Whiting School of Engineering

Research Output

2020

Abstract: Learning to avoid poor images: towards task-aware c-arm cone-beam ct trajectories

Zaech, J. N., Gao, C., Bier, B., Taylor, R., Maier, A., Navab, N. & Unberath, M., Jan 1 2020, Bildverarbeitung für die Medizin 2020 Algorithmen - Systeme - Anwendungen. Proceedings des Workshops. Tolxdorff, T., Deserno, T. M., Handels, H., Maier, A., Maier-Hein, K. H. & Palm, C. (eds.). Springer, 1 p. (Informatik aktuell).

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

Open Access

Analysis of fiber strain in the human tongue during speech

Gomez, A. D., Stone, M. L., Woo, J., Xing, F. & Prince, J. L., Jan 1 2020, (Accepted/In press) In : Computer Methods in Biomechanics and Biomedical Engineering.

Research output: Contribution to journalArticle

An Individualized, Data-Driven Digital Approach for Precision Behavior Change

Wongvibulsin, S., Martin, S. S., Saria, S., Zeger, S. L. & Murphy, S. A., May 1 2020, In : American Journal of Lifestyle Medicine. 14, 3, p. 289-293 5 p.

Research output: Contribution to journalReview article

Automated detection & classification of knee arthroplasty using deep learning

Yi, P. H., Wei, J., Kim, T. K., Sair, H. I., Hui, F. K., Hager, G. D., Fritz, J. & Oni, J. K., Mar 2020, In : Knee. 27, 2, p. 535-542 8 p.

Research output: Contribution to journalArticle

Automatic annotation of hip anatomy in fluoroscopy for robust and efficient 2D/3D registration

Grupp, R. B., Unberath, M., Gao, C., Hegeman, R. A., Murphy, R. J., Alexander, C. P., Otake, Y., McArthur, B. A., Armand, M. & Taylor, R. H., Jan 1 2020, (Accepted/In press) In : International Journal of Computer Assisted Radiology and Surgery.

Research output: Contribution to journalArticle

Better together: Elements of successful scientific software development in a distributed collaborative community

RosettaCommons Consortium, May 1 2020, In : PLoS computational biology. 16, 5, p. e1007507

Research output: Contribution to journalReview article

Open Access

Combating COVID-19-The role of robotics in managing public health and infectious diseases

Yang, G. Z., Nelson, B. J., Murphy, R. R., Choset, H., Christensen, H., Collins, S. H., Dario, P., Goldberg, K., Ikuta, K., Jacobstein, N., Kragic, D., Taylor, R. H. & McNutt, M., Mar 25 2020, In : Science Robotics. 5, 40, eabb5589.

Research output: Contribution to journalEditorial

Open Access

Comparison of Automated Activity Recognition to Provider Observations of Patient Mobility in the ICU

Rawat, N., Rao, V., Peven, M., Shrock, C., Reiter, A., Saria, S. & Ali, H., Jan 1 2020, (Accepted/In press) In : Critical care medicine. p. 1232-1234 3 p.

Research output: Contribution to journalArticle

Dynamic organelle distribution initiates actin-based spindle migration in mouse oocytes

Duan, X., Li, Y., Yi, K., Guo, F., Wang, H. Y., Wu, P. H., Yang, J., Mair, D. B., Morales, E. A., Kalab, P., Wirtz, D., Sun, S. X. & Li, R., Dec 1 2020, In : Nature communications. 11, 1, 277.

Research output: Contribution to journalArticle

Open Access

From development to deployment: dataset shift, causality, and shift-stable models in health AI

Subbaswamy, A. & Saria, S., Apr 1 2020, In : Biostatistics (Oxford, England). 21, 2, p. 345-352 8 p.

Research output: Contribution to journalArticle

Multimodal training by demonstration for robot-assisted surgery

Abdelaal, A. E., Hager, G. D. & Salcudean, S. E., Mar 23 2020, HRI 2020 - Companion of the 2020 ACM/IEEE International Conference on Human-Robot Interaction. IEEE Computer Society, p. 549-551 3 p. (ACM/IEEE International Conference on Human-Robot Interaction).

