Collective Logic Lab


a paper

Identifying a developmental transition in honey bees using gene expression data.
Bryan C. Daniels, Ying Wang, Robert E. Page, Jr, and Gro V. Amdam.

Phase Transitions and Criticality in the Collective Behavior of Animals — Self-Organization and Biological Function.
Pawel Romanczuk and Bryan C. Daniels.
In Order, Disorder and Criticality. Advanced Problems of Phase Transition Theory, vol. VII, ed. Yu. Holovatch.
World Scientific Publishing (2022).

Subcritical escape waves in schooling fish.
Winnie Poel, Bryan C. Daniels, Matthew M. G. Sosna, Colin R. Twomey, Simon P. Leblanc, Iain D. Couzin, and Pawel Romanczuk.
Science Advances 8, eabm6385 (2022).

Discovering sparse control strategies in neural activity.
Edward D. Lee, Xiaowen Chen, and Bryan C. Daniels.
PLoS Computational Biology 18 (5), e1010072 (2022).

The basis of easy controllability in Boolean networks.
Enrico Borriello and Bryan C. Daniels.
Nature Communications 12, 5227 (2021).
Press release.

Quantifying the impact of network structure on speed and accuracy in collective decision-making.
Bryan C. Daniels and Pawel Romanczuk.
Theory in Biosciences 140, 379 (2021).
Arxiv version.

Innovations are disproportionately likely in the periphery of a scientific network.
Deryc T. Painter, Bryan C. Daniels, and Manfred Laubichler.
Theory in Biosciences 140, 391 (2021).

Neet: Simulating and Analyzing Dynamical Network Models
Douglas G. Moore, Harrison B. Smith, Bryan C. Daniels, Hyunju Kim, Bradley Karas, Siyu Zhou, and Sara I. Walker.

Quantifying dynamical high-order interdependencies from the O-information: An application to neural spiking dynamics.
Sebastiano Stramaglia, Tomas Scagliarini, Bryan C. Daniels, and Daniele Marinazzo.
Frontiers in Physiology 11, 595736 (2021).

Inferring the Logic of Collective Information Processors.
Bryan C. Daniels.
In Advances in Info-Metrics: Information and Information Processing Across Disciplines, ed. Min Chen, J. Michael Dunn, Amos Golan, and Aman Ullah.
Oxford University Press (2021).

Tyramine and its receptor TYR1 linked behavior QTL to reproductive physiology in honey bee workers (Apis mellifera).
Ying Wang, Gro V. Amdam, Bryan C. Daniels, and Robert E. Page, Jr.
Journal of Insect Physiology 126, 104093 (2020).

Scaling theory of armed-conflict avalanches.
Edward D. Lee, Bryan C. Daniels, Christopher R. Myers, David C. Krakauer, and Jessica C. Flack.
Phys. Rev. E 102, 042312 (2020).

Individual and collective encoding of risk in animal groups.
Matthew M. G. Sosna, Colin R. Twomey, Joseph Bak-Coleman, Winnie Poel, Bryan C. Daniels, Pawel Romanczuk, and Iain D. Couzin.
PNAS 116, 20556 (2019).
Press release.

Emergent regularities and scaling in armed conflict data.
Edward D. Lee, Bryan C. Daniels, Christopher R. Myers, David C. Krakauer, and Jessica C. Flack.

Automated, predictive, and interpretable inference of Caenorhabditis elegans escape dynamics.
Bryan C. Daniels, William S. Ryu, and Ilya Nemenman.
PNAS 116, 7226 (2019).
Sir Isaac code on GitHub. arXiv version.

Convenient Interface to Inverse Ising (ConIII): A Python 3 package for solving Ising-type maximum entropy models.
Edward D. Lee and Bryan C. Daniels.
Journal of Open Research Software 7, 3 (2019).
ConIII code on GitHub.

Network Analysis for the Digital Humanities: Principles, Problems, Extensions.
Deryc T. Painter, Bryan C. Daniels, and Jürgen Jost.
Isis 110, 538-554 (2019).

Criticality distinguishes the ensemble of biological regulatory networks.
Bryan C. Daniels, Hyunju Kim, Douglas Moore, Siyu Zhou, Harrison Smith, Bradley Karas, Stuart A. Kauffman, and Sara I. Walker.
Phys. Rev. Lett. 121, 138102 (2018).
Press release. Neet code on GitHub.

Locating decision-making circuits in a heterogeneous neural network.
Emerson Arehart, Tangxin Jin, and Bryan C. Daniels.
Frontiers in Applied Mathematics and Statistics 4, 11 (2018).

