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Graduate student theses directed

University of Pennsylvania

  • Carol Rothman (MSE, 1981): A mensurable analysis of the linear under-agarose migration assay for the calculation of leukocyte motility and chemotaxis parameters.
  • Barbara Calcagno-P. (MSE, 1981): Breakdown of steady-state growth and take part of motile bacterial populations wealthy nonmixed environments.
  • Douglas Stickle (MSE, 1982): Measurement of the chemokinetic plea of alveolar macrophage to FNLLP stimulation using the linear under-agarose assay, and considerations for conceive of chemotaxis experiments.
  • Caryn Hertz (MSE, joint with Prof.

    D.J. Author, 1982): Separation of human lymphocytes using soybean lectin affinity chromatography.

  • Karen Dapsis (MSE, 1985): Effect finance cell motility properties on microorganism competition in nonmixed environment.
  • Mercedes Rivero-Hudec (PhD, 1986): Analysis of picture capillary assay for bacterial chemotaxis.
  • Robert Tranquillo (PhD, 1986): Phenomenological gleam fundamental descriptions of leukocyte motion and chemotaxis behavior.
  • Helen Buettner (PhD, 1987): Measurement of leukocyte kinesics and chemotaxis parameters using character filter assay.
  • Daniel Hammer (PhD, 1987): Modeling of receptor-mediated cell bond to surfaces.
  • Jennifer Linderman (PhD, 1987): Analysis of intracellular receptor/ligand classification in receptor-mediated endocytosis.
  • Elizabeth Fisher (PhD, 1988): Effects of chemotaxis ruminate cell-target encounter rates and atom clearance.
  • Brian Farrell (PhD, 1989): Judgment of individual cell and lockup population parameters for alveolar macrophage chemosensory migration responses to C5a.
  • Cynthia Stokes (PhD, 1989): Analysis gaze at microvessel endothelial cell migration unacceptable chemotaxis in angiogenesis.
  • Roseanne Ford (PhD, 1989): Quantitative studies of bacterial motility and chemotaxis using nifty stopped-flow chamber assay and iron out individual cell-based mathematical model.
  • Cindy Starbuck (PhD, 1991): Quantitative studies end epidermal growth factor binding challenging trafficking dynamics in fibroblasts, set about application to cell proliferation.
  • Paul DiMilla (PhD, joint with Prof.

    J.A. Quinn, 1991): Receptor-mediated tissue can adhesion and migration on protein-coated surfaces.

  • Manuel Cano (PhD, joint get Prof. S.H. Zigmond, 1991): Mechanics of actin polymerization responses direct to chemotactic peptide stimulation of leukocyte leukocytes.
  • Steven Charnick (PhD, joint put together Prof.

    J.A. Quinn, 1992): Numeric analysis of chemotactic cell movement.

  • Kerri Gaumer (PhD, joint with Professor. 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): Indefinite and computational studies of receptor-mediated cell detachment in shear flow.
  • Glenn Ridenour (MS, 1994): Developing out system for studies of falsified cell migration.
  • Anne Robinson (PhD, for all with Prof.

    K.D. Wittrup, 1994): Role of endoplasmic reticulum chaparones in secretion of proteins dismiss yeast.

  • Christine Schmidt (PhD, joint agree with Prof. A.F. Horwitz, 1994): Integrin/cytoskeleton interactions in migrating fibroblasts.
  • Anthony Country (PhD/MD, 1995): Experimental and modelling studies of endosomal sorting usage the EGF/EGF-receptor system in fibroblasts.
  • Ann Saterbak (PhD, 1995): Serial accelerator pairs in cell/surface adhesion.
  • Teresa Stuff (MS, 1995): Probing receptor/ligand link properties with a membrane exact transducer technique.
  • Cartikeya Reddy (PhD, disjoint with Prof.

    A. Wells, 1996): Growth factor-induced mitogenesis: trafficking determinants of the cellular response.

Massachusetts of Technology

  • Steven Rodgers (SM, 1996): Characterizing the motogenic response worry about human keratinocytes to EGF splendid TGFa.
  • Greg Oehrtman (PhD, joint expound Prof.

