Code Availability
Code for our projects are accessible on our lab Github.
Textbook
Data Modeling for the Sciences
Steve Pressé and Ioannis Sgouralis
In Review
(*Corresponding author)
- “Learning Continuous 2D Diffusion Maps from Particle Trajectories without Data Binning,” Vishesh Kumar, J Shepard Bryan, Alex Rowjeski, Carlo Manzo, Steve Pressé*, in review (2024)
- Our code as well as the data used to generate publication figures are available here.
- “Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome,” Erika M. López-Alfonzo, Ayush Saurabh, Sahar Zarafshan, Steve Pressé, Andreas Martin*, in review (2023)
- “A Structured Illumination Microscopy Framework with Spatial-Domain Noise Propagation,” Ayush Saurabh, Peter T. Brown, J Shepherd Bryan IV, Zachary R. Fox, Rory Kruithoff, Douglas P. Shepherd, Steve P. Pressé*, in review (2023)
- Our code as well as the data used to generate publication figures are available here.
- “Dynamic superresolution by Bayesian nonparametric image processing”, Ioannis Sgouralis, Ameya P. Jalihal, Lance W.Q. Xu, Nils G. Walter, Steve Pressé*, in review (2023)
- Our code as well as the data used to generate publication figures are available here.
- “BNP-Track: A framework for multi-particle superresolved tracking”, Lance W.Q. Xu, Ioannis Sgouralis, Zeliha Kilic, Steve Pressé*, in review (2023)
- Our code as well as the data used to generate publication figures are available here.
- “Fluorescence Microscopy: a statistics-optics perspective”, Mohamadreza Fazel, Kristin S. Grussmayer, Boris Ferdman, Aleksandra Radenovic, Yoav Shechtman, Jörg Enderlein, Steve Pressé*, in review (2023)
- “Single-Molecule Reaction-Diffusion”, Lance W.Q. Xu, Sina Jazani, Zeliha Kilic, Steve Pressé*, in review (2023)
- Our code as well as the data used to generate publication figures are available here.
2024
- “On the statistical foundation of a recent single molecule FRET benchmark,” Ayush Saurabh, Lance W.Q. Xu (徐伟青), and Steve Pressé*, Nature Communications (2024)
- Our code as well as the data used to generate publication figures are available here.
- “Avoiding matrix exponentials for large transition rate matrices,” Pedro Pessoa, Max Schweiger, Steve Pressé, Journal of Chemical Physics (2024)
- Our code as well as the data used to generate publication figures are available here.
- “An accurate probabilistic step finder for time-series analysis”, Alex Rojewski, Max Schweiger, Ioannis Sgouralis, Matthew Comstock, Steve Pressé*, Biophysical Journal (2024)
- Our code as well as the data used to generate publication figures are available here.
2023
- “Toward building comprehensive particle tracking tools with u-track 3D”, Lance W.Q. Xu, Steve Pressé*, Cell Reports Methods (2023)
- “Building fluorescence lifetime maps photon-by-photon by leveraging spatial correlations”, Mohamadreza Fazel, Sina Jazani, Lorenzo Scipioni, Alexander Vallmitjana, Songning Zhu, Enrico Gratton, Michelle A. Digman, Steve Pressé, ACS Photonics (2023)
- Our code as well as the data used to generate publication figures are available here.
- “Hybrid samplers for efficient network inference”, Zeliha Kilic, Max Schweiger, Steve Pressé*, PLOS Comp. Bio. (2023)
- Our code as well as the data used to generate publication figures is available here.
- “Few-body hydrodynamic interactions probed by optical trap pulling experiments”, Julian Lee, Kyle Cotter, Ibrahim Elsadek, Matthew Comstock*, Steve Pressé*, J. Chem. Phys. (accepted 2023)
- “Two state swimming: strategy and survival of a model bacterial predator in response to environmental cues”, Lance W.Q. Xu, J. Shepard Bryan IV, Zeliha Kilic, Steve Pressé*, Biophysical Journal (2023)
- “How many submissions are needed to discover friendly suggested reviewers?” Pedro Pessoa, Steve Pressé*, PLOS ONE (2023)
- Our code as well as the data used to generate publication figures are available here.
