99 Publications (Page 1 of 4)
2024
A multiscale model of the mammalian liver circadian clock supports synchronization of autonomous oscillations by intercellular communication
2023
Efficacy of Rapamycin for Increasing Female Reproductive Longevity in Old Rhesus Macaques. Zenodo
 
Efficacy of Rapamycin for Increasing Female Reproductive Longevity in Old Rhesus Macaques. Zenodo
 
PhenoCellPy: A Python package for biological cell behavior modeling
Gianlupi, J.F.⋅Sego, T.J.⋅Sluka, J.P. and Glazier, J.A.
 
Tissue Forge: Interactive biological and biophysics simulation environment. PLOS Computational Biology
. | Journal Article
 
Toward a common standard for data and specimen provenance in life sciences
Wittner, R.⋅Holub, P.⋅Mascia, C.⋅Frexia, F.⋅Müller, H.⋅Plass, M.⋅Allocca, C.⋅Betsou, F.⋅Burdett, T.⋅Cancio, I.⋅Chapman, A.⋅Chapman, M.⋅Courtot, M.⋅Curcin, V.⋅Eder, J.⋅Elliot, M.⋅Exter, K.⋅Goble, C.⋅Golebiewski, M.⋅Kisler, B.⋅Kremer, A.⋅Leo, S.⋅Lin-Gibson, S.⋅Marsano, A.⋅Mattavelli, M.⋅Moore, J.⋅Nakae, H.⋅Perseil, I.⋅Salman, A.⋅Sluka, J.⋅Soiland-Reyes, S.⋅Strambio-De-Castillia, C.⋅Sussman, M.⋅Swedlow, J.R.⋅Zatloukal, K. and Geiger, J.
Learning Health Systems. | Journal Article
2022
Computational modelling of nephron progenitor cell movement and aggregation during kidney organogenesis
Tikka, P.⋅Tikka, Pauli⋅Mercker, Moritz⋅Mercker, M.⋅Skovorodkin, Ilya⋅Skovorodkin, I.⋅Saarela, Ulla⋅Saarela, U.⋅Vainio, S.⋅Vainio, Seppo⋅Ronkainen, V.-P.⋅Ronkainen, Veli-Pekka⋅Sluka, J.P.⋅Sluka, James P⋅Glazier, James A⋅Glazier, J.A.⋅Marciniak-Czochra, A.⋅Marciniak-Czochra, Anna⋅Schaefer, Franz and Schaefer, F.
Mathematical Biosciences, vol. 344. | Journal Article
 
Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2
Gianlupi, J.F.⋅Ferrari Gianlupi, Juliano⋅Mapder, Tarunendu⋅Sego, T J⋅Sluka, James P⋅Sluka, J.P.⋅Quinney, Sara K⋅Craig, Morgan⋅Stratford, Robert E and Glazier, James A
Viruses. | Journal Article
 
Tissue Forge: Interactive Biological and Biophysics Simulation Environment
2021
A computational model of liver tissue damage and repair
Adhyapok, P.⋅Adhyapok, Priyom⋅Adhyapok, P.⋅Fu, X.⋅Fu, Xiao⋅Fu, X.⋅Sluka, James P⋅Sluka, J.P.⋅Sluka, J.P.⋅Clendenon, S.G.⋅Clendenon, S.G.⋅Clendenon, Sherry G⋅Sluka, Victoria D⋅Sluka, V.D.⋅Sluka, V.D.⋅Wang, Z.⋅Wang, Zemin⋅Wang, Z.⋅Dunn, Kenneth⋅Dunn, K.⋅Dunn, K.⋅Klaunig, J.E.⋅Klaunig, J.E.⋅Klaunig, James E⋅Glazier, J.A.⋅Glazier, J.A. and Glazier, James A
PLoS ONE, vol. 15. | Journal Article
 
Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations
Toledo-Marín, J.Q.⋅Fox, G.⋅Sluka, J.P. and Glazier, J.A.
Frontiers in Physiology, vol. 12. | Journal Article
 
Deep learning approaches to surrogates for solving the diffusion equation for mechanistic real-world simulations: A preprint
Toledo-Marín, J.Q.⋅Fox, G.⋅Sluka, J.P. and Glazier, J.A.
 
