Graduate student theses directed

University of Pennsylvania

  • Carol Rothman (MSE, 1981): A quantitative analysis of the linear under-agarose migration assay for the measurement of leukocyte motility and chemotaxis parameters.
  • Barbara Calcagno-P. (MSE, 1981): Analysis of steady-state growth and competition of motile bacterial populations in nonmixed environments.
  • Douglas Stickle (MSE, 1982): Measurement of the chemokinetic response of alveolar macrophage to FNLLP stimulation using the linear under-agarose assay, and considerations for design of chemotaxis experiments.
  • Caryn Hertz (MSE, joint with Prof. D.J. Graves, 1982): Separation of human lymphocytes using soybean lectin affinity chromatography.
  • Karen Dapsis (MSE, 1985): Effect of cell motility properties on microbial competition in nonmixed environment.
  • Mercedes Rivero-Hudec (PhD, 1986): Analysis of the capillary assay for bacterial chemotaxis.
  • Robert Tranquillo (PhD, 1986): Phenomenological and fundamental descriptions of leukocyte motility and chemotaxis behavior.
  • Helen Buettner (PhD, 1987): Measurement of leukocyte motility and chemotaxis parameters using the filter assay.
  • Daniel Hammer (PhD, 1987): Modeling of receptor-mediated cell adhesion to surfaces.
  • Jennifer Linderman (PhD, 1987): Analysis of intracellular receptor/ligand sorting in receptor-mediated endocytosis.
  • Elizabeth Fisher (PhD, 1988): Effects of chemotaxis on cell-target encounter rates and particle clearance.
  • Brian Farrell (PhD, 1989): Measurement of individual cell and cell population parameters for alveolar macrophage chemosensory migration responses to C5a.
  • Cynthia Stokes (PhD, 1989): Analysis of microvessel endothelial cell migration and chemotaxis in angiogenesis.
  • Roseanne Ford (PhD, 1989): Quantitative studies of bacterial motility and chemotaxis using a stopped-flow chamber assay and an individual cell-based mathematical model.
  • Cindy Starbuck (PhD, 1991): Quantitative studies of epidermal growth factor binding and trafficking dynamics in fibroblasts, with application to cell proliferation.
  • Paul DiMilla (PhD, joint with Prof. J.A. Quinn, 1991): Receptor-mediated tissue cell adhesion and migration on protein-coated surfaces.
  • Manuel Cano (PhD, joint with Prof. S.H. Zigmond, 1991): Kinetics of actin polymerization responses to chemotactic peptide stimulation of neutrophil leukocytes.
  • Steven Charnick (PhD, joint with Prof. J.A. Quinn, 1992): Quantitative analysis of chemotactic cell movement.
  • Kerri Gaumer (PhD, joint with Prof. E.D. Glandt, 1993): Simulation studies of cell shape and adhesion.

University of Illinois

  • Kim Forsten (PhD, 1993): Computational studies of autocrine ligand binding.
  • Suzanne Kuo (PhD, 1994): Experimental and computational studies of receptor-mediated cell detachment in shear flow.
  • Glenn Ridenour (MS, 1994): Developing a system for studies of engineered cell migration.
  • Anne Robinson (PhD, joint with Prof. K.D. Wittrup, 1994): Role of endoplasmic reticulum chaparones in secretion of proteins from yeast.
  • Christine Schmidt (PhD, joint with Prof. A.F. Horwitz, 1994): Integrin/cytoskeleton interactions in migrating fibroblasts.
  • Anthony French (PhD/MD, 1995): Experimental and modeling studies of endosomal sorting using the EGF/EGF-receptor system in fibroblasts.
  • Ann Saterbak (PhD, 1995): Serial protein pairs in cell/surface adhesion.
  • Teresa Stone (MS, 1995): Probing receptor/ligand bond properties with a membrane force transducer technique.
  • Cartikeya Reddy (PhD, joint with Prof. A. Wells, 1996): Growth factor-induced mitogenesis: trafficking determinants of the cellular response.

Massachusetts Institute of Technology

  • Steven Rodgers (SM, 1996): Characterizing the motogenic response of human keratinocytes to EGF and TGFa.
