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Type
Author(s)
Title
Link
Date
Paper
Kiseok Lee, Siqi Liu, Kyle Crocker, Mikhail Tikhonov, Madhav Mani, Seppe Kuehn
Functional regimes define the response of the soil microbiome to environmental change
2024
Paper
Madeline Melzer, Yogesh Goyal
Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms
2024
Paper
Wioletta I. Nawrocka, Shouqiang Cheng, Bingjie Hao, Matthew C. Rosen, Elena Cortés, Elana E. Baltrusaitis, Zainab Aziz, István A. Kovács and Engin Özkan
Nematode Extracellular Protein Interactome Expands Connections between Signaling Pathways
2024
Paper
Madeline Melzer, Yogesh Goyal
Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells
2024
Paper
David Sabatini, Matthew Kaufman
Reach-dependent reorientation of rotational dynamics in motor cortex
2024
Paper
Chris Chi, Jonathan Weare, and Aaron R. Dinner
Sampling parameters of ordinary differential equations with Langevin dynamics that satisfy constraints
2024
Paper
Lunjun Zhang, Bradly Stadie
D2 Actor Critic: Diffusion Actor Meets Distributional Critic
2024
Paper
Benjamin Hoshal, Caroline Holmes, Kyle Bojanek, Jared Salisbury, Michael Berry, Olivier Marre, Stephanie Palmer
Stimulus invariant aspects of the retinal code drive discriminability of natural scenes
2024
Paper
Guy Amichay
Biological Coupled Oscillators in the Real World
2024
Paper
Stephen M Lander, Garth Fisher, Blake A Everett, Peter Tran, Arthur Prindle
Secreted nucleases reclaim extracellular DNA during biofilm development
2024
Paper
Melissa Adrian, Jake A. Soloff, Rebecca Willett
Stabilizing black-box model selection with the inflated argmax
2024
Paper
Jared Salisbury, Stephanie Palmer
A dynamic scale-mixture model of motion in natural scenes
2024
Paper
Matthew Capek, Oscar M Arenas, Michael H Alpert, Emanuela E Zaharieva, Iván D Méndez-González, José Miguel Simões, Hamin Gil, Aldair Acosta, Yuqing Su, Alessia Para, Marco Gallio
Evolution of temperature preference in flies of the genus Drosophila
2025
Paper
Haibei Zhang, Miles T. Wetherington, Hungtang Ko, Cody E. FitzGerald, Edwin M. Munro, Jasmine A Nirody
Bacterial motility patterns adapt smoothly in response to spatial confinement and disorder
2024
Paper
Xiaowen Chen, Kyle Crocker, Seppe Kuehn, Aleksandra M. Walczak, Thierry Mora
Inferring resource competition in microbial communities from time series
2025
Paper
Kyle Crocker, Abigail Skwara, Rathi Kannan, Arvind Murugan, Seppe Kuehn
Microbial functional guilds respond cohesively to rapidly fluctuating environments
2025
Paper
Melissa Adrian, Jake A. Soloff, Rebecca Willett
Stabilizing black-box model selection with the inflated argmax
2025
Paper
Adela DePavia, Vasileios Charisopoulos, Rebecca Willett
Faster Adaptive Optimization via Expected Gradient Outer Product Reparameterization
2025
Paper
Hannah Laus, Suzanna Parkinson, Vasileios Charisopoulos, Felix Krahmer, Rebecca Willett
Solving Inverse Problems with Deep Linear Networks: Global Convergence Guarantees for Gradient Descent with Weight Decay
2025
Paper
Vasileios Charisopoulos, Rebecca Willett
Nonlinear tomographic reconstruction via nonsmooth optimization
2025
Paper
Mahmoud Yousef, Kiseok Keith Lee, Jonathan Tang, Vasileios Charisopoulos, Rebecca Willett, Seppe Kuehn
Collective Microbial Effects Drive Toxin Bioremediation and Enable Rational Design
2025
Paper
M. H. Alpert, N. Ding, W. L. Kath, M. Gallio
Cellular and molecular properties of a hot-sensing circuit in Drosophila
2024
Paper
Ziyu Zhao, Dae-Sung Hwangbo, Sumit Saurabh, Clark Rosensweig, Ravi Allada, William L. Kath, Rosemary Braun
Modeling Transient Changes in Circadian Rhythms
2024
Paper
Hanna M. Hieromnimon, Anna Trzcinska, Frank T. Wen, Frederick M. Howard, James M. Dolezal, Emma Dyer, Sara Kochanny, Jefree J Schulte, Cindy Wang, Heather Chen, Jeffrey Chin, Elizabeth Blair, Nishant Agrawal, Ari Rosenberg, Everett Vokes, Rohan Katipally, Aditya Juloori, Evgeny Izumchenko, Mark W. Lingen, Nicole Cipriani, Jalal B. Jalaly, Devraj Basu, Samantha J. Riesenfeld, Alexander T. Pearson
Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas
2025
Paper
Arthur N. Montanari, Ana E.D. Barioni,, Chao Duan, Adilson E. Motter
Optimal flock formation induced by agent heterogeneity
2025
Paper
Carlos Floyd, Aaron Dinner, Arvind Murugan, Suriyanarayanan Vaikuntanathan
Limits on the computational experssivity of non-equilibrium biological processes
2024
Paper
HA Faizi, R Granek, PM Vlahovska
Curvature fluctuations of fluid vesicles reveal hydrodynamic dissipation within the bilayer
2024
Paper
Doran B.A., Chen R.Y., Giba H., Behera V., Barat B., Sundararajan A., Lin H., Sidebottom A., Pamer E.G., Raman A.S.
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom
2025
Paper
Behera V., Giba H., Pen U., Di Lello A., Doran B.A., Esposito A., Pezeshk A., Bestvina C.M., Kline J., Garassino M.C., Raman A.S.
Conserved principles of spatial biology define tumor heterogeneity and response to immunotherapy
2025
Software
Chris Chi and Aaron Dinner
Constrained Langevin and Hamiltonian Monte Carlo samplers
2024
Software
Bingjie Hao and István A. Kovács
Maximum-entropy based background correction
2024
Software
Madeline Melzer, Yogesh Goyal
Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells
2024
Research Products
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