Using digital twins in viral infection
Laubenbacher, R.⋅Laubenbacher, Reinhard⋅Sluka, J.P.⋅Sluka, James P⋅Glazier, J.A. and Glazier, James A
Science, vol. 371, pp. 1105-1106. | Journal Article
2020
Computational Modelling of Cell Movements and Aggregations during Kidney Organogenesis
Tikka, Pauli⋅Mercker, Moritz⋅Skovorodkin, Ilya⋅Saarela, Ulla⋅Vainio, Seppo J⋅Marciniak-Czochra, Anna⋅Schaefer, Franz⋅Sluka, James P.⋅Glazier, James A. and Ronkainen, Veli-Pekka
Cold Spring Harbor Laboratory
 
Computational Modelling of Nephron Progenitor Cell Movement and Aggregation During Kidney Organogenesis
Tikka, P.⋅Mercker, M.⋅Skovorodkin, I.⋅Saarela, U.⋅Vainio, S.⋅Ronkainen, V.-P.⋅Sluka, J.P.⋅Glazier, J.A.⋅Marciniak-Czochra, A. and Schaefer, F.
 
Construction and usage of a human body common coordinate framework comprising clinical, semantic, and spatial ontologies
Börner, K.⋅Quardokus, E.M.⋅Herr, B.W.⋅Cross, L.E.⋅Record, E.G.⋅Ju, Y.⋅Bueckle, A.D.⋅Sluka, J.P.⋅Silverstein, J.C.⋅Browne, K.M.⋅Jain, S.⋅Wasserfall, C.H.⋅Jorgensen, M.L.⋅Spraggins, J.M.⋅Patterson, N.H.⋅Musen, M.A. and Weber, G.M.
 
Mitochondrial depolarization and repolarization in the early stages of acetaminophen hepatotoxicity in mice
Dunn, K.W.⋅Dunn, Kenneth W⋅Dunn, Kenneth W⋅Martinez, M.M.⋅Martinez, Michelle M⋅Martinez, Michelle M⋅Wang, Zemin⋅Wang, Z.⋅Wang, Zemin⋅Mang, H.E.⋅Mang, Henry E⋅Mang, Henry E⋅Clendenon, Sherry G⋅Clendenon, S.G.⋅Clendenon, Sherry G⋅Sluka, J.P.⋅Sluka, James P⋅Sluka, James P⋅Glazier, James A⋅Glazier, James A⋅Glazier, J.A.⋅Klaunig, James E⋅Klaunig, James E and Klaunig, J.E.
Toxicology, vol. 439. | Journal Article
2019
A simple automated method for continuous fieldwise measurement of microvascular hemodynamics
Clendenon, Jeffrey L⋅Clendenon, Sherry G⋅Clendenon, Sherry G⋅Fu, Xiao⋅Fu, Xiao⋅Von Hoene, Robert A⋅Von Hoene, Robert A⋅Clendenon, Jeffrey L⋅Sluka, James P⋅Sluka, James P⋅Winfree, Seth⋅Winfree, Seth⋅Mang, Henry⋅Mang, Henry⋅Martinez, Michelle⋅Martinez, Michelle⋅Filson, Adele J⋅Filson, Adele J⋅Klaunig, James E⋅Klaunig, James E⋅Glazier, James A⋅Glazier, James A⋅Dunn, Kenneth W and Dunn, Kenneth W
Microvascular Research, vol. 123, pp. 13, May 2019. | Journal Article
 
Learning everywhere: Pervasive machine learning for effective high-performance computation
Fox, G.⋅Glazier, J.⋅Kadupitiya, J.C.S.⋅Jadhao, V.⋅Kim, M.⋅Qiu, J.⋅Sluka, J.P.⋅Somogy, E.⋅Marathe, M.⋅Adiga, A.⋅Chen, J.⋅Beckstein, O. and Jha, S.
(pp. 422-429)
 