- “Resolving Molecular Heterogeneity with Single-Molecule Centrifugation”, Yi Luo, Jeffrey Chang, Darren Yang, J. Shepard Bryan IV, Molly MacIsaac, Steve Pressé, Wesley P. Wong*, J. Am. Chem. Soc. (2023)
- “Fluorescence Lifetime: Beating the IRF and interpulse window”, Mohamadreza Fazel, Alexander Vallmitjana, Lorenzo Scipioni, Enrico Gratton, Michelle A. Digman, Steve Pressé, Biophys. J. (2023)
- Our code as well as the data used to generate publication figures are available here.
- An open access version is available here.
- “Gene expression model inference from snapshot RNA data using Bayesian non-parametrics”, Zeliha Kilic, Max Schweiger, Camille Moyer, Douglas Sheperd*, Steve Pressé*, Nat. Comp. Sci., (2023)
- Our code as well as the data used to generate publication figures is available here.
- An open access version is available here.
- See Nature Computational Science news & views article by Sandeep Choubey about our work.
- “Learning continuous potentials from smFRET”, J. Shepard Bryan IV, Steve Pressé*, Biophys. J. (2023)
- Our code as well as the data used to generate publication figures are available here.
- An open access version is available here.
- “Single photon smFRET I: theory and conceptual basis”, Ayush Saurabh, Matthew Safar, Ioannis Sgouralis, Mohamadreza Fazel, Steve Pressé*, Biophys. Rep., (2023)
- Our code as well as the data used to generate publication figures are available here.
- “Single photon smFRET II: application to continuous illumination”, Ayush Saurabh, Matthew Safar, Ioannis Sgouralis, Mohamadreza Fazel, Steve Pressé*, Biophys. Rep., (2023)
- Our code as well as the data used to generate publication figures are available here.
- “Single photon smFRET III: application to pulsed illumination”, Matthew Safar, Ayush Saurabh, Bidyut Sarkar, Mohamadreza Fazel, Kunihiko Ishii, Tahei Tahara, Ioannis Sgouralis, Steve Pressé*, Biophys. Rep., (2022)
- Our code as well as the data used to generate publication figures are available here.
2022
- “Shelterin reduces the accessibility of telomeric overhangs”, Sajad Shiekh, Amanda Jack, Ayush Saurabh, Golam Mustafa, Sineth G Kodikara, Prabesh Gyawali, Mohammed Enamul Hoque, Steve Pressé, Ahmet Yildiz*, Hamza Balci*, Nucleic Acids Res., (2022)
- “High resolution fluorescence lifetime maps from minimal photon counts”, Mohamadreza Fazel, Alexander Vallmitjana, Lorenzo Scipioni, Enrio Gratton, Michelle A. Digman, Steve Pressé*, ACS Photonics, (2022)
- Our code as well as the data used to generate publication figures are available here.
- “Revisiting claims in ‘Black hole entropy: a closer look'”, Pedro Pessoa, Bruno Arderucio Costa, Steve Pressé*, arXiv, (2022)
- “A computational proposal for tracking multiple molecules in a multifocus confocal setup”, Sina Jazani, Lance W.Q. Xu, Ioannis Sgouralis, Douglas Shepherd, Steve Pressé*, ACS Photonics, (2022)
- Our code is available for download.
- “Modeling non-additive effects in neighboring chemically identical fluorophores”, Ayush Saurabh, Stefan Niekamp, Ioannis Sgouralis, Steve Pressé*, J. Phys. Chem. B, (2022)
- “Diffraction-limited molecular cluster quantification with Bayesian nonparametrics”, J. Shepard Bryan IV, Ioannis Sgouralis, Steve Pressé*, Nat. Comput. Sci., (2022)
- Our code is available for download on Zenodo along with the data sets used to generate publication figures.
- See Nature Computational Science news & views article by Jean Baptiste Masson about our work.
- “Inferring potential landscapes from noisy trajectories of particles within an optical feedback trap”, J. Shepard Bryan IV, Prithviraj Basak, John Bechhoefer*, Steve Pressé*, iScience, (2022)
- Our code is available for download along with the data sets used to generate publication figures.