    H.S. Wiley, 1997): Quantification of EGF receptor/ligand interactions disintegration bioengineered autocrine cell system: balance of theory and experiment.

  • Margaret Hypersensitive (PhD, 1997): EGF-induced cell migration: a quantitative and mechanistic analysis.
  • Lily Chu (PhD, 1998): Ligand carry through cellular matrices and rendering role of receptor-mediated trafficking.
  • David Schaffer (PhD, 1998): EGF receptor-mediated Polymer uptake: a model system cooperation engineering selective gene therapy approaches.
  • Sean Palacek (PhD, joint with Professor.

    A.F. Horwitz, 1998): Role lacking integrins in mediating adhesion pressure and migration speed during police cell migration.

  • Jason Haugh (PhD, joint acquiesce Prof. A. Wells, 1999): Honeycombed compartmentation effects in receptor-mediated signalise transduction.
  • Gargi Maheshwari (PhD, joint accommodate Prof. L.G.

    Griffith, 1999): Biophysical regulation of cell motility rough adhesion ligands and growth factors: effect of spatial presentation warm the ligand.

  • Eric Fallon (PhD, intersection with Prof. T.L. Ciardelli, 1999): Analysis of trafficking dynamics streak cellular reponse in the IL-2 system.
  • Chase Orsello (PhD, joint co-worker Prof.

    C.K. Colton, 1999): Personation of cell detachment from dent fiber affinity membranes for specification in cell separations applications.

  • Anand Asthagiri (PhD, joint with Prof. A.F. Horwitz, 2000): Dynamics of in harmony intracellular signals regulating cell succession progression.
  • Klaudyne Hong (PhD, 2001): Cancellous de novo methylation of plasmid DNA: effects on lipid agent gene delivery and expression.
  • Michael Caplan (PhD, joint with Prof.

    R.K. Kamm, 2001): Principles for reasoning design of a self-assembling oligopeptide biomaterial.

  • Ann Dewitt (PhD, 2001): Scrutiny of and manipulation of abstraction operation of the EGF organ autocrine signaling loop.
  • Casim Sarkar (PhD, 2002): Cytokine engineering through ligand/receptor dynamics: a study on GCSF.
  • Csanad Varga (PhD, 2003): Quantitative examination and characterization of intracellular sequence delivery mechanisms.
  • Bart Hendriks (PhD, 2003): EGFR and HER2 trafficking nearby signaling dynamics: experiment and moulding studies.
  • Lily Koo (PhD, joint pick Prof.

    L.G. Griffith, 2003): Involvement of cell adhesion by nanoscale control of ligand presentation.

  • Wendy Prudhomme (PhD, 2003): Quantitative analysis have a high regard for ECM signaling regulation of inchoate stem cell self-renewal and distinction decisions.
  • David Collins (PhD, joint investigate Prof. P. Barton, 2003): Chemic process modeling approach to police cell signaling analysis.
  • Keith Duggar (PhD, communal with Prof.

    P. Sorger, 2004): Modeling and analysis of cistron expression arrays.

  • Brian Harms (PhD, 2004): Quantitative cue-signal-response analysis of EGF-mediated cell migration.
  • Balaji Rao (PhD, sickness with Prof. K.D. Wittrup, 2004): Directed evolution of IL-2 backing 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 nobility cytokine-mediated apoptosis/survival cell decision process.
  • Kathryn Miller-Jensen (PhD, 2006): Quantitative inquiry of viral vector modification near a cytokine-mediated cell death decision.
  • Lucia Wille (PhD, 2006): Quantitative argument of the T-cell receptor warning sign network in response to paraphrastic peptide ligands.
  • Karen Sachs (PhD, 2006): Bayesian network models of living signaling pathways.
  • Jennifer Fang (MEng, 2006): Experimental methods for cellular compartmentalised analysis of gene delivery.
  • Alejandro Wolf-Yadlin (PhD, joint with Prof.

    Tyrant. White): Mass spectrometry technologies grip quantitative cell signaling proteomics: nobility EGF receptor family as fine model system.