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

Open Access

Particle tracking microrheology of cancer cells in living subjects

Wu, P. H., Gambhir, S. S., Hale, C. M., Chen, W. C., Wirtz, D. & Smith, B. R., Jan 1 2020, (Accepted/In press) In : Materials Today.

Research output: Contribution to journalArticle

Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane

Alford, R. F., Fleming, P. J., Fleming, K. G. & Gray, J. J., Apr 21 2020, In : Biophysical journal. 118, 8, p. 2042-2055 14 p.

Research output: Contribution to journalArticle

Revisiting a controversy: The effect of EGF on EGFR dimer stability

Singh, D. R., King, C., Salotto, M. & Hristova, K., Jan 1 2020, In : Biochimica et Biophysica Acta - Biomembranes. 1862, 1, 183015.

Research output: Contribution to journalArticle

SCADE: Simultaneous Sensor Calibration and Deformation Estimation of FBG-Equipped Unmodeled Continuum Manipulators

Alambeigi, F., Aghajani Pedram, S., Speyer, J. L., Rosen, J., Iordachita, I., Taylor, R. H. & Armand, M., Feb 2020, In : IEEE Transactions on Robotics. 36, 1, p. 222-239 18 p., 8886726.

Research output: Contribution to journalArticle

Single-cell morphology encodes metastatic potential

Wu, P. H., Gilkes, D. M., Phillip, J. M., Narkar, A., Cheng, T. W. T., Marchand, J., Lee, M. H., Li, R. & Wirtz, D., Jan 22 2020, In : Science Advances. 6, 4, eaaw6938.

Research output: Contribution to journalArticle

Open Access

Spatial Radiation Dose Influence on Xerostomia Recovery and Its Comparison to Acute Incidence in Patients With Head and Neck Cancer

Guo, Y., Jiang, W., Lakshminarayanan, P., Han, P., Cheng, Z., Bowers, M., Hui, X., Shpitser, I., Siddiqui, S., Taylor, R. H., Quon, H. & McNutt, T., Mar 1 2020, In : Advances in Radiation Oncology. 5, 2, p. 221-230 10 p.

Research output: Contribution to journalArticle

Open Access

Supramolecular Design of Unsymmetric Reverse Bolaamphiphiles for Cell-Sensitive Hydrogel Degradation and Drug Release

Chakroun, R. W., Sneider, A., Anderson, C. F., Wang, F., Wu, P. H., Wirtz, D. & Cui, H., Jan 1 2020, (Accepted/In press) In : Angewandte Chemie - International Edition.

Research output: Contribution to journalArticle

Surgical data science: The new knowledge domain

Vedula, S. S. & Hager, G. D., Sep 1 2020, In : Innovative Surgical Sciences. 2, 3, p. 109-121 13 p.

Research output: Contribution to journalReview article

Open Access

Three-dimensional visualization of cleared human pancreas cancer reveals that sustained epithelial-to-mesenchymal transition is not required for venous invasion

Hong, S. M., Jung, D. J., Kiemen, A., Gaida, M. M., Yoshizawa, T., Braxton, A. M., Noë, M., Lionheart, G., Oshima, K., Thompson, E. D., Burkhart, R., Wu, P. H., Wirtz, D., Hruban, R. H. & Wood, L. D., Apr 1 2020, In : Modern Pathology. 33, 4, p. 639-647 9 p.

Research output: Contribution to journalArticle

TrkA overexpression in non-tumorigenic human breast cell lines confers oncogenic and metastatic properties

Kyker-Snowman, K., Hughes, R. M., Yankaskas, C. L., Cravero, K., Karthikeyan, S., Button, B., Waters, I., Rosen, D. M., Dennison, L., Hunter, N., Donaldson, J., Christenson, E. S., Konstantopoulos, K., Hurley, P. J., Croessmann, S. & Park, B. H., Feb 1 2020, In : Breast Cancer Research and Treatment. 179, 3, p. 631-642 12 p.

Research output: Contribution to journalArticle

2019

2019 data fusion contest

Le Saux, B., Yokoya, N., Hansch, R., Brown, M. & Hager, G., Mar 1 2019, IEEE Geoscience and Remote Sensing Magazine, 7, 1, p. 103-105 3 p.

