Reeves Lab | Dynamics of Cellular Decision-Making

Publications List

Note: asterisk indicates shared first authorship.

    2024

  1. Shaikh, R.; Larson, N. J.; Kam, J.; Hanjaya-Putra, D.; Zartman, J.; Umulis, D. M.; Li, L. & Reeves, G. T. (2024). Optimal performance objectives in the highly conserved bone morphogenetic protein signaling pathway. npj Systems Biology and Applications, 10: 1-13.
  2. Al Asafen, H.; Beseli, A.; Chen, H.-Y.; Hiremath, S.; Williams, C. M. & Reeves, G. T. (2024). Dynamics of BMP signaling and stable gene expression in the early Drosophila embryo. Biology Open, 13: bio061646.

    3. 2023

  3. Bandodkar, P. U.*; Shaikh, R. R.* & Reeves, G. T. (2023). ISRES+: An improved evolutionary strategy for function minimization to estimate the free parameters of Systems Biology models. Bioinformatics 39 (7):btad403.

    4. 2022

  4. McArthur, N.; Cruz-Teran, C.; Thatavarty, A.; Reeves, G. T. & Rao, B. M. (2022). Experimental and Analytical Framework for “Mix-and-Read” Assays Based on Split Luciferase. ACS Omega, 7: 24551-24560. doi: 10.1021/acsomega.2c02319

    5. 2020

  5. Bowen, J. D.; Schloop, A. E.; Reeves, G. T.; Menegatti, S. & Rao, B. M. (2020). Discovery of membrane-permeating cyclic peptides via mRNA display. Bioconjugate Chemistry, 31: 2325-2338. doi: 10.1021/acs.bioconjchem.0c00413
  6. Jacobsen, T.; Yi, G.; Al Asafen, H.; Jermusyk, A. A.; Beisel, C. L. & Reeves, G. T. (2020). Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems. PLoS One, 15: e0232046. doi: 10.1371/journal.pone.0232046
  7. Schloop, A. E.; Bandodkar, P. U. & Reeves, G. T. (2020). Formation, interpretation, and regulation of the Drosophila Dorsal/NF-κB gradient. Current Topics in Developmental Biology 137: 143-191.doi: 10.1016/bs.ctdb.2019.11.007 [Invited review.]
  8. Al Asafen, H.; Bandodkar, P. U.; Carrell-Noel, S.; Schloop, A. E.; Friedman, J. & Reeves, G. T. (2020). Robustness of the Dorsal morphogen gradient with respect to morphogen dosage. PLoS Computational Biology, 16: e1007750. doi: 10.1371/journal.pcbi.1007750
  9. Bandodkar, P. U.; Al Asafen, H. & Reeves, G. T. (2020). Spatiotemporal control of gene expression boundaries using a feedforward loop. Dev Dyn, 249: 369-382. doi: 10.1002/dvdy.150 [Invited for a special issue: “50 Years of Positional information in Development, Disease, and Regeneration.”]
  10. Schloop, A. E.; Carrell-Noel, S.; Friedman, J.; Thomas, A. & Reeves, G. T. (2020). Mechanism and implications of morphogen shuttling: Lessons learned from dorsal and Cactus in Drosophila. Developmental Biology, 461: 13-18.

    11. 2019

  11. Reeves, G. T. (2019). The engineering principles of combining a transcriptional incoherent feedforward loop with negative feedback. Journal of Biological Engineering, 13: 62. doi: 10.1186/s13036-019-0190-3

    12. 2017

  12. Carrell, S. N.*; O’Connell M. D.*; Jacobsen, T.; Pomeroy, A. E.; Hayes, S. M. & Reeves, G. T. (2017). A facilitated diffusion mechanism establishes the Drosophila Dorsal gradient. Development, 144: 4450-4461. doi: 10.1242/dev.155549
  13. Hrischuk, C. E. & Reeves, G. T. (2017). The Cell Embodies Standard Engineering Principles. J Bioinf Com Sys Biol, 1: 106. Note: Appendix can be found here.

    14. 2016

  14. Jermusyk A.; Murphy, N. P. & Reeves, G. T. (2016). Analyzing negative feedback using a synthetic gene network expressed in the Drosophila melanogaster embryo. BMC Systems Biology, 10: 85. doi: 10.1186/s12918-016-0330-z
  15. Reeves, G. T. & Hrischuk, C. E. (2016). Survey of Engineering Models for Systems Biology. Computational Biology Journal, 2016: 1-12. doi: 10.1155/2016/4106329
  16. Jermusyk A. & Reeves, G. T. (2016). Transcription Factor Networks. Encyclopedia of Cell Biology, 4: 63-71. doi: 10.1016/B978-0-12-394447-4.40010-6

    17. 2015

  17. O’Connell, M. D. & Reeves, G. T. (2015). The presence of nuclear Cactus in the early Drosophila embryo may extend the dynamic range of the Dorsal gradient. PLoS Comput Biol, 11: e1004159. doi: 10.1371/journal.pcbi.1004159
  18. Carrell, S. N. & Reeves, G. T. (2015). Imaging the Dorsal-Ventral Axis of Live and Fixed Drosophila melanogaster Embryos. Methods Mol Biol, 1189: 63-78. doi: 10.1007/978-1-4939-1164-6_5

