Genomic analysis using a yeast artificial chromosome library with mouse DNA inserts.”, Proc Natl Acad Sci U S A, vol. 89, no. 6, pp. 2456-60, 1992.
P. A. Leighton, Saam, J. R., Ingram, R. S., Stewart, C. L., and Tilghman, S. M., “An enhancer deletion affects both H19 and Igf2 expression.”, Genes Dev, vol. 9, no. 17, pp. 2079-89, 1995.
N. S. Tolwinski and Wieschaus, E., “A nuclear function for armadillo/beta-catenin.”, PLoS Biol, vol. 2, no. 4, p. E95, 2004.
B. T. Spear and Tilghman, S. M., “Role of alpha-fetoprotein regulatory elements in transcriptional activation in transient heterokaryons.”, Mol Cell Biol, vol. 10, no. 10, pp. 5047-54, 1990.
T. Caspary, Cleary, M. A., Baker, C. C., Guan, X. J., and Tilghman, S. M., “Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster.”, Mol Cell Biol, vol. 18, no. 6, pp. 3466-74, 1998.
R. Menon, Otto, E. A., Kokoruda, A., Zhou, J., Zhang, Z., Yoon, E., Chen, Y. - C., Troyanskaya, O., Spence, J. R., Kretzler, M., and Cebrián, C., “Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.”, Development, vol. 145, no. 16, 2018.
B. P. Berman, Nibu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M., and Eisen, M. B., “Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.”, Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 757-62, 2002.
J. V. Schmidt, Matteson, P. G., Jones, B. K., Guan, X. J., and Tilghman, S. M., “The Dlk1 and Gtl2 genes are linked and reciprocally imprinted.”, Genes Dev, vol. 14, no. 16, pp. 1997-2002, 2000.
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. Vacher and Tilghman, S. M., “Dominant negative regulation of the mouse alpha-fetoprotein gene in adult liver.”, Science, vol. 250, no. 4988, pp. 1732-5, 1990.
R. Godbout, Ingram, R. S., and Tilghman, S. M., “Fine-structure mapping of the three mouse alpha-fetoprotein gene enhancers.”, Mol Cell Biol, vol. 8, no. 3, pp. 1169-78, 1988.
J. Miller, Zeng, C., Wingreen, N. S., and Tang, C., “Emergence of highly designable protein-backbone conformations in an off-lattice model.”, Proteins, vol. 47, no. 4, pp. 506-12, 2002.
G. Tkačik, Callan, C. G., and Bialek, W., “Information flow and optimization in transcriptional regulation.”, Proc Natl Acad Sci U S A, vol. 105, no. 34, pp. 12265-70, 2008.
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.
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.
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.
G. Tkačik, Gregor, T., and Bialek, W., “The role of input noise in transcriptional regulation.”, PLoS One, vol. 3, no. 7, p. e2774, 2008.
C. Jang, Hui, S., Lu, W., Cowan, A. J., Morscher, R. J., Lee, G., Liu, W., Tesz, G. J., Birnbaum, M. J., and Rabinowitz, J. D., “The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids.”, Cell Metab, vol. 27, no. 2, pp. 351-361.e3, 2018.
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.
L. J. Kurihara, Semenova, E., Levorse, J. M., and Tilghman, S. M., “Expression and functional analysis of Uch-L3 during mouse development.”, Mol Cell Biol, vol. 20, no. 7, pp. 2498-504, 2000.
B. Haley, Hendrix, D., Trang, V., and Levine, M., “A simplified miRNA-based gene silencing method for Drosophila melanogaster.”, Dev Biol, vol. 321, no. 2, pp. 482-90, 2008.
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.
C. S. Greene and Troyanskaya, O. G., “PILGRM: an interactive data-driven discovery platform for expert biologists.”, Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
T. Gregor, Tank, D. W., Wieschaus, E. F., and Bialek, W., “Probing the limits to positional information.”, Cell, vol. 130, no. 1, pp. 153-64, 2007.
