101 Publications (Page 1 of 5)
2023
A multiscale model of pulmonary micrometastasis and immune surveillance: towards cancer patient digital twins
 
An agent-based modeling approach for lung fibrosis in response to COVID-19. PLOS Computational Biology
. | Journal Article
 
PhysiCell Studio: a graphical tool to make agent-based modeling more accessible
2022
A model of multicellular communication mediated through extracellular matrix microstructure
 
An agent-based modeling approach for lung fibrosis in response to COVID-19
 
Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation.
Stahlberg, Eric A⋅Stahlberg, Eric A.⋅Stahlberg, Eric A⋅Abdel-Rahman, Mohamed⋅Abdel-Rahman, Mohamed⋅Abdel-Rahman, Mohamed⋅Aguilar, Boris⋅Aguilar, Boris⋅Aguilar, Boris⋅Asadpoure, Alireza⋅Asadpoure, Alireza⋅Asadpoure, Alireza⋅Beckman, Robert A⋅Beckman, Robert A⋅Beckman, Robert A.⋅Borkon, Lynn L⋅Borkon, Lynn L.⋅Borkon, Lynn L⋅Bryan, Jeffrey N.⋅Bryan, Jeffrey N⋅Bryan, Jeffrey N⋅Cebulla, Colleen M⋅Cebulla, Colleen M⋅Cebulla, Colleen M.⋅Chang, Young Hwan⋅Chang, Young Hwan⋅Chang, Young Hwan⋅Chatterjee, Ansu⋅Chatterjee, Ansu⋅Chatterjee, Ansu⋅Deng, Jun⋅Deng, Jun⋅Deng, Jun⋅Dolatshahi, Sepideh⋅Dolatshahi, Sepideh⋅Dolatshahi, Sepideh⋅Gevaert, Olivier⋅Gevaert, Olivier⋅Gevaert, Olivier⋅Greenspan, Emily J.⋅Greenspan, Emily J⋅Greenspan, Emily J⋅Hao, Wenrui⋅Hao, Wenrui⋅Hao, Wenrui⋅Hernandez-Boussard, Tina⋅Hernandez-Boussard, Tina⋅Hernandez-Boussard, Tina⋅Jackson, Pamela R.⋅Jackson, Pamela R⋅Jackson, Pamela R⋅Kuijjer, Marieke⋅Kuijjer, Marieke⋅Kuijjer, Marieke⋅Lee, Adrian⋅Lee, Adrian⋅Lee, Adrian⋅Macklin, Paul⋅Macklin, Paul⋅Macklin, Paul⋅Madhavan, Subha⋅Madhavan, Subha⋅Madhavan, Subha⋅McCoy, Matthew D.⋅McCoy, Matthew D⋅McCoy, Matthew D⋅Mohammad Mirzaei, Navid⋅Mohammad Mirzaei, Navid⋅Mohammad Mirzaei, Navid⋅Razzaghi, Talayeh⋅Razzaghi, Talayeh⋅Razzaghi, Talayeh⋅Rocha, Heber L⋅Rocha, Heber L⋅Rocha, Heber L.⋅Shahriyari, Leili⋅Shahriyari, Leili⋅Shahriyari, Leili⋅Shmulevich, Ilya⋅Shmulevich, Ilya⋅Shmulevich, Ilya⋅Stover, Daniel G⋅Stover, Daniel G⋅Stover, Daniel G.⋅Sun, Yi⋅Sun, Yi⋅Sun, Yi⋅Syeda-Mahmood, Tanveer⋅Syeda-Mahmood, Tanveer⋅Syeda-Mahmood, Tanveer⋅Wang, Jinhua⋅Wang, Jinhua⋅Wang, Jinhua⋅Wang, Qi⋅Wang, Qi⋅Wang, Qi⋅Zervantonakis, Ioannis⋅Zervantonakis, Ioannis and Zervantonakis, Ioannis
Frontiers in digital health, vol. 4, pp. 1007784, 2022. | Journal Article
 
PhysiCell training apps: Cloud hosted open-source apps to learn cell-based simulation software
Sundus, Aneequa⋅Kurtoglu, Furkan⋅Konstantinopoulos, Kali⋅Chen, Mary⋅Willis, Drew⋅Heiland, Randy and Macklin, Paul
Cold Spring Harbor Laboratory
 
