Departmental Papers (BE)

Departmental Papers (BE)

 
The Department of Bioengineering, one of the first nationally, was established in 1973 with graduate degrees offered since 1961. Rated one of the top Bioengineering programs in the country, the Department presents the strong intellectual interdisciplinary infrastructure and collaborative culture that links Engineering, Life Sciences and Medicine at the University of Pennsylvania.

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Papers from 2016

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Optogenetic Control of Calcium Oscillation Waveform Defines NFAT as an Integrator of Calcium Load, Pimkhuan Hannanta-anan and Brian Y. Chow

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Toolbox for Exploring Modular Gene Regulation in Synthetic Biology Training, Michael S. Magaraci, Jessica G. Bermudez, Deeksha Yogish, Daniel H. Pak, Viktor Mollov, Josh Tycko, David Issadore, Sevile G. Mannickarottu, and Brian Y. Chow

Papers from 2015

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Noninvasive Metrics for Identification of Brain Injury Deficits in Piglets, Samer A. Jaber, Sarah Sullivan, and Susan S. Margulies

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Peripheral Blood Mitochondrial DNA as a Biomarker of Cerebral Mitochondrial Dysfunction Following Traumatic Brain Injury in a Porcine Model, Todd Kilbaugh, Maria Lvova, Michael Karlsson, Zhe Zhang, Jeremy Leipzig, Douglas C. Wallace, and Susan S. Margulies

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Persistently Altered Brain Mitochondrial Bioenergetics After Apparently Successful Resuscitation From Cardiac Arrest, Todd Kilbaugh, Robert M. Sutton, Michael Karlsson, Magnus J. Hansson, Maryam Y. Naim, Ryan W. Morgan, George Bratinov, Joshua Willard Lampe, Vinay Nadkarni, Lance Becker, Susan S. Margulies, and Robert A. Berg

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Establishing a Clinically Relevant Large Animal Model Platform for TBI Therapy Development: Using Cyclosporin A as a Case Study, Susan S. Margulies, Todd Kilbaugh, Sarah Sullivan, Colin Smtih, Kathleen J. Propert, Melissa Byro, Kristen Saliga, Beth A. Costine, and Ann-Christine Duhaime

Papers from 2013

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The Anesthetic Effects on Vasopressor Modulation of Cerebral Blood Flow in an Immature Swine Model, Benjamin Bruins, Todd Kilbaugh, Susan S. Margulies, and Stuart H. Friess

Papers from 2012

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Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation, Pamela A. Barendt, Najaf A. Shah, Gregory A. Barendt, and Casim A. Sarkar

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Ischemia Induces P-Selectin-Mediated Selective Progenitor Cell Engraftment in the Isolated-Perfused Heart, Jason A. Burdick, Jeremy A. Elser, Brendan P. Purcell, Irshad A. Allana, and Kenneth B. Margulies

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Scanner-Free and Wide-Field Endoscopic Imaging by Using a Single Multimode Optical Fiber, Youngwoon Choi, Changhyeong Yoon, Moonseok Kim, Taeseok Daniel Yang, Christopher Fang-Yen, Ramchandra R. Dasari, Kyoung Jin Lee, and Wonshik Choi

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Finite Element Model Predictions of Intracranial Hemorrhage From Non-impact, Rapid Head Rotations in the Piglet, Brittany Coats, Stephanie A. Eucker, Sarah Sullivan, and Susan S. Margulies

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Sepsis Enhances Epithelial Permeability With Stretch in an Actin Dependent Manner, Taylor Sitarik Cohen, Brian Christopher DiPaolo, Gladys Gray Lawrence, and Susan S. Margulies

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Uses of Remnant Human Lung Tissue for Mechanical Stretch Studies, Nurit Davidovich, Peter Chhour, and Susan S. Margulies

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Rho Kinase Signaling Pathways During Stretch in Primary Alveolar Epithelia, Brian Christopher DiPaolo and Susan S. Margulies

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Effects of Size Polydispersity on the Extinction Spectra of Colloidal Nanoparticle Aggregates, Alexander E. Ershov, Ivan L. Isaev, Polina N. Semina, Vadim A. Markel, and Sergei V. Karpov

