Simulating biological processes: stochastic physics from whole cells to colonies
Earnest, Tyler M, Cole, John A, Luthey-Schulten, Zaida
Published in Reports on progress in physics (01.05.2018)
Published in Reports on progress in physics (01.05.2018)
Get full text
Journal Article
Essential metabolism for a minimal cell
Breuer, Marian, Earnest, Tyler M, Merryman, Chuck, Wise, Kim S, Sun, Lijie, Lynott, Michaela R, Hutchison, Clyde A, Smith, Hamilton O, Lapek, John D, Gonzalez, David J, de Crécy-Lagard, Valérie, Haas, Drago, Hanson, Andrew D, Labhsetwar, Piyush, Glass, John I, Luthey-Schulten, Zaida
Published in eLife (18.01.2019)
Published in eLife (18.01.2019)
Get full text
Journal Article
Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly
Earnest, Tyler M., Lai, Jonathan, Chen, Ke, Hallock, Michael J., Williamson, James R., Luthey-Schulten, Zaida
Published in Biophysical journal (15.09.2015)
Published in Biophysical journal (15.09.2015)
Get full text
Journal Article
Reverse-Chaperoning Activity of an AAA+ Protein
Liu, Cheng, McKinney, Mary C., Chen, Yi-Hsing, Earnest, Tyler M., Shi, Xinghua, Lin, Li-Jung, Ishino, Yoshizumi, Dahmen, Karin, Cann, Isaac K.O., Ha, Taekjip
Published in Biophysical journal (02.03.2011)
Published in Biophysical journal (02.03.2011)
Get full text
Journal Article
Fundamental behaviors emerge from simulations of a living minimal cell
Thornburg, Zane R., Bianchi, David M., Brier, Troy A., Gilbert, Benjamin R., Earnest, Tyler M., Melo, Marcelo C.R., Safronova, Nataliya, Sáenz, James P., Cook, András T., Wise, Kim S., Hutchison, Clyde A., Smith, Hamilton O., Glass, John I., Luthey-Schulten, Zaida
Published in Cell (20.01.2022)
Published in Cell (20.01.2022)
Get full text
Journal Article
Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations
Earnest, Tyler M, Watanabe, Reika, Stone, John E, Mahamid, Julia, Baumeister, Wolfgang, Villa, Elizabeth, Luthey-Schulten, Zaida
Published in The journal of physical chemistry. B (20.04.2017)
Published in The journal of physical chemistry. B (20.04.2017)
Get full text
Journal Article
DNA looping increases the range of bistability in a stochastic model of the lac genetic switch
Earnest, Tyler M, Roberts, Elijah, Assaf, Michael, Dahmen, Karin, Luthey-Schulten, Zaida
Published in Physical biology (01.04.2013)
Published in Physical biology (01.04.2013)
Get full text
Journal Article
Ribosome biogenesis in replicating cells: Integration of experiment and theory
Earnest, Tyler M., Cole, John A., Peterson, Joseph R., Hallock, Michael J., Kuhlman, Thomas E., Luthey‐Schulten, Zaida
Published in Biopolymers (01.10.2016)
Published in Biopolymers (01.10.2016)
Get full text
Journal Article
Hybrid CME–ODE method for efficient simulation of the galactose switch in yeast
Bianchi, David M, Peterson, Joseph R, Earnest, Tyler M, Hallock, Michael J, Luthey-Schulten, Zaida
Published in IET systems biology (01.08.2018)
Published in IET systems biology (01.08.2018)
Get full text
Journal Article
Need for systematic de-escalation of care in HER2+ breast cancer patients
Pandey, Tushar, Earnest, Tyler M, Cole, John A, Braun, Eduardo
Published in Journal of clinical oncology (20.05.2020)
Published in Journal of clinical oncology (20.05.2020)
Get full text
Journal Article