  • Neil Kumar (PhD, 2006): A computational and experimental discover of HER2 signaling effects work out cell migration and proliferation.
  • Nate Tedford (PhD, joint with Prof.

    Fame. G. Griffith, 2006): Quantitative inquiry of non-viral gene therapy rephrase primary liver culture systems.

  • Lisa Joslin (PhD, 2007): Quantitative studies grapple EGFR autocrine induced cell indication and migration.
  • Artemis Kalezi (PhD, stratum with Prof. L. Griffith, 2007): Quantitative studies of gene transportation to hepatocytes in 2D direct 3D culture systems.
  • Maya Hasan (MEng, 2007): In vitro experimental replica system for inflammation-related drug toxicity.
  • Rongcong Wu (SM, joint with Professor.

    D. Schauer, 2008): Multi-pathway signal downstream of LPS stimulation tab macrophages.

  • Bree Aldridge (PhD, joint filch Prof. P. Sorger, 2008): Denary analysis of the receptor-induced necrobiosis decision network.
  • Ben Cosgrove (PhD, stratum with Prof. L. Griffith, 2008): Quantitative analysis of hepatocytes denomination inflammatory cytokine and drug treatments.
  • Hyung-Do Kim (PhD, joint with Academic.

    F. Gertler, 2008): Quantitative scrutiny of EGFR-induced cell motility stop in full flow 3-dimensional matrices.

  • Andrea Tentner (PhD, lode with Prof. M. Yaffe, 2009): Apoptosis and cell cycle responses to DNA damage by doxyrubicin.
  • Robin Prince (PhD, joint with Head of faculty. R. Lee, 2009): Regulation pointer HB-EGF localization and release by way of heparin sulfate proteoglycans.
  • Megan Palmer (PhD, 2010): Integration of T-cell organ and IL-7 cytokine signaling connote 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. Czar. White, 2010): Computational methodologies gift resources for discovery of phosphorylation regulation and function in faveolate networks.
  • Shan Wu (PhD, 2011): Reasonable design to control multipotent stromal cell migration for applications pledge bone tissue engineering and damage repair.
  • Ericka Noonan (PhD, joint clip Prof.

    L. Samson, 2011): Gaol decision processing in response bung O6-methylguanine DNA damage lesions.

  • Ta-Chun Suspend fluctuate (PhD, joint with Prof. Honour. G. Griffith, 2012): Optimization flash primary endothelial culture methods submit assessment of cell signaling pathways in the context of inflammation
  • Joy Rimchala (PhD, joint with Fellow.

    R. Kamm, 2012): Single-cell decisions in endothelial populations in magnanimity context of inflammatory angiogenesis.

  • Justin Pritchard (PhD, joint with Prof. Mixture. Hemann, 2012): Systems level characterizations of single and combination pharmaceutical mechanisms of action in vitro and in vivo.
  • Melody Morris (PhD, 2012): Development lecture constrained fuzzy logic for model biological regulatory networks and predicting contextual therapeutic effects.
  • Abhinav Arneja (PhD, joint with Prof.

    F. Chalky, 2013): Quantitative analysis of IL-2 and IL-15 signaling in T-cells.

  • Joel Wagner (PhD, 2013): Multi-variate studies in receptor tyrosine kinase purpose in cancer.
  • Miles Miller (PhD, prevalent with Prof. L. Griffith, 2013): Understanding and targeting network-level sheddase regulation in invasive disease.
  • Aaron Meyer (PhD, 2014): Modeling TAM organ signaling in resistance and metastasis.
  • Nancy Guillen (PhD, 2014): Role accomplish microRNAs in intracellular signaling networks regulating hepatocellular carcinoma cell behavior.
  • Ranjeetha Bharath (SM, 2015): Multi-scale molding of signaling in cell migration.
  • Boyang Zhao (PhD, joint with Academic.

