Whiting School of Engineering

Research Output

2018

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

Brain and retinal atrophy in African-Americans versus Caucasian-Americans with multiple sclerosis: A longitudinal study

Caldito, N. G., Saidha, S., Sotirchos, E. S., Dewey, B. E., Cowley, N. J., Glaister, J., Fitzgerald, K., Al-Louzi, O., Nguyen, J., Rothman, A., Ogbuokiri, E., Fioravante, N., Feldman, S., Kwakyi, O., Risher, H., Kimbrough, D., Frohman, T. C., Frohman, E., Balcer, L., Crainiceanu, C. M. & 7 others, Van Zijl, P. C., Mowry, E. M., Reich, D. S., Oh, J., Pham, D. L., Prince, J. L. & Calabresi, P., Nov 1 2018, In : Brain. 141, 11, p. 3115-3129 15 p.

Research output: Contribution to journalArticle

Cell tension and mechanical regulation of cell volume

Gonzalez, N. P., Tao, J., Rochman, N. D., Vig, D., Chiu, E., Wirtz, D. & Sun, S. X., Oct 15 2018, In : Molecular Biology of the Cell. 29, 21, p. 2591-2600 10 p.

Research output: Contribution to journalArticle

Chiral switching in biomineral suprastructures induced by homochiral l-amino acid

Jiang, W., Pacella, M. S., Vali, H., Gray, J. J. & McKee, M. D., Aug 1 2018, In : Science advances. 4, 8, eaas9819.

Research output: Contribution to journalArticle

Comparing fully automated state-of-the-art cerebellum parcellation from magnetic resonance images

Carass, A., Cuzzocreo, J. L., Han, S., Hernandez-Castillo, C. R., Rasser, P. E., Ganz, M., Beliveau, V., Dolz, J., Ben Ayed, I., Desrosiers, C., Thyreau, B., Romero, J. E., Coupé, P., Manjón, J. V., Fonov, V. S., Collins, D. L., Ying, S. H., Onyike, C. U., Crocetti, D., Landman, B. A. & 3 others, Mostofsky, S. H., Thompson, P. M. & Prince, J. L., Dec 2018, In : NeuroImage. 183, p. 150-172 23 p.

Research output: Contribution to journalArticle

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: Contribution to journalArticle

Controlling excitable wave behaviors through the tuning of three parameters

Bhattacharya, S. & Iglesias, P. A., Jan 1 2018, (Accepted/In press) In : Biological Cybernetics.

Research output: Contribution to journalArticle

Counterfactual normalization: Proactively addressing dataset shift using causal mechanisms

Subbaswamy, A. & Saria, S., Jan 1 2018, 34th Conference on Uncertainty in Artificial Intelligence 2018, UAI 2018. Silva, R., Globerson, A. & Globerson, A. (eds.). Association For Uncertainty in Artificial Intelligence (AUAI), Vol. 2. p. 947-957 11 p.

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

Cross-modality image synthesis from unpaired data using cyclegan: Effects of gradient consistency loss and training data size

Hiasa, Y., Otake, Y., Takao, M., Matsuoka, T., Takashima, K., Carass, A., Prince, J. L., Sugano, N. & Sato, Y., Jan 1 2018, Simulation and Synthesis in Medical Imaging - Third International Workshop, SASHIMI 2018, Held in Conjunction with MICCAI 2018, Proceedings. Goksel, O., Oguz, I., Gooya, A. & Burgos, N. (eds.). Springer Verlag, p. 31-41 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11037 LNCS).

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

Crowdsourcing annotation of surgical instruments in videos of cataract surgery

Kim, T. S., Malpani, A., Reiter, A., Hager, G., Sikder, S. & Swaroop Vedula, S., Jan 1 2018, Intravascular Imaging and Computer Assisted Stenting and Large-Scale Annotation of Biomedical Data and Expert Label Synthesis - 7th Joint International Workshop, CVII-STENT 2018 and Third International Workshop, LABELS 2018 Held in Conjunction with MICCAI 2018. Lee, S-L., Trucco, E., Maier-Hein, L., Moriconi, S., Albarqouni, S., Jannin, P., Balocco, S., Zahnd, G., Mateus, D., Taylor, Z., Demirci, S., Stoyanov, D., Sznitman, R., Martel, A., Cheplygina, V., Granger, E. & Duong, L. (eds.). Springer Verlag, p. 121-130 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11043 LNCS).

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

Deep harmonization of inconsistent mr data for consistent volume segmentation

Dewey, B. E., Zhao, C., Carass, A., Oh, J., Calabresi, P., Van Zijl, P. C. & Prince, J. L., Jan 1 2018, Simulation and Synthesis in Medical Imaging - Third International Workshop, SASHIMI 2018, Held in Conjunction with MICCAI 2018, Proceedings. Goksel, O., Oguz, I., Gooya, A. & Burgos, N. (eds.). Springer Verlag, p. 20-30 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11037 LNCS).