T. Gregor, Bialek, W., van Steveninck, R. R. de Ruyte, Tank, D. W., and Wieschaus, E. F., “Diffusion and scaling during early embryonic pattern formation.”, Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18403-7, 2005.
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.
G. Tkačik, Walczak, A. M., and Bialek, W., “Optimizing information flow in small genetic networks.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 3 Pt 1, p. 031920, 2009.
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.
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
A. Stathopoulos, Tam, B., Ronshaugen, M., Frasch, M., and Levine, M., “pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos.”, Genes Dev, vol. 18, no. 6, pp. 687-99, 2004.
D. T. Burke, Rossi, J. M., Leung, J., Koos, D. S., and Tilghman, S. M., “A mouse genomic library of yeast artificial chromosome clones.”, Mamm Genome, vol. 1, no. 1, p. 65, 1991.
V. D. Nair, Ge, Y., Balasubramaniyan, N., Kim, J., Okawa, Y., Chikina, M., Troyanskaya, O., and Sealfon, S. C., “Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells.”, Mol Cell Biol, vol. 32, no. 23, pp. 4861-76, 2012.
S. C. Little, Tikhonov, M., and Gregor, T., “Precise developmental gene expression arises from globally stochastic transcriptional activity.”, Cell, vol. 154, no. 4, pp. 789-800, 2013.
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.
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.
C. D. van Raamsdonk and Tilghman, S. M., “Optimizing the detection of nascent transcripts by RNA fluorescence in situ hybridization.”, Nucleic Acids Res, vol. 29, no. 8, pp. E42-2, 2001.
M. Levine, Cattoglio, C., and Tjian, R., “Looping back to leap forward: transcription enters a new era.”, Cell, vol. 157, no. 1, pp. 13-25, 2014.
K. Pfeifer, Leighton, P. A., and Tilghman, S. M., “The structural H19 gene is required for transgene imprinting.”, Proc Natl Acad Sci U S A, vol. 93, no. 24, pp. 13876-83, 1996.
M. Levine and Tjian, R., “Transcription regulation and animal diversity.”, Nature, vol. 424, no. 6945, pp. 147-51, 2003.
E. Semenova, Wang, X. F., Jablonski, M. M., Levorse, J., and Tilghman, S. M., “An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina.”, Hum Mol Genet, vol. 12, no. 11, pp. 1301-12, 2003.
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J., “A method for detecting and correcting feature misidentification on expression microarrays.”, BMC Genomics, vol. 5, p. 64, 2004.
J. Vacher, Camper, S. A., Krumlauf, R., Compton, R. S., and Tilghman, S. M., “raf regulates the postnatal repression of the mouse alpha-fetoprotein gene at the posttranscriptional level.”, Mol Cell Biol, vol. 12, no. 2, pp. 856-64, 1992.
M. van de Rijn, Perou, C. M., Tibshirani, R., Haas, P., Kallioniemi, O., Kononen, J., Torhorst, J., Sauter, G., Zuber, M., Köchli, O. R., Mross, F., Dieterich, H., Seitz, R., Ross, D., Botstein, D., and Brown, P., “Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome.”, Am J Pathol, vol. 161, no. 6, pp. 1991-6, 2002.
P. B. Vrana, Guan, X. J., Ingram, R. S., and Tilghman, S. M., “Genomic imprinting is disrupted in interspecific Peromyscus hybrids.”, Nat Genet, vol. 20, no. 4, pp. 362-5, 1998.
J. M. Rossi, Chen, H., and Tilghman, S. M., “Genetic map of the fused locus on mouse chromosome 17.”, Genomics, vol. 23, no. 1, pp. 178-84, 1994.
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.
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.
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.
H. G. Garcia, Tikhonov, M., Lin, A., and Gregor, T., “Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning.”, Curr Biol, vol. 23, no. 21, pp. 2140-5, 2013.
