Whiting School of Engineering

Research Output

2018

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

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

Research output: Contribution to journalArticle

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

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

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. A., Mar 19 2018, (Accepted/In press) In : Unknown Journal.

Research output: Contribution to journalArticle

Preface

Dong, C., Zahir, N. & Konstantopoulos, K., Jan 1 2018, In : Advances in Experimental Medicine and Biology. 1092, p. v-vi

Research output: Contribution to journalEditorial

Preliminary evaluation of an online estimation method for organ geometry and tissue stiffness

Chalasani, P., Wang, L., Yasin, R., Simaan, N. & Taylor, R. H., Jul 1 2018, In : IEEE Robotics and Automation Letters. 3, 3, p. 1816-1823 8 p.

Research output: Contribution to journalArticle

Radio-morphology: Parametric shape-based features in radiotherapy

Lakshminarayanan, P., Jiang, W., Robertson, S. P., Cheng, Z., Han, P., Bowers, M., Moore, J. A., Shpitser, I., Siddiqui, S. A., Quon, H., Taylor, R. H. & McNutt, T., Jan 1 2018, (Accepted/In press) In : Medical Physics.

Research output: Contribution to journalArticle

Real-time robotic airway measurement: An additional benefit of a novel steady-hand robotic platform

Razavi, C. R., Creighton, F., Wilkening, P. R., Peine, J., Taylor, R. H. & Akst, L. M., Jan 1 2018, (Accepted/In press) In : Laryngoscope.

Research output: Contribution to journalArticle

Regularizing face verification nets for pain intensity regression

Wang, F., Xiang, X., Liu, C., Tran, T. D., Reiter, A., Hager, G. D., Quon, H., Cheng, J. & Yuille, A. L., Feb 20 2018, 2017 IEEE International Conference on Image Processing, ICIP 2017 - Proceedings. IEEE Computer Society, p. 1087-1091 5 p. (Proceedings - International Conference on Image Processing, ICIP; vol. 2017-September).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

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

S3D: Stacking Segmental P3D for Action Quality Assessment

Xiang, X., Tian, Y., Reiter, A., Hager, G. & Tran, T. D., Aug 29 2018, 2018 IEEE International Conference on Image Processing, ICIP 2018 - Proceedings. IEEE Computer Society, p. 928-932 5 p. 8451364. (Proceedings - International Conference on Image Processing, ICIP).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Scalable Joint Models for Reliable Uncertainty-Aware Event Prediction

Soleimani, H., Hensman, J. & Saria, S., Aug 1 2018, In : IEEE Transactions on Pattern Analysis and Machine Intelligence. 40, 8, p. 1948-1963 16 p.

Research output: Contribution to journalArticle

Self super-resolution for magnetic resonance images using deep networks

Zhao, C., Carass, A., Dewey, B. E. & Prince, J. L., May 23 2018, 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018. IEEE Computer Society, Vol. 2018-April. p. 365-368 4 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Self-supervised learning for dense depth estimation in monocular endoscopy

Liu, X., Sinha, A., Unberath, M., Ishii, M., Hager, G., Taylor, R. H. & Reiter, A., Jan 1 2018, OR 2.0 Context-Aware Operating Theaters, Computer Assisted Robotic Endoscopy, Clinical Image-Based Procedures, and Skin Image Analysis - 1st International Workshop, OR 2.0 2018 5th International Workshop, CARE 2018, 7th International Workshop, CLIP 2018, 3rd International Workshop, ISIC 2018 Held in Conjunction with MICCAI 2018. Malpani, A., Zenati, M. A., Oyarzun Laura, C., Celebi, M. E., Sarikaya, D., Codella, N. C., Halpern, A., Erdt, M., Maier-Hein, L., Xiongbiao, L., Wesarg, S., Stoyanov, D., Taylor, Z., Drechsler, K., Dana, K., Martel, A., Shekhar, R., De Ribaupierre, S., Reichl, T., McLeod, J., González Ballester, M. A., Collins, T. & Linguraru, M. G. (eds.). Springer Verlag, p. 128-138 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11041 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Shortcomings of ventricle segmentation using deep convolutional networks

