Paul Macklin's Math Cancer Lab Website

People

Research Faculty

Paul Macklin

Paul Macklin, Ph.D., MMCL Leader

Education

Selected Honors

  • 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

Recent positions

  • Co-Founder and Co-Director, Consortium for Integrative Computational Oncology (CICO), U. of Southern California, May 2011-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

Research Interests

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.

CV: Curriculum Vitae (March 9, 2014)
Contact: Click here

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Postdoctoral Students

Samuel Friedman

Samuel Friedman, Ph.D., Postdoctoral Student

Education

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.

Website: MathCancer.org

Time in MMCL: October 2013-present

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Unnamed Scientist, Ph.D., Postdoctoral Student

Education

  • Ph.D. in Mathematics, Physics, Computer Science, or Engineering

Selected Honors

  • A strong history of multidisciplinary research in mathematical and computational biology

Short Bio and Research Interests

The ideal student will have a strong background in computational biology in C/C++ or a comparable language. Experience in cancer biology is a definite plus. The best candidate will have a passion for moving cancer modeling from the blackboard to the clinic.

Please see the job posting here!

Website: MathCancer.org

Time in MMCL: Starting late 2011

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Graduate Students

Edwin Rosales

Edwin F. Juárez Rosales • Ph.D. student • electrical engineering (control systems group)

Mr. Rosales is a second-year 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

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Undergraduate Students

Kelsi Chesney

Kelsi Chesney • B.S. student • neuroscience

Ms. Chesney is a Junior from Wisconsin who is studying at the University of Southern California, majoring in Neuroscience and minoring in Health Care Studies. Ms. Chesney is involved in the URAP-funded multidisciplinary team project to develop user-friendly 3-D computational cancer simulators. (more info here) She wants to become a surgeon and learn how to make pottery. She plans on reaching her goals with the help of her coffee and sweettart mini addictions.

Time in MMCL: June 2013-present

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Jasmine McAllister

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-present

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Demi Nguyen

Demi Nguyen • B.S. student • computer engineering & computer science

Ms. Nguyen is a third year B.S. student majoring in computer engineering and computer science at USC. She comes from the small town of Erie, Pennsylvania, and her academic interests include molecular biology and computer science. She is part of the URAP-funded multidisciplinary team project to develop user-friendly 3-D computational cancer simulators. (more info here) In her spare time, she enjoys baking, playing piano, and solving sudoku puzzles.

Time in MMCL: June 2013-present

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Brian Shaw

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

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Interns, Staff, and Temporary Visitors