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Premedication With Meloxicam Exacerbates Intracranial Hemorrhage in an Immature Swine Model of Non-impact Inertial Head Injury, Stuart H. Friess, Maryam Y. Naim, Todd Kilbaugh, Jill Ralston, and Susan S. Margulies

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Early Cerebral Perfusion Pressure Augmentation With Phenylephrine After Traumatic Brain Injury May Be Neuroprotective in a Pediatric Swine Model, Stuart H. Friess, Colin Smith, Todd Kilbaugh, Suzanne G. Frangos, Jill Ralston, Mark A. Helfaer, and Susan S. Margulies

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Influence of Age and Fall Type on Head Injuries in Infants and Toddlers, Nicole G. Ibrahim, Joanne Wood, Susan S. Margulies, and Cindy W. Christian

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Three-dimensional differential interference contrast microscopy using synthetic aperture imaging, Moonseok Kim, Youngwoon Choi, Christopher Fang-Yen, Yongjin Sung, Kwanhyung Kim, Ramachandra R. Dasari, Michael S. Feld, and Wonshik Choi

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Comment on “Green’s function theory for infinite and semi-infinite particle chains”, Vadim A. Markel and Andrey K. Sarychev

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MicroRNA Modulate Alveolar Epithelial Response to Cyclic Stretch, Nadir Yehya, Adi Yerrapureddy, John Tobias, and Susan S. Margulies

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Spin-Labeling Magnetic Resonance Imaging Detects Increased Myocardial Blood Flow After Endothelial Cell Transplantation in the Infarcted Heart, HuaLei Zhang, Hui Qiao, Rachel S. Frank, Bin Huang, Kathleen J. Propert, Susan S. Margulies, Victor A. Ferrari, Jonathan A. Epstein, and Rong Zhou

Papers from 2011

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Generalized Langevin dynamics of a nanoparticle using a finite element approach: Thermostating with correlated noise, Uma Balakrishnan, T. N. Swaminathan, Portonovo S. Ayyaswamy, David M. Eckmann, and Ravi Radhakrishnan

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Schwann Cell Proliferation and Macrophage Infiltration Are Evident at Day 14 after Painful Cervical Nerve Root Compression in the Rat, Yu-Wen Chang and Beth A. Winkelstein

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Overcoming the Diffraction Limit Using Multiple Light Scattering in a Highly Disordered Medium, Youngwoon Choi, Taeseok Daniel Yang, Christopher Fang-Yen, Pilsung Kang, Kyoung Jin Lee, Ramachandra R. Dasari, Michael S. Feld, and Wonshik Choi

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Physiological and Histopathological Responses Following Closed Rotational Head Injury Depend on Direction of Head Motion, Stephanie A. Eucker

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Neurocritical Care Monitoring Correlates with Neuropathology in a Swine Model of Pediatric Traumatic Brain Injury, Stuart H. Friess, Jill Ralston, Stephanie A. Eucker, Mark A. Helfaer, Colin Smith, and Susan S. Margulies

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Robust Network Topologies for Generating Switch-Like Cellular Responses, Najaf A. Shah and Casim A. Sarkar

Papers from 2010

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Inverse Scattering and Acousto-Optic Imaging, Giullaume Bal and John C. Schotland

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Radiometric Bimolecular Beacons for Sensitive Detection of RNA in Single Living Cells, Antony K. Chen, Olga Davydenko, Mark A. Behlke, and Andrew Tsourkas

MAPk Activation Modulates Permeability of Isolated Rat Alveolar Epithelial Cell Monolayers Following Cyclic Stretch, Taylor Sitarik Cohen, Galadys Gray Lawrence, Amit Khasgiwala, and Susan S. Margulies

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Cultured Alveolar Epithelial Cells From Septic Rats Mimic in Vivo Septic Lung, Taylor Sitarik Cohen, Gladys Gray Lawrence, and Susan S. Margulies

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Polymer - Xerogel Composites for Controlled Release Wound Dressings, Marius C. Costache, Haibo Qu, Paul Ducheyne, and David Devore

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Stretch Magnitude and Frequency-Dependent Actin Cytoskeleton Remodeling in Alveolar Epithelia, Brian Christopher DiPaolo; Guillaume Lenormand,; Jeffrey J. Fredberg; and Susan S. Margulies

