Whiting School of Engineering

Research Output

2019

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. & 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

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 2019, In : Critical care medicine. 47, 9, p. 1232-1234 3 p.

Research output: Contribution to journalArticle

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 : 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
Open Access

DeepHarmony: A deep learning approach to contrast harmonization across scanner changes

Dewey, B. E., Zhao, C., Reinhold, J. C., Carass, A., Fitzgerald, K. C., Sotirchos, E. S., Saidha, S., Oh, J., Pham, D. L., Calabresi, P. A., van Zijl, P. C. M. & Prince, J. L., Dec 2019, In : Magnetic Resonance Imaging. 64, p. 160-170 11 p.

Research output: Contribution to journalArticle

Deep-Learning-Based Semantic Labeling for 2D Mammography and Comparison of Complexity for Machine Learning Tasks

Yi, P. H., Lin, A., Wei, J., Yu, A. C., Sair, H. I., Hui, F. K., Hager, G. D. & Harvey, S. C., Aug 15 2019, In : Journal of Digital Imaging. 32, 4, p. 565-570 6 p.

Research output: Contribution to journalArticle

Open Access

Deep learning based topology guaranteed surface and MME segmentation of multiple sclerosis subjects from retinal OCT

He, Y., Carass, A., Liu, Y., Jedynak, B. M., Solomon, S. D., Saidha, S., Calabresi, P. A. & Prince, J. L., Oct 1 2019, In : Biomedical Optics Express. 10, 10, p. 5042-5058 17 p.

Research output: Contribution to journalArticle

Deep Learning Method for Automated Classification of Anteroposterior and Posteroanterior Chest Radiographs

Kim, T. K., Yi, P. H., Wei, J., Shin, J. W., Hager, G., Hui, F. K., Sair, H. I. & Lin, C. T., Dec 1 2019, In : Journal of Digital Imaging. 32, 6, p. 925-930 6 p.

Research output: Contribution to journalArticle

Differentiating post-cancer from healthy tongue muscle coordination patterns during speech using deep learning

Woo, J., Xing, F., Prince, J. L., Stone, M., Green, J. R., Goldsmith, T., Reese, T. G., Wedeen, V. J. & El Fakhri, G., May 1 2019, In : Journal of the Acoustical Society of America. 145, 5, p. EL423-EL429

Research output: Contribution to journalArticle

Open Access

Dissecting cellular mechanics: Implications for aging, cancer, and immunity

Harris, M. J., Wirtz, D. & Wu, P. H., Sep 2019, In : Seminars in Cell and Developmental Biology. 93, p. 16-25 10 p.

Research output: Contribution to journalReview article

Do no harm: a roadmap for responsible machine learning for health care

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., Jan 1 2019, (Accepted/In press) In : Nature medicine.

Research output: Contribution to journalArticle

Open Access

Dose/Volume histogram patterns in Salivary Gland subvolumes influence xerostomia injury and recovery

Han, P., Lakshminarayanan, P., Jiang, W., Shpitser, I., Hui, X., Lee, S. H., Cheng, Z., Guo, Y., Taylor, R. H., Siddiqui, S. A., Bowers, M., Sheikh, K., Kiess, A. P., Page, B., Lee, J., Quon, H. & McNutt, T., Dec 1 2019, In : Scientific reports. 9, 1, 3616.

Research output: Contribution to journalArticle

Open Access

Enabling machine learning in X-ray-based procedures via realistic simulation of image formation

Unberath, M., Zaech, J. N., Gao, C., Bier, B., Goldmann, F., Lee, S. C., Fotouhi, J., Taylor, R., Armand, M. & Navab, N., Sep 1 2019, In : International Journal of Computer Assisted Radiology and Surgery. 14, 9, p. 1517-1528 12 p.

Research output: Contribution to journalArticle

Enabling migration by moderation: YAP/TAZ are essential for persistent migration

Nair, P. R. & Wirtz, D., Apr 1 2019, In : Journal of Cell Biology. 218, 4, p. 1092-1093 2 p.

