Whiting School of Engineering

Research Output

2017

Multi-atlas-based CT synthesis from conventional MRI with patch-based refinement for MRI-based radiotherapy planning

Lee, J., Carass, A., Jog, A., Zhao, C. & Prince, J. L., 2017, Medical Imaging 2017: Image Processing. SPIE, Vol. 10133. 101331I

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

Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology

Kim, J. K., Louhghalam, A., Lee, G., Schafer, B. W., Wirtz, D. & Kim, D. H., Dec 1 2017, In : Nature Communications. 8, 1, 2123.

Research output: Contribution to journalArticle

Objective Assessment of Surgical Technical Skill and Competency in the Operating Room

Vedula, S. S., Ishii, M. & Hager, G., Jun 21 2017, In : Annual Review of Biomedical Engineering. 19, p. 301-325 25 p.

Research output: Contribution to journalArticle

On the reproducibility of expert-operated and robotic ultrasound acquisitions

Kojcev, R., Khakzar, A., Fuerst, B., Zettinig, O., Fahkry, C., DeJong, R., Richmon, J., Taylor, R. H., Sinibaldi, E. & Navab, N., Mar 20 2017, (Accepted/In press) In : International journal of computer assisted radiology and surgery. p. 1-9 9 p.

Research output: Contribution to journalArticle

Phase Vector Incompressible Registration Algorithm for Motion Estimation from Tagged Magnetic Resonance Images

Xing, F., Woo, J., Gomez, A. D., Pham, D. L., Bayly, P. V., Stone, M. & Prince, J. L., Oct 2017, In : IEEE transactions on medical imaging. 36, 10, p. 2116-2128 13 p., 7967856.

Research output: Contribution to journalArticle

pH-triggered, macromolecule-sized poration of lipid bilayers by synthetically evolved peptides

Wiedman, G., Kim, S. Y., Zapata-Mercado, E., Wimley, W. C. & Hristova, K. A., Jan 18 2017, In : Journal of the American Chemical Society. 139, 2, p. 937-945 9 p.

Research output: Contribution to journalArticle

Pluri-IQ: Quantification of Embryonic Stem Cell Pluripotency through an Image-Based Analysis Software

Perestrelo, T., Chen, W., Correia, M., Le, C., Pereira, S., Rodrigues, A. S., Sousa, M. I., Ramalho-Santos, J. & Wirtz, D., Aug 8 2017, In : Stem Cell Reports. 9, 2, p. 697-709 13 p.

Research output: Contribution to journalArticle

Pose-aware C-arm for automatic re-initialization of interventional 2D/3D image registration

Fotouhi, J., Fuerst, B., Johnson, A., Lee, S. C., Taylor, R. H., Osgood, G., Navab, N. & Armand, M., Jul 1 2017, In : International journal of computer assisted radiology and surgery. 12, 7, p. 1221-1230 10 p.

Research output: Contribution to journalArticle

Preface

Tsaftaris, S. A., Gooya, A., Frangi, A. F. & Prince, J. L., Jan 1 2017, In : Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 10557 LNCS, p. V-VI

Research output: Contribution to journalEditorial

Probabilistic tractography using Lasso bootstrap

Ye, C. & Prince, J. L., Jan 1 2017, In : Medical Image Analysis. 35, p. 544-553 10 p.

Research output: Contribution to journalArticle

Proof of Concept of a Tracheoesophageal Voice Prosthesis Insufflator for Speech Production After Total Laryngectomy

Starmer, H., Taylor, R. H., Noureldine, S. I. & Richmon, J. D., 2017, (Accepted/In press) In : Journal of Voice.

Research output: Contribution to journalArticle

Quantifying the Interaction between EGFR Dimers and Grb2 in Live Cells

Del Piccolo, N. & Hristova, K. A., 2017, (Accepted/In press) In : Biophysical Journal.

Research output: Contribution to journalArticle

Random forest regression for magnetic resonance image synthesis

Jog, A., Carass, A., Roy, S., Pham, D. L. & Prince, J. L., Jan 1 2017, In : Medical Image Analysis. 35, p. 475-488 14 p.

Research output: Contribution to journalArticle

Reliable decision support using counterfactual models

Schulam, P. & Saria, S., Jan 1 2017, In : Advances in neural information processing systems. 2017-December, p. 1698-1709 12 p.

Research output: Contribution to journalConference article

Reproducible RNA-seq analysis using recount2

Collado-Torres, L., Nellore, A., Kammers, K., Ellis, S. E., Taub, M. A., Hansen, K. D., Jaffe, A., Langmead, B. & Leek, J. T., Apr 11 2017, In : Nature Biotechnology. 35, 4, p. 319-321 3 p.

Research output: Contribution to journalLetter

Residue-centric modeling and design of saccharide and glycoconjugate structures

Labonte, J. W., Adolf-Bryfogle, J., Schief, W. R. & Gray, J. J., Feb 15 2017, In : Journal of Computational Chemistry. 38, 5, p. 276-287 12 p.

Research output: Contribution to journalArticle

Resting-state functional connectivity and cognitive dysfunction correlations in spinocerebelellar ataxia type 6 (SCA6)

Pereira, L., Airan, R. D., Fishman, A., Pillai, J. J., Kansal, K., Onyike, C. U., Prince, J. L., Ying, S. H. & Sair, H. I., Jun 2017, In : Human Brain Mapping. 38, 6, p. 3001-3010 10 p.

