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    Biological Transport and Networks Integrating computation, theory and experimental data to decipher the inner workings of living processes.

    Biomolecular Design Using exotic building blocks to design novel heteropolymers that fold into well-defined 3D structures.

    Biophysical Modeling Modeling and simulating the complex systems that arise in biology and soft condensed matter physics.

    CCBScope Observatory The Flatiron Institute's in-house, state-of-the-art imaging facility for live-cell confocal microscopy.

    CCBx Uniting theorists and experimentalists to develop and test theories of biological systems.

    COMPASS Connecting researchers working on molecular sampling, simulation and design.

    Developmental Dynamics Combining experiment, theory and computing to elucidate the inner workings of embryonic development.

    Genomics Working to unravel the complexity of the genome, its regulation and its phenotypic consequences.

    Statistical Biophysics Developing a nonequilibrium physics of living systems and learning machines.

    Structural and Molecular Biophysics Developing novel mathematical approaches to decipher the molecular mechanisms involved in key biological processes.

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Flatiron Institute Computational Biology

Computational Biology: Publications

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  1. Confirmations, correlatons and instabilities of a flexible fiber in an active fluid

    Physical Review Fluids, December 6, 2023

    S. Weady, D. Stein, Alexandra Zidovska, and M. Shelley

  2. Uniqueness and characteristic flow for a non strictly convex singular variational problem

    ArXiv, December 4, 2023

    Jean-FrançoisBabadjian and G. Francfort

  3. A dynamical model of growth and maturation in Drosophila

    Proceedings of the National Academy of Sciences, November 28, 2023

    John J. Tyson, Amirali Monshizadeh, S. Shvartsman, and Alexander W. Shingleton

  4. Morphogens enable interacting supracellular phases that generate organ architecture

    Science, November 24, 2023

    Sichen Yang, et al.

  5. Microscopic Theory, Analysis, and Interpretation of Conductance Histograms in Molecular Junctions

    Nature Communications, November 23, 2023

    Leopoldo Mejía, P. Cossio, and Ignacio Franco

  6. Bacterial diffusion in disordered media, by forgetting the media

    arXiv:2311.10612, November 17, 2023

    H. Mattingly

  7. Sculpting the Sphinx

    PHYSICAL REVIEW FLUIDS, November 16, 2023

    Samuel Boury, S. Weady, and Leif Ristroph

  8. Dispersion of run-and-tumble microswimmers through disordered media

    Physical Review E, November 15, 2023

    D. Saintillan

  9. The power of weak, transient interactions across biology: A paradigm of emergent behavior

    Physica D: Nonlinear Phenomena, November 15, 2023

    Paula A. Vasquez and C. Edelmaier

  10. A chemomechanical model of sperm locomotion reveals two modes of swimming

    Physical Review Fluids, November 15, 2023

    Chenji Li, et al.

  11. A model of replicating coupled oscillators generates naturally occurring cell networks

    Development, November 13, 2023

    M. Smart, S. Shvartsman, and H. Nunley

  12. IIM2FieldII: A Framework for Validating Ultrasound Measurements of Volumetric Flow and WSS in Complex Carotid Plaque Geometries

    2023 IEEE International Ultrasonics Symposium (IUS), November 7, 2023

    Keerthi S. Anand, E. Kolahdouz, Boyce E. Griffith, and Caterina M. Gallippi

  13. Protein-Engineered Fibers For Drug Encapsulation Traceable via 19F Magnetic Resonance

    ACS Applied Nano Materials, November 6, 2023

    Dustin Britton, et al.

  14. Extracting thermodynamic properties from van ’t Hoff plots with emphasis on temperature-sensing ion channels

    Temperature, November 2, 2023

    Jakob T. Bullerjahn and S. Hanson

  15. Universal scaling of shear thickening transitions

    Journal of Rheology, November 1, 2023

    Meera Ramaswamy, et al.

  16. Contrastive power-efficient physical learning in resistor networks

    OpenReview, November 1, 2023

    Menachem Stern, et al.

  17. Nonlinear Classification Without a Processor

    OpenReview, November 1, 2023

    Sam Dillavou, et al.

  18. Phase plane dynamics of ERK phosphorylation

    Journal of Biological Chemistry, November 1, 2023

    S. Shvartsman, Sarah McFann, Martin Wühr, and Boris Y. Rubinstein

  19. Stochastic force inference via density estimation

    NeurIPS 2023 AI for Science Workshop, October 27, 2023

    V. Chardès, S. Maddu, and M. Shelley

  20. Lack of chromokinesin Klp-19 creates a more rigid midzone and affects force transmission during anaphase in C. elegans

    bioRxiv, October 26, 2023

    Vitaly Zimyanin, et al.