Abstract P4-06-02: Clinically feasible pharmacokinetic model of dynamic contrast-enhanced MRI is prognostic of recurrence free survival in breast cancer patients treated with neoadjuvant therapy
Peterson, Joseph R, Earnest, Tyler M., Huang, Wei, Abe, Hiroyuki, Cole, John A
Published in Cancer research (Chicago, Ill.) (15.02.2022)
Published in Cancer research (Chicago, Ill.) (15.02.2022)
Get full text
Journal Article
Using a multimodal approach to elucidate racial disparities in breast cancer biology by integrating tumor imaging and -omics data
Liadis, Nicole, Earnest, Tyler M, Braun, Eduardo, Antony, Anu K., Hallock, Micahel J, Team, The SimBioSys, Cook, Daniel
Published in Journal of clinical oncology (01.06.2022)
Published in Journal of clinical oncology (01.06.2022)
Get full text
Journal Article
Abstract P5-13-34: A multi-modal biomarker of immunotherapy response
Pfeiffer, JR, Peterson, Joseph R., Howard, Frederick, Earnest, Tyler M., Pandey, Tushar, He, Gong, Nanda, Rita
Published in Cancer research (Chicago, Ill.) (15.02.2022)
Published in Cancer research (Chicago, Ill.) (15.02.2022)
Get full text
Journal Article
Abstract P1-06-04: SimBioSys TumorScope: Spatio-temporal modeling of the breast tumor microenvironment accurately predicts chemotherapeutic response
Cole, John A, Peterson, Joseph R., Earnest, Tyler M., Hallock, Michael J., Braun, Eduardo
Published in Cancer research (Chicago, Ill.) (15.02.2020)
Published in Cancer research (Chicago, Ill.) (15.02.2020)
Get full text
Journal Article
Abstract P1-08-31: Simbiosys tumorscope: Biophysical modeling of patient-specific response to chemotherapy
Cole, John A, Peterson, Joseph R, Earnest, Tyler M, Hallock, Michael J, Cook, Daniel J, Braun, Eduardo, Antony, Anu, Pfeiffer, John R, Pandey, Tushar
Published in Cancer research (Chicago, Ill.) (15.02.2022)
Published in Cancer research (Chicago, Ill.) (15.02.2022)
Get full text
Journal Article
SimBioSys TumorScope: Spatio-temporal modeling of the tumor microenvironment to predict chemotherapeutic response
Cole, John A, Peterson, Joseph R, Earnest, Tyler M, Hallock, Micahel J, Pfeiffer, John R, Pandey, Tushar, Braun, Eduardo
Published in Journal of clinical oncology (20.05.2020)
Published in Journal of clinical oncology (20.05.2020)
Get full text
Journal Article
Variability in metabolic cross-feeding behaviors in breast cancer and response to neoadjuvant chemotherapy
Peterson, Joseph R, Cole, John A, Earnest, Tyler M, Hallock, Micahel J, Pandey, Tushar, Ritchie, Katherine, Braun, Eduardo
Published in Journal of clinical oncology (20.05.2020)
Published in Journal of clinical oncology (20.05.2020)
Get full text
Journal Article
Perfusion kinetics from clinical DCE mris increase the accuracy of predictions of tumor response to chemotherapy
Cole, John A, Peterson, Joseph R, Earnest, Tyler M, Hallock, Micahel J, Pfeiffer, John R, Pandey, Tushar, Braun, Eduardo
Published in Journal of clinical oncology (20.05.2020)
Published in Journal of clinical oncology (20.05.2020)
Get full text
Journal Article
Abstract P1-06-03: Breast cancers exhibit diverse metabolic cross-feeding behaviors associated with differing long-term survival
Peterson, Joseph R, Cole, John A, Earnest, Tyler M., Hallock, Michael J., Pandey, Tushar, Ritchie, Katherine, Braun, Eduardo
Published in Cancer research (Chicago, Ill.) (15.02.2020)
Published in Cancer research (Chicago, Ill.) (15.02.2020)
Get full text
Journal Article