Whiting School of Engineering

Research Output 1966 2018

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2018

A comparison of methods to assess cell mechanical properties

Wu, P. H. , Aroush, D. R. B. , Asnacios, A. , Chen, W. C. , Dokukin, M. E. , Doss, B. L. , Durand-Smet, P. , Ekpenyong, A. , Guck, J. , Guz, N. V. , Janmey, P. A. , Lee, J. S. H. , Moore, N. M. , Ott, A. , Poh, Y. C. , Ros, R. , Sander, M. , Sokolov, I. , Staunton, J. R. , Wang, N. & 2 others Whyte, G. & Wirtz, D. Jun 18 2018 (Accepted/In press) In : Nature Methods. p. 1-8 8 p.

Research output: Contribution to journalArticle

Cellular Microenvironment
Mechanical Stress
Rheology
Atomic Force Microscopy
Elastic Modulus

A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces

Lubin, J. H., Pacella, M. S. & Gray, J. J. May 8 2018 In : Langmuir. 34, 18, p. 5279-5289 11 p.

Research output: Contribution to journalArticle

Unsaturated polymers
Photosensitizers
Self assembled monolayers
Peptides
peptides

Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality

Koehler Leman, J., D'Avino, A. R., Bhatnagar, Y. & Gray, J. J. Jan 1 2018 In : Proteins: Structure, Function and Bioinformatics. 86, 1, p. 57-74 18 p.

Research output: Contribution to journalArticle

Photosensitizers
Membrane Proteins
Membranes
X Ray Crystallography

EB1 and cytoplasmic dynein mediate protrusion dynamics for efficient 3-dimensional cell migration

Jayatilaka, H., Giri, A., Karl, M., Aifuwa, I., Trenton, N. J., Phillip, J. M., Khatau, S. & Wirtz, D. Mar 1 2018 In : FASEB Journal. 32, 3, p. 1207-1221 15 p.

Research output: Contribution to journalArticle

Slip forming
Cytoplasmic Dyneins
Condensation reactions
Paclitaxel
Microtubules
Navigation systems
Surgery
Nasolacrimal Duct
Endoscopes
Paranasal Sinuses

Factors associated with physicians' prescriptions for rheumatoid arthritis drugs not filled by patients

Kan, H. J., Dyagilev, K., Schulam, P., Saria, S., Kharrazi, H., Bodycombe, D., Molta, C. T. & Curtis, J. R. May 2 2018 In : Arthritis Research and Therapy. 20, 1, 79

Research output: Contribution to journalArticle

Methotrexate
Prescriptions
Biological Products
Rheumatoid Arthritis
Physicians

Immunolabeling of Cleared Human Pancreata Provides Insights into Three-Dimensional Pancreatic Anatomy and Pathology

Noë, M., Rezaee, N., Asrani, K., Skaro, M., Groot, V. P., Wu, P. H., Olson, M. T., Hong, S. M., Kim, S. J., Weiss, M. J., Wolfgang, C. L., Makary, M. A., He, J., Cameron, J. L., Wirtz, D., Roberts, N. J., Offerhaus, G. J. A., Brosens, L. A. A., Wood, L. D. & Hruban, R. H. Jul 1 2018 In : American Journal of Pathology. 188, 7, p. 1530-1535 6 p.

Research output: Contribution to journalArticle

Pancreas
Anatomy
Pathology
Pancreatic Neoplasms
Paraffin

Inhibition of ovarian tumor cell invasiveness by targeting SYK in the tyrosine kinase signaling pathway

Yu, Y., Suryo Rahmanto, Y., Lee, M. H., Wu, P. H., Phillip, J. M., Huang, C. H., Vitolo, M. I., Gaillard, S., Martin, S. S., Wirtz, D., Shih, I. M. & Wang, T. L. Apr 11 2018 (Accepted/In press) In : Oncogene. p. 1-12 12 p.