S. C. Little, Tkačik, G., Kneeland, T. B., Wieschaus, E. F., and Gregor, T., “The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA.”, PLoS Biol, vol. 9, no. 3, p. e1000596, 2011.
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.
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.
D. Mancini-Dinardo, Steele, S. J. S., Levorse, J. M., Ingram, R. S., and Tilghman, S. M., “Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes.”, Genes Dev, vol. 20, no. 10, pp. 1268-82, 2006.
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.
J. A. Drocco, Grimm, O., Tank, D. W., and Wieschaus, E., “Measurement and perturbation of morphogen lifetime: effects on gradient shape.”, Biophys J, vol. 101, no. 8, pp. 1807-15, 2011.
S. M. Tilghman, Bartolomei, M. S., Webber, A. L., Brunkow, M. E., Saam, J., Leighton, P. A., Pfeifer, K., and Zemel, S., “Parental imprinting of the H19 and Igf2 genes in the mouse.”, Cold Spring Harb Symp Quant Biol, vol. 58, pp. 287-95, 1993.
C. D. van Raamsdonk and Tilghman, S. M., “Dosage requirement and allelic expression of PAX6 during lens placode formation.”, Development, vol. 127, no. 24, pp. 5439-48, 2000.
M. A. Gelbart, He, B., Martin, A. C., Thiberge, S. Y., Wieschaus, E. F., and Kaschube, M., “Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis.”, Proc Natl Acad Sci U S A, vol. 109, no. 47, pp. 19298-303, 2012.
B. K. Jones, Levorse, J., and Tilghman, S. M., “A human H19 transgene exhibits impaired paternal-specific imprint acquisition and maintenance in mice.”, Hum Mol Genet, vol. 11, no. 4, pp. 411-8, 2002.
T. Caspary, Cleary, M. A., Perlman, E. J., Zhang, P., Elledge, S. J., and Tilghman, S. M., “Oppositely imprinted genes p57(Kip2) and igf2 interact in a mouse model for Beckwith-Wiedemann syndrome.”, Genes Dev, vol. 13, no. 23, pp. 3115-24, 1999.
W. Ju, Greene, C. S., Eichinger, F., Nair, V., Hodgin, J. B., Bitzer, M., Lee, Y. -suk, Zhu, Q., Kehata, M., Li, M., Jiang, S., Rastaldi, M. Pia, Cohen, C. D., Troyanskaya, O. G., and Kretzler, M., “Defining cell-type specificity at the transcriptional level in human disease.”, Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
Q. Wang, J Taliaferro, M., Klibaite, U., Hilgers, V., Shaevitz, J. W., and Rio, D. C., “The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.”, Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 2016.
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.
T. Gregor, Wieschaus, E. F., McGregor, A. P., Bialek, W., and Tank, D. W., “Stability and nuclear dynamics of the bicoid morphogen gradient.”, Cell, vol. 130, no. 1, pp. 141-52, 2007.
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.
D. J. Katz, Beer, M. A., Levorse, J. M., and Tilghman, S. M., “Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region.”, Mol Cell Biol, vol. 25, no. 10, pp. 3855-63, 2005.
J. O. Dubuis, Tkačik, G., Wieschaus, E. F., Gregor, T., and Bialek, W., “Positional information, in bits.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
D. Mancini-Dinardo, Steele, S. J. S., Ingram, R. S., and Tilghman, S. M., “A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer.”, Hum Mol Genet, vol. 12, no. 3, pp. 283-94, 2003.
J. J. Kamphorst, Cross, J. R., Fan, J., de Stanchina, E., Mathew, R., White, E. P., Thompson, C. B., and Rabinowitz, J. D., “Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids.”, Proc Natl Acad Sci U S A, vol. 110, no. 22, pp. 8882-7, 2013.
M. K. Shin, Russell, L. B., and Tilghman, S. M., “Molecular characterization of four induced alleles at the Ednrb locus.”, Proc Natl Acad Sci U S A, vol. 94, no. 24, pp. 13105-10, 1997.