  • Greg Oehrtman (PhD, joint with Prof. H.S. Wiley, 1997): Quantification of EGF receptor/ligand interactions in bioengineered autocrine cell system: comparison of theory and experiment.
  • Margaret Ware (PhD, 1997): EGF-induced cell migration: a quantitative and mechanistic analysis.
  • Lily Chu (PhD, 1998): Ligand transport through cellular matrices and the role of receptor-mediated trafficking.
  • David Schaffer (PhD, 1998): EGF receptor-mediated DNA uptake: a model system for engineering selective gene therapy approaches.
  • Sean Palacek (PhD, joint with Prof. A.F. Horwitz, 1998): Role of integrins in mediating adhesion strength and migration speed during cell migration.
  • Jason Haugh (PhD, joint with Prof. A. Wells, 1999): Cellular compartmentation effects in receptor-mediated signal transduction.
  • Gargi Maheshwari (PhD, joint with Prof. L.G. Griffith, 1999): Biophysical regulation of cell motility by adhesion ligands and growth factors: effect of spatial presentation of the ligand.
  • Eric Fallon (PhD, joint with Prof. T.L. Ciardelli, 1999): Analysis of trafficking dynamics and cellular reponse in the IL-2 system.
  • Chase Orsello (PhD, joint with Prof. C.K. Colton, 1999): Characterization of cell detachment from hollow fiber affinity membranes for use in cell separations applications.
  • Anand Asthagiri (PhD, joint with Prof. A.F. Horwitz, 2000): Dynamics of synergistic intracellular signals regulating cell cycle progression.
  • Klaudyne Hong (PhD, 2001): Cellular de novo methylation of plasmid DNA: effects on lipid vector gene delivery and expression.
  • Michael Caplan (PhD, joint with Prof. R.K. Kamm, 2001): Principles for rational design of a self-assembling oligopeptide biomaterial.
  • Ann Dewitt (PhD, 2001): Analysis of and manipulation of spatial operation of the EGF receptor autocrine signaling loop.
  • Casim Sarkar (PhD, 2002): Cytokine engineering through ligand/receptor dynamics: a study on GCSF.
  • Csanad Varga (PhD, 2003): Quantitative analysis and characterization of intracellular gene delivery mechanisms.
  • Bart Hendriks (PhD, 2003): EGFR and HER2 trafficking and signaling dynamics: experiment and modeling studies.
  • Lily Koo (PhD, joint with Prof. L.G. Griffith, 2003): Regulation of cell adhesion by nanoscale control of ligand presentation.
  • Wendy Prudhomme (PhD, 2003): Quantitative analysis of ECM signaling regulation of embryonic stem cell self-renewal and differentiation decisions.
  • David Collins (PhD, joint with Prof. P. Barton, 2003): Chemical process modeling approach to cell signaling analysis.
  • Keith Duggar (PhD, joint with Prof. P. Sorger, 2004): Modeling and analysis of gene expression arrays.
  • Brian Harms (PhD, 2004): Quantitative cue-signal-response analysis of EGF-mediated cell migration.
  • Balaji Rao (PhD, joint with Prof. K.D. Wittrup, 2004): Directed evolution of IL-2 for improved therapeutic effectiveness.
  • Maya Said (PhD, joint with Prof. A. Oppenheim, 2004): Biological signal processing: proteins, networks, and cells.
  • Kevin Janes (PhD, joint with Prof. M. Yaffe, 2005): Quantitative analysis of the cytokine-mediated apoptosis/survival cell decision process.
  • Kathryn Miller-Jensen (PhD, 2006): Quantitative analysis of viral vector modification of a cytokine-mediated cell death decision.
  • Lucia Wille (PhD, 2006): Quantitative analysis of the T-cell receptor signaling network in response to altered peptide ligands.
  • Karen Sachs (PhD, 2006): Bayesian network models of biological signaling pathways.
  • Jennifer Fang (MEng, 2006): Experimental methods for cellular compartmental analysis of gene delivery.
  • Alejandro Wolf-Yadlin (PhD, joint with Prof. F. White): Mass spectrometry technologies for quantitative cell signaling proteomics: the EGF receptor family as a model system.
  • Neil Kumar (PhD, 2006): A computational and experimental study of HER2 signaling effects on cell migration and proliferation.