    19. 2013

  19. Garcia, M.; Nahmad, M.; Reeves, G. T. & Stathopoulos, A. (2013). Size-dependent regulation of dorsal-ventral patterning in the early Drosophila embryo. Developmental Biology, 381: 286-299. doi: 10.1016/j.ydbio.2013.06.020
  20. Trisnadi, N.; Altinok, A.; Stathopoulos, A. & Reeves, G. T. (2012). Image analysis and empirical modeling of gene and protein expression. Methods, 62: 68-78. doi: 10.1016/j.ymeth.2012.09.016

    21. 2012

  21. Reeves, G. T.*; Trisnadi, N.*; Truong, T. V.; Nahmad, M.; Katz, S. & Stathopoulos, A. (2012). Dorsal-Ventral Gene Expression in the Drosophila Embryo Reflects the Dynamics and Precision of the Dorsal Nuclear Gradient. Dev Cell, 22: 544-557. doi: 10.1016/j.devcel.2011.12.007

    22. 2010

  22. McMahon, A.; Reeves, G. T.; Supatto, W. & Stathopoulos, A. (2010). Mesoderm migration in Drosophila is a multi-step process requiring FGF signaling and integrin activity. Development, 137: 2167-2175. doi: 10.1242/dev.051573.

    23. 2009

  23. Liberman, L. M.*; Reeves, G.T.* & Stathopoulos, A. (2009). Quantitative imaging of the Dorsal nuclear gradient reveals limitations to threshold-dependent patterning in Drosophila. Proc Natl Acad Sci U S A, 106: 22317-22322. doi: 10.1073/pnas.0906227106.
  24. Reeves, G.T. & Stathopoulos, A. (2009). Cold Spring Harb Perspect Biol, “Perspectives on Generation and Interpretation of Morphogen Gradients.” doi: 10.1101/cshperspect.a000836.
  25. Reeves, G.T. & Fraser, S.E. (2009). Biological systems from an engineer’s point of view. PLoS Biol 7: e21. doi: 10.1371/journal.pbio.1000021.

    26. 2006

  26. Reeves, G.T.; Muratov, C.B.; Schüpbach, T. & Shvartsman, S.Y. (2006). Quantitative models of developmental pattern formation. Dev. Cell, 11: 289-300.
  27. Goentoro, L.A.; Reeves, G.T.; Kowal, C.P.; Martinelli, L.; Schüpbach, T. & Shvartsman, S.Y. (2006). Quantifying the Gurken morphogen gradient in Drosophila oogenesis. Dev. Cell, 11: 263-272.

    28. 2005

  28. Reeves, G.T.; Kalifa, R.; Klein, D.E.; Lemmon, M.A. & Shvartsman, S.Y. (2005). Computational analysis of EGFR inhibition by Argos. Dev. Biol., 284: 523-535.

    29. 2004

  29. Pilyugin, S.S.; Reeves, G.T. & Narang, A. (2004). Predicting stability of mixed microbial cultures from single species experiments: 1. Phenomenological model. Math Biosci., 192: 85-109.
  30. Pilyugin, S.S.; Reeves, G.T. & Narang, A. (2004). Predicting stability of mixed microbial cultures from single species experiments: 2. Physiological model. Math Biosci., 192: 111-136.
  31. Klein, D.E.; Nappi, V.M.; Reeves, G.T.; Shvartsman, S.Y. & Lemmon, M.A. (2004). Argos inhibits Epidermal Growth Factor Receptor signaling by ligand sequestration. Nature, 430: 1040-1044.
  32. Reeves, G.T.; Narang, A. & Pilyugin, S.S. (2004). Growth of mixed cultures on mixtures of substitutable substrates: the operating diagram for a structured model. J. Theor. Biol., 226: 143-157.

    33. 2003

  33. Shoemaker, J.; Reeves, G.T.; Gupta, S.; Pilyugin, S.S.; Egli, T. & Narang, A. (2003). The dynamics of single-substrate continuous cultures: the role of transport enzymes. J. Theor. Biol., 222: 307-322.


Feedforward control stabilizes morphogen gradients that vary in both space and time. Figure modified from Bandodkar et al., 2020.
 


Dorsal target gene expression is unexpectedly robust. Mechanistic modeling reveals why. Figure modified from Al Asafen et al., 2020.
 


A signaling gradient goes against the grain: diffusion causes accumulation instead of spreading. Figure modified from Carrell et al., 2017.
 


Transcription factor networks show similar global properties to man-made networks. Figure modified from Jermusyk and Reeves, 2016.
 


Computational modeling of the Dorsal gradient suggests that Dorsal/Cactus complex is present in the nucleus. Figure modified from O’Connell and Reeves, 2015.
 

Detailed, quantitative measurements of the Dorsal gradient found it to be surprisingly narrow. Figure modified from Liberman et al., 2009.