Research output: Contribution to journalArticle

Protein-Tyrosine Kinases
Ovarian Neoplasms
Cortactin
Neoplasms
Cell Movement

Interactions between NRP1 and VEGFR2 molecules in the plasma membrane

King, C., Wirth, D., Workman, S. & Hristova, K. Jan 1 2018 (Accepted/In press) In : Biochimica et Biophysica Acta - Biomembranes.

Research output: Contribution to journalArticle

Neuropilin-1
Vascular Endothelial Growth Factor Receptor-2
Cell Membrane
Ligands
Vascular Endothelial Growth Factor Receptor-1

Isomeric control of the mechanical properties of supramolecular filament hydrogels

Lin, Y. A., Kang, M., Chen, W. C., Ou, Y. C., Cheetham, A. G., Wu, P. H., Wirtz, D., Loverde, S. M. & Cui, H. Jan 1 2018 In : Biomaterials Science. 6, 1, p. 216-224 9 p.

Research output: Contribution to journalArticle

Hydrogels
Hydrocarbons
Peptides
Mechanical properties
Tuning

Multi-nucleated cells use ROS to induce breast cancer chemo-resistance in vitro and in vivo

Parekh, A. , Das, S. , Parida, S. , Das, C. K. , Dutta, D. , Mallick, S. K. , Wu, P. H. , Kumar, B. N. P. , Bharti, R. , Dey, G. , Banerjee, K. , Rajput, S. , Bharadwaj, D. , Pal, I. , Dey, K. K. , Rajesh, Y. , Jena, B. C. , Biswas, A. , Banik, P. , Pradhan, A. K. & 7 others Das, S. K., Das, A. K., Dhara, S., Fisher, P. B., Wirtz, D., Mills, G. B. & Mandal, M. May 10 2018 (Accepted/In press) In : Oncogene. p. 1-16 16 p.

Research output: Contribution to journalArticle

Reactive Oxygen Species
Breast Neoplasms
Vascular Endothelial Growth Factor A
Neoplasms
Apoptosis Regulatory Proteins

Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell

Athanasiadou, D., Jiang, W., Goldbaum, D., Saleem, A., Basu, K., Pacella, M. S., Böhm, C. F., Chromik, R. R., Hincke, M. T., Rodríguez-Navarro, A. B., Vali, H., Wolf, S. E., Gray, J. J., Bui, K. H. & McKee, M. D. Mar 30 2018 In : Science Advances. 4, 3, aar3219

Research output: Contribution to journalArticle

Egg Shell
Osteopontin
Nanostructures
Hardness
Dinosaurs

Photoacoustic-based catheter tracking: Simulation, phantom, and in vivo studies

Cheng, A., Kim, Y., Itsarachaiyot, Y., Zhang, H. K., Weiss, C. R., Taylor, R. H. & Boctor, E. M. Apr 1 2018 In : Journal of Medical Imaging. 5, 2, 021223

Research output: Contribution to journalArticle

Catheters
Acoustics
Technology
Electromagnetic Phenomena
Fluoroscopy

Piezo2 channel regulates RhoA and actin cytoskeleton to promote cell mechanobiological responses

Pardo-Pastor, C., Rubio-Moscardo, F., Vogel-González, M., Serra, S. A., Afthinos, A., Mrkonjic, S., Destaing, O., Abenza, J. F., Fernández-Fernández, J. M., Trepat, X., Albiges-Rizo, C., Konstantopoulos, K. & Valverde, M. A. Feb 20 2018 In : Proceedings of the National Academy of Sciences of the United States of America. 115, 8, p. 1925-1930 6 p.

Research output: Contribution to journalArticle

Stress Fibers
Actin Cytoskeleton
Focal Adhesions
Plasminogen Activator Inhibitor 2
Calpain

Plan in 2-D, execute in 3-D: An augmented reality solution for cup placement in total hip arthroplasty

Fotouhi, J., Alexander, C. P., Unberath, M., Taylor, G., Lee, S. C., Fuerst, B., Johnson, A., Osgood, G., Taylor, R. H., Khanuja, H., Armand, M. & Navab, N. Apr 1 2018 In : Journal of Medical Imaging. 5, 2, 021205

Research output: Contribution to journalArticle

Arthroplasty
Hip
Arm
X-Rays
Radiation

Potent macromolecule-sized poration of lipid bilayers by the macrolittins, a synthetically evolved family of pore-forming peptides

Li, S., Kim, S. Y., Pittman, A. E., King, G. M., Wimley, W. C. & Hristova, K. Mar 19 2018 (Accepted/In press) In : Unknown Journal.