  • Nate Tedford (PhD, joint with Prof. L. G. Griffith, 2006): Quantitative analysis of non-viral gene therapy in primary liver culture systems.
  • Lisa Joslin (PhD, 2007): Quantitative studies of EGFR autocrine induced cell signaling and migration.
  • Artemis Kalezi (PhD, joint with Prof. L. Griffith, 2007): Quantitative studies of gene delivery to hepatocytes in 2D and 3D culture systems.
  • Maya Hasan (MEng, 2007): In vitro experimental model system for inflammation-related drug toxicity.
  • Rongcong Wu (SM, joint with Prof. D. Schauer, 2008): Multi-pathway signaling downstream of LPS stimulation in macrophages.
  • Bree Aldridge (PhD, joint with Prof. P. Sorger, 2008): Quantitative analysis of the receptor-induced apoptosis decision network.
  • Ben Cosgrove (PhD, joint with Prof. L. Griffith, 2008): Quantitative analysis of hepatocytes to inflammatory cytokine and drug treatments.
  • Hyung-Do Kim (PhD, joint with Prof. F. Gertler, 2008): Quantitative analysis of EGFR-induced cell motility in 3-dimensional matrices.
  • Andrea Tentner (PhD, joint with Prof. M. Yaffe, 2009): Apoptosis and cell cycle responses to DNA damage by doxyrubicin.
  • Robin Prince (PhD, joint with Prof. R. Lee, 2009): Regulation of HB-EGF localization and release by heparin sulfate proteoglycans.
  • Megan Palmer (PhD, 2010): Integration of T-cell receptor and IL-7 cytokine signaling for network control of naïve CD8+ T-cell fate.
  • Laura Sontag Kleiman (PhD, joint with Prof. P. Sorger, 2010): Quantitative analysis of EGFR phosphorylation and dephosphorylation dynamics.
  • Kristen Naegle (PhD, joint with Prof. F. White, 2010): Computational methodologies and resources for discovery of phosphorylation regulation and function in cellular networks.
  • Shan Wu (PhD, 2011): Rational design to control multipotent stromal cell migration for applications in bone tissue engineering and injury repair.
  • Ericka Noonan (PhD, joint with Prof. L. Samson, 2011): Cell decision processing in response to O6-methylguanine DNA damage lesions.
  • Ta-Chun Hang (PhD, joint with Prof. L. G. Griffith, 2012): Optimization of primary endothelial culture methods and assessment of cell signaling pathways in the context of inflammation
  • Joy Rimchala (PhD, joint with Prof. R. Kamm, 2012): Single-cell decisions in endothelial populations in the context of inflammatory angiogenesis.
  • Justin Pritchard (PhD, joint with Prof. M. Hemann, 2012): Systems level characterizations of single and combination drug mechanisms of action in vitro and in vivo.
  • Melody Morris (PhD, 2012): Development of constrained fuzzy logic for modeling biological regulatory networks and predicting contextual therapeutic effects.
  • Abhinav Arneja (PhD, joint with Prof. F. White, 2013): Quantitative analysis of IL-2 and IL-15 signaling in T-cells.
  • Joel Wagner (PhD, 2013): Multi-variate studies in receptor tyrosine kinase function in cancer.
  • Miles Miller (PhD, joint with Prof. L. Griffith, 2013): Understanding and targeting network-level sheddase regulation in invasive disease.
  • Aaron Meyer (PhD, 2014): Modeling TAM receptor signaling in resistance and metastasis.
  • Nancy Guillen (PhD, 2014): Role of microRNAs in intracellular signaling networks regulating hepatocellular carcinoma cell behavior.
  • Ranjeetha Bharath (SM, 2015): Multi-scale modeling of signaling in cell migration.
  • Boyang Zhao (PhD, joint with Prof. M. Hemann, 2015): Rational design of drug combinations against intratumoral heterogeneity.