Research output: Contribution to specialist publicationArticle

A 3D Computational Head Model Under Dynamic Head Rotation and Head Extension Validated Using Live Human Brain Data, Including the Falx and the Tentorium

Lu, Y. C., Daphalapurkar, N. P., Knutsen, A. K., Glaister, J., Pham, D. L., Butman, J. A., Prince, J. L., Bayly, P. V. & Ramesh, K. T., Jan 1 2019, In : Annals of biomedical engineering.

Research output: Contribution to journalArticle

Active learning for decision-making from imbalanced observational data

Sundin, I., Schulam, P., Siivola, E., Vehtari, A., Saria, S. & Kaski, S., Jan 1 2019, 36th International Conference on Machine Learning, ICML 2019. International Machine Learning Society (IMLS), p. 10578-10587 10 p. (36th International Conference on Machine Learning, ICML 2019; vol. 2019-June).

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

A direct podocalyxin–dynamin-2 interaction regulates cytoskeletal dynamics to promote migration and metastasis in pancreatic cancer cells

Wong, B. S., Shea, D. J., Mistriotis, P., Tuntithavornwat, S., Law, R. A., Bieber, J. M., Zheng, L. & Konstantopoulos, K., Jun 1 2019, In : Cancer Research. 79, 11, p. 2878-2891 14 p.

Research output: Contribution to journalArticle

A humanized yeast system to analyze cleavage of prelamin A by ZMPSTE24

Spear, E., Alford, R. F., Babatz, T. D., Wood, K. M., Mossberg, O. W., Odinammadu, K., Shilagardi, K., Gray, J. J. & Michaelis, S. D., Jan 1 2019, (Accepted/In press) In : Methods.

Research output: Contribution to journalArticle

Alterations in the retinal vasculature occur in multiple sclerosis and exhibit novel correlations with disability and visual function measures

Murphy, O. C., Kwakyi, O., Iftikhar, M., Zafar, S., Lambe, J., Pellegrini, N., Sotirchos, E. S., Gonzalez-Caldito, N., Ogbuokiri, E., Filippatou, A., Risher, H., Cowley, N., Feldman, S., Fioravante, N., Frohman, E. M., Frohman, T. C., Balcer, L. J., Prince, J. L., Channa, R., Calabresi, P. & 1 others, Saidha, S., Jan 1 2019, In : Multiple Sclerosis Journal.

Research output: Contribution to journalArticle

A microfluidic assay for the quantification of the metastatic propensity of breast cancer specimens

Yankaskas, C. L., Thompson, K. N., Paul, C. D., Vitolo, M. I., Mistriotis, P., Mahendra, A., Bajpai, V. K., Shea, D. J., Manto, K. M., Chai, A. C., Varadarajan, N., Kontrogianni-Konstantopoulos, A., Martin, S. S. & Konstantopoulos, K., Jan 1 2019, In : Nature biomedical engineering.

Research output: Contribution to journalArticle

A Novel Semi-Autonomous Control Framework for Retina Confocal Endomicroscopy Scanning

Li, Z., Yang, G. Z., Taylor, R. H., Shahbazi, M., Patel, N., Sullivan, E. O., Zhang, H., Vyas, K., Chalasani, P., Gehlbach, P. L. & Iordachita, I., Nov 2019, 2019 IEEE/RSJ International Conference on Intelligent Robots and Systems, IROS 2019. Institute of Electrical and Electronics Engineers Inc., p. 7083-7090 8 p. 8967751. (IEEE International Conference on Intelligent Robots and Systems).

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

Applications of a deep learning method for anti-aliasing and super-resolution in MRI

Zhao, C., Shao, M., Carass, A., Li, H., Dewey, B. E., Ellingsen, L. M., Woo, J., Guttman, M. A., Blitz, A. M., Stone, M., Calabresi, P. A., Halperin, H. & Prince, J. L., Jan 1 2019, In : Magnetic Resonance Imaging.