Research output: Contribution to journalArticle

Unsaturated polymers
Water recycling
Lipid bilayers
Lipid Bilayers
Macromolecules

Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification

Jeliazkov, J. R., Sljoka, A., Kuroda, D., Tsuchimura, N., Katoh, N., Tsumoto, K. & Gray, J. J. Mar 2 2018 In : Frontiers in Immunology. 9, MAR, 413

Research output: Contribution to journalArticle

Complementarity Determining Regions
Antibodies
Antibody Binding Sites
Antigens
Antibody Affinity

Role of membrane-tension gated Ca2+ flux in cell mechanosensation

He, L., Tao, J., Maity, D., Si, F., Wu, Y., Wu, T., Prasath, V., Wirtz, D. & Sun, S. X. Feb 1 2018 In : Journal of Cell Science. 131, 4, jcs208470

Research output: Contribution to journalArticle

Myosins
Membranes
Lab-On-A-Chip Devices
Cytoskeleton
Cytoplasm

Single Proteoliposome High Content Analysis Reveals Differences in the Homo-Oligomerization of GPCRs

Walsh, S. M., Mathiasen, S., Christensen, S. M., Fay, J. F., King, C., Provasi, D., Borrero, E., Rasmussen, S. G. F., Fung, J. J., Filizola, M., Hristova, K., Kobilka, B., Farrens, D. L. & Stamou, D. Jan 1 2018 (Accepted/In press) In : Biophysical journal.

Research output: Contribution to journalArticle

Hominidae
G-Protein-Coupled Receptors
Opsins
Cannabinoid Receptors
Fluorescence Microscopy

Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors

Kalin, J. H. , Wu, M. , Gomez, A. V. , Song, Y. , Das, J. , Hayward, D. , Adejola, N. , Wu, M. , Panova, I. , Chung, H. J. , Kim, E. , Roberts, H. J. , Roberts, J. M. , Prusevich, P. , Jeliazkov, J. R. , Roy Burman, S. S. , Fairall, L. , Milano, C. , Eroglu, A. , Proby, C. M. & 14 others Dinkova-Kostova, A. T., Hancock, W. W., Gray, J. J., Bradner, J. E., Valente, S., Mai, A., Anders, N. M., Rudek, M. A., Hu, Y., Ryu, B., Schwabe, J. W. R., Mattevi, A., Alani, R. M. & Cole, P. A. Dec 1 2018 In : Nature Communications. 9, 1, 53

Research output: Contribution to journalArticle

cells and cell components
Histone Demethylases
enzyme activity
Histone Deacetylase Inhibitors
gene expression

Toward Semi-autonomous Cryoablation of Kidney Tumors via Model-Independent Deformable Tissue Manipulation Technique

Alambeigi, F., Wang, Z., Liu, Y. H., Taylor, R. H. & Armand, M. Jun 19 2018 (Accepted/In press) In : Annals of Biomedical Engineering. p. 1-13 13 p.

Research output: Contribution to journalArticle

Tumors
Tissue
Biomedical engineering
Needles
Experiments

Using Big Data Analytics to Advance Precision Radiation Oncology

McNutt, T. R., Benedict, S. H., Low, D. A., Moore, K., Shpitser, I., Jiang, W., Lakshminarayanan, P., Cheng, Z., Han, P., Hui, X., Nakatsugawa, M., Lee, J., Moore, J. A., Robertson, S. P., Shah, V., Taylor, R., Quon, H., Wong, J. & DeWeese, T. Jun 1 2018 In : International Journal of Radiation Oncology Biology Physics. 101, 2, p. 285-291 7 p.