Supporting Computational Apprenticeship Through Educational and Software Infrastructure: A Case Study in a Mathematical Oncology Research Lab.
Madamanchi, Aasakiran⋅Madamanchi, Aasakiran⋅Thomas, Madison⋅Thomas, Madison⋅Magana, Alejandra⋅Magana, Alejandra⋅Heiland, Randy⋅Heiland, Randy⋅Macklin, Paul and Macklin, Paul
PRIMUS : problems, resources, and issues in mathematics undergraduate studies, vol. 32, (no. 3 Pt 2), pp. 446-467, 2022. | Journal Article
2021
A persistent invasive phenotype in post-hypoxic tumor cells is revealed by fate mapping and computational modeling.
Rocha, Heber L⋅Godet, Inês⋅Kurtoglu, Furkan⋅Metzcar, John⋅Konstantinopoulos, Kali⋅Bhoyar, Soumitra⋅Gilkes, Daniele M and Macklin, Paul
iScience, vol. 24, (no. 9), pp. 102935, September 24, 2021. | Journal Article
 
A persistent invasive phenotype in post-hypoxic tumor cells is revealed by novel fate-mapping and computational modeling
Rocha, Heber L⋅Rocha, H.L.⋅Godet, I.⋅Godet, Inês⋅Kurtoglu, Furkan⋅Kurtoglu, F.⋅Metzcar, J.⋅Metzcar, John⋅Konstantinopoulos, Kali⋅Konstantinopoulos, K.⋅Bhoyar, Soumitra⋅Bhoyar, S.⋅Gilkes, D.M.⋅Gilkes, Daniele M⋅Macklin, Paul and Macklin, P.
Cold Spring Harbor Laboratory
 
DAPT: A package enabling distributed automated parameter testing
Gigabyte. | Journal Article
 
Digital twins for predictive oncology will be a paradigm shift for precision cancer care
Hernandez-Boussard, Tina⋅Macklin, Paul⋅Greenspan, Emily J⋅Gryshuk, Amy L and Stahlberg, Eric
(pp. 2065-2066). Dec 2021
 
Digital twins for predictive oncology will be a paradigm shift for precision cancer care.
Hernandez Boussard, Tina⋅Hernandez-Boussard, Tina⋅Macklin, Paul⋅Macklin, Paul⋅Greenspan, Emily J.⋅Greenspan, Emily J⋅Gryshuk, Amy L.⋅Gryshuk, Amy L⋅Stahlberg, Eric⋅Stahlberg, Eric⋅Syeda-Mahmood, Tanveer⋅Syeda-Mahmood, Tanveer⋅Shmulevich, Ilya and Shmulevich, Ilya
November 25, 2021
 
Elucidating tumor-stromal metabolic crosstalk in colorectal cancer through integration of constraint-based models and LC-MS metabolomics.
Wang, Junmin⋅Delfarah, Alireza⋅Gelbach, Patrick⋅Fong, Emma⋅Macklin, Paul⋅Mumenthaler, Shannon M⋅Graham, Nicholas A and Finley, Stacey
Metabolic engineering, November 25, 2021. | Journal Article
 
Elucidating Tumor-stromal Metabolic Crosstalk in Colorectal Cancer through Integration of Constraint-Based Models and LC-MS Metabolomics
Wang, Junmin⋅Delfarah, Alireza⋅Gelbach, Patrick⋅Fong, Emma⋅Macklin, Paul⋅Mumenthaler, Shannon⋅Graham, Nicholas Alexander and Finley, Stacey D
Cold Spring Harbor Laboratory
 
Envisioning the future of precision oncology trials
Madhavan, Subha⋅Madhavan, Subha⋅Beckman, Robert A⋅Beckman, Robert A.⋅McCoy, Matthew D.⋅McCoy, Matthew D⋅Pishvaian, Michael J⋅Pishvaian, Michael J.⋅Brody, Jonathan R.⋅Brody, Jonathan R⋅Macklin, Paul and Macklin, Paul
Nature Cancer. | Journal Article
 
High-throughput microscopy reveals the impact of multifactorial environmental perturbations on colorectal cancer cell growth.
Chiang, Chun-Te⋅Lau, Roy⋅Ghaffarizadeh, Ahmadreza⋅Brovold, Matthew⋅Vyas, Dipen⋅Juárez, Edwin F⋅Atala, Anthony⋅Agus, David B⋅Soker, Shay⋅Macklin, Paul⋅Ruderman, Daniel and Mumenthaler, Shannon M
GigaScience, vol. 10, (no. 4), April 19, 2021. | Journal Article
 
