Paul Macklin

According to our database, Paul Macklin authored at least 19 papers between 2006 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Toward mechanistic medical digital twins: some use cases in immunology.

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

Frontiers Digit. Health, 2024

Building multiscale models with PhysiBoSS, an agent-based modeling tool.

Marco Ruscone, Andrea Checcoli, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Laurence Calzone, Vincent Noël

Briefings Bioinform., 2024

2023

An agent-based modeling approach for lung fibrosis in response to COVID-19.

Mohammad Aminul Islam, Michael Getz, Paul Macklin, Ashlee N. Ford Versypt

PLoS Comput. Biol., December, 2023

Aboveground biomass and carbon stock estimation using UAV photogrammetry in Indonesian mangroves and other competing land uses.

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

Ecol. Informatics, November, 2023

2022

Building digital twins of the human immune system: toward a roadmap.

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

npj Digit. Medicine, 2022

Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation.

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

Frontiers Digit. Health, 2022

OpenACC Acceleration of an Agent-Based Biological Simulation Framework.

Matt Stack, Paul Macklin, Robert Searles, Sunita Chandrasekaran

Comput. Sci. Eng., 2022

2020

OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics.

Zaki Hasnain, Andrew K. Fraser, Dan Georgess, Alex Choi, Paul Macklin, Joel S. Bader, Shelly R. Peyton, Andrew J. Ewald, Paul K. Newton

Bioinform., 2020

2019

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

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

Nat., 2019

xml2jupyter: Mapping parameters between XML and Jupyter widgets.

Randy W. Heiland, Daniel Mishler, Tyler Zhang, Eric Bower, Paul Macklin

J. Open Source Softw., 2019

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling.

Gaëlle Letort, Arnau Montagud, Gautier Stoll, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Andrei Yu. Zinovyev, Laurence Calzone

Bioinform., 2019

Students' Use of Metacognitive Skills in Undergraduate Research Experiences in Computational Modeling.

Aasakiran Madamanchi, Randy W. Heiland, Paul Macklin, Alejandra J. Magana

Proceedings of the IEEE Frontiers in Education Conference, 2019

2018

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems.

Ahmadreza Ghaffarizadeh, Randy W. Heiland, Samuel H. Friedman, Shannon M. Mumenthaler, Paul Macklin

PLoS Comput. Biol., 2018

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow.

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

BMC Bioinform., 2018

2016

An Evolutionary Model of Tumor Cell Kinetics and the Emergence of Molecular Heterogeneity Driving Gompertzian Growth.

Jeffrey West, Zaki Hasnain, Paul Macklin, Paul K. Newton

SIAM Rev., 2016

Quantifying differences in cell line population dynamics using CellPD.

Edwin F. Juarez, Roy Lau, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Edmond A. Jonckheere, David B. Agus, Shannon M. Mumenthaler, Paul Macklin

BMC Syst. Biol., 2016

BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations.

Ahmadreza Ghaffarizadeh, Samuel H. Friedman, Paul Macklin

Bioinform., 2016

2008

A New Ghost Cell/Level Set Method for Moving Boundary Problems: Application to Tumor Growth.

Paul Macklin, John S. Lowengrub

J. Sci. Comput., 2008

2006

An improved geometry-aware curvature discretization for level set methods: Application to tumor growth.

Paul Macklin, John S. Lowengrub

J. Comput. Phys., 2006