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MicroRNA-10a Regulation of Proinflammatory Phenotype in Athero-susceptible Endothelium in Vivo and in Vitro, Yun Fang, Congzhu Shi, Elisabetta Manduchi, Mete Civelek, and Peter F. Davies

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Single-scattering Optical Tomography: Simultaneous Reconstruction of Scattering and Absorption, Lucia Florescu, Vadim A. Markel, and John C. Schotland

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The Rho Pathway Mediates Transition to an Alveolar Type I Cell Phenotype During Static Stretch of Alveolar Type II Cells, Cherie D. Foster, Linda S. Varghese, Linda W. Gonzales, Susan S. Margulies, and Susan H. Guttentag

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Biomechanics of the Toddler Head During Low-height Falls: An Anthropomorphic Dummy Analysis Laboratory Investigation, Nicole G. Ibrahim and Susan S. Margulies

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Biomechanics of Toddler Head During Low-height Falls: An Anthorpomorphic Dummy Analysis, Nicole G. Ibrahim and Susan S. Margulies

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Injectable Hydrogel Properties Influence Infarct Expansion and Extent of Postinfarction Left Ventricular Remodeling in an Ovine Model, Jamie L. Ifkovits, Elena Tous, Masahito Minakawa, J. Daniel Robb, Kevin J. Koomalsingh, Joseph H. Gorman III, Robert C. Gorman, and Jason A. Burdick

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Mechanical Tugging Force Regulates the Size of Cell-Cell Junctions, Zhijun Liu, John L. Tan, Daniel M. Cohen, Michael T. Yang, Nathan J. Sniadecki, Sami Alom Ruiz, Celeste M. Nelson, and Christopher S. Chen

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Detecting Mutually-Salient Landmark Pairs with MRF Regularization, Yangming Ou, Ahmed Besbes, Michel Bilello, Mohamed Mansour, Christos Davatzikos, and Nikos Paragios

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Quantum Imaging and Inverse Scattering, John C. Schotland

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The ErbB3/HER3 Intracellular Domain is Competent to Bind ATP and Catalyze Autophosphorylation, Fumin Shi, Shannon Telesco, Yingting Liu, Ravi Radhakrishnan, and Mark Lemmon

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Mining Terabytes of Submillimeter-resolution ECoG Datasets for Neurophysiologic Biomarkers, Jonathan Viventi, Justin Blanco, and Brian Litt

Papers from 2009

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Calculation of free energies in fluid membranes subject to heterogeneous curvature fields, Neeraj J. Agrawal and Ravi Radhakrishnan

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Sub-cellular trafficking and functionality of 2'-O-methyl and 2'-O-methyl-phosphorothioate molecular beacons, Anthony K. Chen, Mark A. Behlke, and Andrew Tsourkas

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Single-scattering optical tomography, Lucia Florescu, John C. Schotland, and Vadim A. Markel

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Phaseless Three-Dimensional Optical Nanoimaging, Alexander A. Govyadinov, George Y. Panasyuk, and John C. Schotland

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Novel nano-composite biomaterials that respond to light, Kolin C. Hribar, Robert B. Metter, and Jason A. Burdick

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Tuning hydrogel properties for applications in tissue engineering, Sudhir Khetan, Cindy Chung, and Jason A. Burdick

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Ketamine Modulates Theta and Gamma Oscillations, Maciej T. Lazarewicz, Richard S. Ehrilichman, Christina R. Maxwell, Michael J. Gandal, Leif H. Finkel, and Steven J. Siegel

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DRAMMS: deformable registration via attribute matching and mutual-saliency weighting, Yangming Ou and Christos Davatzikos

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Non-Rigid Registration between Histological and MR Images of the Prostate: A Joint Segmentation and Registration Framework, Yangming Ou, Dinggang Shen, Michael Feldman, John Tomaszewski, and Christos Davatzikos

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Sampling the spatial patterns of cancer: Optimized biopsy procedures for estimating prostate cancer volume and Gleason Score, Yangming Ou, Dinggang Shen, Jianchao Zeng, Leon Sun, Judd Moul, and Christos Davatzikos

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Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior, Jeremy E. Purvis, Ravi Radhakrishnan, and Scott L. Diamond

