Publications (PDFs)

Nikolić M, Antonetti V, Liu F, Muhaxheri G, Petkova MD, Scheeler M, Smith EM, Bialek W, Gregor T. Scale invariance in early embryonic development. Proceedings of the National Academy of Science 121 (46), e2403265121
(2024).

McGough L, Casademunt H, Nikolić M, Aridor Z, Petkova MD, Gregor T, Bialek W. Finding the last bits of positional information. PRX Life 2 (1), 013016 (2024).

Merle M, Friedman L, Chureau C, Shoushtarizadeh A, Gregor T. Precise and scalable self-organization in mammalian pseudo-embryos. Nature Structural & Molecular Biology 31, 896–902 (2024).

Haroush N, Levo M, Wieschaus EF, Gregor T.  Functional analysis of the Drosophila eve locus in response to non-canonical combinations of gap gene expression levels. Developmental Cell 58(23), 2789-2801.e5 (2023).

Brückner DB, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science 380 (6652), 1357–62 (2023).

Davidescu MR, Romanczuk P, Gregor T, Cousin ID. Growth produces coordination trade-offs in Trichoplax adhaerens, an animal lacking a central nervous system. Proceedings of the National Academy of Science 120 (11), e2206163120 (2023). 

Rossine FW, Vercelli G, Tarnita C, Gregor T.  Structured foraging of soil predators unveils functional responses to bacterial defenses. Proceedings of the National Academy of Science 119(52): e2210995119 (2022).

Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology 31: 100435 (2022).

Voortman L, Anderson C, Urban E, Yuan R, Tran S, Neuhaus-Follini A, Derrick J, Gregor T, Johnston RJ Jr.  Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. Developmental Cell 57(15), 1817–1832.e5 (2022).

Seyboldt R, Lavoie J, Henry A, Vanaret J, Petkova MD, Gregor T, François P. Latent space of a small genetic network: Geometry of dynamics and information. Proceedings of the National Academy of Science 119 (26): e2113651119 (2022).

Levo M, Raimundo J, Bing, XY, Sisco Z, Batut PJ, Ryabichko S, Gregor T, Levine MS. Transcriptional coupling of distant regulatory genes in living embryos. Nature 605, 754–760 (2022). 

Singh AP, Wu P, Ryabichko S, Raimundo J, Swan M, Wieschaus E, Gregor T, Toettcher JE. Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation. Cell Reports 38, 110543 (2022).

Wang MD, Nicodemi M, Dekker NH, Gregor T, Holcman D, van Oijen AM, Manley S. Physics meets biology: The joining of two forces to further our understanding of cellular function. Molecular Cell. 81(15):3033–3037 (2021).

Bauer M, Petkova MD, Gregor T, Wieschaus EF, Bialek W. Trading bits in the readout from a genetic network. Proceedings of the National Academy of Science 118 (46): e2109011118 (2021).

Nollmann M, Bennabi I, Götz M, Gregor T. The Impact of Space and Time on the Functional Output of the Genome. Cold Spring Harb Perspect Biol.:a040378. doi: 10.1101/cshperspect.a040378 (2021).

Tkačik G, Gregor T. The many bits of positional information. Development 148: dev176065 (2021).

Chen H, Gregor T. Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos. In: Heinlein M. (eds) RNA Tagging. Methods in Molecular Biology, vol 2166. Humana, New York, NY (2020).

Rossine FW, Martinez-Garcia R, Sgro AE, Sgro, Gregor T, Tarnita C. Eco-evolutionary significance of ‘loners’. PLoS Biology 18(3): e3000642 (2020).

Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv.org:1912.08579 [q-bio.SC] (2019).

Petkova MD, Tkacik G, Bialek W, Wieschaus EF, Gregor T (2019). Optimal decoding of cellular identities in a genetic network. Cell 176(4), 844–855 (2019).

Zoller B, Little SC, Gregor T. Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting Cell 175(3), 835–847 (2018).

Chen H, Levo M, Barinov L, Fujioka M, Jaynes JB, Gregor T (2018). Dynamic interplay between enhancer-promoter topology and gene activity. Nature Genetics 50, 1296–1303.

Little SC, Gregor T (2018). Single mRNA Molecule Detection in Drosophila. In: Gaspar I. (eds) RNA Detection. Methods in Molecular Biology, vol 1649. Humana Press, New York, NY

Garcia HG, Gregor T (2018). Live Imaging of mRNA Synthesis in Drosophila. In: Gaspar I. (eds) RNA Detection. Methods in Molecular Biology, vol 1649. Humana Press, New York, NY

Gregor T (2017). Beyond D’Arcy Thompson: Future challenges for quantitative biology. Mechanisms of Development 145: 10–12.

Tikhonov M, Little SC, Gregor T (2015). Only accessible information is useful: insights from gradient-mediated patterning. Roy. Soc. Open Sci. 2: 150486.