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.
A. K. Wong, Park, C. Y., Greene, C. S., Bongo, L. A., Guan, Y., and Troyanskaya, O. G., “IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.”, Nucleic Acids Res, vol. 40, no. Web Server issue, pp. W484-90, 2012.
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.
G. Tkačik, Callan, C. G., and Bialek, W., “Information capacity of genetic regulatory elements.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, no. 1 Pt 1, p. 011910, 2008.
J. A. Drocco, Wieschaus, E. F., and Tank, D. W., “The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs.”, Phys Biol, vol. 9, no. 5, p. 055004, 2012.
M. A. Cleary, van Raamsdonk, C. D., Levorse, J., Zheng, B., Bradley, A., and Tilghman, S. M., “Disruption of an imprinted gene cluster by a targeted chromosomal translocation in mice.”, Nat Genet, vol. 29, no. 1, pp. 78-82, 2001.
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. J. Vasicek, Zeng, L., Guan, X. J., Zhang, T., Costantini, F., and Tilghman, S. M., “Two dominant mutations in the mouse fused gene are the result of transposon insertions.”, Genetics, vol. 147, no. 2, pp. 777-86, 1997.
M. S. Bartolomei, Webber, A. L., Brunkow, M. E., and Tilghman, S. M., “Epigenetic mechanisms underlying the imprinting of the mouse H19 gene.”, Genes Dev, vol. 7, no. 9, pp. 1663-73, 1993.
S. M. Tilghman, “The sins of the fathers and mothers: genomic imprinting in mammalian development.”, Cell, vol. 96, no. 2, pp. 185-93, 1999.
M. Tipping, Kim, Y., Kyriakakis, P., Tong, M., Shvartsman, S. Y., and Veraksa, A., “β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.”, EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
M. D. Chikina, Huttenhower, C., Murphy, C. T., and Troyanskaya, O. G., “Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.”, PLoS Comput Biol, vol. 5, no. 6, p. e1000417, 2009.
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.
C. S. Greene and Troyanskaya, O. G., “Integrative systems biology for data-driven knowledge discovery.”, Semin Nephrol, vol. 30, no. 5, pp. 443-54, 2010.
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Y. Guan, Gorenshteyn, D., Burmeister, M., Wong, A. K., Schimenti, J. C., Handel, M. Ann, Bult, C. J., Hibbs, M. A., and Troyanskaya, O. G., “Tissue-specific functional networks for prioritizing phenotype and disease genes.”, PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
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.
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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.
A. L. Webber, Ingram, R. S., Levorse, J. M., and Tilghman, S. M., “Location of enhancers is essential for the imprinting of H19 and Igf2 genes.”, Nature, vol. 391, no. 6668, pp. 711-5, 1998.
J. A. Emerson, Vacher, J., Cirillo, L. A., Tilghman, S. M., and Tyner, A. L., “The zonal expression of alpha-fetoprotein transgenes in the livers of adult mice.”, Dev Dyn, vol. 195, no. 1, pp. 55-66, 1992.
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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.
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.
N. S. Tolwinski and Wieschaus, E., “Rethinking WNT signaling.”, Trends Genet, vol. 20, no. 4, pp. 177-81, 2004.
S. M. Tilghman, “Lessons learned, promises kept: a biologist's eye view of the Genome Project.”, Genome Res, vol. 6, no. 9, pp. 773-80, 1996.
S. De Renzis, Elemento, O., Tavazoie, S., and Wieschaus, E. F., “Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo.”, PLoS Biol, vol. 5, no. 5, p. e117, 2007.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., “A genomewide functional network for the laboratory mouse.”, PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
N. S. Tolwinski, Wehrli, M., Rives, A., Erdeniz, N., DiNardo, S., and Wieschaus, E., “Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity.”, Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
M. Lagha, Bothma, J. P., Esposito, E., Ng, S., Stefanik, L., Tsui, C., Johnston, J., Chen, K., Gilmour, D. S., Zeitlinger, J., and Levine, M. S., “Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.”, Cell, vol. 153, no. 5, pp. 976-87, 2013.
