Pribyl, Michal, Cyrill B Muratov, and Stanislav Y Shvartsman. (2003) 2003. “Transitions in the Model of Epithelial Patterning.”. Dev Dyn 226 (1): 155-9.

Kim, Yoosik, Ze’ev Paroush, Knud Nairz, Ernst Hafen, Gerardo Jiménez, and Stanislav Y Shvartsman. (2011) 2011. “Substrate-Dependent Control of MAPK Phosphorylation in Vivo.”. Mol Syst Biol 7: 467.

Sourjik, Victor, and Ned S Wingreen. (2012) 2012. “Responding to Chemical Gradients: Bacterial Chemotaxis.”. Curr Opin Cell Biol 24 (2): 262-8.

Coppey, Mathieu, Alistair N Boettiger, Alexander M Berezhkovskii, and Stanislav Y Shvartsman. (2008) 2008. “Nuclear Trapping Shapes the Terminal Gradient in the Drosophila Embryo.”. Curr Biol 18 (12): 915-9.

Adelman, Thomas L, William Bialek, and Robert M Olberg. (2003) 2003. “The Information Content of Receptive Fields.”. Neuron 40 (4): 823-33.

Shvartsman, Stanislav Y, Mathieu Coppey, and Alexander M Berezhkovskii. (2008) 2008. “Dynamics of Maternal Morphogen Gradients in Drosophila.”. Curr Opin Genet Dev 18 (4): 342-7.

Jiménez, Gerardo, Stanislav Y Shvartsman, and Ze’ev Paroush. (2012) 2012. “The Capicua Repressor--a General Sensor of RTK Signaling in Development and Disease.”. J Cell Sci 125 (Pt 6): 1383-91.

Kaletsky, Rachel, Vanisha Lakhina, Rachel Arey, April Williams, Jessica Landis, Jasmine M Ashraf, and Coleen T Murphy. (2016) 2016. “The C. Elegans Adult Neuronal IIS FOXO Transcriptome Reveals Adult Phenotype Regulators.”. Nature 529 (7584): 92-6. doi:10.1038/nature16483.

Christiaen, Lionel, Brad Davidson, Takeshi Kawashima, Weston Powell, Hector Nolla, Karen Vranizan, and Michael Levine. (2008) 2008. “The Transcription Migration Interface in Heart Precursors of Ciona Intestinalis.”. Science 320 (5881): 1349-52.

Batsilas, Lazaros, Alexander M Berezhkovskii, and Stanislav Y Shvartsman. (2003) 2003. “Stochastic Model of Autocrine and Paracrine Signals in Cell Culture Assays.”. Biophys J 85 (6): 3659-65.

Ahmed, Yashi, S Hayashi, A Levine, and E Wieschaus. (1998) 1998. “Regulation of Armadillo by a Drosophila APC Inhibits Neuronal Apoptosis During Retinal Development.”. Cell 93 (7): 1171-82.

Tolwinski, Nicholas S, and Eric Wieschaus. (2004) 2004. “A Nuclear Function for Armadillo Beta-Catenin.”. PLoS Biol 2 (4): E95.

Terry, Laura J, Livia Vastag, Joshua D Rabinowitz, and Thomas Shenk. (2012) 2012. “Human Kinome Profiling Identifies a Requirement for AMP-Activated Protein Kinase During Human Cytomegalovirus Infection.”. Proc Natl Acad Sci U S A 109 (8): 3071-6.

Cheung, Lily S, David S A Simakov, Alisa Fuchs, George Pyrowolakis, and Stanislav Y Shvartsman. (2013) 2013. “Dynamic Model for the Coordination of Two Enhancers of Broad by EGFR Signaling.”. Proc Natl Acad Sci U S A 110 (44): 17939-44.

Luo, Shijing, and Coleen T Murphy. (2011) 2011. “Caenorhabditis Elegans Reproductive Aging: Regulation and Underlying Mechanisms.”. Genesis 49 (2): 53-65.

DiLoreto, Race, and Coleen T Murphy. (2015) 2015. “The Cell Biology of Aging.”. Mol Biol Cell 26 (25): 4524-31. doi:10.1091/mbc.E14-06-1084.

Shakoury-Elizeh, Minoo, John Tiedeman, Jared Rashford, Tracey Ferea, Janos Demeter, Emily Garcia, Ronda Rolfes, Patrick O Brown, David Botstein, and Caroline C Philpott. (2004) 2004. “Transcriptional Remodeling in Response to Iron Deprivation in Saccharomyces Cerevisiae.”. Mol Biol Cell 15 (3): 1233-43.

Lembong, Jessica, Nir Yakoby, and Stanislav Y Shvartsman. (2008) 2008. “Spatial Regulation of BMP Signaling by Patterned Receptor Expression.”. Tissue Eng Part A 14 (9): 1469-77.

Long, Tao, Kimberly C Tu, Yufang Wang, Pankaj Mehta, N P Ong, Bonnie L Bassler, and Ned S Wingreen. (2009) 2009. “Quantifying the Integration of Quorum-Sensing Signals With Single-Cell Resolution.”. PLoS Biol 7 (3): e68.

Tolwinski, Nicholas S, and Eric Wieschaus. (2004) 2004. “A Nuclear Escort for Beta-Catenin.”. Nat Cell Biol 6 (7): 579-80.

Emberly, Eldon, and Ned S Wingreen. (2006) 2006. “Hourglass Model for a Protein-Based Circadian Oscillator.”. Phys Rev Lett 96 (3): 038303.