  • Sarah Schrier (PhD, 2016): Systems Analysis of Cytokine Mediated Communication and Signaling
  • Jennifer Wilson (PhD, 2016): Network analyses for functional genomic screens in cancer
  • Allison Claas (PhD, 2017): Systems modeling of quantitative kinetic data identifies receptor tyrosine kinase-specific resistance mechanisms to MAPK pathway inhibition in cancer
  • Simon Gordonov (PhD, 2017): Understanding the effects of chemotherapy on cellular signaling, structure, and function with phosphoproteomics and bioimage informatics
  • Abby Hill (PhD, 2018): Integrated experimental and computational analysis of inter-cellular communication with application to endometriosis.
  • Samantha Dale Strasser (PhD, 2019): Phosphoproteomic data interpretation applied to studies of cancer and inflammatory bowel disease.
  • Manu Kumar (PhD, 2019): Systems analysis of tumor microenvironment cell-cell communication.
  • Stephanie Wang (PhD, 2019): Tumor/macrophage signaling and crosstalk in ovarian cancer kinase inhibitor resistance.
  • Simona Dalin (PhD, joint with M. Hemann, 2019): Systems analysis of tumor cell chemotherapeutics resistance.
  • Stephen Van Nostrand (SM, 2020): Analysis of tumor microenvironment via single-cell RNAsequence transcriptomics.
  • Lauren Stopfer (PhD, joint with F. White, 2021): Proteomic investigation of adaptive responses in cancer therapeutics.
  • Divya Ravinder (MEng, 2021): Cross-species translation of vaccine studies.
  • Meelim Lee (PhD, 2022): Integrated computational and experimental studies of cellular mechanisms underlying Alzheimer’s Disease
  • Tomar Zohar (PhD, joint with G. Alter, 2022): Methods, models, and machine learning for understanding pathogen-specific humoral immunity
  • Krista Pullen (PhD, 2024): Data-driven translation of the pathogeninduced
    immune responses across species

Post-doctoral associates advised

  • Yong-Ho Khang (1990-1991): Epidermal growth factor binding/trafficking properties and cell proliferation.
  • Paul Wu (1991-1993): Modulation of endothelial cell migration by integrin binding competitors.
  • Michael Lassle (1996-2000): Epidermal growth factor trafficking and signal transduction.
  • Fred Allen (1997-2000): Forces involved in fibroblast migration responses to epidermal growth factor.
  • Peter Zandstra (1997-1998): Cytokine dynamics and stem cell expansion.
  • Atul Narang (1999-2000): Mathematical modeling of membrane phospholipid signaling in cell motility.
  • Stas Shvartsman (1999-2001): Computational cell biology: analysis of autocrine loops.
  • Daniel Kamei (2001-2003): Computational modeling for design of Fc-conjugated therapeutic proteins.
  • Birgit Schoeberl (2001-2003): Computational modeling of EGFR signaling in autocrine cell migration behavior.
  • Peter Woolf (2002-2004): Computational modeling of signaling in cell migration and development.
  • Ivan Maly (2003-2004): Analysis of mechanosignaling networks.
  • Melissa Kemp (2003-2006): Quantitative analysis of cell signaling in apoptosis.
  • Muhamman Zaman (2003-2006): Computational modeling of cell migration in 3-dimensional matrices.
  • Sampsa Hauteniemi (2004-2006): Bioinformatic analysis of cell signaling networks.
  • Matt Lazzara (2004-2006): Endocytic trafficking dynamics of TNFR.
  • Catherine Cresson (2004-2006): Quantitative analysis of EGFR vIII trafficking and signaling dynamics.
  • Yuefeng Han (2005-2006): Biophysical model of cell adhesion dynamics.
  • Evi Farazi (2005-2006): Hepatocyte signaling in inflammation-related drug toxicity.
  • Matt Lazzara (2004-2007): Modulation of EGFR-targeted therapeutics effects by receptor/ligand dynamics.
  • John Burke (2003-2008, joint w/ Prof. P. Sorger): Dynamic analysis of cell signaling networks.
  • Arthur Goldsipe (2006-2008): p38 signaling pathway modeling and analysis.
  • Greg Riddick (2007-2008): Transcriptional regulation in T-cells by signaling networks.
  • Manu Platt (2006-2008, joint w/ Prof. L. Griffith): Signaling networks regulating mesenchymal stem cell differentiation.
  • Pamela Kreeger (2005-2008): Systems models of mutant ras effects in inflammation-induced colon epithelial cell apoptosis.