Research output: Contribution to journalArticle

Applied Force during Piston Prosthesis Placement in a 3D-Printed Model: Freehand vs Robot-Assisted Techniques

Razavi, C. R., Wilkening, P. R., Yin, R., Lamaison, N., Taylor, R. H., Carey, J. P. & Creighton, F., Feb 1 2019, In : Otolaryngology - Head and Neck Surgery (United States). 160, 2, p. 320-325 6 p.

Research output: Contribution to journalArticle

Aquaporin-4 IgG seropositivity is associated with worse visual outcomes after optic neuritis than MOG-IgG seropositivity and multiple sclerosis, independent of macular ganglion cell layer thinning

Sotirchos, E. S., Filippatou, A., Fitzgerald, K. C., Salama, S., Pardo, S., Wang, J., Ogbuokiri, E., Cowley, N. J., Pellegrini, N., Murphy, O. C., Mealy, M. A., Prince, J. L., Levy, M., Calabresi, P. A. & Saidha, S., Jan 1 2019, (Accepted/In press) In : Multiple Sclerosis Journal.

Research output: Contribution to journalArticle

Artificial intelligence to diagnose ischemic stroke and identify large vessel occlusions: A systematic review

Murray, N. M., Unberath, M., Hager, G. & Hui, F., Jan 1 2019, (Accepted/In press) In : Journal of neurointerventional surgery.

Research output: Contribution to journalReview article

A sparse non-negative matrix factorization framework for identifying functional units of tongue behavior from MRI

Woo, J., Prince, J. L., Stone, M., Xing, F., Gomez, A. D., Green, J. R., Hartnick, C. J., Brady, T. J., Reese, T. G., Wedeen, V. J. & El Fakhri, G., Mar 2019, In : IEEE transactions on medical imaging. 38, 3, p. 730-740 11 p., 8467354.

Research output: Contribution to journalArticle

Assessment of Automated Identification of Phases in Videos of Cataract Surgery Using Machine Learning and Deep Learning Techniques

Yu, F., Silva Croso, G., Kim, T. S., Song, Z., Parker, F., Hager, G., Reiter, A., Vedula, S. S., Ali, H. & Sikder, S., Apr 5 2019, In : JAMA network open. 2, 4, p. e191860

Research output: Contribution to journalArticle

Association between Surgical Trainee Daytime Sleepiness and Intraoperative Technical Skill When Performing Septoplasty

Tseng, Y. W., Vedula, S. S., Malpani, A., Ahmidi, N., Boahene, K. D. O., Papel, I. D., Kontis, T. C., Maxwell, J., Wanamaker, J. R., Byrne, P. J., Malekzadeh, S., Hager, G. D., Ishii, L. E. & Ishii, M., Mar 1 2019, In : JAMA Facial Plastic Surgery. 21, 2, p. 104-109 6 p.

Research output: Contribution to journalArticle

Atlas-based tongue muscle correlation analysis from tagged and high- resolution magnetic resonance imaging

Xing, F., Stone, M., Goldsmith, T., Prince, J. L., Fakhri, G. E. & Woo, J., Jul 2019, In : Journal of Speech, Language, and Hearing Research. 62, 7, p. 2258-2269 12 p.

Research output: Contribution to journalArticle

Author Correction: Do no harm: a roadmap for responsible machine learning for health care (Nature Medicine, (2019), 25, 9, (1337-1340), 10.1038/s41591-019-0548-6)

Wiens, J., Saria, S., Sendak, M., Ghassemi, M., Liu, V. X., Doshi-Velez, F., Jung, K., Heller, K., Kale, D., Saeed, M., Ossorio, P. N., Thadaney-Israni, S. & Goldenberg, A., Oct 1 2019, In : Nature medicine. 25, 10, 1 p.

Research output: Contribution to journalComment/debate

Open Access

Automated semantic labeling of pediatric musculoskeletal radiographs using deep learning

Yi, P. H., Kim, T. K., Wei, J., Shin, J., Hui, F., Sair, H., Hager, G. & Fritz, J., Jan 1 2019, In : Pediatric radiology.