Research output: Contribution to journalShort survey

Open Access

Engineering immunity with quantitative tools

Jewell, C. M. & Gray, J. J., Aug 1 2019, In : Molecular Systems Design and Engineering. 4, 4, p. 677-678 2 p.

Research output: Contribution to journalEditorial

Engineering nanomolar peptide ligands that differentially modulate EphA2 receptor signaling

Gomez-Soler, M., Gehring, M. P., Lechtenberg, B. C., Zapata-Mercado, E., Hristova, K. & Pasquale, E. B., May 31 2019, In : Journal of Biological Chemistry. 294, 22, p. 8791-8805 15 p.

Research output: Contribution to journalArticle

Open Access
Open Access

Evaluating the impact of intensity normalization on MR image synthesis

Reinhold, J. C., Dewey, B. E., Carass, A. & 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, 109493H. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10949).

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

Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes

Roy Burman, S. S., Yovanno, R. A. & Gray, J. J., Jun 4 2019, In : Structure. 27, 6, p. 1041-1051.e8

Research output: Contribution to journalArticle

Open Access

Fully convolutional boundary regression for retina OCT segmentation

He, Y., Carass, A., Liu, Y., Jedynak, B. M., Solomon, S. D., Saidha, S., Calabresi, P. A. & Prince, J. L., 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. 120-128 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11764 LNCS).

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

Hierarchical Parcellation of the Cerebellum

Han, S., Carass, A. & Prince, J. L., 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. 484-491 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11766 LNCS).

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

How the mechanobiome drives cell behavior, viewed through the lens of control theory

Kothari, P., Johnson, C., Sandone, C., Iglesias, P. A. & Robinson, D., Sep 2 2019, In : Journal of cell science. 132, 17

Research output: Contribution to journalReview article

Open Access

Image-Guided Mastoidectomy with a Cooperatively Controlled ENT Microsurgery Robot

Razavi, C. R., Wilkening, P. R., Yin, R., Barber, S. R., Taylor, R. H., Carey, J. P. & Creighton, F., Jan 1 2019, (Accepted/In press) In : Otolaryngology - Head and Neck Surgery (United States).

Research output: Contribution to journalArticle

ISMORE: An iterative self super-resolution algorithm

Zhao, C., Son, S., Kim, Y. & Prince, J. L., Jan 1 2019, Simulation and Synthesis in Medical Imaging - 4th International Workshop, SASHIMI 2019, Held in Conjunction with MICCAI 2019, Proceedings. Burgos, N., Gooya, A. & Svoboda, D. (eds.). Springer, p. 130-139 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11827 LNCS).

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

Large-scale parcellation of the ventricular system using convolutional neural networks

Atlason, H. E., Shao, M., Robertsson, V., Sigurdsson, S., Gudnason, V., Prince, J. L. & Ellingsen, L. M., Jan 1 2019, Medical Imaging 2019: Biomedical Applications in Molecular, Structural, and Functional Imaging. Gimi, B. & Krol, A. (eds.). SPIE, 109530N. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10953).

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

Layer boundary evolution method for macular OCT layer segmentation

Liu, Y., Carass, A., He, Y., Antony, B. J., Filippatou, A., Saidha, S., Solomon, S., Calabresi, P. & Prince, J. L., Mar 1 2019, In : Biomedical Optics Express. 10, 3, p. 1064-1080 17 p., 349227.

Research output: Contribution to journalArticle

Learning models from data with measurement error: Tackling underreporting

Adams, R., Ji, Y., Wang, X. & Saria, S., Jan 1 2019, 36th International Conference on Machine Learning, ICML 2019. International Machine Learning Society (IMLS), p. 95-104 10 p. (36th International Conference on Machine Learning, ICML 2019; vol. 2019-June).