Parameter Estimation, Sloppiness, and Model Identifiability.
Bryan C. Daniels, Dirk Fey, and Maciej Dobrzyński.
In Quantitative Biology: Theory, Computational Methods, and Models, ed. B. Munsky, W. Hlavacek, and L. Tsimring. MIT Press (2018).

Collective memory in macaque conflict implied by temporal scaling collapse.
Edward D. Lee, Bryan C. Daniels, David C. Krakauer, and Jessica C. Flack.
J. Royal Society Interface 14, 20170223 (2017).
Press release.

Dual coding theory explains biphasic collective computation in neural decision-making.
Bryan C. Daniels, Jessica C. Flack, and David C. Krakauer.
Frontiers in Neuroscience 11, 313 (2017).
Press release.

Control of finite critical behaviour in a small-scale social system.
Bryan C. Daniels, David C. Krakauer, and Jessica C. Flack.
Nature Communications 8, 14301 (2017).
Press release.

Quantifying collectivity.
Bryan C. Daniels, Christopher J. Ellison, David C. Krakauer, and Jessica C. Flack.
Current Opinion in Neurobiology 37, 106 (2016).

Automated adaptive inference of coarse-grained dynamical models.
Bryan C. Daniels and Ilya Nemenman.
Nature Communications 6, 8133 (2015).
Sir Isaac code on GitHub. Press release.

Sloppiness and emergent theories in physics, biology, and beyond.
Mark K. Transtrum, Benjamin Machta, Kevin Brown, Bryan C. Daniels, Christopher R. Myers and James P. Sethna.
J. Chem. Phys. 143, 010901 (2015).
arXiv version.

Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression.
Bryan C. Daniels and Ilya Nemenman.
PLOS ONE 10, e0119821 (2015).

Sparse code of conflict in an animal society.
Bryan C. Daniels, David C. Krakauer, and Jessica C. Flack.
PNAS 109, 14259 (2012). PDF
Press release.

Nucleation at the DNA supercoiling transition.
Bryan C. Daniels and James P. Sethna.
Phys. Rev. E 83, 041924 (2011).
arXiv version.

Saturation Probabilities of Continuous-Time Sigmoidal Networks.
Randall D. Beer and Bryan C. Daniels.
arXiv version.

Discontinuities at the DNA supercoiling transition.
Bryan C. Daniels, Scott Forth, Maxim Y. Sheinin, Michelle D. Wang, and James P. Sethna.
Phys. Rev. E. 80, 040901(R) (2009).
arXiv version.
Poster [pdf] for 2009 Biophysical Society Meeting. Presentation [pdf] for 2009 APS March Meeting.

Mesoscopic statistical properties of multistep enzyme-mediated reactions.
Wiet H. de Ronde, Bryan C. Daniels, Andrew Mugler, Nikolai A. Sinitsyn, and Ilya Nemenman.
IET Systems Biology 3, 429 (2009).
arXiv version.
Andrew's poster [pdf] for 2009 q-bio Conference.

Sloppiness, robustness, and evolvability in systems biology.
Bryan C. Daniels, Yan-Jiun Chen, James P. Sethna, Ryan N. Gutenkunst, and Christopher R. Myers.
Current Opinion in Biotechnology 19, 389 (2008).
arXiv version.
Poster [pdf] for 2008 q-bio Conference.

Abrupt Buckling Transition Observed during the Plectoneme Formation of Individual DNA Molecules.
Scott Forth, Christopher Deufel, Maxim Y. Sheinin, Bryan Daniels, James P. Sethna, and Michelle D. Wang.
Phys. Rev. Lett. 100, 148301 (2008).

Synchronization of Globally Coupled Nonlinear Oscillators: The Rich Behavior of the Kuramoto Model.
Bryan C. Daniels.
Website and paper for senior project at Ohio Wesleyan University.

Absence of Kondo lattice coherence effects in Ce0.6La0.4Pb3: A magnetic field study.
Richard Pietri, Costel R. Rotundu, Bohdan Andraka, Bryan C. Daniels, and Kevin Ingersent.
J. Appl. Phys. 97, 10A510 (2005).

Using NRG to solve quantum impurity models for heavy-fermion systems. [pdf]
Bryan Daniels and Kevin Ingersent.
Paper for University of Florida Summer 2004 REU program.

Synchronization of Coupled Rotators: Josephson Junction Ladders and the Locally-Coupled Kuramoto Model.
B. C. Daniels, S. T. M. Dissanayake, and B. R. Trees.
Phys. Rev. E 67, 026216 (2003).