Research output: Contribution to journalArticle

Automated Surgical Activity Recognition with One Labeled Sequence

DiPietro, R. & Hager, G. D., Jan 1 2019, Medical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Proceedings. Shen, D., Yap, P-T., Liu, T., Peters, T. M., Khan, A., Staib, L. H., Essert, C. & Zhou, S. (eds.). Springer, p. 458-466 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11768 LNCS).

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

Automatic quality control using hierarchical shape analysis for cerebellum parcellation

Zuo, L., Han, S., Carass, A., Ying, S. H., Onyike, C. U. & Prince, J. L., Jan 1 2019, Medical Imaging 2019: Image Processing. Angelini, E. D., Angelini, E. D., Angelini, E. D. & Landman, B. A. (eds.). SPIE, 109490J. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10949).

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

Brain ventricle parcellation using a deep neural network: Application to patients with ventriculomegaly

Shao, M., Han, S., Carass, A., Li, X., Blitz, A. M., Shin, J., Prince, J. L. & Ellingsen, L. M., Jan 1 2019, In : NeuroImage: Clinical. 23, 101871.

Research output: Contribution to journalArticle

Open Access

Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation

Santiago-Frangos, A., Fröhlich, K. S., Jeliazkov, J. R., Małecka, E. M., Marino, G., Gray, J. J., Luisi, B. F., Woodson, S. A. & Hardwick, S. W., May 28 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 166, 22, p. 10978-10987 10 p.

Research output: Contribution to journalArticle

Open Access

Cell sensing and decision-making in confinement: The role of TRPM7 in a tug of war between hydraulic pressure and cross-sectional area

Zhao, R., Afthinos, A., Zhu, T., Mistriotis, P., Li, Y., Serra, S. A., Zhang, Y., Yankaskas, C. L., He, S., Valverde, M. A., Sun, S. X. & Konstantopoulos, K., Jul 24 2019, In : Science Advances. 5, 7, eaaw7243.

Research output: Contribution to journalArticle

Open Access

Cerebellum parcellation with convolutional neural networks

Han, S., He, Y., Carass, A., Ying, S. H. & Prince, J. L., Jan 1 2019, Medical Imaging 2019: Image Processing. Angelini, E. D., Angelini, E. D., Angelini, E. D. & Landman, B. A. (eds.). SPIE, 109490K. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10949).

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

Computer-based engineering of thermostabilized antibody fragments

Lee, J., Der, B. S., Karamitros, C. S., Li, W., Marshall, N. M., Lungu, O. I., Miklos, A. E., Xu, J., Kang, T. H., Lee, C. H., Tan, B., Hughes, R. A., Jung, S. T., Ippolito, G. C., Gray, J. J., Zhang, Y., Kuhlman, B., Georgiou, G. & Ellington, A. D., Jan 1 2019, (Accepted/In press) In : AIChE Journal. e16864.

Research output: Contribution to journalArticle

Confinement hinders motility by inducing RhoA-mediated nuclear influx, volume expansion, and blebbing

Mistriotis, P., Wisniewski, E. O., Bera, K., Keys, J., Li, Y., Tuntithavornwat, S., Law, R. A., Perez-Gonzalez, N. A., Erdogmus, E., Zhang, Y., Zhao, R., Sun, S. X., Kalab, P., Lammerding, J. & Konstantopoulos, K., Dec 2 2019, In : The Journal of cell biology. 218, 12, p. 4093-4111 19 p.

Research output: Contribution to journalArticle

Open Access

Control of Chemotaxis Through Absolute Concentration Robustness

Bhattacharya, S., Biswas, D., Enciso, G. A. & Iglesias, P. A., Jan 18 2019, 2018 IEEE Conference on Decision and Control, CDC 2018. Institute of Electrical and Electronics Engineers Inc., p. 4360-4365 6 p. 8619195. (Proceedings of the IEEE Conference on Decision and Control; vol. 2018-December).

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

Control theory in biology and medicine: Introduction to the special issue

Thomas, P. J., Olufsen, M., Sepulchre, R., Iglesias, P. A., Ijspeert, A. & Srinivasan, M., Apr 1 2019, In : Biological Cybernetics. 113, 1-2

Research output: Contribution to journalEditorial

Open Access