Impact of tumor-parenchyma biomechanics on liver metastatic progression: a multi-model approach
Wang, Yafei⋅Brodin, Erik⋅Nishii, Kenichiro⋅Frieboes, Hermann B.⋅Mumenthaler, Shannon M.⋅Sparks, Jessica L. and Macklin, Paul
Scientific Reports, vol. 11. | Journal Article
 
Supporting computational apprenticeship through educational and software infrastructure. A case study in a mathematical oncology research lab
Madamanchi, Aasakiran⋅Thomas, Madison⋅Magana, Alejandra⋅Heiland, Randy and Macklin, Paul
PRIMUS, pp. 1–42. | Journal Article
2020
Impact of tumor-parenchyma biomechanics on liver metastatic progression: a multi-model approach
Wang, Yafei⋅Brodin, Erik⋅Nishii, Kenichiro⋅Frieboes, Hermann B⋅Mumenthaler, Shannon⋅Sparks, Jessica L and Macklin, Paul
Cold Spring Harbor Laboratory
 
Maraviroc inhibits SARS-CoV-2 multiplication and s-protein mediated cell fusion in cell culture
Risner, Kenneth⋅Tieu, Katie V⋅Wang, Yafei⋅Bakovic, Allison⋅Bhalla, Nishank⋅Nathan, Steven⋅Conway, Daniel E⋅Macklin, Paul and Narayanan, Aarthi
Cold Spring Harbor Laboratory
 
Maraviroc inhibits SARS-CoV-2 multiplication and s-protein mediated cell fusion in cell culture.
Risner, Kenneth H⋅Tieu, Katie V⋅Wang, Yafei⋅Bakovic, Allison⋅Alem, Farhang⋅Bhalla, Nishank⋅Nathan, Steven⋅Conway, Daniel E⋅Macklin, Paul and Narayanan, Aarthi
bioRxiv : the preprint server for biology, August 13, 2020. | Journal Article
 
OrgDyn: Feature and model based characterization of spatial and temporal organoid dynamics.
Hasnain, Zaki⋅Fraser, Andrew K⋅Georgess, Dan⋅Choi, Alex⋅Macklin, Paul⋅Bader, Joel S⋅Peyton, Shelly R⋅Ewald, Andrew J and Newton, Paul K
Bioinformatics (Oxford, England), February 24, 2020. | Journal Article
 