  21. Scaffold Matcher: A CMA-ES based algorithm for identifying hotspot aligned peptidomimetic scaffolds

    Proteins: Structure, Function, and Bioinformatics, October 24, 2023

    Erin R. Claussen, D. Renfrew, Christian L. Müller, and Kevin Drew

  22. Development shapes the evolutionary diversification of rodent stripe patterns

    Proceedings of the National Academy of Sciences, October 23, 2023

    Merlijn Staps, P. Miller, Corina E. Tarnita, and Ricardo Mallarin

  23. Modeling epithelial tissue and cell deformation dynamics using a viscoelastic slab sculpted by surface forces

    Physical Review Research, October 19, 2023

  24. Adaptive weighting of Bayesian physics informed neural networks for multitask and multiscale forward and inverse problems

    Journal of Computational Physics, October 15, 2023

    Sarah Perez, S. Maddu, Ivo F. Sbalzarini, and Philippe Poncet

  25. From localized to well mixed: How commuter interactions shape disease spread

    Physical Review E, October 11, 2023

    Aaron Winn, Adam Konkol, and E. Katifori

  26. Identifying microscopic factors that influence ductility in disordered solids

    PNAS, October 9, 2023

    Hongyi Xiao, Douglas J. Durian, and Andrea J. Liu

  27. A multifunctional Wnt regulator underlies the evolution of rodent stripe patterns

    Nature Ecology & Evolution, October 9, 2023

    Matthew R. Johnson, et al.

  28. Design principles of Cdr2 node patterns in fission yeast cells

    Molecular Biology of the Cell, October 1, 2023

    Hannah Opalko and Dimitrios Vavylonis

  29. Atlas of primary cell-type-specific sequence models of gene expression and variant effects

    Cell Reports Methods, September 25, 2023

    Ksenia Sokolova, et al.

  30. Mitochondrial electron transport chain, ceramide and Coenzyme Q are linked in a pathway that drives insulin resistance in skeletal muscle

    bioRxiv: 2023.03.10.532020, September 19, 2023

    Alexis Diaz-Vegas, et al.

  31. Scaling behaviour and control of nuclear wrinkling

    Nature Physics, September 18, 2023

    Jonathan A. Jackson, et al.

  32. Hierarchical bubble size distributions in coarsening wet liquid foams

    PNAS, September 14, 2023

    Nicolò Galvani and Douglas J. Durian

  33. Clustering of cortical dynein regulates the mechanics of spindle orientation in human mitotic cells

    bioRxiv, September 12, 2023

    Maya I. Anjur-Dietrich, et al.

  34. Liquid Filled Elastomers: From Linearization to Elastic Enhancement

    ArXiv, arXiv:2309.03630, September 7, 2023

    Juan Casado Dìaz, G. Francfort, Oscar Lopez-Pamies, and Maria Giovanna Mora

  35. Learning Vector Quantized Shape Code for Amodal Blastomere Instance Segmentation

    IEEEX, September 1, 2023

    Won-Dong Jang, et al.

  36. Multi-Task Curriculum Learning for Partially Labeled Data

    2023 IEEE 20th International Symposium on Biomedical Imaging, September 1, 2023

    Won-Dong Jang, et al.

  37. Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel

    Cell Biology, August 21, 2023

    S. Hanson, Jan Scholüke, and Jana Liewald

  38. Discontinuous instabilities in disordered solids

    PNAS, August 16, 2023

    Ding Xu, et al.

  39. Generation and motion of interfaces in a mass-conserving reaction-diffusion system

    SIAM Journal on Applied Dynamical Systems, August 14, 2023

    P. Miller, Daniel Fortunato, Matteo Novaga, S. Shvartsman, and Cyrill B. Muratov

  40. Evolutionary history of MEK1 illuminates the nature of deleterious mutations

    PNAS, August 14, 2023

    Ekaterina P. Andrianova, Robert A. Marmion, S. Shvartsman, and Igor B. Zhulin

  41. Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy

    Current Opinion in Structural Biology, August 1, 2023

    W. Wai Shing, Ellen D. Zhong, S. Hanson, E. Thiede, and P. Cossio

  42. Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data

    Nature Computational Science, July 25, 2023

    O. Troyanskaya, et al.

  43. Maintaining symmetry during body axis elongation

    Current Biology, July 21, 2023

    Celia M. Smits, Sayantan Dutta, Vishank Jain-Sharma, Sebastian J. Streichan, and S. Shvartsman

  44. A note about convected time derivatives for flows of complex fluids

    Soft Matter, July 5, 2023

    Howard A Stone, M. Shelley, and Evgeniy Boyko

  45. P-175 Human cumulus cell telomere length and its association with assisted reproduction outcome

    Human Reproduction, June 22, 2023

    K. Kumar, et al.

  46. Ensemble reweighting using Cryo-EM particles

    Journal of Physical Chemistry B, June 9, 2023

    P. Tang, D. Silva-Sánchez, J. Giraldo-Barreto, B. Carpenter, S. Hanson, A. Barnett, et al.

  47. Dual mechanism of kinetochore microtubule detachment

    bioRxiv, June 7, 2023

    William Conway, Gloria Ha, and D. Needleman

  48. Algebraically rigorous quaternion framework for the neural network pose estimation problem

    IEEE Explore, 2023

    C. Lin, Andrew J. Hanson, and S. Hanson

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