Jaźwińska, A, N Kirov, E Wieschaus, S Roth, and C Rushlow. (1999) 1999. “The Drosophila Gene Brinker Reveals a Novel Mechanism of Dpp Target Gene Regulation.”. Cell 96 (4): 563-73.

Zartman, Jeremiah J, Nir Yakoby, Christopher A Bristow, Xiaofeng Zhou, Karin Schlichting, Christian Dahmann, and Stanislav Y Shvartsman. (2008) 2008. “Cad74A Is Regulated by BR and Is Required for Robust Dorsal Appendage Formation in Drosophila Oogenesis.”. Dev Biol 322 (2): 289-301.

Li, Ling-Bo, Haoyun Lei, Rachel Arey, Pengpeng Li, Jianfeng Liu, Coleen T Murphy, X Z Shawn Xu, and Kang Shen. (2016) 2016. “The Neuronal Kinesin UNC-104 KIF1A Is a Key Regulator of Synaptic Aging and Insulin Signaling-Regulated Memory.”. Curr Biol 26 (5): 605-15. doi:10.1016/j.cub.2015.12.068.

Fuchs, Alisa, Lily S Cheung, Enrica Charbonnier, Stanislav Y Shvartsman, and George Pyrowolakis. (2012) 2012. “Transcriptional Interpretation of the EGF Receptor Signaling Gradient.”. Proc Natl Acad Sci U S A 109 (5): 1572-7.

Cowden, John, and Michael Levine. (2002) 2002. “The Snail Repressor Positions Notch Signaling in the Drosophila Embryo.”. Development 129 (7): 1785-93.

Goentoro, Lea A, Gregory T Reeves, Craig P Kowal, Luigi Martinelli, Trudi Schüpbach, and Stanislav Y Shvartsman. (2006) 2006. “Quantifying the Gurken Morphogen Gradient in Drosophila Oogenesis.”. Dev Cell 11 (2): 263-72.

Stolfi, Alberto, Eileen Wagner, Matthew Taliaferro, Seemay Chou, and Michael Levine. (2011) 2011. “Neural Tube Patterning by Ephrin, FGF and Notch Signaling Relays.”. Development 138 (24): 5429-39.

Lee, Seung-Jae, Coleen T Murphy, and Cynthia Kenyon. (2009) 2009. “Glucose Shortens the Life Span of C. Elegans by Downregulating DAF-16 FOXO Activity and Aquaporin Gene Expression.”. Cell Metab 10 (5): 379-91.

Yakoby, Nir, Jessica Lembong, Trudi Schüpbach, and Stanislav Y Shvartsman. (2008) 2008. “Drosophila Eggshell Is Patterned by Sequential Action of Feedforward and Feedback Loops.”. Development 135 (2): 343-51.

Shaw, Wendy M, Shijing Luo, Jessica Landis, Jasmine M Ashraf, and Coleen T Murphy. (2007) 2007. “The C. Elegans TGF-Beta Dauer Pathway Regulates Longevity via Insulin Signaling.”. Curr Biol 17 (19): 1635-45.

Shi, Cheng, and Coleen T Murphy. (2016) 2016. “Feeding the Germline.”. Genes Dev 30 (3): 249-50. doi:10.1101/gad.276980.115.

Grimm, Oliver, Victoria Sanchez Zini, Yoosik Kim, Jordi Casanova, Stanislav Y Shvartsman, and Eric Wieschaus. (2012) 2012. “Torso RTK Controls Capicua Degradation by Changing Its Subcellular Localization.”. Development 139 (21): 3962-8.

Lenz, Derrick H, Kenny C Mok, Brendan N Lilley, Rahul Kulkarni V, Ned S Wingreen, and Bonnie L Bassler. (2004) 2004. “The Small RNA Chaperone Hfq and Multiple Small RNAs Control Quorum Sensing in Vibrio Harveyi and Vibrio Cholerae.”. Cell 118 (1): 69-82.

Bialek, William. (2013) 2013. “QnAs With William Bialek.”. Proc Natl Acad Sci U S A 110 (41): 16288.

Sharpee, Tatyana, and William Bialek. 2007. “Neural Decision Boundaries for Maximal Information Transmission.”. PLoS One 2 (7): e646.

Diehn, Maximilian, Ash A Alizadeh, Oliver J Rando, Chih Long Liu, Kryn Stankunas, David Botstein, Gerald R Crabtree, and Patrick O Brown. (2002) 2002. “Genomic Expression Programs and the Integration of the CD28 Costimulatory Signal in T Cell Activation.”. Proc Natl Acad Sci U S A 99 (18): 11796-801.

Ahmed, Yashi, Ali Nouri, and Eric Wieschaus. (2002) 2002. “Drosophila Apc1 and Apc2 Regulate Wingless Transduction Throughout Development.”. Development 129 (7): 1751-62.

Christiaen, Lionel, Alberto Stolfi, and Michael Levine. (2010) 2010. “BMP Signaling Coordinates Gene Expression and Cell Migration During Precardiac Mesoderm Development.”. Dev Biol 340 (2): 179-87.

Minhas, Paras S, Ling Liu, Peter K Moon, Amit U Joshi, Christopher Dove, Siddhita Mhatre, Kevin Contrepois, et al. (2019) 2019. “Macrophage De Novo NAD Synthesis Specifies Immune Function in Aging and Inflammation.”. Nat Immunol 20 (1): 50-63. doi:10.1038/s41590-018-0255-3.

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).