N. D. Trinklein, Murray, J. I., Hartman, S. J., Botstein, D., and Myers, R. M., “The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response.”, Mol Biol Cell, vol. 15, no. 3, pp. 1254-61, 2004.
A. L. Tyner, Godbout, R., Compton, R. S., and Tilghman, S. M., “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.
J. Fan, Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., and Rabinowitz, J. D., “Quantitative flux analysis reveals folate-dependent NADPH production.”, Nature, vol. 510, no. 7504, pp. 298-302, 2014.
O. G. Troyanskaya, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
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.
O. G. Troyanskaya, “Integrated analysis of microarray results.”, Methods Mol Biol, vol. 382, pp. 429-37, 2007.
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.
V. S. Chopra, Hendrix, D. A., Core, L. J., Tsui, C., Lis, J. T., and Levine, M., “The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo.”, Mol Cell, vol. 42, no. 6, pp. 837-44, 2011.
S. M. Tilghman, “DNA methylation: a phoenix rises.”, Proc Natl Acad Sci U S A, vol. 90, no. 19, pp. 8761-2, 1993.
O. Troyanskaya, “"Getting started in..": a series not to miss.”, PLoS Comput Biol, vol. 3, no. 10, p. 1841, 2007.
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.
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.
C. Y. Park, Wong, A. K., Greene, C. S., Rowland, J., Guan, Y., Bongo, L. A., Burdine, R. D., and Troyanskaya, O. G., “Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.”, PLoS Comput Biol, vol. 9, no. 3, p. e1002957, 2013.
P. A. Leighton, Saam, J. R., Ingram, R. S., and Tilghman, S. M., “Genomic imprinting in mice: its function and mechanism.”, Biol Reprod, vol. 54, no. 2, pp. 273-8, 1996.
C. I. Brannan, Dees, E. C., Ingram, R. S., and Tilghman, S. M., “The product of the H19 gene may function as an RNA.”, Mol Cell Biol, vol. 10, no. 1, pp. 28-36, 1990.
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.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
Y. Guan, Myers, C. L., Hess, D. C., Barutcuoglu, Z., Caudy, A. A., and Troyanskaya, O. G., “Predicting gene function in a hierarchical context with an ensemble of classifiers.”, Genome Biol, vol. 9 Suppl 1, p. S3, 2008.
A. L. Tyner, Godbout, R., Compton, R. S., and Tilghman, S. M., “The ontogeny of alpha-fetoprotein gene expression in the mouse gastrointestinal tract.”, J Cell Biol, vol. 110, no. 4, pp. 915-27, 1990.
M. van de Rijn, Perou, C. M., Tibshirani, R., Haas, P., Kallioniemi, O., Kononen, J., Torhorst, J., Sauter, G., Zuber, M., Köchli, O. R., Mross, F., Dieterich, H., Seitz, R., Ross, D., Botstein, D., and Brown, P., “Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome.”, Am J Pathol, vol. 161, no. 6, pp. 1991-6, 2002.
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.
A. Stolfi, Wagner, E., J Taliaferro, M., Chou, S., and Levine, M., “Neural tube patterning by Ephrin, FGF and Notch signaling relays.”, Development, vol. 138, no. 24, pp. 5429-39, 2011.
N. S. Tolwinski and Wieschaus, E., “A nuclear escort for beta-catenin.”, Nat Cell Biol, vol. 6, no. 7, pp. 579-80, 2004.
R. Papazyan, Sun, Z., Kim, Y. Hoon, Titchenell, P. M., Hill, D. A., Lu, W., Damle, M., Wan, M., Zhang, Y., Briggs, E. R., Rabinowitz, J. D., and Lazar, M. A., “Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP.”, Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
S. M. Tilghman, “Parental imprinting in the mouse.”, Harvey Lect, vol. 87, pp. 69-84, 1991.
J. H. Millonig, Emerson, J. A., Levorse, J. M., and Tilghman, S. M., “Molecular analysis of the distal enhancer of the mouse alpha-fetoprotein gene.”, Mol Cell Biol, vol. 15, no. 7, pp. 3848-56, 1995.
