Reeves Lab | Dynamics of Cellular Decision-Making

Publications List

Note: Submitted manuscripts included. Asterisk indicates shared authorship; ✉ indicates (co-)corresponding author.

    2026

  1. Dima, S. S. & Reeves, G. T.✉ (2026). Genome-wide mapping of Bicoid/DNA interactions reveals quantitative constraints on transcriptional regulation. bioRχiv, DOI: 10.64898/2026.05.22.727281.
  2. Dima, S. S.; Turner, M. A.; Garcia, H. G. & Reeves, G. T.✉ (2026). Global maps of transcription factor properties reveal threshold-based formation of DNA-bound and mobile clusters. Sci Adv, 12: eady3909.
  3. Shaikh, R.; Frank, C.; Larson, N. J.; Chen, H.-Y.; Pradhan, A. G.; Mendiola, K.; Hanjaya-Putra, D.; Umulis, D. M.; Zartman, J.✉; Reeves, G. T.✉ & Li, L.✉ (2026). Biochemical Principles of SMAD Signaling Across the Animal Kingdom. Preprints.org, DOI: 10.20944/preprints202601.0062.v1.

    4. 2025

  4. Dima, S. S. & Reeves, G. T.✉ (2025). Bulk-level maps of pioneer factor binding dynamics during the Drosophila maternal-to-zygotic transition. Development, 152: dev.204460.
  5. Schloop, A. E.; Hiremath, S. V.; Shaikh, R.; Dima, S. S.; Lizardo, L.; Bhakta, A.; Williams, C. M. & Reeves, G. T.✉ (2025). Spatiotemporal dynamics of NF-κB/Dorsal inhibitor IκBα/Cactus in Drosophila blastoderm embryos. iScience, 28: 112854.
  6. Turner, M. A.; Gravina, N. M.*; Moretti, B.*; Dima, S.*; Martini, G.; Reeves, G. T. & Garcia, H. G.✉ (2025). Novel Fluorescent and Photoconvertible Fusions Reveal Dorsal Activator Dynamics. bioRχiv, DOI: 10.1101/2025.05.12.653543.
  7. Suarez-Gomez, D.; Perez-Rosas, N. C.; Miranda-Contreras, G. I.; Colom-Braña, S. R.; Zhang, W.; Mim, M. S.; Tan, S.; Gazzo, D.; Tepole, A. B.; Deng, Q.; Reeves, G. T.; Isaza-Brando, C. E.; Staiger, C. J.; Umulis, D.; Zartman, J. & Cabrera-Ríos, M.✉ (2025). CalciumInsights: An Open-Source, Tissue-Agnostic Graphical Interface for High-Quality Analysis of Calcium Signals. bioRχiv, DOI: 10.1101/2025.06.04.657923.
  8. Shaikh, R. & Reeves, G. T.✉ (2025). MIDOE: Maximally-informed Design of Experiment to infer experimentally inaccessible transcription factors dynamics. bioRχiv, DOI: 10.1101/2025.08.04.668461.
  9. Reeves, G. T.✉ & Umulis, D. M.✉ (2025). How cells in growing tissues know the time. Newton, 1: 100254.

    10. 2024

  10. Hiremath, S. V.; Goyal, E.; Reeves, G. T.✉ & Williams, C. M.✉ (2024). FRAP analysis: Measuring biophysical kinetic parameters using image analysis. arχiv, DOI: 10.48550/arXiv.2402.16615.
  11. Noel, A.; Eckford, A. W.; Erban, R.; Icardi, M. & Reeves, G. T. (2024). Guest Editorial Special Feature on Seeing Through the Crowd: Molecular Communication in Crowded and Multi-Cellular Environments. IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, 10: 422-424.
  12. 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.
  13. 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.
  14. Shaikh, R. & Reeves, G. T.✉ (2024). Elucidating the role of multiple feedback loops in regulating stem cell decisions. bioRχiv, DOI: 10.1101/2024.09.25.615049.

    15. 2023

  15. 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.

    16. 2022

  16. 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

    17. 2020

  17. 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
  18. 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
  19. 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.]
  20. 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
  21. 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.”]
  22. 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. Dev Biol, 461: 13-18.

    23. 2019

  23. 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

    24. 2017

  24. 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
  25. 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.

    26. 2016

  26. 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
  27. 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
  28. 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

    29. 2015

  29. 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
  30. 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

    31. 2013

  31. 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
  32. 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

    33. 2012

  33. 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

    34. 2010

  34. 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.

    35. 2009

  35. 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.
  36. Reeves, G.T. & Stathopoulos, A.✉ (2009). Cold Spring Harb Perspect Biol, “Perspectives on Generation and Interpretation of Morphogen Gradients.” doi: 10.1101/cshperspect.a000836.
  37. 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.

    38. 2006

  38. Reeves, G.T.; Muratov, C.B.; Schüpbach, T. & Shvartsman, S.Y.✉ (2006). Quantitative models of developmental pattern formation. Dev. Cell, 11: 289-300.
  39. 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.

    40. 2005

  40. 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.

    41. 2004

  41. 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.
  42. 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.
  43. 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.
  44. 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.

    45. 2003

  45. 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.



Dorsal forms clusters above a concentration threshold. Figure modified from Dima and Reeves, 2026.
 



Spatiotemporal dynamics of NF-κB/Dorsal inhibitor IκBα/Cactus in Drosophila blastoderm embryos. Figure modified from Schloop et al., 2025.
 



Feedforward control stabilizes morphogen gradients that vary in both space and time. Figure modified from Shaikh et al., 2024.
 


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.