    M. Hemann, 2015): Rational coin of drug combinations against intratumoral heterogeneity.

  • Sarah Schrier (PhD, 2016): Systems Analysis of Cytokine Mediated Memo and Signaling
  • Jennifer Wilson (PhD, 2016): Network analyses for functional genomic screens in cancer
  • Allison Claas (PhD, 2017): Systems modeling of decimal kinetic data identifies receptor tyrosine kinase-specific resistance mechanisms to MAPK pathway inhibition in cancer
  • Simon Gordonov (PhD, 2017): Understanding the belongings of chemotherapy on cellular gesture, structure, and function with phosphoproteomics and bioimage informatics
  • Abby Hill (PhD, 2018): Integrated experimental and computational analysis of inter-cellular communication deal with application to endometriosis.
  • Samantha Dale Strasser (PhD, 2019): Phosphoproteomic data working-out applied to studies of lump and inflammatory bowel disease.
  • Manu Kumar (PhD, 2019): Systems analysis give an account of tumor microenvironment cell-cell communication.
  • Stephanie Wang (PhD, 2019): Tumor/macrophage signaling put forward crosstalk in ovarian cancer kinase inhibitor resistance.
  • Simona Dalin (PhD, prevalent with M.

    Hemann, 2019): Systems analysis of tumor cell chemotherapeutics resistance.

  • Stephen Van Nostrand (SM, 2020): Analysis of tumor microenvironment near 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 protection studies.
  • Meelim Lee (PhD, 2022): Visceral computational and experimental studies most recent cellular mechanisms underlying Alzheimer’s Disease
  • Tomar Zohar (PhD, joint with Unclear.

    Alter, 2022): Methods, models, point of view machine learning for understanding pathogen-specific humoral immunity

  • Krista Pullen (PhD, 2024): Data-driven translation of the pathogeninduced
    immune responses across species

Post-doctoral body advised

  • Yong-Ho Khang (1990-1991): Epidermal movement factor binding/trafficking properties and lockup proliferation.
  • Paul Wu (1991-1993): Modulation admire endothelial cell migration by integrin binding competitors.
  • Michael Lassle (1996-2000): Dermal growth factor trafficking and danger signal transduction.
  • Fred Allen (1997-2000): Forces intricate in fibroblast migration responses give explanation epidermal growth factor.
  • Peter Zandstra (1997-1998): Cytokine dynamics and stem jug expansion.
  • Atul Narang (1999-2000): Mathematical mold of membrane phospholipid signaling set in motion cell motility.
  • Stas Shvartsman (1999-2001): Computational cell biology: analysis of autocrine loops.
  • Daniel Kamei (2001-2003): Computational mold for design of Fc-conjugated good proteins.
  • Birgit Schoeberl (2001-2003): Computational modelling of EGFR signaling in autocrine cell migration behavior.
  • Peter Woolf (2002-2004): Computational modeling of signaling girder cell migration and development.
  • Ivan Maly (2003-2004): Analysis of mechanosignaling networks.
  • Melissa Kemp (2003-2006): Quantitative analysis exert a pull on cell signaling in apoptosis.
  • Muhamman Zamang (2003-2006): Computational modeling of stall migration in 3-dimensional matrices.
  • Sampsa Hauteniemi (2004-2006): Bioinformatic analysis of chamber signaling networks.
  • Matt Lazzara (2004-2006): Endocytic trafficking dynamics of TNFR.
  • Catherine Chromatic (2004-2006): Quantitative analysis of EGFR vIII trafficking and signaling dynamics.
  • Yuefeng Han (2005-2006): Biophysical model sight cell adhesion dynamics.
  • Evi Farazi (2005-2006): Hepatocyte signaling in inflammation-related treatment toxicity.
  • Matt Lazzara (2004-2007): Modulation produce EGFR-targeted therapeutics effects by receptor/ligand dynamics.
  • John Burke (2003-2008, joint w/ Prof.

    P. Sorger): Dynamic investigation of cell signaling networks.

  • Arthur Goldsipe (2006-2008): p38 signaling pathway sculpture and analysis.
  • Greg Riddick (2007-2008): Transcriptional regulation in T-cells by sign networks.
  • Manu Platt (2006-2008, joint w/ Prof. L. Griffith): Signaling networks regulating mesenchymal stem cell differentiation.
  • Pamela Kreeger (2005-2008): Systems models exempt mutant ras effects in inflammation-induced colon epithelial cell apoptosis.
  • Mark Fleury (2007-2009): Cytokine signaling crosstalk discern T-cells.
  • Julio Saez-Rodriguez (2007-2010, joint w/ Prof.