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

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 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. 11-19 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

Learning to Detect Collisions for Continuum Manipulators Without a Prior Model

Sefati, S., Sefati, S., Iordachita, I., Taylor, R. H. & Armand, M., 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. 182-190 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

Machine Learning Methods Uncover Radiomorphologic Dose Patterns in Salivary Glands that Predict Xerostomia in Patients with Head and Neck Cancer

Jiang, W., Lakshminarayanan, P., Hui, X., Han, P., Cheng, Z., Bowers, M., Shpitser, I., Siddiqui, S., Taylor, R. H., Quon, H. & McNutt, T., Jan 1 2019, (Accepted/In press) In : Advances in Radiation Oncology.

Research output: Contribution to journalArticle

Mechanism of Action of Peptides That Cause the pH-Triggered Macromolecular Poration of Lipid Bilayers

Kim, S. Y., Pittman, A. E., Zapata-Mercado, E., King, G. M., Wimley, W. C. & Hristova, K. A., Apr 24 2019, In : Journal of the American Chemical Society. 141, 16, p. 6706-6718 13 p.

Research output: Contribution to journalArticle

Mosquito pick-and-place: Automating a key step in PfSPZ-based Malaria vaccine production

Phalen, H., Vagdargi, P., Pozin, M., Chakravarty, S., Chirikjian, G. S., Iordachita, I. & Taylor, R. H., Aug 2019, 2019 IEEE 15th International Conference on Automation Science and Engineering, CASE 2019. IEEE Computer Society, p. 12-17 6 p. 8842860. (IEEE International Conference on Automation Science and Engineering; vol. 2019-August).

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

Mosquito Staging Apparatus for Producing PfSPZ Malaria Vaccines

Xu, M., Lyu, S., Xu, Y., Kocabalkanli, C., Chirikjian, B. K., Chirikjian, J. S., Davis, J., Kim, J. S., Iordachita, I., Taylor, R. H. & Chirikjian, G. S., Aug 2019, 2019 IEEE 15th International Conference on Automation Science and Engineering, CASE 2019. IEEE Computer Society, p. 443-449 7 p. 8843147. (IEEE International Conference on Automation Science and Engineering; vol. 2019-August).

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

Multi-mosquito object detection and 2d pose estimation for automation of PfSPZ malaria vaccine production

Wu, H., Mu, J., Da, T., Xu, M., Taylor, R. H., Iordachita, I. & Chirikjian, G. S., Aug 2019, 2019 IEEE 15th International Conference on Automation Science and Engineering, CASE 2019. IEEE Computer Society, p. 411-417 7 p. 8842953. (IEEE International Conference on Automation Science and Engineering; vol. 2019-August).

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

Myosin IIB assembly state determines its mechanosensitive dynamics

Schiffhauer, E. S., Ren, Y., Iglesias, V. A., Kothari, P., Iglesias, P. A. & Robinson, D. N., Mar 1 2019, In : Journal of Cell Biology. 218, 3, p. 895-908 14 p.

Research output: Contribution to journalArticle

Open Access

Non-H3 CDR template selection in antibody modeling through machine learning

Long, X., Jeliazkov, J. R. & Gray, J. J., Jan 1 2019, In : PeerJ. 2019, 1, e6179.

Research output: Contribution to journalArticle

Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37–45

Roy Burman, S. S., Nance, M. L., Jeliazkov, J. R., Labonte, J. W., Lubin, J. H., Biswas, N. & Gray, J. J., Jan 1 2019, (Accepted/In press) In : Proteins: Structure, Function and Bioinformatics.

Research output: Contribution to journalArticle

Objective assessment of intraoperative technical skill in capsulorhexis using videos of cataract surgery

Kim, T. S., O’Brien, M., Zafar, S., Hager, G. D., Sikder, S. & Vedula, S. S., Jun 1 2019, In : International Journal of Computer Assisted Radiology and Surgery. 14, 6, p. 1097-1105 9 p.

Research output: Contribution to journalArticle