  • Mark Fleury (2007-2009): Cytokine signaling crosstalk in T-cells.
  • Julio Saez-Rodriguez (2007-2010, joint w/ Prof. P.K. Sorger): Logic modeling of cell signaling networks.
  • Gerard Ostheimer (2005-2010, joint w/ Prof. M. Yaffe and Prof. L. Samson): Systems biology study of DNA damage/repair networks.
  • Shelly Peyton (2007-2010): joint w/ Prof. L. Griffith): Synthetic matrices for mesenchymal stem cell studies.
  • Dan Kirouac (2009-2011, joint w/ Prof. P. Sorger): Cue-signal-response analysis of inflammatory tissue disease processes.
  • Elma Kurtagic (2010-2011): Systems analysis of inflammatory signaling in colon epithelial cells.
  • Neda Bagheri (2008-2010): Computational analysis of dynamic cytokine signaling responses by individual T cells to resolve and predict complex immune function.
  • Juliesta E. Sylvester (Postdoctoral Associate) Engineering cells and their microenvironment to control metastasis
  • Shannon Hughes-Alford (2008-2012): Dysregulation of EGF receptor-mediated tumor cell migration signaling.
  • Ken Lau (2008-2012, joint w/ Prof. K. Haigis): In vivo systems analysis of inflammatory signaling and pathophysiology.
  • David Clarke (2009-2013): Hepatocyte signaling and function in systemic inflammation.
  • Sarah Kolitz (2010-2013): Quantitative analysis of signal-response behavior in single cells.
  • Michael Beste (2009-2014): Model studies of inflammatory processes in endometriosis.
  • Theresa Ulrich (2011-2014): Scientific Program Manager, DARPA BIOMIMICS.)
  • Levi Wood (2012-2015, joint w/ Prof. K. Haigis): Systems analysis of inflammation signaling in Alzheimer’s disease.
  • Carissa Young (2012-2015): Inflammatory cytokine dynamics in micro-physiological system platforms.
  • Nick Cilfone (2014-2015, joint w/ Prof. L. Griffith): Quantitative systems pharmacology.
  • Kelly [Benedict] Arnold (2010-2015): Systems analysis of cell-cell communication.
  • Douglas Jones (2010-2015): Cue-signal-response analysis of inflammatory tissue disease processes.
  • Jesse Lyons (2011-2016): Response of intestinal epithelial cells to inflammatory stimuli.
  • Wen-Li Kelly Chen (2013-2017): Development of intestinal/immune micro-physiological system platform.
  • Elizabeth Proctor (2014-2018, joint w/ Prof. K. Haigis): Systems analysis of neurodegenerative disease.
  • Annelien Zweemer (2014-2018): Role of receptor tyrosine kinases in cancer drug combinations.
  • Melissa Kinney (2014-2018): Systems biology approach to understanding hematopoietic stem cell regulation.
  • Wen-Han Yu (2013-2018, joint with G. Alter): Computational immunology studies of vaccine design.
  • Jishnu Das (2015-2019, joint w/G. Alter): Computational immunology studies of vaccine responses.
  • Sepideh Dolatshahi (2016-2019, joint w/ G. Alter): Systems modeling of antibody dynamics.
  • Alina Starchenko (2016-2019): Quantitative analysis of inflammatory cell-cell communication.
  • Evan Chiswick (2015-2020, joint w/ L. Griffith): Systems analysis of endometrial inflammatory pathologies.
  • Douglas Brubaker (2016-2020): Translational systems biology analysis of inflammatory pathophysiology.
  • Carolin Loos (2019-2021, joint w/L. Griffith): Systems serology applications in pathogen infection.
  • Lauren Baugh (2018-2021, joint w/L. Griffith): Systems analysis of inflammatory tissue pathophysiology in endometriosis
  • Avlant Nilsson (2019-2023): Multi-scale computational modeling in cell signaling
  • Chuangqi Wang (2019-2022): Machine learning analysis of host immune response in Covid and tuberculosis
  • Shu Wang (2020-2023): Computational analysis of multi-dimensional and multi-modal omics data in systems biology.
  • Yixiang Deng (2022-2024): Computational system serology for vaccine designs
Whitaker Building, MIT