Bothma JP, Garcia HG, Ng S, Perry MW, Gregor T, Levine MS (2015). Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo. eLife 2015; 4: e07956.

Noorbakhsh J, Schwab DJ, Sgro AE, Gregor T, Mehta P (2015). Modeling oscillations and spiral waves in Dictyostelium populations. Physical Review E 91: 062711; arXiv.org:1407.8210 [qbio.CB].

Sgro AE, Schwab DJ, Noorbakhsh J, Mestler T, Mehta P, Gregor T (2015). From Intracellular Signaling to Population Oscillations: Bridging Size and Time Scales in Collective Behavior. Molecular Systems Biology 11: 799.

Tkačik G, Dubuis JO, Petkova MD, Gregor T (2015). Positional information, positional error, and read-out precision in morphogenesis: a mathematical framework. Genetics 199 (1): 39–59.

Gregor T, Garcia HG, Little SC (2014). The embryo as a laboratory: quantifying transcription in Drosophila. Trends in Genetics 30 (8): 364–375.

Bothma JP, Garcia HG, Esposito E, Schlissel G, Gregor T, Levine MS (2014). Dynamic regulation of Eve Stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. Proceedings of the National Academy of Science 111 (29): 10598–10603.

Abouchar L, Petkova MD, Steinhardt CR, Gregor T (2014). Fly wing vein patterns have spatial reproducibility of a single cell. J. Roy. Soc. Interface 11 (97): 20140443.

Petkova MD, Little SC, Liu F, Gregor T (2014). Maternal origins of developmental reproducibility. Current Biology 24 (11): 1283–1288. (For original, pre-peer review version see: arXiv.org:1309.6271 [q-bio.MN]).

Krotov D, Dubuis JO, Gregor T, Bialek W (2014). Morphogenesis at criticality. Proceedings of the National Academy of Science 111 (10): 3683–3688.

Garcia HG, Tikhonov M, Lin A, Gregor T (2013). Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning. Current Biology 23 (21): 2140–2145.

Abouchar L, Petkova MD, Steinhardt CR, Gregor T (2013). Precision and reproducibility of macroscopic developmental patterns. arXiv.org:1309.6273 [q-bio.TO].

Dubuis JO, Tkačik G, Wieschaus EF, Gregor T, Bialek W (2013). Positional information, in bits. Proceedings of the National Academy of Science 110 (41): 16301–16308.

Little SC, Tikhonov M, Gregor T (2013). Precise developmental gene expression arises from globally stochastic transcriptional activity. Cell 154(4): 789–800.

Little SC, Gregor T (2013). Sorting sloppy Sonic. Cell 153 (3): 509.

Liu F, Morrison AH, Gregor T (2013). Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network. Proceedings of the National Academy of Science 110 (17): 6724–6729.

Dubuis JO, Samanta R, Gregor T (2013). Accurate measurements of dynamics and reproducibility in small genetic networks. Molecular Systems Biology 9: 639.

Morrison AH, Scheeler M, Dubuis JO, Gregor T (2012). Quantifying the Bicoid morphogen gradient in living fly embryos. Cold Spring Harb Protoc. 2012 (4): 398–406.

Little SC, Tkačik G, Kneeland T, Wieschaus EF, Gregor T (2011). The formation of the Bicoid morphogen gradient requires protein movement from anteriorily localized mRNA. PLoS Biology 9 (3), e1000596.

Mehta P, Gregor T (2010). Approaching the molecular origins of collective dynamics in oscillating cell populations. Current Opinion in Genetics and Development 20 (6).

Gregor T, Fujimoto K, Masaki N, Sawai S (2010). The onset of collective behavior in social amoebae. Science 328: 1021–1026.

Bialek W, Gregor T, Tank DW, Wieschaus EF (2008). Can we fit all of the data? Cell 132: 17–18.

Gregor T, McGregor AP, Wieschaus EF (2008) Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos. Developmental Biology 316: 350–358.

Tkačik G, Gregor T, Bialek W (2008). The role of input noise in transcriptional regulation. PLoS One 3, e2774.

Gregor T, Wieschaus EF, Tank DW, Bialek W (2007). Probing the limits to positional information. Cell 130: 153–164.

Gregor T, Wieschaus EF, McGregor AP, Bialek W, Tank DW (2007). Stability and nuclear dynamics of the Bicoid morphogen gradient. Cell 130: 141–152.

Gregor T, Bialek W, deRuyter van Steveninck RR, Tank DW, Wieschaus EF (2005). Diffusion and scaling during early embryonic pattern formation. Proceedings of the National Academy of Science 102: 18403–18407.

Gregor T, Car R (2005). Minimization of the potential energy surface of Lennard-Jones clusters by quantum optimization. Chem. Phys. Lett. 412: 125–130.

Gregor T, Mauri F, Car R (1999). A comparison of methods for the calculation of NMR chemical shifts. J. Chem. Phys. 111: 1815–1822.