Paul Macklin, Ph.D., MMCL Leader
- Ph.D. in Mathematics, University of California-Irvine, 2007
- M.S. in Industrial & Applied Mathematics, University of Minnesota-Twin Cities, 2003
- B.A. in Mathematics & German (minors: physics, economics), University of Nebraska-Lincoln, 1999
- U. of Texas Health Science Center SBMI John P. McGovern Award for Outstanding Teaching, 2009
- UC-Irvine Department of Mathematics Kovalesky Outstanding Ph.D. Thesis Award, 2007
- National Science Foundation Graduate Research Fellowship, 1999-2000 & 2001-2003
- U. of Nebraska-Lincoln Chancellor's Scholar, summa cum laude, honors program, 1999
- Barry M. Goldwater Scholarship, 1998
- Co-Founder / Co-Director, Consortium for Integrative Computational Oncology (CICO), U. of Southern California, May 2012-present
- Assistant Professor of Research Medicine, Center for Applied Molecular Medicine, U. of Southern California, Aug. 2011-present
- Lecturer (permanent staff--UK version of tenure-track), Division of Mathematics, U. of Dundee, Feb. 2010-Aug. 2011
- Assistant Professor, School of Biomedical Informatics (formerly School of Health Information Sciences), U. of Texas Health Science Center-Houston, Jul. 2007-Feb. 2010
Dr. Macklin has over 10 years' experience (since 2001) in modeling cancer using continuum, discrete, and multiscale techniques. He has been particularly focused on developing methods to rigorously calibrate mathematical and computational models to patient clinical data, with the hope of moving decades of modeling advances from the blackboard to the clinic to improve patient care. As a critical part of these efforts, Macklin is developing standardizations for exchanging experimental and computational data. A novel creation of this work is the digital cell line—an extensible, standardized representation of a cell line, its physical and behavioral characteristics (phenotype), and corresponding microenvironmental conditions. A repository of ever-improving digital cell lines will allow modelers to more efficiently create, exchange, extend, and recombine models of cancer.
To date, much of Macklin's modeling work has been applied to ductal carcinoma in situ (DCIS: a precursor to invasive breast cancer), which has allowed significant model validation. In his decade of cancer research, Macklin has worked closely with pathologists, radiologists, surgeons, biologists, mathematicians and engineers in exciting, multidisciplinary teams.
For his M.S. and Ph.D. work, he developed a sophisticated computational model of tumor growth as a moving boundary problem, using the level set method (to represent the tumor-host boundary) and high-accuracy ghost fluid methods (to solve nonlinear reaction-diffusion equations on complex moving domains). Significant advances included state-of-the-art, high-order efficient numerical solvers, the first incorporation of the necrotic core dynamics into continuum tumor growth, simulations of dynamic, heterogeneous microenvironments, and coupling of tumor biomechanics, hypoxia, and angiogenesis into a single simulation framework.
More recently, Macklin has developed a cutting-edge agent-based (individual-based) model that can be directly calibrated to patient immunohistochemistry and morphometric measures from hematoxylin and eosin (H & E) stains. The agent model can be straightforwardly coupled with intracellular and intercellular signaling models, as well as with pharmacokinetic/pharmacodynamic (PKPD) models of therapeutic response.
Samuel Friedman, Ph.D., Postdoctoral Student
- Ph.D. in Astronomy, University of Wisconsin-Madison, 2011
- M.S. in Astronomy, University of Wisconsin-Madison, 2006
- B.A. in Physics, University of Chicago, 2004
- B.S. in Mathematics, University of Chicago, 2004
- B.A. in Religion & Humanities, University of Chicago, 2004
Short bio and research interests
Originally from Wisconsin, Dr. Friedman attended the University of Chicago for his undergraduate degrees where he worked in the Kavli Institute for Cosmological Physics with Andrey Kravtsov by creating computional models of galactic cannibalism with the Sagittarius dwarf spheroidal galaxy and the Milky Way. For graduate school, he attended the Astronomy Department at the University of Wisconsin-Madison, first working for Linda Sparke working on local group galaxy dynamics, and then for Sebastian Heinz working on heating mechanisms of shock waves interacting with bubbles as it relates to AGN Feedback and the intergalactic medium (IGM). He next worked as a Systems Programmer on the HTCondor project in the Center for High Throughput Computing in the Computer Sciences Department at the University of Wisconsin-Madison. When he's not at work, he enjoys playing board games, reading maps, watching/riding trains, and competes in ballroom dancing.
Time in MMCL: October 2013-present
Ahmadreza (Farzin) Ghaffarizadeh, Ph.D., Postdoctoral Student
- Ph.D. in Computer Science, Utah State University, 2014
- M.S. in Software Engineering, Arak Azad University, 2010
- B.S. in Software Engineering, Shiraz University, 2007
Short bio and research interests
Hailing from Sirjan, Iran, Dr. Ghaffarizadeh studied software engineering at Shiraz University and later at Arak Azad University, where he earned his M.S. while researching a new efficient algorithm for quantitative trait loci mapping. During his Ph.D. work at Utah State University, he used computational models to study network dynamics driving cellular differentiation at smaller scales, and the role of intercellular interactions in morphogenesis at larger scales. Prior to defending his dissertation, he served as a research scholar at the Institute for Systems Biology, where he worked on multiscale modeling of glioma and immune interactions. Ghaffarizadeh's research interests lie in the development of computational and mathematical approaches for multiscale modeling of biological systems and analyzing large-scale data sets. His main hobbies center around food and soccer; therefore, if you can't find him at work, there is a high chance you find him in a restaurant or in a soccer field!
Time in MMCL: August 2014-present
Edwin F. Juárez Rosales • Ph.D. student • electrical engineering (control systems group)
- M.S. in Electrical Engineering, University of Southern California, 2014
- B.S. in Electrical Engineering, ????, 20??
Short bio and research interests
Mr. Rosales is a Ph.D. student at the Ming Hsieh department of Electrical Engineering at USC, jointly advised by Edmond Jonckheere He was born and raised in El Salvador, and he earned his B.S. in EE from Texas A&M University. His research interest include developing a compartmental model for B-cell lymphoma and applying control theory to regulate the immune system. In his spare time, he loves traveling around the world to find churches to pray, mountains to hike, and places to dance salsa.
Time in MMCL: September 2012-present
Jasmine McAllister • B.A. neuroscience • B.S. mathematics, economics
Ms. McAllister is in her second year as an undergraduate neuroscience B.A. and economics / mathematics B.S. student. Her academic interests include biology, psychology, and mathematics. Outside of the classroom, she is involved in Undergraduate Student Government, leadership fraternity DOZ, and enjoys cooking and hiking.
Time in MMCL: May 2012-May 2013
Brian Shaw • B.S. student • biomedical engineering
Mr. Shaw is a third year student at the University of Southern California, majoring in Biomedical Engineering. From Rolling Hills, California, he has had an affinity for mathematics and the sciences, ever since he could remember. He enjoys applying his knowledge to help others and aspires to enter medical school. Mr. Shaw is part of the URAP-funded multidisciplinary team project to develop user-friendly 3-D computational cancer simulators. (more info here) In his spare time, he listens to classical music, rock, and electronica on top of hanging out with friends. Other hobbies include reading comics, playing the piano, surfing the web, and playing cards and board games.
Time in MMCL: June 2013-present