Shao, M., Han, S., Carass, A., Li, X., Blitz, A. M., Prince, J. L. & Ellingsen, L. M., Jan 1 2018, Understanding and Interpreting Machine Learning in Medical Image Computing Applications - First International Workshops MLCN 2018, DLF 2018, and iMIMIC 2018, Held in Conjunction with MICCAI 2018, Proceedings. Taylor, Z., Reyes, M., Cardoso, M. J., Silva, C. A., Stoyanov, D., Maier-Hein, L., Pereira, S., Kia, S. M., Oguz, I., Landman, B., Martel, A., Duchesnay, E., Lofstedt, T., Marquand, A. F. & Meier, R. (eds.). Springer Verlag, p. 79-86 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11038 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Simulation and Synthesis in Medical Imaging

Frangi, A. F., Tsaftaris, S. A. & Prince, J. L., Mar 2018, In : IEEE transactions on medical imaging. 37, 3, p. 673-679 7 p.

Research output: Contribution to journalArticle

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., Jul 17 2018, In : Biophysical journal. 115, 2, p. 300-312 13 p.

Research output: Contribution to journalArticle

State-of-the-Art Digital Imaging in Dentistry: Advanced Research of MRI, CT, CBCT, and Digital Intraoral Imaging

Honda, E., Prince, J. L. & Fontanella, V. R. C., Jan 1 2018, In : BioMed Research International. 2018, 9057120.

Research output: Contribution to journalEditorial

Strain map of the tongue in normal and ALS speech patterns from tagged and diffusion MRI

Xing, F., Prince, J. L., Stone, M., Reese, T. G., Atassi, N., Wedeen, V. J., El Fakhri, G. & Woo, J., Jan 1 2018, Medical Imaging 2018: Image Processing. Angelini, E. D., Angelini, E. D. & Landman, B. A. (eds.). SPIE, Vol. 10574. 1057411

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Technical note: An augmented reality system for total hip arthroplasty

Fotouhi, J., Alexander, C. P., Unberath, M., Taylor, G., Lee, S. C., Fuerst, B., Alex Johnson, M. D., Greg Osgood, M. D., Taylor, R. H., Khanuja, H., Navab, N. & Armand, M., Jan 1 2018, Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling. Fei, B. & Webster, R. J. (eds.). SPIE, 105760J. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10576).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

The Biophysics of 3D Cell Migration

Wu, P. H., Gilkes, D. & Wirtz, D., May 20 2018, In : Annual Review of Biophysics. 47, p. 549-567 19 p.

Research output: Contribution to journalReview article

The EphA2 receptor is activated through induction of distinct, ligand-dependent oligomeric structures

Singh, D. R., Kanvinde, P., King, C., Pasquale, E. B. & Hristova, K., Dec 1 2018, In : Communications biology. 1, 1, 15.

Research output: Contribution to journalArticle

Open Access

The grand challenges of science robotics

Yang, G. Z., Bellingham, J., Dupont, P. E., Fischer, P., Floridi, L., Full, R., Jacobstein, N., Kumar, V., McNutt, M., Merrifield, R., Nelson, B. J., Scassellati, B., Taddeo, M., Taylor, R. H., Veloso, M., Wang, Z. L. & Wood, R., Jan 31 2018, In : Science Robotics. 3, 14, eaar7650.

Research output: Contribution to journalReview article

The threshold of an excitable system serves as a control mechanism for noise filtering during chemotaxis

Bhattacharya, S. & Iglesias, P. A., Jul 1 2018, In : PLoS One. 13, 7, e0201283.

Research output: Contribution to journalArticle

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., Oct 15 2018, In : Annals of biomedical engineering. 46, 10, p. 1650-1662 13 p.

Research output: Contribution to journalArticle

Tumor cell density regulates matrix metalloproteinases for enhanced migration

Jayatilaka, H., Umanzor, F. G., Shah, V., Meirson, T., Russo, G., Starich, B., Tyle, P., Lee, J. S. H., Khatau, S., Gil-Henn, H. & Wirtz, D., Aug 24 2018, In : Oncotarget. 9, 66, p. 32556-32569 14 p.

