Whiting School of Engineering

Research Output

2019

Parallel deep neural networks for endoscopic oct image segmentation

Li, D., Wu, J., He, Y., Yao, X., Yuan, W., Chen, D., Park, H. C., Yu, S., Prince, J. L. & Li, X., Mar 1 2019, In : Biomedical Optics Express. 10, 3, p. 1126-1135 10 p., #349139.

Research output: Contribution to journalArticle

Phase Image Texture Analysis for Motion Detection in Diffusion MRI (PITA-MDD)

Elsaid, N. M. H., Prince, J. L., Roys, S., Gullapalli, R. P. & Zhuo, J., Oct 2019, In : Magnetic Resonance Imaging. 62, p. 228-241 14 p.

Research output: Contribution to journalArticle

Plasma Cells Are the Most Abundant Gluten Peptide MHC-expressing Cells in Inflamed Intestinal Tissues From Patients With Celiac Disease

Høydahl, L. S., Richter, L., Frick, R., Snir, O., Gunnarsen, K. S., Landsverk, O. J. B., Iversen, R., Jeliazkov, J. R., Gray, J. J., Bergseng, E., Foss, S., Qiao, S. W., Lundin, K. E. A., Jahnsen, J., Jahnsen, F. L., Sandlie, I., Sollid, L. M. & Løset, G. Å., Apr 2019, In : Gastroenterology. 156, 5, p. 1428-1439.e10

Research output: Contribution to journalArticle

Pose Estimation of Periacetabular Osteotomy Fragments with Intraoperative X-Ray Navigation

Grupp, R. B., Hegeman, R., Murphy, R., Alexander, C., Otake, Y., McArthur, B., Armand, M. & Taylor, R. H., Jan 1 2019, In : IEEE Transactions on Biomedical Engineering.

Research output: Contribution to journalArticle

Projection artifact suppression for inner retina in oct angiography

Liu, Y., Carass, A., Filippatou, A., He, Y., Solomon, S. D., Saidha, S., Calabresi, P. A. & Prince, J. L., Apr 2019, ISBI 2019 - 2019 IEEE International Symposium on Biomedical Imaging. IEEE Computer Society, p. 592-596 5 p. 8759466. (Proceedings - International Symposium on Biomedical Imaging; vol. 2019-April).

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

Quantifying Tongue Tip Shape in Apical and Laminal /s/: Contributions of Palate Shape

Stone, M., Gomez, A. D., Zhuo, J., Tchouaga, A. L. & Prince, J. L., Sep 20 2019, In : Journal of speech, language, and hearing research : JSLHR. 62, 9, p. 3149-3159 11 p.

Research output: Contribution to journalArticle

Quantitative vibratory sensation measurement is related to sensory cortical thickness in MS

Fritz, N. E., Eloyan, A., Glaister, J., Dewey, B. E., Al-Louzi, O., Costello, M. G., Chen, M., Prince, J. L., Calabresi, P. A. & Zackowski, K. M., Mar 2019, In : Annals of Clinical and Translational Neurology. 6, 3, p. 586-595 10 p.

Research output: Contribution to journalArticle

Open Access

Recapitulation of molecular regulators of nuclear motion during cell migration

Sneider, A., Hah, J., Wirtz, D. & Kim, D. H., Dec 1 2019, In : Cell adhesion & migration. 13, 1, p. 50-62 13 p.

Research output: Contribution to journalArticle

Open Access

Recovering Physiological Changes in Nasal Anatomy with Confidence Estimates

Sinha, A., Liu, X., Ishii, M., Hager, G. D. & Taylor, R. H., Jan 1 2019, Uncertainty for Safe Utilization of Machine Learning in Medical Imaging and Clinical Image-Based Procedures - 1st International Workshop, UNSURE 2019, and 8th International Workshop, CLIP 2019, Held in Conjunction with MICCAI 2019, Proceedings. Greenspan, H., Tanno, R., Erdt, M., Arbel, T., Baumgartner, C., Dalca, A., Sudre, C. H., Wells, W. M., Drechsler, K., Erdt, M., Linguraru, M. G., Shekhar, R., Oyarzun Laura, C., Wesarg, S. & González Ballester, M. Á. (eds.). Springer, p. 115-124 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11840 LNCS).

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

Segmenting and classifying activities in robot-assisted surgery with recurrent neural networks

DiPietro, R., Ahmidi, N., Malpani, A., Waldram, M., Lee, G. I., Lee, M. R., Vedula, S. S. & Hager, G., Jan 1 2019, In : International Journal of Computer Assisted Radiology and Surgery.

Research output: Contribution to journalArticle

Semantic stereo for incidental satellite images

Bosch, M., Foster, K., Christie, G., Wang, S., Hager, G. & Brown, M., Mar 4 2019, Proceedings - 2019 IEEE Winter Conference on Applications of Computer Vision, WACV 2019. Institute of Electrical and Electronics Engineers Inc., p. 1524-1532 9 p. 8659180. (Proceedings - 2019 IEEE Winter Conference on Applications of Computer Vision, WACV 2019).

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

Solid Stress in Brain Tumors

Gilkes, D. M. & Wirtz, D., May 2019, In : Trends in Cancer. 5, 5, p. 266-268 3 p.

Research output: Contribution to journalShort survey

Special issue on the International Symposium on Robotics Research, 2017

Amato, N. M., Hager, G., Thomas, S. & Torres-Torriti, M., Oct 1 2019, In : International Journal of Robotics Research. 38, 12-13, p. 1327-1328 2 p.

Research output: Contribution to journalArticle

Open Access

Speech Map: a statistical multimodal atlas of 4D tongue motion during speech from tagged and cine MR images

Woo, J., Xing, F., Stone, M., Green, J., Reese, T. G., Brady, T. J., Wedeen, V. J., Prince, J. L. & El Fakhri, G., Jul 4 2019, In : Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization. 7, 4, p. 361-373 13 p.

Research output: Contribution to journalArticle

Spinal cord and infratentorial lesions in radiologically isolated syndrome are associated with decreased retinal ganglion cell/inner plexiform layer thickness

Filippatou, A., Shoemaker, T., Esch, M., Qutab, M., Gonzalez-Caldito, N., Prince, J. L., Mowry, E. M., Calabresi, P. A., Saidha, S. & Sotirchos, E. S., Dec 1 2019, In : Multiple Sclerosis Journal. 25, 14, p. 1878-1887 10 p.

Research output: Contribution to journalArticle

Synthesizing attributes with unreal engine for fine-grained activity analysis

Kim, T. S., Peven, M., Qiu, W., Yuille, A. & Hager, G., Feb 8 2019, Proceedings - 2019 IEEE Winter Conference on Applications of Computer Vision Workshops, WACVW 2019. Institute of Electrical and Electronics Engineers Inc., p. 35-37 3 p. 8638315. (Proceedings - 2019 IEEE Winter Conference on Applications of Computer Vision Workshops, WACVW 2019).

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

Targeting mechanoresponsive proteins in pancreatic cancer: 4-hydroxyacetophenone blocks dissemination and invasion by activating MYH14

Surcel, A., Schiffhauer, E. S., Thomas, D. G., Zhu, Q., DiNapoli, K. T., Herbig, M., Otto, O., West-Foyle, H., Jacobi, A., Krater, M., Plak, K., Guck, J., Jaffee, E. M., Iglesias, P. A., Anders, R. A. & Robinson, D. N., Sep 15 2019, In : Cancer Research. 79, 18, p. 4665-4678 14 p.

Research output: Contribution to journalArticle

Ten robotics technologies of the year

Yang, G. Z., Full, R. J., Jacobstein, N., Fischer, P., Bellingham, J., Choset, H., Christensen, H., Dario, P., Nelson, B. J. & Taylor, R., Jan 16 2019, In : Science Robotics. 4, 26, p. 1-5 5 p., eaaw1826.

Research output: Contribution to journalReview article

The CoSTAR Block Stacking Dataset: Learning with Workspace Constraints

Hundt, A., Jain, V., Lin, C. H., Paxton, C. & Hager, G. D., Nov 2019, 2019 IEEE/RSJ International Conference on Intelligent Robots and Systems, IROS 2019. Institute of Electrical and Electronics Engineers Inc., p. 1797-1804 8 p. 8967784. (IEEE International Conference on Intelligent Robots and Systems).

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

The deformable most-likely-point paradigm

Sinha, A., Billings, S. D., Reiter, A., Liu, X., Ishii, M., Hager, G. & Taylor, R. H., Jul 1 2019, In : Medical Image Analysis. 55, p. 148-164 17 p.

Research output: Contribution to journalArticle

The Mechanism of Membrane Permeabilization by Peptides: Still an Enigma

Wimley, W. C. & Hristova, K., Jan 1 2019, (Accepted/In press) In : Australian Journal of Chemistry.

Research output: Contribution to journalReview article

The RTK Interactome: Overview and Perspective on RTK Heterointeractions

Paul, M. D. & Hristova, K., May 8 2019, In : Chemical Reviews. 119, 9, p. 5881-5921 41 p.

Research output: Contribution to journalReview article

The structure of the colorectal cancer-associated enzyme GalNAc-T12 reveals how nonconserved residues dictate its function

Fernandez, A. J., Daniel, E. J. P., Mahajan, S. P., Gray, J. J., Gerken, T. A., Tabak, L. A. & Samara, N. L., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 41, p. 20404-20410 7 p.

Research output: Contribution to journalArticle

Open Access

Toward computer vision systems that understand real-world assembly processes

Jones, J. D., Hager, G. D. & Khudanpur, S., Mar 4 2019, Proceedings - 2019 IEEE Winter Conference on Applications of Computer Vision, WACV 2019. Institute of Electrical and Electronics Engineers Inc., p. 426-434 9 p. 8659114. (Proceedings - 2019 IEEE Winter Conference on Applications of Computer Vision, WACV 2019).

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

Toward Improving Patient Safety and Surgeon Comfort in a Synergic Robot-Assisted Eye Surgery: A Comparative Study

Ebrahimi, A., Alambeigi, F., Zimmer-Galler, I. E., Gehlbach, P., Taylor, R. H. & Iordachita, I., Nov 2019, 2019 IEEE/RSJ International Conference on Intelligent Robots and Systems, IROS 2019. Institute of Electrical and Electronics Engineers Inc., p. 7075-7082 8 p. 8967806. (IEEE International Conference on Intelligent Robots and Systems).

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

Towards securing the sclera against patient involuntary head movement in robotic retinal surgery

Ebrahimi, A., Urias, M., Patel, N., He, C., Taylor, R. H., Gehlbach, P. & Iordachita, I., Oct 2019, 2019 28th IEEE International Conference on Robot and Human Interactive Communication, RO-MAN 2019. Institute of Electrical and Electronics Engineers Inc., 8956341. (2019 28th IEEE International Conference on Robot and Human Interactive Communication, RO-MAN 2019).

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

Toward the computational design of protein crystals with improved resolution

Jeliazkov, J. R., Robinson, A. C., García-Moreno, B. E., Bergera, J. M. & Gray, J. J., Nov 1 2019, In : Acta Crystallographica Section D: Structural Biology. 75, p. 1015-1027 13 p.

Research output: Contribution to journalArticle

Uncertainty-aware occupancy map prediction using generative networks for robot navigation

Katyal, K., Popek, K., Paxton, C., Burlina, P. & Hager, G. D., May 2019, 2019 International Conference on Robotics and Automation, ICRA 2019. Institute of Electrical and Electronics Engineers Inc., p. 5453-5459 7 p. 8793500. (Proceedings - IEEE International Conference on Robotics and Automation; vol. 2019-May).

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

Visual robot task planning

Paxton, C., Barnoy, Y., Katyal, K., Arora, R. & Hager, G., May 1 2019, 2019 International Conference on Robotics and Automation, ICRA 2019. Institute of Electrical and Electronics Engineers Inc., p. 8832-8838 7 p. 8793736. (Proceedings - IEEE International Conference on Robotics and Automation; vol. 2019-May).

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

Wave patterns organize cellular protrusions and control cortical dynamics

Miao, Y., Bhattacharya, S., Banerjee, T., Abubaker-Sharif, B., Long, Y., Inoue, T., Iglesias, P. A. & Devreotes, P. N., Mar 2019, In : Molecular systems biology. 15, 3, e8585.

Research output: Contribution to journalArticle

Open Access

YAP and TAZ regulate cell volume

Perez-Gonzalez, N. A., Rochman, N. D., Yao, K., Tao, J., Le, M. T. T., Flanary, S., Sablich, L., Toler, B., Crentsil, E., Takaesu, F., Lambrus, B., Huang, J., Fu, V., Chengappa, P., Jones, T. M., Holland, A. J., An, S., Wirtz, D., Petrie, R. J., Guan, K. L. & 1 others, Sun, S. X., Oct 7 2019, In : Journal of Cell Biology. 218, 10, p. 3472-3488 17 p.

Research output: Contribution to journalArticle

Open Access
2018

2D Modeling and Correction of Fan-Beam Scan Geometry in OCT

Chen, M., Gee, J. C., Prince, J. L. & Aguirre, G. K., Jan 1 2018, Computational Pathology and Ophthalmic Medical Image Analysis - First International Workshop, COMPAY 2018, and 5th International Workshop, OMIA 2018, Held in Conjunction with MICCAI 2018, Proceedings. Taylor, Z., Bogunovic, H., Snead, D., Garvin, M. K., Chen, X. J., Ciompi, F., Xu, Y., Maier-Hein, L., Veta, M., Trucco, E., Stoyanov, D., Rajpoot, N., van der Laak, J., Martel, A. & McKenna, S. (eds.). Springer Verlag, p. 328-335 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11039 LNCS).

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

3D Measurements of Acceleration-Induced Brain Deformation via Harmonic Phase Analysis and Finite-Element Models

Gomez, A., Knutsen, A., Xing, F., Chan, D., Lu, Y. C., Pham, D., Bayly, P. V. & Prince, J. L., Jan 1 2018, (Accepted/In press) In : IEEE Transactions on Biomedical Engineering.

Research output: Contribution to journalArticle

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

A computational framework for complementary situational awareness (CSA) in surgical assistant robots

Chalasani, P., Deguet, A., Kazanzides, P. & Taylor, R. H., Apr 2 2018, Proceedings - 2nd IEEE International Conference on Robotic Computing, IRC 2018. Institute of Electrical and Electronics Engineers Inc., Vol. 2018-January. p. 9-16 8 p.

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

A deep learning based anti-aliasing self super-resolution algorithm for MRI

Zhao, C., Carass, A., Dewey, B. E., Woo, J., Oh, J., Calabresi, P., Reich, D. S., Sati, P., Pham, D. L. & Prince, J. L., Jan 1 2018, Medical Image Computing and Computer Assisted Intervention – MICCAI 2018 - 21st International Conference, 2018, Proceedings. Schnabel, J. A., Davatzikos, C., Alberola-López, C., Fichtinger, G. & Frangi, A. F. (eds.). Springer Verlag, p. 100-108 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11070 LNCS).

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

Adversarial deep structured nets for mass segmentation from mammograms

Zhu, W., Xiang, X., Tran, T. D., Hager, G. D. & Xie, X., May 23 2018, 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018. IEEE Computer Society, p. 847-850 4 p. (Proceedings - International Symposium on Biomedical Imaging; vol. 2018-April).

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

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., Mar 4 2018, In : Current Eye Research. 43, 3, p. 415-423 9 p.

Research output: Contribution to journalArticle

Analyzing and exploiting NARX recurrent neural networks for long-term dependencies

DiPietro, R., Rupprecht, C., Navab, N. & Hager, G. D., Jan 1 2018.

Research output: Contribution to conferencePaper

An evolutionary computation approach for optimizing multilevel data to predict patient outcomes

Barnes, S., Saria, S. & Levin, S., Jan 1 2018, In : Journal of Healthcare Engineering. 2018, 7174803.

Research output: Contribution to journalArticle

A novel filtering approach for 3D harmonic phase analysis of tagged MRI

Wang, X., Stone, M. L., Prince, J. L. & Gomez, A., Jan 1 2018, Medical Imaging 2018: Image Processing. Angelini, E. D., Angelini, E. D. & Landman, B. A. (eds.). SPIE, Vol. 10574. 1057414

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

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

Atlas of acceleration-induced brain deformation from measurements in vivo

Gomez, A., Knutsen, A., Chan, D., Lu, Y. C., Pham, D. L., Bayly, P. & Prince, J. L., May 14 2018, Computational Biomechanics for Medicine: Measurements, Models, and Predictions. Springer International Publishing, p. 3-14 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Augmented reality-based feedback for technician-in-the-loop C-arm repositioning

Unberath, M., Fotouhi, J., Hajek, J., Maier, A., Osgood, G., Taylor, R. H., Armand, M. & Navab, N., Jan 1 2018, In : Healthcare Technology Letters. 5, 5, p. 143-147 5 p.

Research output: Contribution to journalArticle

A Unified Framework for Multi-view Multi-class Object Pose Estimation

Li, C., Bai, J. & Hager, G. D., Jan 1 2018, Computer Vision – ECCV 2018 - 15th European Conference, 2018, Proceedings. Weiss, Y., Ferrari, V., Sminchisescu, C. & Hebert, M. (eds.). Springer Verlag, p. 263-281 19 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11220 LNCS).

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

Automatic outlier detection using hidden Markov model for cerebellar lobule segmentation

Zuo, L., Carass, A., Han, S. & Prince, J. L., Jan 1 2018, Medical Imaging 2018: Biomedical Applications in Molecular, Structural, and Functional Imaging. Gimi, B. & Krol, A. (eds.). SPIE, Vol. 10578. 105780D

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

Better medicine through machine learning: What’s real, and what’s artificial?

Saria, S., Butte, A. & Sheikh, A., Jan 1 2018, In : PLoS medicine. 15, 12, e1002721.

Research output: Contribution to journalEditorial

Biomechanical guidance system for periacetabular osteotomy

Armand, M., Grupp, R., Murphy, R., Hegman, R., Armiger, R., Taylor, R. H., McArthur, B. & Lepisto, J., Jan 1 2018, Advances in Experimental Medicine and Biology. Springer New York LLC, p. 169-179 11 p. (Advances in Experimental Medicine and Biology; vol. 1093).

Research output: Chapter in Book/Report/Conference proceedingChapter