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation
Fox, Geoffrey⋅Fox, Geoffrey⋅Fox, Geoffrey⋅Fox, Geoffrey⋅Fox, Geoffrey⋅Fox, Geoffrey⋅Glazier, James A⋅Glazier, James A⋅Glazier, James A⋅Glazier, James A⋅Glazier, James A⋅Glazier, James A⋅Kadupitiya, JCS⋅Kadupitiya, JCS⋅Kadupitiya, JCS⋅Kadupitiya, JCS⋅Kadupitiya, JCS⋅Kadupitiya, JCS⋅Jadhao, Vikram⋅Jadhao, Vikram⋅Jadhao, Vikram⋅Jadhao, Vikram⋅Jadhao, Vikram⋅Jadhao, Vikram⋅Kim, Minje⋅Kim, Minje⋅Kim, Minje⋅Kim, Minje⋅Kim, Minje⋅Kim, Minje⋅Qiu, Judy⋅Qiu, Judy⋅Qiu, Judy⋅Qiu, Judy⋅Qiu, Judy⋅Qiu, Judy⋅Sluka, James P⋅Sluka, James P⋅Sluka, James P⋅Sluka, James P⋅Sluka, James P⋅Sluka, James P⋅Somogyi, Endre⋅Somogyi, Endre⋅Somogyi, Endre⋅Somogyi, Endre⋅Somogyi, Endre⋅Somogyi, Endre⋅Marathe, Madhav⋅Marathe, Madhav⋅Marathe, Madhav⋅Marathe, Madhav⋅Marathe, Madhav⋅Marathe, Madhav⋅Adiga, Abhijin⋅Adiga, Abhijin⋅Adiga, Abhijin⋅Adiga, Abhijin⋅Adiga, Abhijin⋅Adiga, Abhijin⋅Chen, Jiangzhuo⋅Chen, Jiangzhuo⋅Chen, Jiangzhuo⋅Chen, Jiangzhuo⋅Chen, Jiangzhuo⋅Chen, Jiangzhuo⋅Beckstein, Oliver⋅Beckstein, Oliver⋅Beckstein, Oliver⋅Beckstein, Oliver⋅Beckstein, Oliver⋅Beckstein, Oliver⋅Jha, Shantenu⋅Jha, Shantenu⋅Jha, Shantenu⋅Jha, Shantenu⋅Jha, Shantenu and Jha, Shantenu
2019-02-27. | Journal Article
 