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.
W. J. Pavan, Mac, S., Cheng, M., and Tilghman, S. M., “Quantitative trait loci that modify the severity of spotting in piebald mice.”, Genome Res, vol. 5, no. 1, pp. 29-41, 1995.
Animals, Genetically Modified
H. G. Garcia, Tikhonov, M., Lin, A., and Gregor, T., “Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning.”, Curr Biol, vol. 23, no. 21, pp. 2140-5, 2013.
Animals, Newborn
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.
A. B. Bowman, Levorse, J. M., Ingram, R. S., and Tilghman, S. M., “Functional characterization of a testis-specific DNA binding activity at the H19/Igf2 imprinting control region.”, Mol Cell Biol, vol. 23, no. 22, pp. 8345-51, 2003.
J. Vacher and Tilghman, S. M., “Dominant negative regulation of the mouse alpha-fetoprotein gene in adult liver.”, Science, vol. 250, no. 4988, pp. 1732-5, 1990.
E. Semenova, Wang, X. F., Jablonski, M. M., Levorse, J., and Tilghman, S. M., “An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina.”, Hum Mol Genet, vol. 12, no. 11, pp. 1301-12, 2003.
Antibodies, Anti-Idiotypic
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J., “Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”, BMC Immunol, vol. 3, p. 5, 2002.
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J., “Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”, BMC Immunol, vol. 3, p. 5, 2002.
Antibodies, Monoclonal
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.
Antibodies, Monoclonal, Murine-Derived
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.
Antigen Presentation
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., “Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.”, PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
Antigens, CD20
M. L. Whitfield, Finlay, D. R., Murray, J. Isaac, Troyanskaya, O. G., Chi, J. - T., Pergamenschikov, A., McCalmont, T. H., Brown, P. O., Botstein, D., and M Connolly, K., “Systemic and cell type-specific gene expression patterns in scleroderma skin.”, Proc Natl Acad Sci U S A, vol. 100, no. 21, pp. 12319-24, 2003.
Antigens, Nuclear
D. J. Katz, Beer, M. A., Levorse, J. M., and Tilghman, S. M., “Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region.”, Mol Cell Biol, vol. 25, no. 10, pp. 3855-63, 2005.
Antineoplastic Agents
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.
Antineoplastic Combined Chemotherapy Protocols
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.
Apoenzymes
J. A. Capra, Laskowski, R. A., Thornton, J. M., Singh, M., and Funkhouser, T. A., “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
Apoptosis
C. D. van Raamsdonk and Tilghman, S. M., “Dosage requirement and allelic expression of PAX6 during lens placode formation.”, Development, vol. 127, no. 24, pp. 5439-48, 2000.
Arabidopsis
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.
A. Pop, Huttenhower, C., Iyer-Pascuzzi, A., Benfey, P. N., and Troyanskaya, O. G., “Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.”, BMC Syst Biol, vol. 4, p. 180, 2010.
Arabidopsis Proteins
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.
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.
Area Under Curve
K. M. Chen, Cofer, E. M., Zhou, J., and Troyanskaya, O. G., “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
J. Zhou and Troyanskaya, O. G., “Global quantitative modeling of chromatin factor interactions.”, PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
J. A. Capra, Laskowski, R. A., Thornton, J. M., Singh, M., and Funkhouser, T. A., “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
C. Huttenhower and Troyanskaya, O. G., “Bayesian data integration: a functional perspective.”, Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
Armadillo Domain Proteins
N. S. Tolwinski, Wehrli, M., Rives, A., Erdeniz, N., DiNardo, S., and Wieschaus, E., “Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity.”, Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
N. S. Tolwinski and Wieschaus, E., “Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan.”, Development, vol. 128, no. 11, pp. 2107-17, 2001.
