Tipping, Marla, Yoosik Kim, Phillip Kyriakakis, Mei Tong, Stanislav Y Shvartsman, and Alexey Veraksa. (2010) 2010. “β-Arrestin Kurtz Inhibits MAPK and Toll Signalling in Drosophila Development.”. EMBO J 29 (19): 3222-35.

Welch, Aaron Z, Patrick A Gibney, David Botstein, and Douglas E Koshland. (2013) 2013. “TOR and RAS Pathways Regulate Desiccation Tolerance in Saccharomyces Cerevisiae.”. Mol Biol Cell 24 (2): 115-28.

Park, Christopher Y, David C Hess, Curtis Huttenhower, and Olga G Troyanskaya. 2010. “Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components.”. PLoS Comput Biol 6 (11): e1001009.

Stathopoulos, Angelike, Bergin Tam, Matthew Ronshaugen, Manfred Frasch, and Michael Levine. (2004) 2004. “Pyramus and Thisbe: FGF Genes That Pattern the Mesoderm of Drosophila Embryos.”. Genes Dev 18 (6): 687-99.

Markowetz, Florian, Dennis Kostka, Olga G Troyanskaya, and Rainer Spang. (2007) 2007. “Nested Effects Models for High-Dimensional Phenotyping Screens.”. Bioinformatics 23 (13).

Murphy, Coleen T, Steven A McCarroll, Cornelia I Bargmann, Andrew Fraser, Ravi S Kamath, Julie Ahringer, Hao Li, and Cynthia Kenyon. (2003) 2003. “Genes That Act Downstream of DAF-16 to Influence the Lifespan of Caenorhabditis Elegans.”. Nature 424 (6946): 277-83.

De Renzis, Stefano, J Yu, R Zinzen, and Eric Wieschaus. (2006) 2006. “Dorsal-Ventral Pattern of Delta Trafficking Is Established by a Snail-Tom-Neuralized Pathway.”. Dev Cell 10 (2): 257-64.

Yan, Shian-Jang, Jeremiah J Zartman, Minjie Zhang, Anthony Scott, Stanislav Y Shvartsman, and Willis X Li. 2009. “Bistability Coordinates Activation of the EGFR and DPP Pathways in Drosophila Vein Differentiation.”. Mol Syst Biol 5: 278.

Menon, Rajasree, Edgar A Otto, Austin Kokoruda, Jian Zhou, Zidong Zhang, Euisik Yoon, Yu-Chih Chen, et al. (2018) 2018. “Single-Cell Analysis of Progenitor Cell Dynamics and Lineage Specification in the Human Fetal Kidney.”. Development 145 (16). doi:10.1242/dev.164038.

Gibney, Patrick A, Charles Lu, Amy A Caudy, David C Hess, and David Botstein. (2013) 2013. “Yeast Metabolic and Signaling Genes Are Required for Heat-Shock Survival and Have Little Overlap With the Heat-Induced Genes.”. Proc Natl Acad Sci U S A 110 (46).

Guan, Yuanfang, Dmitriy Gorenshteyn, Margit Burmeister, Aaron K Wong, John C Schimenti, Mary Ann Handel, Carol J Bult, Matthew A Hibbs, and Olga G Troyanskaya. 2012. “Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes.”. PLoS Comput Biol 8 (9): e1002694.

Berezhkovskii, Alexander M, Mathieu Coppey, and Stanislav Y Shvartsman. (2009) 2009. “Signaling Gradients in Cascades of Two-State Reaction-Diffusion Systems.”. Proc Natl Acad Sci U S A 106 (4): 1087-92.

Costa, M, E T Wilson, and E Wieschaus. (1994) 1994. “A Putative Cell Signal Encoded by the Folded Gastrulation Gene Coordinates Cell Shape Changes During Drosophila Gastrulation.”. Cell 76 (6): 1075-89.

Sample, Christine, and Stanislav Y Shvartsman. (2010) 2010. “Multiscale Modeling of Diffusion in the Early Drosophila Embryo.”. Proc Natl Acad Sci U S A 107 (22): 10092-6.

Kim, Yoosik, María José Andreu, Bomyi Lim, Kwanghun Chung, Mark Terayama, Gerardo Jiménez, Celeste A Berg, Hang Lu, and Stanislav Y Shvartsman. (2011) 2011. “Gene Regulation by MAPK Substrate Competition.”. Dev Cell 20 (6): 880-7.

Stathopoulos, Angelike, and Michael Levine. (2002) 2002. “Dorsal Gradient Networks in the Drosophila Embryo.”. Dev Biol 246 (1): 57-67.