Research output: Contribution to journalArticle

Radiation Oncology
Oncology
learning
health
Precision Medicine

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

Moretti, R., Lyskov, S., Das, R., Meiler, J. & Gray, J. J. Jan 1 2018 In : Protein science : a publication of the Protein Society. 27, 1, p. 259-268 10 p.

Research output: Contribution to journalArticle

Molecular modeling
Servers
Network protocols
Proteins
Biopolymers

Why policymakers should care about “big data” in healthcare

Bates, D. W., Heitmueller, A., Kakad, M. & Saria, S. Jan 1 2018 (Accepted/In press) In : Health Policy and Technology.

Research output: Contribution to journalArticle

Health
Delivery of Health Care
Privacy
Medicine
Research Personnel
2017

3-DOF Force-Sensing Motorized Micro-Forceps for Robot-Assisted Vitreoretinal Surgery

Gonenc, B., Chamani, A., Handa, J., Gehlbach, P., Taylor, R. H. & Iordachita, I. Jun 1 2017 In : IEEE Sensors Journal. 17, 11, p. 3526-3541 16 p., 7903591

Research output: Contribution to journalArticle

robots
surgery
Surgery
Robots
Sensors

A Benchmarking Study of Peptide-Biomineral Interactions

Pacella, M. S. & Gray, J. J. Jan 23 2017 In : Crystal Growth and Design. 18, 2, p. 607-616 10 p.

Research output: Contribution to journalArticle

Unsaturated polymers
Biomineralization
Bins
Benchmarking
Bioinformatics

Accurate structure prediction of CDR H3 loops enabled by a novel structure-based C-terminal constraint

Weitzner, B. D. & Gray, J. J. Jan 1 2017 In : Journal of Immunology. 198, 1, p. 505-515 11 p.

Research output: Contribution to journalArticle

Benchmarking
Antibodies
Proteins

Acidic C-terminal domains autoregulate the RNA chaperone Hfq

Santiago-Frangos, A., Jeliazkov, J. R., Gray, J. J. & Woodson, S. A. Aug 9 2017 In : eLife. 6, e27049

Research output: Contribution to journalArticle

RNA
Escherichia coli
Bacterial RNA
Peptide Nucleic Acids
Messenger RNA

Activation of tumor suppressor LKB1 by honokiol abrogates cancer stem-like phenotype in breast cancer via inhibition of oncogenic Stat3

Sengupta, S. , Nagalingam, A. , Muniraj, N. , Bonner, M. Y. , Mistriotis, P. , Afthinos, A. , Kuppusamy, P. , Lanoue, D. , Cho, S. , Korangath, P. , Shriver, M. , Begum, A. , Merino, V. F. , Huang, C. Y. , Arbiser, J. L. , Matsui, W. , Györffy, B. , Konstantopoulos, K. , Sukumar, S. , Marignani, P. A. & 2 others Saxena, N. K. & Sharma, D. Oct 12 2017 In : Oncogene. 36, 41, p. 5709-5721 13 p.

Research output: Contribution to journalArticle

Phosphotransferases
Breast Neoplasms
Phenotype
Liver
Neoplasms

A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design

Alford, R. F., Leaver-Fay, A., Gonzales, L., Dolan, E. L. & Gray, J. J. Dec 1 2017 In : PLoS Computational Biology. 13, 12, e1005837

Research output: Contribution to journalArticle

molecular conformation
Molecular Conformation
self-efficacy
Self-efficacy
Structure Prediction

A Dataset and Benchmarks for Segmentation and Recognition of Gestures in Robotic Surgery

Ahmidi, N., Tao, L., Sefati, S., Gao, Y., Lea, C., Haro, B. B., Zappella, L., Khudanpur, S., Vidal, R. & Hager, G. D. Sep 1 2017 In : IEEE Transactions on Biomedical Engineering. 64, 9, p. 2025-2041 17 p., 7805258

Research output: Contribution to journalArticle

Hidden Markov models
Benchmarking
Time series
Dynamical systems
Kinematics

Affine and non-affine deformations quantified in cytoskeletal networks through three-dimensional form-finding model

Wang, Y., Gong, J., Wirtz, D. & Schafer, B. W. Aug 1 2017 In : Journal of the Mechanical Behavior of Biomedical Materials. 72, p. 52-65 14 p.

Research output: Contribution to journalArticle

Actins
Finite element method
Fluidics
Bending moments
Strain energy

A high throughput mutagenic analysis of yeast sumo structure and function

Newman, H. A., Meluh, P. B., Lu, J., Vidal, J., Carson, C., Lagesse, E., Gray, J. J., Boeke, J. D. & Matunis, M. J. Feb 1 2017 In : PLoS Genetics. 13, 2, e1006612

Research output: Contribution to journalArticle

Sumoylation
Libraries
yeast
Yeasts
yeasts

Altering the threshold of an excitable signal transduction network changes cell migratory modes

Miao, Y., Bhattacharya, S., Edwards, M., Cai, H., Inoue, T., Iglesias, P. A. & Devreotes, P. N. Mar 27 2017 (Accepted/In press) In : Nature Cell Biology.

Research output: Contribution to journalArticle

Signal Transduction
Cell Surface Extensions
Dictyostelium
Phosphatidylinositols
Cell Movement

Analysis of Agreement of Retinal-Layer Thickness Measures Derived from the Segmentation of Horizontal and Vertical Spectralis OCT Macular Scans

Gonzalez Caldito, N., Antony, B., He, Y., Lang, A., Nguyen, J., Rothman, A., Ogbuokiri, E., Avornu, A., Balcer, L., Frohman, E., Frohman, T. C., Bhargava, P., Prince, J., Calabresi, P. A. & Saidha, S. Dec 15 2017 (Accepted/In press) In : Current Eye Research. p. 1-9 9 p.

Research output: Contribution to journalArticle

Retinaldehyde
Optical Coherence Tomography
Multiple Sclerosis
Nerve Fibers
Ganglia

A new method to study heterodimerization of membrane proteins and its application to fibroblast growth factor receptors

Del Piccolo, N., Sarabipour, S. & Hristova, K. Jan 27 2017 In : Journal of Biological Chemistry. 292, 4, p. 1188-1301 114 p.

Research output: Contribution to journalArticle

Fibroblast Growth Factor Receptors
Receptor Protein-Tyrosine Kinases
Membrane Proteins
Cell membranes
Cell Membrane

A tandem simulation framework for predicting mapping quality

Langmead, B. Aug 10 2017 In : Genome Biology. 18, 1, 152

Research output: Contribution to journalArticle

simulation
methodology
alignment
method

A Three-Dimensional Computational Human Head Model That Captures Live Human Brain Dynamics

Ganpule, S., Daphalapurkar, N. P., Ramesh, K. T., Knutsen, A. K., Pham, D. L., Bayly, P. V. & Prince, J. L. Jul 1 2017 In : Journal of Neurotrauma. 34, 13, p. 2154-2166 13 p.

Research output: Contribution to journalArticle

Head
Brain
Wounds and Injuries
Diffuse Axonal Injury
Limbic System

Biophysical and biomolecular determination of cellular age in humans

Phillip, J. M., Wu, P. H., Gilkes, D. M., Williams, W., McGovern, S., Daya, J., Chen, J., Aifuwa, I., Lee, J. S. H., Fan, R., Walston, J. & Wirtz, D. Jun 30 2017 In : Nature Biomedical Engineering. 1, 7, 0093

Research output: Contribution to journalArticle

Aging of materials
Fibroblasts
Progeria
Metabolism
Gene expression

Cancer Protrusions on a Tightrope: Nanofiber Curvature Contrast Quantitates Single Protrusion Dynamics

Koons, B., Sharma, P., Ye, Z., Mukherjee, A., Lee, M. H., Wirtz, D., Behkam, B. & Nain, A. S. Dec 26 2017 In : ACS Nano. 11, 12, p. 12037-12048 12 p.

Research output: Contribution to journalArticle

cytology
Cytology
Nanofibers
Cell culture
debris

Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate

Jiang, W., Pacella, M. S., Athanasiadou, DI., Nelea, V., Vali, H., Hazen, R. M., Gray, J. J. & McKee, M. D. Apr 13 2017 In : Nature Communications. 8, 15066

Research output: Contribution to journalArticle

Acidic Amino Acids
Enantiomers
Calcium Carbonate
calcium carbonates
enantiomers

Cooperative interactions between VEGFR2 extracellular Ig-like subdomains ensure VEGFR2 dimerization

King, C., Wirth, D., Workman, S. & Hristova, K. Nov 1 2017 In : Biochimica et Biophysica Acta - General Subjects. 1861, 11, p. 2559-2567 9 p.

Research output: Contribution to journalArticle

Dimerization
Cell membranes
Photons
Oligomers
Dimers

Cross contrast multi-channel image registration using image synthesis for MR brain images

Chen, M., Carass, A., Jog, A., Lee, J., Roy, S. & Prince, J. L. Feb 1 2017 In : Medical Image Analysis. 36, p. 2-14 13 p.

Research output: Contribution to journalArticle

Image registration
Brain
Image fusion
Atlases
Proxy

Disease-modifying therapies modulate retinal atrophy in multiple sclerosis: A retrospective study

Button, J., Al-Louzi, O., Lang, A., Bhargava, P., Newsome, S. D., Frohman, T., Balcer, L. J., Frohman, E. M., Prince, J., Calabresi, P. A. & Saidha, S. Feb 7 2017 In : Neurology. 88, 6, p. 525-532 8 p.

Research output: Contribution to journalArticle

Optical Coherence Tomography
Multiple Sclerosis
Atrophy
Relapsing-Remitting Multiple Sclerosis
Retrospective Studies

Ebola virus delta peptide is a viroporin

He, J., Melnik, L. I., Komin, A., Wiedman, G., Fuselier, T., Morris, C. F., Starr, C. G., Searson, P. C., Gallaher, W. R., Hristova, K., Garry, R. F. & Wimley, W. C. Aug 1 2017 In : Journal of Virology. 91, 16, e00438-17

Research output: Contribution to journalArticle

Ebolavirus
peptides
Peptides
Ebola Hemorrhagic Fever
polypeptides

Editorial overview: Biological engineering: Stem cell engineering

Gerecht, S. & Konstantopoulos, K. 2017 (Accepted/In press) In : Current Opinion in Chemical Engineering.

Research output: Contribution to journalArticle

Cell engineering
Stem cells
Bioengineering

E-selectin-mediated rolling facilitates pancreatic cancer cell adhesion to hyaluronic acid

Shea, D. J., Li, Y. W., Stebe, K. J. & Konstantopoulos, K. Nov 1 2017 In : FASEB Journal. 31, 11, p. 5078-5086 9 p.

Research output: Contribution to journalArticle

Neoplasm Proteins
E-Selectin
Flash memory
Hyaluronic Acid
Tumor Cell Line

Excitable signal transduction networks in directed cell migration

Devreotes, P. N., Bhattacharya, S., Edwards, M., Iglesias, P. A., Lampert, T. & Miao, Y. Oct 6 2017 In : Annual Review of Cell and Developmental Biology. 33, p. 103-125 23 p.

Research output: Contribution to journalArticle

Pseudopodia
Eukaryotic Cells
Cell Movement
Signal Transduction
Cell Surface Extensions

Expanding the toolkit for membrane protein modeling in Rosetta

Leman, J. K., Mueller, B. K. & Gray, J. J. 2017 In : Bioinformatics. 33, 5, p. 754-756 3 p.

Research output: Contribution to journalArticle

Membrane Protein
Membrane Proteins
Proteins
Membranes
Membrane

Flexible expressed region analysis for RNA-seq with derfinder

Collado-Torres, L., Nellore, A., Frazee, A. C., Wilks, C., Love, M. I., Langmead, B., Irizarry, R. A., Leek, J. T. & Jaffe, A. E. Jan 1 2017 In : Nucleic Acids Research. 45, 2, p. e9

Research output: Contribution to journalArticle

RNA Sequence Analysis
Genome
Genes
Software
Genotype