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ORCIDPaul Macklin
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2020 – today
- 2024
[j17]Reinhard C. Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James A. Glazier, Tomás Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt
, Thomas E. Yankeelov, Tjalf Ziemssen:
Toward mechanistic medical digital twins: some use cases in immunology. Frontiers Digit. Health 6 (2024)- [i2]Marco Ruscone, Andrea Checcoli, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Laurence Calzone, Vincent Noël:
Building multiscale models with PhysiBoSS, an agent-based modeling tool. CoRR abs/2406.18371 (2024) - 2023
- [j16]Mohammad Basyuni, Anindya Wirasatriya, Sigit Bayhu Iryanthony, Rizka Amelia, Bejo Slamet, Nurdin Sulistiyono, Rudhi Pribadi, Elham Sumarga, Syaiful Eddy, Shofiyah S. Al Mustaniroh, Sigit D. Sasmito, Frida Sidik, Tadashi Kajita, Hayssam M. Ali, Paul Macklin, Virni B. Arifanti:
Aboveground biomass and carbon stock estimation using UAV photogrammetry in Indonesian mangroves and other competing land uses. Ecol. Informatics 77: 102227 (2023) - [j15]Mohammad Aminul Islam, Michael Getz, Paul Macklin, Ashlee N. Ford Versypt:
An agent-based modeling approach for lung fibrosis in response to COVID-19. PLoS Comput. Biol. 19(12) (2023) - 2022
- [j14]Matt Stack, Paul Macklin, Robert Searles, Sunita Chandrasekaran:
OpenACC Acceleration of an Agent-Based Biological Simulation Framework. Comput. Sci. Eng. 24(5): 53-63 (2022) - [j13]Eric A. Stahlberg, Mohamed Abdel-Rahman, Boris Aguilar, Alireza Asadpoure, Robert A. Beckman, Lynn L. Borkon, Jeffrey N. Bryan, Colleen M. Cebulla, Young Hwan Chang, Ansu Chatterjee, Jun Deng, Sepideh Dolatshahi, Olivier Gevaert, Emily J. Greenspan, Wenrui Hao, Tina Hernandez-Boussard, Pamela R. Jackson, Marieke L. Kuijjer, Adrian Lee, Paul Macklin, Subha Madhavan, Matthew D. McCoy, Navid Mohammad Mirzaei, Talayeh Razzaghi, Heber L. Rocha, Leili Shahriyari, Ilya Shmulevich, Daniel G. Stover, Yi Sun, Tanveer F. Syeda-Mahmood, Jinhua Wang, Qi Wang, Ioannis K. Zervantonakis:
Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation. Frontiers Digit. Health 4 (2022) - [j12]Reinhard C. Laubenbacher, Anna Niarakis, Tomás Helikar, Gary An, B. Shapiro, Rahuman S. Malik-Sheriff, T. J. Sego, Adam C. Knapp, Paul Macklin, James A. Glazier:
Building digital twins of the human immune system: toward a roadmap. npj Digit. Medicine 5 (2022) - 2021
- [i1]Matt Stack, Paul Macklin, Robert Searles, Sunita Chandrasekaran:
OpenACC Acceleration of an Agent-Based Biological Simulation Framework. CoRR abs/2110.13368 (2021) - 2020
- [j11]Zaki Hasnain, Andrew K. Fraser, Dan Georgess, Alex Choi, Paul Macklin, Joel S. Bader, Shelly R. Peyton, Andrew J. Ewald, Paul K. Newton:
OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics. Bioinform. 36(10): 3292-3294 (2020)
2010 – 2019
- 2019
- [j10]Gaëlle Letort, Arnau Montagud, Gautier Stoll, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Andrei Yu. Zinovyev, Laurence Calzone:
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. Bioinform. 35(7): 1188-1196 (2019) - [j9]Randy W. Heiland, Daniel Mishler, Tyler Zhang, Eric Bower, Paul Macklin:
xml2jupyter: Mapping parameters between XML and Jupyter widgets. J. Open Source Softw. 4(39): 1408 (2019) - [j8]Michael P. Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Cole Trapnell, Dana Jackson, Garry P. Nolan, William James Greenleaf, Sylvia K. Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Xin Sun, Sanjay Jain, James S. Hagood, Gloria Pryhuber, Peter V. Kharchenko, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark P. de Caestecker, Agnes B. Fogo, Raf Van de Plas, Ken Lau, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Dong Hye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma Anand Akoju, Matthew Ruffalo, Margaret Vella, Chuck McCallum, Leonard E. Cross, Samuel H. Friedman, Randy W. Heiland, Bruce William Herr II, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Philip D. Blood, Alexander Ropelewski, William Shirey, Robin M. Scibek, Paula M. Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, John C. Marioni, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Gökcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth L. Wilder, James Anderson:
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nat. 574(7777): 187-192 (2019) - [c1]Aasakiran Madamanchi, Randy W. Heiland, Paul Macklin, Alejandra J. Magana:
Students' Use of Metacognitive Skills in Undergraduate Research Experiences in Computational Modeling. FIE 2019: 1-5 - 2018
- [j7]Jonathan Ozik, Nicholson T. Collier, Justin M. Wozniak, Charles M. Macal, Chase Cockrell, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Randy W. Heiland, Gary An, Paul Macklin:
High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow. BMC Bioinform. 19-S(18): 81-97 (2018) - [j6]Ahmadreza Ghaffarizadeh, Randy W. Heiland, Samuel H. Friedman, Shannon M. Mumenthaler, Paul Macklin:
PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems. PLoS Comput. Biol. 14(2) (2018) - 2016
- [j5]Ahmadreza Ghaffarizadeh, Samuel H. Friedman, Paul Macklin:
BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. Bioinform. 32(8): 1256-1258 (2016) - [j4]Edwin F. Juarez, Roy Lau, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Edmond A. Jonckheere, David B. Agus, Shannon M. Mumenthaler, Paul Macklin:
Quantifying differences in cell line population dynamics using CellPD. BMC Syst. Biol. 10: 92 (2016) - [j3]Jeffrey West, Zaki Hasnain, Paul Macklin, Paul K. Newton:
An Evolutionary Model of Tumor Cell Kinetics and the Emergence of Molecular Heterogeneity Driving Gompertzian Growth. SIAM Rev. 58(4): 716-736 (2016)
2000 – 2009
- 2008
- [j2]Paul Macklin, John S. Lowengrub:
A New Ghost Cell/Level Set Method for Moving Boundary Problems: Application to Tumor Growth. J. Sci. Comput. 35(2-3): 266-299 (2008) - 2006
- [j1]Paul Macklin, John S. Lowengrub:
An improved geometry-aware curvature discretization for level set methods: Application to tumor growth. J. Comput. Phys. 215(2): 392-401 (2006)
Coauthor Index
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