Daniel M Zuckerman (D M Zuckerman, Daniel Zuckerman)

ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 41

Top Venues

PLoS computational biology

Journal of chemical theory and computation

bioRxiv : the preprint server for biology

Communications biology

Oregon Health & Science University

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Oregon Health & Science University

United States

Professor :: Biomedical Engineering

Publications

Daniel M Zuckerman, August George
Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo. Journal of chemical theory and computation 20 (8) (2024)
Daniel M Zuckerman, August George
Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo. Journal of chemical theory and computation 20 (8) (2024)
Daniel M Zuckerman, August George
Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo. Journal of chemical theory and computation 20 (8) (2024)
Jeremy Copperman, Ian C McLean, Sean M Gross, Jalim Singh, Young Hwan Chang, Daniel M Zuckerman, Laura M Heiser
Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change. bioRxiv : the preprint server for biology (2024)
Jeremy Copperman, Ian C McLean, Sean M Gross, Jalim Singh, Young Hwan Chang, Daniel M Zuckerman, Laura M Heiser
Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change. bioRxiv : the preprint server for biology (2024)
Jeremy Copperman, Ian C McLean, Sean M Gross, Young Hwan Chang, Daniel M Zuckerman, Laura M Heiser
Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change. bioRxiv : the preprint server for biology (2024)
August George, Daniel M Zuckerman
From Average Transient Transporter Currents to Microscopic Mechanism─A Bayesian Analysis. The journal of physical chemistry. B (2024)
August George, Daniel M Zuckerman
From Average Transient Transporter Currents to Microscopic Mechanism─A Bayesian Analysis. The journal of physical chemistry. B 128 (8) (2024)
August George, Daniel M Zuckerman
From Average Transient Transporter Currents to Microscopic Mechanism─A Bayesian Analysis. The journal of physical chemistry. B 128 (8) (2024)
Jeremy Copperman, Ian C McLean, Sean M Gross, Jalim Singh, Young Hwan Chang, Daniel M Zuckerman, Laura M Heiser
Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change. bioRxiv : the preprint server for biology (2024)
Daniel M Zuckerman, August George
Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo. Journal of chemical theory and computation (2024)
Daniel M Zuckerman, August George
Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo. Journal of chemical theory and computation 20 (8) (2024)
Jeremy Copperman, Ian C McLean, Sean M Gross, Young Hwan Chang, Daniel M Zuckerman, Laura M Heiser
Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change. bioRxiv : the preprint server for biology (2024)
Aidan B Estelle, August George, Elisar J Barbar, Daniel M Zuckerman
Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. PLoS computational biology 19 (4) (2023)
Jeremy Copperman, Sean M Gross, Young Hwan Chang, Laura M Heiser, Daniel M Zuckerman
Morphodynamical cell state description via live-cell imaging trajectory embedding. Communications biology 6 (1) (2023)
Aidan B Estelle, August George, Elisar J Barbar, Daniel M Zuckerman
Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. PLoS computational biology 19 (4) (2023)
Aidan B Estelle, August George, Elisar J Barbar, Daniel M Zuckerman
Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. PLoS computational biology 19 (4) (2023)
Jeremy Copperman, Sean M Gross, Young Hwan Chang, Laura M Heiser, Daniel M Zuckerman
Morphodynamical cell state description via live-cell imaging trajectory embedding. Communications biology 6 (1) (2023)
Aidan B Estelle, August George, Elisar J Barbar, Daniel M Zuckerman
Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. PLoS computational biology 19 (4) (2023)
Jeremy Copperman, Sean M Gross, Young Hwan Chang, Laura M Heiser, Daniel M Zuckerman
Morphodynamical cell state description via live-cell imaging trajectory embedding. Communications biology 6 (1) (2023)
David Aristoff, Jeremy Copperman, Gideon Simpson, Robert J Webber, Daniel M Zuckerman
