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: Research - peer-reviewArticle

Membrane Proteins
Photosensitizers
Membranes
X Ray Crystallography
Datasets

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: Research - peer-reviewArticle

Hydrogels
Mechanical properties
Hydrocarbons
Peptides
Tuning

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: Research - peer-reviewArticle

Molecular modeling
Servers
Network protocols
Proteins
Specifications
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: Research - peer-reviewArticle

Surgery
Robots
Sensors
robots
surgery

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

RNA
Escherichia coli
Messenger RNA
Proteins
Bacterial 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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Molecular Conformation
Self-efficacy
Structure Prediction
Computational Biology
Design

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: Research - peer-reviewArticle

Hidden Markov models
Robotic surgery
Benchmarking
Time series
Dynamical systems

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

yeast
protein
analysis
Sumoylation
Libraries

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Head
Brain
Wounds and Injuries
White Matter
Diffuse Axonal Injury

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: Research - peer-reviewArticle

Aging of materials
Phenotype
Fibroblasts
Metabolism
Gene expression

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Dimerization
Immunoglobulin Domains
Cell membranes
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: Research - peer-reviewArticle

Image registration
Brain
Image fusion
Magnetic resonance
Image analysis

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: Research - peer-reviewArticle

Multiple Sclerosis
Atrophy
Retrospective Studies
Therapeutics
Optical Coherence Tomography

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: Research - peer-reviewArticle

Ebolavirus
peptides
Peptides
polypeptides
cells

Editorial overview: Biological engineering: Stem cell engineering

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

Research output: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Neoplasm Proteins
E-Selectin
Hyaluronic Acid
Tumor Cell Line
Pancreatic Neoplasms

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Membrane Protein
Modeling
Membrane Proteins
Proteins
Membranes

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Geometry
Robots
Bearings (structural)
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: Research - peer-reviewArticle

N-Acetylneuraminic Acid
Esterases
Modulation
Fluxes
Enzymes

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: Research - peer-reviewArticle

Cytokinesis
Cell Shape
Water
Actomyosin
Ion Channels

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: Research - peer-reviewArticle

Integrin alpha5
Breast Neoplasms
Neoplasm Metastasis
Hypoxia
Integrins

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Multiple Sclerosis
Datasets
Research Personnel
Research
White Matter

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: Research - peer-reviewArticle

multiple sclerosis
resources
segmentation
time
website

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: Research - peer-reviewArticle

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

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

NADPH Oxidase
Shear stress
Fluids
Osteocytes
Microtubules

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: Research - peer-reviewArticle

Antibodies
Antigens
Conformations
Network protocols
Complementarity Determining Regions

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: Research - peer-reviewArticle

Neoplasms
Extracellular Matrix
Actomyosin
Mechanics
Cell Adhesion

Motorized Micro-Forceps with Active Motion Guidance based on Common-Path SSOCT for Epiretinal Membranectomy

Cheon, G. W., Gonec, B., Taylor, R. H., Gehlbach, P. L. & Kang, J. U. Sep 4 2017 (Accepted/In press) In : IEEE/ASME Transactions on Mechatronics.

Research output: Research - peer-reviewArticle

Sensors
Optical tomography
Fibers
Monitoring
Polymers

Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology

Kim, J. K., Louhghalam, A., Lee, G., Schafer, B. W., Wirtz, D. & Kim, D. H. Dec 1 2017 In : Nature Communications. 8, 1, 2123

Research output: Research - peer-reviewArticle

harnesses
caps
cables
Lamin Type A
Actins

Objective Assessment of Surgical Technical Skill and Competency in the Operating Room

Vedula, S. S., Ishii, M. & Hager, G. D. Jun 21 2017 In : Annual Review of Biomedical Engineering. 19, p. 301-325 25 p.

Research output: Research - peer-reviewArticle

Operating Rooms
Operating rooms
Surgeons
Safety Management
Quality of Health Care

On the reproducibility of expert-operated and robotic ultrasound acquisitions

Kojcev, R., Khakzar, A., Fuerst, B., Zettinig, O., Fahkry, C., DeJong, R., Richmon, J., Taylor, R., Sinibaldi, E. & Navab, N. Mar 20 2017 (Accepted/In press) In : International Journal of Computer Assisted Radiology and Surgery. p. 1-9 9 p.

Research output: Research - peer-reviewArticle

Robotics
Ultrasonography
Expert Systems
Healthy Volunteers
Thyroid Gland

pH-triggered, macromolecule-sized poration of lipid bilayers by synthetically evolved peptides

Wiedman, G., Kim, S. Y., Zapata-Mercado, E., Wimley, W. C. & Hristova, K. Jan 18 2017 In : Journal of the American Chemical Society. 139, 2, p. 937-945 9 p.

Research output: Research - peer-reviewArticle

Lipid bilayers
Macromolecules
Peptides
Lipid Bilayers
Membranes

Pluri-IQ: Quantification of Embryonic Stem Cell Pluripotency through an Image-Based Analysis Software

Perestrelo, T., Chen, W., Correia, M., Le, C., Pereira, S., Rodrigues, A. S., Sousa, M. I., Ramalho-Santos, J. & Wirtz, D. Aug 8 2017 In : Stem Cell Reports. 9, 2, p. 697-709 13 p.

Research output: Research - peer-reviewArticle

Stem cells
Embryonic Stem Cells
Software
Staining and Labeling
Image analysis

Pose-aware C-arm for automatic re-initialization of interventional 2D/3D image registration

Fotouhi, J., Fuerst, B., Johnson, A., Lee, S. C., Taylor, R., Osgood, G., Navab, N. & Armand, M. Jul 1 2017 In : International Journal of Computer Assisted Radiology and Surgery. 12, 7, p. 1221-1230 10 p.

Research output: Research - peer-reviewArticle

Calibration
Equipment and Supplies
Workflow
Gelatin
Femur

Probabilistic tractography using Lasso bootstrap

Ye, C. & Prince, J. L. Jan 1 2017 In : Medical Image Analysis. 35, p. 544-553 10 p.

Research output: Research - peer-reviewArticle

Fiber reinforced materials
alachlor
Imaging techniques
Diffusion Magnetic Resonance Imaging
Magnetic resonance