Research output: Contribution to journalArticle

Unpaired brain mr-to-ct synthesis using a structure-constrained cyclegan

Yang, H., Sun, J., Carass, A., Zhao, C., Lee, J., Xu, Z. & Prince, J. L., Jan 1 2018, Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 4th International Workshop, DLMIA 2018 and 8th International Workshop, ML-CDS 2018 Held in Conjunction with MICCAI 2018. Maier-Hein, L., Syeda-Mahmood, T., Taylor, Z., Lu, Z., Stoyanov, D., Madabhushi, A., Tavares, J. M. R. S., Nascimento, J. C., Moradi, M., Martel, A., Papa, J. P., Conjeti, S., Belagiannis, V., Greenspan, H., Carneiro, G. & Bradley, A. (eds.). Springer Verlag, p. 174-182 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11045 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Unsupervised Learning for Surgical Motion by Learning to Predict the Future

DiPietro, R. & Hager, G., Jan 1 2018, Medical Image Computing and Computer Assisted Intervention – MICCAI 2018 - 21st International Conference, 2018, Proceedings. Frangi, A. F., Fichtinger, G., Schnabel, J. A., Alberola-López, C. & Davatzikos, C. (eds.). Springer Verlag, p. 281-288 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11073 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Using Big Data Analytics to Advance Precision Radiation Oncology

McNutt, T., 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. H., 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

Using smartphones and machine learning to quantify Parkinson disease severity the mobile Parkinson disease score

Zhan, A., Mohan, S., Tarolli, C., Schneider, R. B., Adams, J. L., Sharma, S., Elson, M. J., Spear, K. L., Glidden, A. M., Little, M. A., Terzis, A., Ray Dorsey, E. & Saria, S., Jul 2018, In : JAMA Neurology. 75, 7, p. 876-880 5 p.

Research output: Contribution to journalArticle

Vision-based calibration of dual RCM-based robot arms in human-robot collaborative minimally invasive surgery

Wang, Z., Liu, Z., Ma, Q., Cheng, A., Liu, Y. H., Kim, S., Deguet, A., Reiter, A., Kazanzides, P. & Taylor, R. H., Apr 1 2018, In : IEEE Robotics and Automation Letters. 3, 2, p. 672-679 8 p.

Research output: Contribution to journalArticle

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

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

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

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

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

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

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., 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

A Curved-Drilling Approach in Core Decompression of the Femoral Head Osteonecrosis Using a Continuum Manipulator

Alambeigi, F., Wang, Y., Sefati, S., Gao, C., Murphy, R. J., Iordachita, I., Taylor, R. H., Khanuja, H. & Armand, M., Jul 2017, In : IEEE Robotics and Automation Letters. 2, 3, p. 1480-1487 8 p., 7855629.

Research output: Contribution to journalArticle

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

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., Sep 1 2017, In : IEEE Transactions on Biomedical Engineering. 64, 9, p. 2025-2041 17 p., 7805258.

Research output: Contribution to journalArticle

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

A four-dimensional motion field atlas of the tongue from tagged and cine magnetic resonance imaging

Xing, F., Prince, J. L., Stone, M., Wedeen, V. J., El Fakhri, G. & Woo, J., 2017, Medical Imaging 2017: Image Processing. SPIE, Vol. 10133. 101331H

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A highly sensitive fiber Bragg Grating shape sensor for continuum manipulators with large deflections

Sefati, S., Pozin, M., Alambeigi, F., Iordachita, I., Taylor, R. H. & Armand, M., Dec 21 2017, IEEE SENSORS 2017 - Conference Proceedings. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-December. p. 1-3 3 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

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

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

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

Research output: Contribution to journalArticle

A supervoxel based random forest synthesis framework for bidirectional MR/CT synthesis

Zhao, C., Carass, A., Lee, J., Jog, A. & Prince, J. L., Jan 1 2017, Simulation and Synthesis in Medical Imaging - 2nd International Workshop, SASHIMI 2017, Held in Conjunction with MICCAI 2017, Proceedings. Springer Verlag, p. 33-40 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10557 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution