Whiting School of Engineering

Research Output 1966 2018

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2018

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

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

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

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

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
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

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, D. I., 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

Force-assisted ultrasound imaging system through dual force sensing and admittance robot control

Fang, T. Y., Zhang, H. K., Finocchi, R., Taylor, R. H. & Boctor, E. M. Mar 25 2017 (Accepted/In press) In : International Journal of Computer Assisted Radiology and Surgery. p. 1-9 9 p.

Research output: Contribution to journalArticle

Robotics
Ultrasonography
Musculoskeletal Pain
Posture
Human Body

Force-controlled exploration for updating virtual fixture geometry in model-mediated telemanipulation

Wang, L., Chen, Z., Chalasani, P., Yasin, R. M., Kazanzides, P., Taylor, R. H. & Simaan, N. Apr 1 2017 In : Journal of Mechanisms and Robotics. 9, 2, 021010

Research output: Contribution to journalArticle

Geometry
Bearings (structural)
Robots
Force control
Motion control

Glycoengineering of Esterase Activity through Metabolic Flux-Based Modulation of Sialic Acid

Mathew, M. P., Tan, E., Labonte, J. W., Shah, S., Saeui, C. T., Liu, L., Bhattacharya, R., Bovonratwet, P., Gray, J. J. & Yarema, K. J. 2017 (Accepted/In press) In : ChemBioChem.

Research output: Contribution to journalArticle

N-Acetylneuraminic Acid
Esterases
Modulation
Fluxes
Polysaccharides

Going with the Flow: Water Flux and Cell Shape during Cytokinesis

Li, Y., He, L., Gonzalez, N. A. P., Graham, J., Wolgemuth, C., Wirtz, D. & Sun, S. X. Dec 5 2017 In : Biophysical Journal. 113, 11, p. 2487-2495 9 p.

Research output: Contribution to journalArticle

Actomyosin
Biological Models
Cytokinesis
Cell Shape
Osmotic Pressure

Hypoxia Selectively Enhances Integrin α5β1 receptor expression in breast cancer to promote metastasis

Ju, J. A., Godet, I., Ye, I. C., Byun, J., Jayatilaka, H., Lee, S. J., Xiang, L., Samanta, D., Lee, M. H., Wu, P. H., Wirtz, D., Semenza, G. L. & Gilkes, D. M. Jun 1 2017 In : Molecular Cancer Research. 15, 6, p. 723-734 12 p.

Research output: Contribution to journalArticle

Integrin alpha5
Breast Neoplasms
Neoplasm Metastasis
Integrins
Hypoxia-Inducible Factor 1

Intracellular Domain Contacts Contribute to Ecadherin Constitutive Dimerization in the Plasma Membrane

Singh, D. R., Ahmed, F., Sarabipour, S. & Hristova, K. Jul 7 2017 In : Journal of Molecular Biology. 429, 14, p. 2231-2245 15 p.

Research output: Contribution to journalArticle

Dimerization
Cadherins
Cell Membrane
Adherens Junctions
Fluorescence Resonance Energy Transfer
Fluoroscopy
Brachytherapy
Prostate
Seeds
X-Rays

Longitudinal multiple sclerosis lesion segmentation: Resource and challenge

Carass, A. , Roy, S. , Jog, A. , Cuzzocreo, J. L. , Magrath, E. , Gherman, A. , Button, J. , Nguyen, J. , Prados, F. , Sudre, C. H. , Jorge Cardoso, M. , Cawley, N. , Ciccarelli, O. , Wheeler-Kingshott, C. A. M. , Ourselin, S. , Catanese, L. , Deshpande, H. , Maurel, P. , Commowick, O. , Barillot, C. & 26 others Tomas-Fernandez, X., Warfield, S. K., Vaidya, S., Chunduru, A., Muthuganapathy, R., Krishnamurthi, G., Jesson, A., Arbel, T., Maier, O., Handels, H., Iheme, L. O., Unay, D., Jain, S., Sima, D. M., Smeets, D., Ghafoorian, M., Platel, B., Birenbaum, A., Greenspan, H., Bazin, P. L., Calabresi, P. A., Crainiceanu, C. M., Ellingsen, L. M., Reich, D. S., Prince, J. L. & Pham, D. L. Mar 1 2017 In : NeuroImage. 148, p. 77-102 26 p.

Research output: Contribution to journalArticle

Multiple Sclerosis
Research Personnel
Research
Datasets

Longitudinal multiple sclerosis lesion segmentation data resource

Carass, A., Roy, S., Jog, A., Cuzzocreo, J. L., Magrath, E., Gherman, A., Button, J., Nguyen, J., Bazin, P. L., Calabresi, P. A., Crainiceanu, C. M., Ellingsen, L. M., Reich, D. S., Prince, J. L. & Pham, D. L. Jun 1 2017 In : Data in Brief. 12, p. 346-350 5 p.

Research output: Contribution to journalArticle

multiple sclerosis
resources
segmentation
website
expert

Loss of giant obscurins alters breast epithelial cell mechanosensing of matrix stiffness

Stroka, K. M., Wong, B. S., Shriver, M., Phillip, J. M., Wirtz, D., Kontrogianni-Konstantopoulos, A. & Konstantopoulos, K. 2017 In : Oncotarget. 8, 33, p. 54004-54020 17 p.

Research output: Contribution to journalArticle

Breast
Epithelial Cells
Cell Movement
rho-Associated Kinases
Down-Regulation

Mammalian cell division in 3D matrices via quantitative confocal reflection microscopy

He, L., Sneider, A., Chen, W., Karl, M., Prasath, V., Wu, P. H., Mattson, G. & Wirtz, D. Nov 29 2017 In : Journal of Visualized Experiments. 2017, 129, e56364

Research output: Contribution to journalArticle

Bioengineering
Confocal Microscopy
Cell Communication
Cell Division
Microscopic examination

Measuring Patient Mobility in the ICU Using a Novel Noninvasive Sensor

Ma, A. J., Rawat, N., Reiter, A., Shrock, C., Zhan, A., Stone, A., Rabiee, A., Griffin, S., Needham, D. M. & Saria, S. Apr 1 2017 In : Critical Care Medicine. 45, 4, p. 630-636 7 p.

Research output: Contribution to journalArticle

Physicians
Walking
Observational Studies
China
Software

Microtubules tune mechanotransduction through NOX2 and TRPV4 to decrease sclerostin abundance in osteocytes

Lyons, J. S., Joca, H. C., Law, R. A., Williams, K. M., Kerr, J. P., Shi, G., Khairallah, R. J., Martin, S. S., Konstantopoulos, K., Ward, C. W. & Stains, J. P. Nov 21 2017 In : Science Signaling. 10, 506, eaan5748

Research output: Contribution to journalArticle

Osteocytes
NADPH Oxidase
Microtubules
Shear stress
Reactive Oxygen Species

Modeling and docking of antibody structures with Rosetta

Weitzner, B. D., Jeliazkov, J. R., Lyskov, S., Marze, N., Kuroda, D., Frick, R., Adolf-Bryfogle, J., Biswas, N., Dunbrack, R. L. & Gray, J. J. Feb 1 2017 In : Nature Protocols. 12, 2, p. 401-416 16 p.

Research output: Contribution to journalArticle

Antibodies
Complementarity Determining Regions
Conformations
Antigens
Network protocols

Modeling the two-way feedback between contractility and matrix realignment reveals a nonlinear mode of cancer cell invasion

Ahmadzadeh, H., Webster, M. R., Behera, R., Valencia, A. M. J., Wirtz, D., Weeraratna, A. T. & Shenoy, V. B. Feb 28 2017 In : Proceedings of the National Academy of Sciences of the United States of America. 114, 9, p. E1617-E1626

Research output: Contribution to journalArticle

Neoplasms
Extracellular Matrix
Actomyosin
Mechanics
Cell Adhesion