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

Deep Supervision with Intermediate Concepts

Li, C., Zia, M. Z., Tran, Q. H., Yu, X., Hager, G. & Chandraker, M., Aug 10 2018, (Accepted/In press) In : IEEE Transactions on Pattern Analysis and Machine Intelligence.

Research output: Contribution to journalArticle

Deformable model reconstruction of the subarachnoid space

Glaister, J., Shao, M., Li, X., Carass, A., Roy, S., Blitz, A. M., Prince, J. L. & Ellingsen, L. M., Jan 1 2018, Medical Imaging 2018: Image Processing. SPIE, Vol. 10574. 1057431

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

Dice overlap measures for objects of unknown number: Application to lesion segmentation

Oguz, I., Carass, A., Pham, D. L., Roy, S., Subbana, N., Calabresi, P., Yushkevich, P. A., Shinohara, R. T. & Prince, J. L., Jan 1 2018, Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries - 3rd International Workshop, BrainLes 2017, Held in Conjunction with MICCAI 2017, Revised Selected Papers. Springer Verlag, p. 3-14 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10670 LNCS).

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

Dictionary-based fiber orientation estimation with improved spatial consistency

Ye, C. & Prince, J. L., Feb 1 2018, In : Medical Image Analysis. 44, p. 41-53 13 p.

Research output: Contribution to journalArticle

Dimerization of the Trk receptors in the plasma membrane: Effects of their cognate ligands

Ahmed, F. & Hristova, K. A., Nov 30 2018, In : Biochemical Journal. 475, 22, p. 3669-3685 17 p.

Research output: Contribution to journalArticle

EB1 and cytoplasmic dynein mediate protrusion dynamics for efficient 3-dimensional cell migration

Jayatilaka, H., Giri, A., Karl, M., Aifuwa, I., Trenton, N. J., Phillip, J. M., Khatau, S. & Wirtz, D., Mar 1 2018, In : FASEB Journal. 32, 3, p. 1207-1221 15 p.

Research output: Contribution to journalArticle

Efficient flexible backbone protein-protein docking for challenging targets

Marze, N. A., Roy Burman, S. S., Sheffler, W. & Gray, J. J., Oct 15 2018, In : Bioinformatics. 34, 20, p. 3461-3469 9 p.

Research output: Contribution to journalArticle

Endoscopic Navigation in the Absence of CT Imaging

Sinha, A., Liu, X., Reiter, A., Ishii, M., Hager, G. & Taylor, R. H., 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. 64-71 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

Erratum: Author Correction: 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., Jan 1 2018, In : Communications biology. 1, 1 p.

Research output: Contribution to journalComment/debate

Open Access

Erratum: Author Correction: Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology (Nature communications (2017) 8 1 (2123))

Kim, J. K., Louhghalam, A., Lee, G., Schafer, B. W., Wirtz, D. & Kim, D. H., Mar 13 2018, In : Nature Communications. 9, 1, 1 p.

Research output: Contribution to journalComment/debate

Erratum: Pluri-IQ: Quantification of Embryonic Stem Cell Pluripotency through an Image-Based Analysis Software (Stem Cell Reports (2017) 9(2) (697–709) (S2213671117302692) (10.1016/j.stemcr.2017.06.006))

Perestrelo, T., Chen, W., Correia, M., Le, C., Pereira, S., Rodrigues, A. S., Sousa, M. I., Ramalho-Santos, J. & Wirtz, D., Aug 14 2018, In : Stem Cell Reports. 11, 2, 1 p.

Research output: Contribution to journalComment/debate

Evaluating Methods for End-User Creation of Robot Task Plans

Paxton, C., Jonathan, F., Hundt, A., Mutlu, B. & Hager, G., Dec 27 2018, 2018 IEEE/RSJ International Conference on Intelligent Robots and Systems, IROS 2018. Institute of Electrical and Electronics Engineers Inc., p. 6086-6092 7 p. 8594127. (IEEE International Conference on Intelligent Robots and Systems).

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

Exploiting Partial Structural Symmetry for Patient-Specific Image Augmentation in Trauma Interventions

Fotouhi, J., Unberath, M., Taylor, G., Farashahi, A. G., Bier, B., Taylor, R. H., Osgood, G., Armand, M. & Navab, N., 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. 107-115 9 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

Exposing cell-itary confinement: Understanding the mechanisms of confined single cell migration

Wong, B. S., Mistriotis, P. & Konstantopoulos, K., Jan 1 2018, Advances in Experimental Medicine and Biology. Springer New York LLC, p. 139-157 19 p. (Advances in Experimental Medicine and Biology; vol. 1092).

Research output: Chapter in Book/Report/Conference proceedingChapter

Factors associated with physicians' prescriptions for rheumatoid arthritis drugs not filled by patients

Kan, H. J., Dyagilev, K., Schulam, P., Saria, S., Kharrazi, H., Bodycombe, D., Molta, C. T. & Curtis, J. R., May 2 2018, In : Arthritis Research and Therapy. 20, 1, 79.

