Topology representing neural networks reconcile biomolecular shape, structure, and dynamics. - Willy Wriggers; Pablo Chacón; Julio A. Kovacs; Florence Tama; Stefan Birmanns (Neurocomputing, 2004)

3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy. - Rubén Nogales-Cadenas; Slavica Jonic; Florence Tama; A. A. Arteni; Daniel Tabas-Madrid; Miguel Vázquez; Alberto D. Pascual-Montano; Carlos Oscar Sánchez Sorzano (Nucleic Acids Res., 2013)

Steered Molecular Dynamics Simulations of a Type IV Pilus Probe Initial Stages of a Force-Induced Conformational Transition. - Joseph L. Baker; Nicolas Biais; Florence Tama (PLoS Comput. Biol., 2013)

Elastic image registration to fully explore macromolecular dynamics by electron microscopy. - Qiyu Jin; Carlos Oscar Sánchez Sorzano; Isabelle Callebaut; Florence Tama; Slavica Jonic (ICIP, 2014)

Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. - Osamu Miyashita; Chigusa Kobayashi; Takaharu Mori; Yuji Sugita; Florence Tama (J. Comput. Chem., 2017)

Searching for 3D structural models from a library of biological shapes using a few 2D experimental images. - Sandhya P. Tiwari; Florence Tama; Osamu Miyashita (BMC Bioinform., 2018)

Poisson image denoising by piecewise principal component analysis and its application in single-particle X-ray diffraction imaging. - Qiyu Jin; Osamu Miyashita; Florence Tama; Jie Yang 002; Slavica Jonic (IET Image Process., 2018)

Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps. - Sandhya P. Tiwari; Sahil Chhabra; Florence Tama; Osamu Miyashita (J. Chem. Inf. Model., 2020)

Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns. - Sandhya P. Tiwari; Florence Tama; Osamu Miyashita (J. Chem. Inf. Model., 2021)

Identifying Structural Properties of Proteins from X-ray Free Electron Laser Diffraction Patterns. - Paula Olaya; Silvina Caíno-Lores; Vanessa Lama; Ria Patel; Ariel Keller Rorabaugh; Osamu Miyashita; Florence Tama; Michela Taufer (e-Science, 2022)

A Methodology to Generate Efficient Neural Networks for Classification of Scientific Datasets. - Ria Patel; Ariel Keller Rorabaugh; Paula Olaya; Silvina Caíno-Lores; Georgia Channing; Catherine D. Schuman; Osamu Miyashita; Florence Tama; Michela Taufer (e-Science, 2022)

Composable Workflow for Accelerating Neural Architecture Search Using In Situ Analytics for Protein Classification. - Georgia Channing; Ria Patel; Paula Olaya; Ariel Keller Rorabaugh; Osamu Miyashita; Silvina Caíno-Lores; Catherine D. Schuman; Florence Tama; Michela Taufer (ICPP, 2023)

Xphase3d: Memory-Distributed Phase Retrieval for Reconstructing Large-Scale 3D Density Maps of Biological Macromolecules. - Wenyang Zhao; Osamu Miyashita; Miki Nakano; Florence Tama (CLUSTER, 2024)

Energy-Efficient Neural Network Training for Scientific Datasets with Advanced Similarity Analytics and Orchestration. - Kin Wai Ng; Orcun Yildiz; Tom Peterka; Florence Tama; Osamu Miyashita; Catherine D. Schuman; Michela Taufer (ICCS (1), 2025)