Rabinowitz, Joshua D, and Eileen White. (2010) 2010. “Autophagy and Metabolism.”. Science 330 (6009): 1344-8.

Müller, H A, R Samanta, and E Wieschaus. (1999) 1999. “Wingless Signaling in the Drosophila Embryo: Zygotic Requirements and the Role of the Frizzled Genes.”. Development 126 (3): 577-86.

Murphy, Coleen T, Seung-Jae Lee, and Cynthia Kenyon. (2007) 2007. “Tissue Entrainment by Feedback Regulation of Insulin Gene Expression in the Endoderm of Caenorhabditis Elegans.”. Proc Natl Acad Sci U S A 104 (48): 19046-50.

Bejsovec, A, and E Wieschaus. (1995) 1995. “Signaling Activities of the Drosophila Wingless Gene Are Separately Mutable and Appear to Be Transduced at the Cell Surface.”. Genetics 139 (1): 309-20.

Ng, Wai-Leung, Yunzhou Wei, Lark J Perez, Jianping Cong, Tao Long, Matthew Koch, Martin F Semmelhack, Ned S Wingreen, and Bonnie L Bassler. (2010) 2010. “Probing Bacterial Transmembrane Histidine Kinase Receptor-Ligand Interactions With Natural and Synthetic Molecules.”. Proc Natl Acad Sci U S A 107 (12): 5575-80.

Bothma, Jacques P, Michael Levine, and Alistair N Boettiger. (2010) 2010. “Morphogen Gradients: Limits to Signaling or Limits to Measurement?”. Curr Biol 20 (5).

Irvine, K D, and E Wieschaus. (1994) 1994. “Fringe, a Boundary-Specific Signaling Molecule, Mediates Interactions Between Dorsal and Ventral Cells During Drosophila Wing Development.”. Cell 79 (4): 595-606.

Pribyl, Michal, Cyrill B Muratov, and Stanislav Y Shvartsman. (2003) 2003. “Discrete Models of Autocrine Cell Communication in Epithelial Layers.”. Biophys J 84 (6): 3624-35.

Tolwinski, N S, and E Wieschaus. (2001) 2001. “Armadillo Nuclear Import Is Regulated by Cytoplasmic Anchor Axin and Nuclear Anchor DTCF Pan.”. Development 128 (11): 2107-17.

Peifer, M, D Sweeton, M Casey, and E Wieschaus. (1994) 1994. “Wingless Signal and Zeste-White 3 Kinase Trigger Opposing Changes in the Intracellular Distribution of Armadillo.”. Development 120 (2): 369-80.

Oleksiuk, Olga, Vladimir Jakovljevic, Nikita Vladimirov, Ricardo Carvalho, Eli Paster, William S Ryu, Yigal Meir, Ned S Wingreen, Markus Kollmann, and Victor Sourjik. (2011) 2011. “Thermal Robustness of Signaling in Bacterial Chemotaxis.”. Cell 145 (2): 312-21.

Muratov, Cyrill B, and Stanislav Y Shvartsman. (2004) 2004. “Signal Propagation and Failure in Discrete Autocrine Relays.”. Phys Rev Lett 93 (11): 118101.

Meir, Yigal, Vladimir Jakovljevic, Olga Oleksiuk, Victor Sourjik, and Ned S Wingreen. (2010) 2010. “Precision and Kinetics of Adaptation in Bacterial Chemotaxis.”. Biophys J 99 (9): 2766-74.

Chung, Kwanghun, Yoosik Kim, Jitendra S Kanodia, Emily Gong, Stanislav Y Shvartsman, and Hang Lu. (2011) 2011. “A Microfluidic Array for Large-Scale Ordering and Orientation of Embryos.”. Nat Methods 8 (2): 171-6.

Dawes-Hoang, Rachel E, Kush M Parmar, Audrey E Christiansen, Chris B Phelps, Andrea H Brand, and Eric F Wieschaus. (2005) 2005. “Folded Gastrulation, Cell Shape Change and the Control of Myosin Localization.”. Development 132 (18): 4165-78.

Hibbs, Matthew A, Chad L Myers, Curtis Huttenhower, David C Hess, Kai Li, Amy A Caudy, and Olga G Troyanskaya. (2009) 2009. “Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis.”. PLoS Comput Biol 5 (3): e1000322.

Klein, Daryl E, Valerie M Nappi, Gregory T Reeves, Stanislav Y Shvartsman, and Mark A Lemmon. (2004) 2004. “Argos Inhibits Epidermal Growth Factor Receptor Signalling by Ligand Sequestration.”. Nature 430 (7003): 1040-4.

Stathopoulos, Angelike, and Michael Levine. (2004) 2004. “Whole-Genome Analysis of Drosophila Gastrulation.”. Curr Opin Genet Dev 14 (5): 477-84.