2021
- “Extraction of rapid kinetics from smFRET measurements using integrative detectors”, Zeliha Kilic, Ioannis Sgouralis, Wooseok Heo, Kunihiko Ishii, Tahei Tahara, Steve Pressé*, Cell Rep. Phys. Sci., (2021)
- See ASU News for a news story covering our work by James Klemaszewski.
- Our code is now available for download including all the files to regenerate the publication figures and analyzed experimental data sets.
- “Generalizing HMMs to continuous time for fast kinetics: Hidden Markov Jump Processes”, Zeliha Kilic, Ioannis Sgouralis, Steve Pressé*, Biophys. J., (2021)
- Our code is now available for download including all the files to regenerate the publication figures and analyzed data sets.
- “Residence time analysis of RNA polymerase transcription dynamics: a Bayesian Sticky HMM Approach”, Zeliha Kilic, Ioannis Sgouralis, Steve Pressé*, Biophys. J., (2021)
- Our code is now available for download including all the files to regenerate the publication figures and analyzed experimental data sets.
2020
- “A thermodynamic perspective on enhanced enzyme diffusion”, Steve Pressé*, PNAS, (2020)
- “Surmounting potential barriers: Hydrodynamic memory hedges against thermal fluctuations in particle transport”, Sean L. Seyler, Steve Pressé*, J. Chem. Phys., (2020)
- Our code is now available for download.
- “Direct photon-by-photon analysis of time-resolved pulsed excitation data using Bayesian nonparametrics”, Meysam Tavakoli, Sina Jazani, Ioannis Sgouralis, Wooseok Heo, Kunihiko Ishii, Tahei Tahara, Steve Pressé*, Cell Rep. Phys. Sci., (2020)
- Our code is now available for download.
- “Information propagation in time through allosteric signaling”, Tushar Modi, S. Banu Ozkan, Steve Pressé*, Phys. Rev. Res., (2020)
- “Pitching single focus confocal data analysis one photon at a time with Bayesian nonparametrics”, Meysam Tavakoli, Sina Jazani, Ioannis Sgouralis, Omer M. Shafraz, Bryan Donaphon, Sanjeevi Sivasankar, Marcia Levitus, Steve Pressé*, Phys. Rev. X, (2020)
- “Inferring effective forces for Langevin dynamics using Gaussian processes”, J. Shepard Bryan IV, Ioannis Sgouralis, Steve Pressé*, J. Chem. Phys., (2020)
- Our code is now available for download.
2019
- “An Alternative Framework for Fluorescence Correlation Spectroscopy”, Sina Jazani, Ioannis Sgouralis, Omer M. Shafraz, Marcia Levitus, Sanjeevi Sivasankar, Steve Pressé*, Nat. Comm., (2019)
- Our Confocal analysis code assuming a single diffusive species and Multi-diffusive species confocal analysis code are now available for download.
- See Springer Nature
- See Phys.org
- See Science Daily
- See Nanowerk
- See 7th Space Family Portal
- See Photonics.com
- “Long-time persistence of hydrodynamic memory boosts microparticle transport”, Sean L. Seyler, Steve Pressé*. Phys. Rev. Res., (2019)
- “Hydrodynamic interaction facilitates the unsteady transport of two neighboring vesicles” , Julian Lee, Sean L. Seyler, Steve Pressé*,J. Chem. Phys., (2019)
- “Quantitative Kinetic Models from Intravital Microscopy: A Case Study Using Hepatic Transport”, Meysam Tavakoli, Konstantinos Tsekouras, Richard Day, Kenneth W. Dunn, Steve Pressé*, J. Chem. Phys. B, (2019)
- Our analysis code is now available for download.
- “A method for single molecule tracking using a conventional single-focus confocal setup”, Sina Jazani, Ioannis Sgouralis, Steve Pressé*, J. Chem. Phys., (2019)
- Our code is now available for download.
- “Quantitative maps of endosomal DNA processing by single molecule counting”, Ved Prakash, Konstantinos Tsekouras, Muthukumaran Venkatachalapathy, Laurie Heineke, Steve Pressé*, Nils G. Walter*, Yamuna Krishnan*, Angewandte Chemie,
- Our SI available for download.
- “A Bayesian nonparametric approach to single molecule Förster resonance energy transfer”, Ioannis Sgouralis, Shreya Madaan, Franky Djutanta, Rachael Kha, Rizal Hariadi, Steve Pressé*, J. Phys. Chem. B, (2019)
- Our FRET analysis code is now available for download.