Mapping the Human Body at Cellular Resolution – The NIH Common Fund Human BioMolecular Atlas Program
Snyder, M.P.⋅Lin, S.⋅Posgai, A.⋅Atkinson, M.⋅Regev, A.⋅Rood, J.⋅Rozenblatt-Rosen, O.⋅Gaffney, L.⋅Hupalowska, A.⋅Satija, R.⋅Gehlenborg, N.⋅Shendure, J.⋅Laskin, J.⋅Harbury, P.⋅Nystrom, N.A.⋅Bar-Joseph, Z.⋅Zhang, K.⋅Börner, K.⋅Lin, Y.⋅Conroy, R.⋅Procaccini, D.⋅Roy, A.L.⋅Pillai, A.⋅Brown, M.⋅Galis, Z.S.⋅Cai, L.⋅Trapnell, C.⋅Lin, S.⋅Jackson, D.⋅Lin, S.⋅Nolan, G.⋅Greenleaf, W.J.⋅Lin, Y.⋅Plevritis, S.⋅Ahadi, S.⋅Lin, Y.⋅Lee, H.⋅Nevins, S.⋅Esplin, E.⋅Horning, A.⋅Bahmani, A.⋅Zhang, K.⋅Sun, X.⋅Zhang, K.⋅Jain, S.⋅Hagood, J.⋅Kharchenko, P.⋅Atkinson, M.⋅Bodenmiller, B.⋅Kharchenko, P.⋅Atkinson, M.⋅Brusko, T.⋅Clare-Salzler, M.⋅Nick, H.⋅Otto, K.⋅Posgai, A.⋅Wasserfall, C.⋅Posgai, A.⋅Maffioletti, S.⋅Caprioli, R.M.⋅Spraggins, J.M.⋅Gutierrez, D.⋅Patterson, N.H.⋅Neumann, E.K.⋅Harris, R.⋅deCaestecker, M.⋅Plas, R.V.⋅Lau, K.⋅Cai, L.⋅Yuan, G.-C.⋅Cai, L.⋅Zhu, Q.⋅Dries, R.⋅Yin, P.⋅Saka, S.K.⋅Kishi, J.Y.⋅Wang, Y.⋅Goldaracena, I.⋅Laskin, J.⋅Ye, D.⋅Laskin, J.⋅Burnum-Johnson, K.E.⋅Piehowski, P.D.⋅Ansong, C.⋅Zhu, Y.⋅Harbury, P.⋅Desai, T.⋅Harbury, P.⋅Mulye, J.⋅Chou, P.⋅Nagendran, M.⋅Bar-Joseph, Z.⋅Teichmann, S.A.⋅Bar-Joseph, Z.⋅Paten, B.⋅Murphy, R.F.⋅Ma, J.⋅Kiselev, V.Y.⋅Kingsford, C.⋅Ricarte, A.⋅Ruffalo, M.⋅Gehlenborg, N.⋅Kharchenko, P.⋅Gehlenborg, N.⋅Vella, M.⋅McCallum, C.⋅Kharchenko, P.⋅Börner, K.⋅Cross, L.E.⋅Börner, K.⋅Friedman, S.H.⋅Heiland, R.⋅Herr, B.⋅Macklin, P.⋅Quardokus, E.M.⋅Record, L.⋅Sluka, J.P.⋅Weber, G.M.⋅Nystrom, N.A.⋅Silverstein, J.C.⋅Nystrom, N.A.⋅Blood, P.D.⋅Ropelewski, A.J.⋅Shirey, W.E.⋅Mabee, P.⋅Lenhardt, W.C.⋅Robasky, K.⋅Michailidis, S.⋅Satija, R.⋅Marioni, J.⋅Regev, A.⋅Satija, R.⋅Butler, A.⋅Regev, A.⋅Stuart, T.⋅Fisher, E.⋅Ghazanfar, S.⋅Rood, J.⋅Gaffney, L.⋅Rood, J.⋅Ersalan, G.⋅Biancalani, T.⋅Gaffney, L.⋅Conroy, R.⋅Procaccini, D.⋅Roy, A.⋅Conroy, R.⋅Procaccini, D.⋅Pillai, A.⋅Brown, M.⋅Galis, Z.⋅Pillai, A.⋅Srinivas, P.⋅Brown, M.⋅Pawlyk, A.⋅Sechi, S.⋅Wilder, E. and Anderson, J.
 
Spatial Temporal Analysis of Fieldwise Flow in Microvasculature
Clendenon, Sherry G⋅Clendenon, Sherry G⋅Clendenon, Sherry G⋅Clendenon, Sherry G⋅Clendenon, Sherry G⋅Fu, Xiao⋅Fu, Xiao⋅Fu, Xiao⋅Fu, Xiao⋅Fu, Xiao⋅Von Hoene, Robert A⋅Von Hoene, Robert A⋅Von Hoene, Robert A⋅Von Hoene, Robert A⋅Von Hoene, Robert A⋅Clendenon, Jeffrey L⋅Clendenon, Jeffrey L⋅Clendenon, Jeffrey L⋅Clendenon, Jeffrey L⋅Clendenon, Jeffrey L⋅Sluka, James P⋅Sluka, James P⋅Sluka, James P⋅Sluka, James P⋅Sluka, James P⋅Winfree, Seth⋅Winfree, Seth⋅Winfree, Seth⋅Winfree, Seth⋅Winfree, Seth⋅Mang, Henry⋅Mang, Henry⋅Mang, Henry⋅Mang, Henry⋅Mang, Henry⋅Martinez, Michelle⋅Martinez, Michelle⋅Martinez, Michelle⋅Martinez, Michelle⋅Martinez, Michelle⋅Filson, Adele⋅Filson, Adele⋅Filson, Adele⋅Filson, Adele⋅Filson, Adele⋅Klaunig, James E⋅Klaunig, James E⋅Klaunig, James E⋅Klaunig, James E⋅Klaunig, James E⋅Glazier, James A⋅Glazier, James A⋅Glazier, James A⋅Glazier, James A⋅Glazier, James A⋅Dunn, Kenneth W⋅Dunn, Kenneth W⋅Dunn, Kenneth W⋅Dunn, Kenneth W and Dunn, Kenneth W
Journal of Visualized Experiments, (no. 153), 11-2019. | Journal Article
 