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Vector Correlation Technique for Pixel-wise Detection of Collagen Fiber Realignment During Injurious Tensile Loading, Kyle P. Quinn and Beth A. Winkelstein

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Nanoscale Optical Tomography using Volume-scanning Near-field Microscopy, Jin Sun, John C. Schotland, Rainer Hillenbrand, and P. Scott Carney

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Calpain mediates proteolysis of the voltage-gated sodium channel alpha-subunit, Catherine R. von Reyn, Jennifer M. Spaethling, Mahlet N. Mesfin, Marek Ma, Robert W. Neumar, Douglas H. Smith, Robert Siman, and David F. Meaney

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Parallel Hopfield Networks, Robert C. Wilson

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Diffuse Optical Monitoring of Hemodynamic Changes in Piglet Brain With Closed Head Injury, Chao Zhou, Stephanie A. Eucker, Turgut Durduran, Guoqiang Yu, Jill Ralston, Stuart H. Friess, Rebecca N. Ichord, Susan S. Margulies, and Arjun G. Yodh

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Diffuse optical monitoring of hemodynamic changes in piglet brain with closed head injury, Chao Zhou, Stephanie A. Eucker, Turgut Durduran, Guoqiang Yu, Jill Ralston, Stuart H. Friess, Rebecca N. Ichord, Susan S. Margulies, and Arjun G. Yodh

Papers from 2008

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Geometry of mediating protein affects the probability of loop formation in DNA., Neeraj J. Agrawal, Ravi Radhakrishnan, and Prashant K. Purohit

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The inhibition of Staphylococcus epidermidis biofilm formation by vancomycinmodified titanium alloy and implications for the treatment of periprosthetic infection, Valentin Antoci Jr., Christopher S. Adams, Javad Parvizi, Helen M. Davidson, Russell J. Composto, Theresa A. Freeman, Eric Wickstrom, Paul Ducheyne, Donald Jungkind, Irving M. Shapiro, and Noreen J. Hickok

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Cytoplasmic BKCa channel intron-containing mRNAs contribute to the intrinsic excitability of hippocampal neurons, Thomas J. Bell, Kevin Y. Miyashiro, Jai-Yoon Sul, Ronald McCullough, Peter T. Buckley, Jeanine Jochems, David F. Meaney, Phil Haydon, Charles R. Cantor, Thomas D. Parsons, and James Eberwine

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Sequential Effects on the Detectability of a Tone Added to a Multitone Masker, Xiang Cao, Rong Huang, and Virginia M. Richards

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Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA, Antony K. Chen, Mark A. Behlke, and Andrew Tsourkas

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Potential for Head Injuries in Infants From Low-Height Falls Laboratory Investigation, Brittany Coats and Susan S. Margulies

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Potential for head injuries in infants from low-height falls: Laboratory investigation, Brittany Coats and Susan S. Margulies

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Response to: Closer but not there yet: models in child injury research, Brittany Coats and Susan S. Margulies

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The Bad Truth about Laplace's Transform, Charles L. Epstein and John C. Schotland

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Adhesive Dynamics Simulations of the Shear Threshold Effect for Leukocytes, Kelly Kaputo, Dooyoung Lee, Michael R. King, and Daniel A. Hammer

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Effect of rapidly resorbable bone substitute materials on the temporal expression of the osteoblastic phenotype in vitro, C. Knabe, A. Houshmand, G. Berger, Paul Ducheyne, R. Gildenhaar, I. Kranz, and M. Stiller

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Validation of a novel device to objectively measure adherence to long-term oxygen therapy, Sun-Kai V. Lin, Daniel K. Bogen, and Samuel T. Kuna

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In vitro surface reaction layer formation and dissolution of calcium phosphate cement – bioactive glass composites, Changsheng Liu, Chien-Wen Chen, and Paul Ducheyne

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Rigid model-based 3D segmentation of the bones of joints in MR and CT images for motion analysis, Jiamin Liu, Jayaram K. Udupa, Punam K. Saha, Dewey Odhner, Bruce E. Hirsch, Sorin Seigler, Scott Simon, and Beth A. Winkelstein

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Can the Imaginary Part of Permeability be Negative?, Vadim A. Markel

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Optimized biopsy procedures for estimating Gleason Score and prostate cancer volume, Yangming Ou, Dinggang Shen, Yong Fan, Jianchao Zeng, Leon Sun, and Christos Davatzikos