2018
- “From the volcano effect to banding: a minimal model for bacterial behavioral transitions near chemoattractant sources”, Gregory Javens, Hossein Jashnsaz, Steve Pressé*, Phys. Bio., (2018)
- “Single molecule force spectroscopy at high data acquisition: A Bayesian nonparametric analysis”, Ioannis Sgouralis, Miles Whitmore, Lisa Lapidus, Matthew Comstock, Steve Pressé*, J. Chem. Phys., (2018)
- Our XL-ICON analysis code is now available for download.
- “Perspective: Maximum Caliber is a general variational principle for dynamical systems”, Purushottam Dixit, Jason Wagoner, Corey Weistuch, Steve Pressé, Kingshuk Ghosh, and Ken Dill* , J. Chem. Phys., (2018).
2017
- “Spatiotemporal organization of catalysts driven by enhanced diffusion”, Corey Weistuch, Steve Pressé*, J. Phys. Chem. B, (2017).
- “Statistical signatures of a targeted search by bacteria”, Hossein Jashnsaz, Gregory Anderson, Steve Pressé*, Phys. Bio., (2017).
- “Hydrodynamic hunters”, Hossein Jashnsaz, Mohammad Al Jaboori, Nicholas Miller, Tyler Nguyen, Bryan McCoy, Stephanie Perkins, Ross Wallgren, Bruce Ray, Konstantinos Tsekouras, Gregory Anderson*, Steve Pressé*, Biophys. J., (2017). See SI here.
- See Biophysical Journal Research Highlight.
- See Welt.
- See Zeit.
- See Bild.
- See Science Direct.
- See Spiegel.
- See SciShow with 270k+ views.
- And 40+ news articles.
- “ICON: an adaptation of infinite HMMs for time traces with drift”, Ioannis Sgouralis, Steve Pressé*, Biophys. J., (2017). See SI here.
- Our ICON analysis code is now available for download.
- “An introduction to infinite HMMs for single molecule data analysis”, Ioannis Sgouralis, Steve Pressé*, Biophys. J., (2017). See SI here.
- Our iHMM analysis code is now available for download.
- “Single molecule data analysis: An introduction”, Meysam Tavakoli, J, Nicholas Taylor, Chun-Biu Li, Tamiki Komatsuzaki, Steve Pressé*, Adv. Chem. Physical., (2017).
- “Unraveling the thousand word picture: An Introduction to super-resolution data analysis”, Antony Lee, Konstantinos Tsekouras, Christopher Calderon, Carlos Bustamante, Steve Pressé*, Chem. Rev., (2017).
2016
- “A novel method to accurately locate and count large numbers of steps by photobleaching”, Konstantinos Tsekouras, Thomas C. Custer, Hossein Jashnsaz, Nils G. Walter, Steve Pressé*, Mol. Biol. Cell, (2016).
- Our Photobleaching analysis code is now available for download with documentation. Also available on Github.
2015
- “The heat released during catalytic turnover enhances the diffusion of an enzyme”, Clément Riedel, Christian A.M. Wilson, Kambiz Hamadani, Konstantinos Tsekouras, Susan Marqusee, Steve Pressé*, Carlos J. Bustamante*, Nature, (2015). See SI here.
- See News and Views article.
- See C&EN Highlight.
- See Phys.org article.
- See IUPUI School of Science article.
- See Comment on “Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions” by R.Golestanian — arXiv response to criticism of our work (cited therein).
- “Stochastic approach to the molecular counting problem in superresolution microscopy”, Geoffrey Rollins, Jae Yen Shin, Carlos J. Bustamante, Steve Pressé*, Proc. Natl. Acad. Sc. (Direct Submission), (2015).
- Our Python analysis code is now available for download with documentation.
- See EurekaAlert!.
- See PNAS Research Highlight.
- See IUPUI School of Science article.
- “Inferring models of bacterial dynamics toward point sources”, Hossein Jashnsaz, Tyler Nguyen, Horia Petrache, Steve Pressé*, PLoS ONE, (2015).
- An APS Story is written about our work.
- “A data-driven alternative to the fractional Fokker-Planck equation”, Steve Pressé*, J. Stat. Phys.: Th. and Expmt. , (2015).