The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.
Xavier, Joao B⋅Xavier, Joao B⋅Xavier, J.B.⋅Xavier, Joao B⋅Xavier, Joao B⋅Xavier, Joao B⋅Young, Vincent B⋅Young, V.B.⋅Young, Vincent B⋅Young, Vincent B⋅Young, Vincent B⋅Young, Vincent B⋅Skufca, Joseph⋅Skufca, J.⋅Skufca, Joseph⋅Skufca, Joseph⋅Skufca, Joseph⋅Skufca, Joseph⋅Ginty, Fiona⋅Ginty, Fiona⋅Ginty, Fiona⋅Ginty, Fiona⋅Ginty, F.⋅Ginty, Fiona⋅Testerman, Traci⋅Testerman, Traci⋅Testerman, Traci⋅Testerman, Traci⋅Testerman, Traci⋅Testerman, T.⋅Pearson, Alexander T⋅Pearson, Alexander T⋅Pearson, Alexander T⋅Pearson, A.T.⋅Pearson, Alexander T⋅Pearson, Alexander T⋅Macklin, Paul⋅Macklin, Paul⋅Macklin, Paul⋅Macklin, Paul⋅Macklin, P.⋅Macklin, Paul⋅Mitchell, A.⋅Mitchell, Amir⋅Mitchell, Amir⋅Mitchell, Amir⋅Mitchell, Amir⋅Mitchell, Amir⋅Shmulevich, I.⋅Shmulevich, Ilya⋅Shmulevich, Ilya⋅Shmulevich, Ilya⋅Shmulevich, Ilya⋅Shmulevich, Ilya⋅Xie, Lei⋅Xie, Lei⋅Xie, Lei⋅Xie, Lei⋅Xie, Lei⋅Xie, L.⋅Caporaso, J Gregory⋅Caporaso, J.G.⋅Caporaso, J Gregory⋅Caporaso, J Gregory⋅Caporaso, J Gregory⋅Caporaso, J Gregory⋅Crandall, K.A.⋅Crandall, Keith A⋅Crandall, Keith A⋅Crandall, Keith A⋅Crandall, Keith A⋅Crandall, Keith A⋅Simone, N.L.⋅Simone, Nicole L⋅Simone, Nicole L⋅Simone, Nicole L⋅Simone, Nicole L⋅Simone, Nicole L⋅Godoy-Vitorino, Filipa⋅Godoy-Vitorino, Filipa⋅Godoy-Vitorino, Filipa⋅Godoy-Vitorino, Filipa⋅Godoy-Vitorino, Filipa⋅Godoy-Vitorino, F.⋅Griffin, Timothy J⋅Griffin, Timothy J⋅Griffin, T.J.⋅Griffin, Timothy J⋅Griffin, Timothy J⋅Griffin, Timothy J⋅Whiteson, Katrine L⋅Whiteson, Katrine L⋅Whiteson, Katrine L⋅Whiteson, Katrine L⋅Whiteson, K.L.⋅Whiteson, Katrine L⋅Gustafson, Heather H⋅Gustafson, H.H.⋅Gustafson, Heather H⋅Gustafson, Heather H⋅Gustafson, Heather H⋅Gustafson, Heather H⋅Slade, Daniel J⋅Slade, Daniel J⋅Slade, Daniel J⋅Slade, Daniel J⋅Slade, D.J.⋅Slade, Daniel J⋅Schmidt, Thomas M⋅Schmidt, Thomas M⋅Schmidt, Thomas M⋅Schmidt, Thomas M⋅Schmidt, T.M.⋅Schmidt, Thomas M⋅Walther-Antonio, M.R.S.⋅Walther-Antonio, Marina R S⋅Walther-Antonio, Marina R S⋅Walther-Antonio, Marina R S⋅Walther-Antonio, Marina R S⋅Walther-Antonio, Marina R S⋅Korem, T.⋅Korem, Tal⋅Korem, Tal⋅Korem, Tal⋅Korem, Tal⋅Korem, Tal⋅Webb-Robertson, Bobbie-Jo M⋅Webb-Robertson, B.-J.M.⋅Webb-Robertson, Bobbie-Jo M⋅Webb-Robertson, Bobbie-Jo M⋅Webb-Robertson, Bobbie-Jo M⋅Webb-Robertson, Bobbie-Jo M⋅Styczynski, Mark P⋅Styczynski, Mark P⋅Styczynski, M.P.⋅Styczynski, Mark P⋅Styczynski, Mark P⋅Styczynski, Mark P⋅Johnson, W Evan⋅Johnson, W Evan⋅Johnson, W.E.⋅Johnson, W Evan⋅Johnson, W Evan⋅Johnson, W Evan⋅Jobin, Christian⋅Jobin, Christian⋅Jobin, Christian⋅Jobin, Christian⋅Jobin, C.⋅Jobin, Christian⋅Ridlon, Jason M⋅Ridlon, J.M.⋅Ridlon, Jason M⋅Ridlon, Jason M⋅Ridlon, Jason M⋅Ridlon, Jason M⋅Koh, Andrew Y⋅Koh, Andrew Y⋅Koh, Andrew Y⋅Koh, Andrew Y⋅Koh, Andrew Y⋅Koh, A.Y.⋅Yu, M.⋅Yu, Michael⋅Yu, Michael⋅Yu, Michael⋅Yu, Michael⋅Yu, Michael⋅Kelly, L.⋅Kelly, Libusha⋅Kelly, Libusha⋅Kelly, Libusha⋅Kelly, Libusha⋅Kelly, Libusha⋅Wargo, Jennifer A⋅Wargo, Jennifer A⋅Wargo, Jennifer A⋅Wargo, Jennifer A⋅Wargo, J.A. and Wargo, Jennifer A
Trends in cancer, vol. 6, (no. 3), pp. 192-204, March 2020. | Journal Article
2019
A Review of Cell-Based Computational Modeling in Cancer Biology
Metzcar, John⋅Wang, Yafei⋅Heiland, Randy and Macklin, Paul
JCO Clinical Cancer Informatics. | Journal Article