Luo, Shijing, Gunnar A Kleemann, Jasmine M Ashraf, Wendy M Shaw, and Coleen T Murphy. (2010) 2010. “TGF-β and Insulin Signaling Regulate Reproductive Aging via Oocyte and Germline Quality Maintenance.”. Cell 143 (2): 299-312.

Shvartsman, Stanislav Y. (2002) 2002. “Shooting from the Hip: Spatial Control of Signal Release by Intracellular Waves.”. Proc Natl Acad Sci U S A 99 (14): 9087-9.

Bialek, William, and Sima Setayeshgar. (2005) 2005. “Physical Limits to Biochemical Signaling.”. Proc Natl Acad Sci U S A 102 (29): 10040-5.

Shvartsman, Stanislav Y, and Ruth E Baker. (2012) 2012. “Mathematical Models of Morphogen Gradients and Their Effects on Gene Expression.”. Wiley Interdiscip Rev Dev Biol 1 (5): 715-30.

Shi, Weiyang, Sara M Peyrot, Edwin Munro, and Michael Levine. (2009) 2009. “FGF3 in the Floor Plate Directs Notochord Convergent Extension in the Ciona Tadpole.”. Development 136 (1): 23-8.

Neumann, Silke, Clinton H Hansen, Ned S Wingreen, and Victor Sourjik. (2010) 2010. “Differences in Signalling by Directly and Indirectly Binding Ligands in Bacterial Chemotaxis.”. EMBO J 29 (20): 3484-95.

Teng, Shu-Wen, Jessica N Schaffer, Kimberly C Tu, Pankaj Mehta, Wenyun Lu, N P Ong, Bonnie L Bassler, and Ned S Wingreen. (2011) 2011. “Active Regulation of Receptor Ratios Controls Integration of Quorum-Sensing Signals in Vibrio Harveyi.”. Mol Syst Biol 7: 491.

Tolwinski, Nicholas S, Marcel Wehrli, Anna Rives, Naz Erdeniz, Stephen DiNardo, and Eric Wieschaus. (2003) 2003. “Wg/Wnt/Signal/Can/Be/Transmitted/through/Arrow/LRP5,6/and/Axin/Independently/of/Zw3/Gsk3beta/Activity.”. Dev Cell 4 (3): 407-18.

Luo, Shijing, Wendy M Shaw, Jasmine M Ashraf, and Coleen T Murphy. (2009) 2009. “TGF-Beta Sma Mab Signaling Mutations Uncouple Reproductive Aging from Somatic Aging.”. PLoS Genet 5 (12): e1000789.

Greenfield, Derek, Ann L McEvoy, Hari Shroff, Gavin E Crooks, Ned S Wingreen, Eric Betzig, and Jan Liphardt. (2009) 2009. “Self-Organization of the Escherichia Coli Chemotaxis Network Imaged With Super-Resolution Light Microscopy.”. PLoS Biol 7 (6): e1000137.

Cheung, Lily S, Trudi Schüpbach, and Stanislav Y Shvartsman. (2011) 2011. “Pattern Formation by Receptor Tyrosine Kinases: Analysis of the Gurken Gradient in Drosophila Oogenesis.”. Curr Opin Genet Dev 21 (6): 719-25.

Kim, Yoosik, Mathieu Coppey, Rona Grossman, Leiore Ajuria, Gerardo Jiménez, Ze’ev Paroush, and Stanislav Y Shvartsman. (2010) 2010. “MAPK Substrate Competition Integrates Patterning Signals in the Drosophila Embryo.”. Curr Biol 20 (5): 446-51.

Wagner, Eileen, and Michael Levine. (2012) 2012. “FGF Signaling Establishes the Anterior Border of the Ciona Neural Tube.”. Development 139 (13): 2351-9.

Slavov, Nikolai, and David Botstein. (2013) 2013. “Decoupling Nutrient Signaling from Growth Rate Causes Aerobic Glycolysis and Deregulation of Cell Size and Gene Expression.”. Mol Biol Cell 24 (2): 157-68.

Goyal, Sidhartha, Jie Yuan, Thomas Chen, Joshua D Rabinowitz, and Ned S Wingreen. (2010) 2010. “Achieving Optimal Growth through Product Feedback Inhibition in Metabolism.”. PLoS Comput Biol 6 (6): e1000802.

Mok, Kenny C, Ned S Wingreen, and Bonnie L Bassler. (2003) 2003. “Vibrio Harveyi Quorum Sensing: A Coincidence Detector for Two Autoinducers Controls Gene Expression.”. EMBO J 22 (4): 870-81.