N. S. Tolwinski and Wieschaus, E., “A nuclear function for armadillo/beta-catenin.”, PLoS Biol, vol. 2, no. 4, p. E95, 2004.
Arrestins
M. Tipping, Kim, Y., Kyriakakis, P., Tong, M., Shvartsman, S. Y., and Veraksa, A., “β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.”, EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
M. Tipping, Kim, Y., Kyriakakis, P., Tong, M., Shvartsman, S. Y., and Veraksa, A., “β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development.”, EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
Artificial Intelligence
C. Huttenhower, Schroeder, M., Chikina, M. D., and Troyanskaya, O. G., “The Sleipnir library for computational functional genomics.”, Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
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.
W. Ju, Greene, C. S., Eichinger, F., Nair, V., Hodgin, J. B., Bitzer, M., Lee, Y. -suk, Zhu, Q., Kehata, M., Li, M., Jiang, S., Rastaldi, M. Pia, Cohen, C. D., Troyanskaya, O. G., and Kretzler, M., “Defining cell-type specificity at the transcriptional level in human disease.”, Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
M. A. Hibbs, Dirksen, N. C., Li, K., and Troyanskaya, O. G., “Visualization methods for statistical analysis of microarray clusters.”, BMC Bioinformatics, vol. 6, p. 115, 2005.
M. D. Chikina, Huttenhower, C., Murphy, C. T., and Troyanskaya, O. G., “Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.”, PLoS Comput Biol, vol. 5, no. 6, p. e1000417, 2009.
Asian Continental Ancestry Group
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.
Asparaginase
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.
Asparagine
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.
ATP-Binding Cassette Transporters
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.
Autism Spectrum Disorder
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
Autistic Disorder
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.
Autophagy
J. J. Kamphorst, Cross, J. R., Fan, J., de Stanchina, E., Mathew, R., White, E. P., Thompson, C. B., and Rabinowitz, J. D., “Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids.”, Proc Natl Acad Sci U S A, vol. 110, no. 22, pp. 8882-7, 2013.
C. Huttenhower, Haley, E. M., Hibbs, M. A., Dumeaux, V., Barrett, D. R., Coller, H. A., and Troyanskaya, O. G., “Exploring the human genome with functional maps.”, Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
Axin Protein
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.
T. J. Vasicek, Zeng, L., Guan, X. J., Zhang, T., Costantini, F., and Tilghman, S. M., “Two dominant mutations in the mouse fused gene are the result of transposon insertions.”, Genetics, vol. 147, no. 2, pp. 777-86, 1997.
Azetidinecarboxylic Acid
E. W. Trotter, Kao, C. M. - F., Berenfeld, L., Botstein, D., Petsko, G. A., and Gray, J. V., “Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 47, pp. 44817-25, 2002.
B-Lymphocyte Subsets
M. L. Whitfield, Finlay, D. R., Murray, J. Isaac, Troyanskaya, O. G., Chi, J. - T., Pergamenschikov, A., McCalmont, T. H., Brown, P. O., Botstein, D., and M Connolly, K., “Systemic and cell type-specific gene expression patterns in scleroderma skin.”, Proc Natl Acad Sci U S A, vol. 100, no. 21, pp. 12319-24, 2003.
B-Lymphocytes
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.
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.
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.
Bacterial Proteins
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.
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.
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.
T. Long, Tu, K. C., Wang, Y., Mehta, P., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Quantifying the integration of quorum-sensing signals with single-cell resolution.”, PLoS Biol, vol. 7, no. 3, p. e68, 2009.
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.
Y. Wang, Tu, K. C., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit.”, Biophys J, vol. 100, no. 12, pp. 3045-53, 2011.

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