The 2019 mathematical oncology roadmap
Rockne, Russell C⋅Rockne, Russell C⋅Rockne, Russell C⋅Rockne, Russell C⋅Rockne, R.C.⋅Rockne, Russell C⋅Hawkins-Daarud, Andrea⋅Hawkins-Daarud, Andrea⋅Hawkins-Daarud, Andrea⋅Hawkins-Daarud, A.⋅Hawkins-Daarud, Andrea⋅Hawkins-Daarud, Andrea⋅Swanson, K.R.⋅Swanson, Kristin R⋅Swanson, Kristin R⋅Swanson, Kristin R⋅Swanson, Kristin R⋅Swanson, Kristin R⋅Sluka, James P⋅Sluka, James P⋅Sluka, James P⋅Sluka, J.P.⋅Sluka, James P⋅Sluka, James P⋅Glazier, J.A.⋅Glazier, James A⋅Glazier, James A⋅Glazier, James A⋅Glazier, James A⋅Glazier, James A⋅Macklin, Paul⋅Macklin, Paul⋅Macklin, Paul⋅Macklin, Paul⋅Macklin, P.⋅Macklin, Paul⋅Hormuth, David A⋅Hormuth, David A⋅Hormuth, David A⋅Hormuth, David A⋅Hormuth, D.A.⋅Hormuth, David A⋅Jarrett, Angela M⋅Jarrett, Angela M⋅Jarrett, Angela M⋅Jarrett, A.M.⋅Jarrett, Angela M⋅Jarrett, Angela M⋅Lima, Ernesto A B F⋅Lima, E.A.B.F.⋅Lima, Ernesto A B F⋅Lima, Ernesto A B F⋅Lima, Ernesto A B F⋅Lima, Ernesto A B F⋅Tinsley Oden, J⋅Tinsley Oden, J⋅Tinsley Oden, J.⋅Tinsley Oden, J⋅Tinsley Oden, J⋅Tinsley Oden, J⋅Biros, George⋅Biros, George⋅Biros, George⋅Biros, George⋅Biros, George⋅Biros, G.⋅Yankeelov, Thomas E⋅Yankeelov, T.E.⋅Yankeelov, Thomas E⋅Yankeelov, Thomas E⋅Yankeelov, Thomas E⋅Yankeelov, Thomas E⋅Curtius, K.⋅Curtius, Kit⋅Curtius, Kit⋅Curtius, Kit⋅Curtius, Kit⋅Curtius, Kit⋅Al Bakir, Ibrahim⋅Al Bakir, Ibrahim⋅Al Bakir, Ibrahim⋅Al Bakir, Ibrahim⋅Al Bakir, Ibrahim⋅Al Bakir, I.⋅Wodarz, D.⋅Wodarz, Dominik⋅Wodarz, Dominik⋅Wodarz, Dominik⋅Wodarz, Dominik⋅Wodarz, Dominik⋅Komarova, Natalia⋅Komarova, Natalia⋅Komarova, N.⋅Komarova, Natalia⋅Komarova, Natalia⋅Komarova, Natalia⋅Aparicio, Luis⋅Aparicio, L.⋅Aparicio, Luis⋅Aparicio, Luis⋅Aparicio, Luis⋅Aparicio, Luis⋅Bordyuh, Mykola⋅Bordyuh, Mykola⋅Bordyuh, Mykola⋅Bordyuh, M.⋅Bordyuh, Mykola⋅Bordyuh, Mykola⋅Rabadan, Raul⋅Rabadan, Raul⋅Rabadan, Raul⋅Rabadan, R.⋅Rabadan, Raul⋅Rabadan, Raul⋅Finley, Stacey D⋅Finley, Stacey D⋅Finley, S.D.⋅Finley, Stacey D⋅Finley, Stacey D⋅Finley, Stacey D⋅Enderling, Heiko⋅Enderling, H.⋅Enderling, Heiko⋅Enderling, Heiko⋅Enderling, Heiko⋅Enderling, Heiko⋅Caudell, Jimmy⋅Caudell, Jimmy⋅Caudell, Jimmy⋅Caudell, J.⋅Caudell, Jimmy⋅Caudell, Jimmy⋅Moros, E.G.