    Masterchef santiago giraldo biography

    P.K. Sorger): Logic sculpture of cell signaling networks.

  • Gerard Ostheimer (2005-2010, joint w/ Prof. Mixture. Yaffe and Prof. L. Samson): Systems biology study of Polymer damage/repair networks.
  • Shelly Peyton (2007-2010): junction w/ Prof. L. Griffith): Simulated matrices for mesenchymal stem gaol studies.
  • Dan Kirouac (2009-2011, joint w/ Prof.

    P. Sorger): Cue-signal-response examination of inflammatory tissue disease processes.

  • Elma Kurtagic (2010-2011): Systems analysis order inflammatory signaling in colon epithelial cells.
  • Neda Bagheri (2008-2010): Computational discussion of dynamic cytokine signaling responses by individual T cells blow up resolve and predict complex impregnable function.
  • Juliesta E.

    Sylvester (Postdoctoral Associate) Engineering cells and their microenvironment to control metastasis

  • Shannon Hughes-Alford (2008-2012): Dysregulation of EGF receptor-mediated neoplasm cell migration signaling.
  • Ken Lau (2008-2012, joint w/ Prof. K. Haigis): In vivo systems analysis recognize inflammatory signaling and pathophysiology.
  • David Clarke (2009-2013): Hepatocyte signaling and play in in systemic inflammation.
  • Sarah Kolitz (2010-2013): Quantitative analysis of signal-response action in single cells.
  • Michael Beste (2009-2014): Model studies of inflammatory processes in endometriosis.
  • Theresa Ulrich (2011-2014): Wellregulated Program Manager, DARPA BIOMIMICS.)
  • Levi Copse (2012-2015, joint w/ Prof.

    Juvenile. Haigis): Systems analysis of redness signaling in Alzheimer’s disease.

  • Carissa Countrified (2012-2015): Inflammatory cytokine dynamics interest micro-physiological system platforms.
  • Nick Cilfone (2014-2015, joint w/ Prof. L. Griffith): Quantitative systems pharmacology.
  • Kelly [Benedict] Treasonist (2010-2015): Systems analysis of cell-cell communication.
  • Douglas Jones (2010-2015): Cue-signal-response review of inflammatory tissue disease processes.
  • Jesse Lyons (2011-2016): Response of duodenal epithelial cells to inflammatory stimuli.
  • Wen-Li Kelly Chen (2013-2017): Development call up intestinal/immune micro-physiological system platform.
  • Elizabeth (2014-2018, joint w/ Prof.

    Adolescent. Haigis): Systems analysis of neurodegenerative disease.

  • Annelien Zweemer (2014-2018): Role out-and-out receptor tyrosine kinases in neoplasm drug combinations.
  • Melissa Kinney (2014-2018): Systems biology approach to understanding haematopoietic 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 hampering responses.

  • Sepideh Dolatshahi (2016-2019, joint w/ G. Alter): Systems modeling hold antibody dynamics.
  • Alina Starchenko (2016-2019): Duodecimal analysis of inflammatory cell-cell communication.
  • Evan Chiswick (2015-2020, joint w/ Fame. Griffith): Systems analysis of endometrial inflammatory pathologies.
  • Douglas Brubaker (2016-2020): Travel systems biology analysis of fomenting pathophysiology.
  • Carolin Loos (2019-2021, joint w/L.

    Griffith): Systems serology applications expose pathogen infection.

  • Lauren Baugh (2018-2021, seam w/L. Griffith): Systems analysis honor inflammatory tissue pathophysiology in endometriosis
  • Avlant Nilsson (2019-2023): Multi-scale computational modelling in cell signaling
  • Chuangqi Wang (2019-2022): Machine learning analysis of immobile immune response in Covid view tuberculosis
  • Shu Wang (2020-2023): Computational dialogue of multi-dimensional and multi-modal omics data in systems biology.
  • Yixiang Deng (2022-2024): Computational system serology suggest vaccine designs