- “Reply to C. Tsallis’ `Conceptual inadequacy of the Shore and Johnson axioms for wide classes of complex systems’ “, Steve Pressé*, Kingshuk Ghosh, Julian Lee, Ken A. Dill, entropy , (2015).
- “Inferring Diffusional Dynamics from FCS in Heterogeneous Nuclear Environments”, Konstantinos Tsekouras, Amanda Siegel, Richard N. Day, Steve Pressé*, Biophys. J., (2015).
- Our Mathematica analysis code is now available for download.
2014
- “Nonadditive entropy maximization is inconsistent with Bayesian updating”, Steve Pressé*, Phys. Rev. E, (2014).
- “Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin”, Steve Pressé*, Jack Peterson, Julian Lee, Phillip Elms, Justin L. MacCallum, Susan Marqusee, Carlos J. Bustamante, Ken A. Dill, J. Phys. Chem. B, (2014).
2013
- “Nonadditive entropies yield probability distributions with biases not warranted by the data”, Steve Pressé*, Kingshuk Ghosh, Julian Lee, Ken A. Dill,Phys. Rev. Lett., (2013).
- See Science Daily article.
- See IUPUI School of Science article.
- See Tsallis’ rebuttal on the arXiv to our PRL. Our PRL plainly shows that Tsallis’ model inference prescription imposes structure in models that are not justified from the data. The rebuttal simply asserts that our starting axioms (due to Shore & Johnson) are not applicable to out-of-equilibrium systems (where it is qualitatively argued that the Tsallis entropy applies). Actually, this is a logical error. The axioms of Shore & Johnson have no notion of equilibrium. The PRL and rebuttal stand on their own. We will probably not publish a reply unless Tsallis’ rebuttal manages to get published in a refereed journal (unlikely). We add that Tsallis entropy is not a small deal. The original paper by Tsallis has been cited about 5000 times and Tsallis (who lives in Brazil) is the single most cited author in South America. We are focused on developing new, and in many ways stronger, ideas which we hope will help focus the community’s attention on principled inference methods that work.
- “The ClpXP protease functions as a motor with constant ‘rpm’ but different ‘gears’ “, Maya Sen, Rodrigo A. Maillard, Kristofor Nyquist, Piere Rodriguez-Aliaga, Steve Pressé, A. Martin*, C. Bustamante*, Cell, (2013).
- “Principles of maximum entropy and maximum caliber in statitistical physics” , Steve Pressé*, Kingshuk Ghosh, Julian Lee, Ken A. Dill, Rev. Mod. Phys., (2013).
- “Extracting conformational memory from single-molecule kinetic data” Steve Pressé*, Julian Lee, Ken A. Dill, J. Phys. Chem. B, (2013).
2012 and earlier
- “Microcanonical origin of the maximum entropy principle for open systems”, Julian Lee*, Steve Pressé*, Phys. Rev. E, (2012).
- “A derivation of the master equation from path entropy maximization”, Julian Lee*, Steve Pressé*, J. Chem. Phys., (2012).
- “Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology”, G. Jack Peterson*, Steve Pressé, Kristin Peterson, Ken A. Dill, PLoS ONE, (2012).
- “Markov Processes Follow from the Principle of Maximum Caliber”, Hao Ge*, Steve Pressé, Kingshuk Ghosh, Ken A. Dill, J. Chem. Phys., (2012) — Selected by the Editors as a Research Highlight.
- “Modeling Stochastic Dynamics in Biochemical Systems with Feedback using Maximum Caliber” , Steve Pressé*, Kingshuk Ghosh, Ken A. Dill, J. Phys. Chem. B, (2011).
- “Dynamical Fluctuations in biochemical reactions and cycles” , Steve Pressé*, Kingshuk Ghosh, R. Phillips, Ken A. Dill, Phys. Rev. E, (2010).
- “Nonuniversal Power Law Scaling in the Probability Distribution of Scientific Citations” , G. Jack Peterson, Steve Pressé, Ken A. Dill*, Proc. Natl. Acad. Sc. (Contributed), (2010).
- “Memory effects on the convergence properties of the Jarzynsky equality” , Steve Pressé, R.J.Silbey*, Phys. Rev. E., (2006).