⋅Moros, Eduardo G⋅Moros, Eduardo G⋅Moros, Eduardo G⋅Moros, Eduardo G⋅Moros, Eduardo G⋅Anderson, Alexander R A⋅Anderson, Alexander R A⋅Anderson, Alexander R A⋅Anderson, Alexander R A⋅Anderson, Alexander R A⋅Anderson, A.R.A.⋅Gatenby, Robert A⋅Gatenby, Robert A⋅Gatenby, R.A.⋅Gatenby, Robert A⋅Gatenby, Robert A⋅Gatenby, Robert A⋅Kaznatcheev, Artem⋅Kaznatcheev, Artem⋅Kaznatcheev, A.⋅Kaznatcheev, Artem⋅Kaznatcheev, Artem⋅Kaznatcheev, Artem⋅Jeavons, P.⋅Jeavons, Peter⋅Jeavons, Peter⋅Jeavons, Peter⋅Jeavons, Peter⋅Jeavons, Peter⋅Krishnan, Nikhil⋅Krishnan, Nikhil⋅Krishnan, Nikhil⋅Krishnan, N.⋅Krishnan, Nikhil⋅Krishnan, Nikhil⋅Pelesko, Julia⋅Pelesko, Julia⋅Pelesko, Julia⋅Pelesko, Julia⋅Pelesko, J.⋅Pelesko, Julia⋅Wadhwa, Raoul R⋅Wadhwa, Raoul R⋅Wadhwa, Raoul R⋅Wadhwa, Raoul R⋅Wadhwa, R.R.⋅Wadhwa, Raoul R⋅Yoon, Nara⋅Yoon, Nara⋅Yoon, Nara⋅Yoon, Nara⋅Yoon, Nara⋅Yoon, N.⋅Nichol, Daniel⋅Nichol, Daniel⋅Nichol, Daniel⋅Nichol, Daniel⋅Nichol, D.⋅Nichol, Daniel⋅Marusyk, Andriy⋅Marusyk, A.⋅Marusyk, Andriy⋅Marusyk, Andriy⋅Marusyk, Andriy⋅Marusyk, Andriy⋅Hinczewski, Michael⋅Hinczewski, Michael⋅Hinczewski, Michael⋅Hinczewski, Michael⋅Hinczewski, M.⋅Hinczewski, Michael⋅Scott, Jacob G⋅Scott, Jacob G⋅Scott, Jacob G⋅Scott, Jacob G⋅Scott, Jacob G and Scott, J.G.
Physical biology, vol. 16, (no. 4), pp. 041005, 2019-Jun-19. | Journal Article
2018
Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models
Fu, Xiao⋅Fu, Xiao⋅Sluka, James P⋅Sluka, James P⋅Clendenon, Sherry G⋅Clendenon, Sherry G⋅Dunn, Kenneth W⋅Dunn, Kenneth W⋅Wang, Zemin⋅Wang, Zemin⋅Klaunig, James E⋅Klaunig, James E⋅Glazier, James A and Glazier, James A
PloS one, vol. 13, (no. 9), pp. e0198060, 2018-00-00. | Journal Article
2016
A Liver-Centric Multiscale Modeling Framework for Xenobiotics
Sluka, James P.⋅James P Sluka⋅Sluka, James P⋅Sluka, James P⋅Fu, Xiao⋅Fu, Xiao⋅Xiao Fu⋅Fu, Xiao⋅Swat, Maciej⋅Swat, Maciej⋅Maciej Swat⋅Swat, Maciej⋅Belmonte, Julio M⋅Belmonte, Julio M.⋅Julio M Belmonte⋅Belmonte, Julio M⋅Alin Cosmanescu⋅Cosmanescu, Alin⋅Cosmanescu, Alin⋅Cosmanescu, Alin⋅Clendenon, Sherry G⋅Clendenon, Sherry G.⋅Clendenon, Sherry G⋅Sherry G Clendenon⋅John F Wambaugh⋅Wambaugh, John F.⋅Wambaugh, John F⋅Wambaugh, John F⋅Glazier, James A⋅Glazier, James A.⋅Glazier, James A and James A Glazier
PloS one, vol. 11, (no. 9), pp. e0162428, 2016-00-00. | Journal Article