Research output: Contribution to journalArticle

FBG-Based Control of a Continuum Manipulator Interacting with Obstacles∗

Sefati, S., Murphy, R. J., Alambeigi, F., Pozin, M., Iordachita, I., Taylor, R. H. & Armand, M., Dec 27 2018, 2018 IEEE/RSJ International Conference on Intelligent Robots and Systems, IROS 2018. Institute of Electrical and Electronics Engineers Inc., p. 6477-6483 7 p. 8594407. (IEEE International Conference on Intelligent Robots and Systems).

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

Guide Me: Interacting with Deep Networks

Rupprecht, C., Laina, I., Navab, N., Hager, G. & Tombari, F., Dec 14 2018, Proceedings - 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, CVPR 2018. IEEE Computer Society, p. 8551-8561 11 p. 8578990. (Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition).

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

Immunolabeling of Cleared Human Pancreata Provides Insights into Three-Dimensional Pancreatic Anatomy and Pathology

Noë, M., Rezaee, N., Asrani, K., Skaro, M., Groot, V. P., Wu, P. H., Olson, M. T., Hong, S. M., Kim, S. J., Weiss, M. J., Wolfgang, C., Makary, M. A., He, J., Cameron, J. L., Wirtz, D., Roberts, N., Offerhaus, G. J. A., Brosens, L. A. A., Wood, L. D. & Hruban, R. H., Jul 1 2018, In : American Journal of Pathology. 188, 7, p. 1530-1535 6 p.

Research output: Contribution to journalArticle

Improving self super resolution in magnetic resonance images

Goyal, S., Zhao, C., Jog, A., Prince, J. L. & Carass, A., Jan 1 2018, Medical Imaging 2018: Biomedical Applications in Molecular, Structural, and Functional Imaging. Gimi, B. & Krol, A. (eds.). SPIE, Vol. 10578. 1057814

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

Individualized sepsis treatment using reinforcement learning

Saria, S., Nov 1 2018, In : Nature Medicine. 24, 11, p. 1641-1642 2 p.

Research output: Contribution to journalComment/debate

Inhibition of ovarian tumor cell invasiveness by targeting SYK in the tyrosine kinase signaling pathway

Yu, Y., Suryo Rahmanto, Y., Lee, M. H., Wu, P. H., Phillip, J. M., Huang, C. H., Vitolo, M. I., Gaillard, S., Martin, S. S., Wirtz, D., Shih, I. M. & Wang, T-L., Apr 11 2018, (Accepted/In press) In : Oncogene. p. 1-12 12 p.

Research output: Contribution to journalArticle

Intensity inhomogeneity correction of SD-OCT data using macular flatspace

Lang, A., Carass, A., Jedynak, B. M., Solomon, S. D., Calabresi, P. A. & Prince, J. L., Jan 2018, In : Medical image analysis. 43, p. 85-97 13 p.

Research output: Contribution to journalArticle

Interactions between NRP1 and VEGFR2 molecules in the plasma membrane

King, C., Wirth, D., Workman, S. & Hristova, K. A., Jan 1 2018, (Accepted/In press) In : Biochimica et Biophysica Acta - Biomembranes.

Research output: Contribution to journalArticle

Inter-scanner variation independent descriptors for constrained diffeomorphic demons registration of retina OCT

Reaungamornrat, S., Carass, A., He, Y., Saidha, S., Calabresi, P. & Prince, J. L., Jan 1 2018, Medical Imaging 2018: Image Processing. SPIE, Vol. 10574. 105741B

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

Inverse biomechanical modeling of the tongue via machine learning and synthetic training data

Tolpadi, A. A., Stone, M. L., Carass, A., Prince, J. L. & Gomez, A., Jan 1 2018, Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling. Fei, B. & Webster, R. J. (eds.). SPIE, Vol. 10576. 1057606

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

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 2018, In : Biomaterials science. 6, 1, p. 216-224 9 p.

Research output: Contribution to journalArticle

Laplace-based modeling of fiber orientation in the tongue

Gomez, A., Elsaid, N., Stone, M. L., Zhuo, J. & Prince, J. L., Aug 1 2018, In : Biomechanics and Modeling in Mechanobiology. 17, 4, p. 1119-1130 12 p.

Research output: Contribution to journalArticle

Mechanics of the cell nucleus

Kim, D. H., Hah, J. & Wirtz, D., Jan 1 2018, Advances in Experimental Medicine and Biology. Springer New York LLC, p. 41-55 15 p. (Advances in Experimental Medicine and Biology; vol. 1092).

Research output: Chapter in Book/Report/Conference proceedingChapter

Metabolic and Mechanical Cues Regulating Pluripotent Stem Cell Fate

Perestrelo, T., Correia, M., Ramalho-Santos, J. & Wirtz, D., Jan 1 2018, (Accepted/In press) In : Trends in Cell Biology.

Research output: Contribution to journalArticle

Modulation of calcium oxalate dihydrate growth by phosphorylated osteopontin peptides

Chien, Y. C., Mansouri, A., Jiang, W., Khan, S. R., Gray, J. J. & McKee, M. D., Jan 1 2018, (Accepted/In press) In : Journal of Structural Biology.

Research output: Contribution to journalArticle