Weighted ensemble: Recent mathematical developments. The Journal of chemical physics 158 (1) (2023)
Jeremy Copperman, Sean M Gross, Young Hwan Chang, Laura M Heiser, Daniel M Zuckerman
Morphodynamical cell state description via live-cell imaging trajectory embedding. Communications biology 6 (1) (2023)
Jeremy Copperman, Sean M Gross, Young Hwan Chang, Laura M Heiser, Daniel M Zuckerman
Morphodynamical cell state description via live-cell imaging trajectory embedding. Communications biology 6 (1) (2023)
Aidan B Estelle, August George, Elisar J Barbar, Daniel M Zuckerman
Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. PLoS computational biology 19 (4) (2023)
Aidan B Estelle, August George, Elisar J Barbar, Daniel M Zuckerman
Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. PLoS computational biology 19 (4) (2023)
Aidan B Estelle, August George, Elisar J Barbar, Daniel M Zuckerman
Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. PLoS computational biology 19 (4) (2023)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
John D Russo, She Zhang, Jeremy M G Leung, Anthony T Bogetti, Jeff P Thompson, Alex J DeGrave, Paul A Torrillo, A J Pratt, Kim F Wong, Junchao Xia, Jeremy Copperman, Joshua L Adelman, Matthew C Zwier, David N LeBard, Daniel M Zuckerman, Lillian T Chong
WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications. Journal of chemical theory and computation 18 (2) (2022)
Ernesto Suárez, Rafal P Wiewiora, Chris Wehmeyer, Frank Noé, John D Chodera, Daniel M Zuckerman
What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models. Journal of chemical theory and computation 17 (5) (2021)
Daniel M Zuckerman, John D Russo
A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications. American journal of physics 89 (11) (2021)
Min Woo Sung, Zhongying Yang, Camden M Driggers, Bruce L Patton, Barmak Mostofian, John D Russo, Daniel M Zuckerman, Show-Ling Shyng
Vascular K ATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides. Proceedings of the National Academy of Sciences of the United States of America 118 (44) (2021)
Abigail C Dommer, Lorenzo Casalino, Fiona L Kearns, Mia A Rosenfeld, Nicholas A Wauer, Surl-Hee Ahn, John D Russo, Sofia Oliveira, Clare Morris, Anthony T Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel G A Smith, Zhuoran Qiao, Sai Krishna Sirumalla, Michael O'Connor, Frederick R Manby, Anima Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John E Stone, Daniel M Zuckerman, Adrian Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol. bioRxiv : the preprint server for biology (2021)
Jonathan A Flores, Bassam G Haddad, Kimberly A Dolan, Janette B Myers, Craig C Yoshioka, Jeremy Copperman, Daniel M Zuckerman, Steve L Reichow
Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å. Nature communications 11 (1) (2020)
August George, Paola Bisignano, John M Rosenberg, Michael Grabe, Daniel M Zuckerman
A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms. PLoS computational biology 16 (7) (2020)
Yerim Lee, Carey Phelps, Tao Huang, Barmak Mostofian, Lei Wu, Ying Zhang, Kai Tao, Young Hwan Chang, Philip Js Stork, Joe W Gray, Daniel M Zuckerman, Xiaolin Nan
High-throughput, single-particle tracking reveals nested membrane domains that dictate KRasG12D diffusion and trafficking. eLife 8 (2019)
Barmak Mostofian, Daniel M Zuckerman
Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping. Journal of chemical theory and computation 15 (6) (2019)
Jeremy Copperman, David Aristoff, Dmitrii E Makarov, Gideon Simpson, Daniel M Zuckerman
Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture. The Journal of chemical physics 151 (17) (2019)
Efrem Braun, Justin Gilmer, Jacob I Monroe, Samarjeet Prasad, Daniel M Zuckerman
Best Practices for Foundations in Molecular Simulations [Article v1.0]. Living journal of computational molecular science 1 (1) (2018)

Daniel M Zuckerman.css-eqlu8i{font-size:small;padding-left:4px;} (D M Zuckerman, Daniel Zuckerman)

Publication Activity (10 Years)

Top Topics

Top Venues

Daniel M Zuckerman (D M Zuckerman, Daniel Zuckerman)