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Classical Theory of Optical Nonlinearity in Conducting Nanoparticles, George Y. Panasyuk, John C. Schotland, and Vadim A. Markel

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The controlled release of drugs from emulsified, sol gel processed silica microspheres, Shula Radin, Paul Ducheyne, and Tiffany Chen

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Emergence of Patterned Stem Cell Differentiation Within Multicellular Structures, Sami Alom Ruiz and Christopher S. Chen

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Geometrical optics limit of stochastic electromagnetic fields, Robert W. Schoonover, Adam M. Zysk, P. Scott Carney, John C. Schotland, and Emil Wolfe

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Molecular Systems Biology of ErbB1 Signaling: Bridging the Gap through Multiscale Modeling and High-Performance Computing, Andrew Shih, Jeremy Purvis, and Ravi Radhakrishnan

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Magnetic microposts for mechanical stimulation of biological cells: Fabrication, characterization, and analysis, Nathan J. Sniadecki, Corinne M. Lamb, Yaohua Liu, Christopher S. Chen, and Daniel H. Reich

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Size, charge and concentration dependent uptake of iron oxide particles by non-phagocytic cells, Daniel L.J. Thorek and Andrew Tsourkas

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Computational Study of the Force Dependence of Phosphoryl Transfer during DNA Synthesis by a High Fidelity Polymerase, Ravindra Venkatramani and Ravi Radhakrishnan

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The effect of oxidatively damaged DNA on the active site pre-organization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus, Ravindra Venkatramani and Ravi Radhakrishnan

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Multiparametric Tissue Characterization of Brain Neoplasms and Their Recurrence Using Pattern Classification of MR Images, Raginia Verma, Evangelia I. Zacharaki, Yangming Ou, Hongmin Cai, Sanjeev Chawla, Seung-Koo Lee, Elias R. Melhem, Ronald Wolf, and Christos Davatzikos

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Integrin-mediated signalling through the MAP-kinase pathway, Ka Lai Yee, V. M. Weaver, and Daniel A. Hammer

Papers from 2007

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Probabilistic Segmentation of Brain Tumors Based on Multi-Modality Magnetic Resonance Images, Hongmin Cai, Ragini Verma, Yangming Ou, Seung-Koo Lee, Elias R. Melhem, and Christos Davatzikos

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Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells, Antony K. Chen, Mark A. Behlke, and Andrew Tsourkas

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Separate but not equal: Differential mechanical roles for myosin isoforms, Christopher S. Chen

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Polymorphic Variation in Human Meiotic Recombination, Vivian G. Cheung, Joshua T. Burdick, Deborah Hirschmann, and Michael Morley

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mGluR5 stimulates gliotransmission in the nucleus accumbens., Marcello D'Ascenzo, Tommaso Fellin, Miho Terunuma, Raquel Revilla-Sanchez, David F. Meaney, Yves P. Auberson, Stephen J. Moss, and Philip G. Haydon

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Enhanced Astrocytic Ca2+ Signals Contribute to Neuronal Excitotoxicity after Status Epilepticus, Shinghua Ding, Tommaso Fellin, Yingzi Zhu, So-Young Lee, Yves P. Auberson, David F. Meaney, Douglas A. Coulter, Giorgio Carmignoto, and Philip G. Haydon

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Photoacoustic effect for multiply scattered light, Andrew R. Fisher, Andrew J. Schissler, and John C. Schotland

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RFID Inside: The Murky Ethics of Implanted Chips, Kenneth R. Foster and Jan Jaeger

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Hyaluronic acid hydrogel for controlled self-renewal and differentiation of human embryonic stem cells, Sharon Gerecht, Jason A. Burdick, Lino S. Ferreira, Seth A. Townsend, Robert Langer, and Gordana Vunjak-Novakovic

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Transient Cervical Nerve Root Compression Modulates Pain: Load Thresholds for Allodynia and Sustained Changes in Spinal Neuropeptide Expression, Raymond D. Hubbard, Zen Chen, and Beth A. Winkelstein

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Thermodynamically Equivalent Silicon Models of Voltage-Dependent Ion Channels, Kai M. Hynna and Kwabena A. Boahen