Research output: Contribution to journalArticle

Robotic microlaryngeal phonosurgery: Testing of a "steady-hand" microsurgery platform

Akst, L. M., Olds, K. C., Balicki, M., Chalasani, P. & Taylor, R. H., 2017, (Accepted/In press) In : Laryngoscope.

Research output: Contribution to journalArticle

Safe tissue manipulation in retinal microsurgery via motorized instruments with force sensing

Gonenc, B., Gehlbach, P., Taylor, R. H. & Iordachita, I., 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

Simulation and synthesis in medical imaging: Second international workshop, SASHIMI 2017 held in conjunction with MICCAI 2017 Québec city, QC, Canada, September 10, 2017 proceedings

Tsaftaris, S. A., Gooya, A., Frangi, A. F. & Prince, J. L., Jan 1 2017, Simulation and Synthesis in Medical Imaging - 2nd International Workshop, SASHIMI 2017, Held in Conjunction with MICCAI 2017, Proceedings. Gooya, A., Frangi, A. F., Tsaftaris, S. A. & Prince, J. L. (eds.). Springer Verlag, (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

Simultaneous segmentation and correspondence improvement using statistical modes

Sinha, A., Reiter, A., Leonard, S., Ishii, M., Hager, G. & Taylor, R. H., 2017, Medical Imaging 2017: Image Processing. SPIE, Vol. 10133. 101331B

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

Software architecture of the da vinci research kit

Chen, Z., Deguet, A., Taylor, R. H. & Kazanzides, P., May 11 2017, Proceedings - 2017 1st IEEE International Conference on Robotic Computing, IRC 2017. Institute of Electrical and Electronics Engineers Inc., p. 180-187 8 p. 7926536

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

Sphingolipids facilitate age asymmetry of membrane proteins in dividing yeast cells

Singh, P., Ramachandran, S. K., Zhu, J., Kim, B. C., Biswas, D., Ha, T., Iglesias, P. A. & Li, R., Oct 1 2017, In : Molecular Biology of the Cell. 28, 20, p. 2712-2722 11 p.

Research output: Contribution to journalArticle

Structural cerebellar correlates of cognitive and motor dysfunctions in cerebellar degeneration

Kansal, K., Yang, Z., Fishman, A. M., Sair, H., Ying, S. H., Jedynak, B. M., Prince, J. L. & Onyike, C. U., Mar 1 2017, In : Brain : a journal of neurology. 140, 3, p. 707-720 14 p.

Research output: Contribution to journalArticle

Structure-based cross-docking analysis of antibody-antigen interactions

Kilambi, K. P. & Gray, J. J., Dec 1 2017, In : Scientific Reports. 7, 1, 8145.

Research output: Contribution to journalArticle

Surgical data science for next-generation interventions

Maier-Hein, L., Vedula, S. S., Speidel, S., Navab, N., Kikinis, R., Park, A., Eisenmann, M., Feussner, H., Forestier, G., Giannarou, S., Hashizume, M., Katic, D., Kenngott, H., Kranzfelder, M., Malpani, A., März, K., Neumuth, T., Padoy, N., Pugh, C., Schoch, N. & 5 others, Stoyanov, D., Taylor, R., Wagner, M., Hager, G. D. & Jannin, P., Sep 1 2017, In : Nature biomedical engineering. 1, 9, p. 691-696 6 p.

Research output: Contribution to journalComment/debate

Synergistic IL-6 and IL-8 paracrine signalling pathway infers a strategy to inhibit tumour cell migration

Jayatilaka, H., Tyle, P., Chen, J. J., Kwak, M., Ju, J., Kim, H. J., Lee, J. S. H., Wu, P. H., Gilkes, D., Fan, R. & Wirtz, D., May 26 2017, In : Nature Communications. 8, 15584.

Research output: Contribution to journalArticle

Tactile object recognition and localization using spatially-varying appearance

Pezzementi, Z. & Hager, G. D., Jan 1 2017, Robotics Research - The 15th International Symposium ISRR. Christensen, H. I. & Khatib, O. (eds.). Springer Verlag, p. 201-217 17 p. (Springer Tracts in Advanced Robotics; vol. 100).

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

Temporal convolutional networks for action segmentation and detection

Lea, C., Flynn, M. D., Vidal, R., Reiter, A. & Hager, G. D., Nov 6 2017, Proceedings - 30th IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2017. Institute of Electrical and Electronics Engineers Inc., p. 1003-1012 10 p. (Proceedings - 30th IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2017; vol. 2017-January).

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

Temporal order of Alzheimer's disease-related cognitive marker changes in BLSA and WRAP longitudinal studies

Bilgel, M., Koscik, R. L., An, Y., Prince, J. L., Resnick, S. M., Johnson, S. C. & Jedynak, B. M., Jan 1 2017, In : Journal of Alzheimer's Disease. 59, 4, p. 1335-1347 13 p.

Research output: Contribution to journalArticle

Test suite for image-based motion estimation of the brain and tongue

Ramsey, J., Prince, J. L. & Gomez, A., 2017, Medical Imaging 2017: Biomedical Applications in Molecular, Structural, and Functional Imaging. SPIE, Vol. 10137. 101371G

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

Thalamus segmentation using multi-modal feature classification: Validation and pilot study of an age-matched cohort

Glaister, J., Carass, A., NessAiver, T., Stough, J. V., Saidha, S., Calabresi, P. & Prince, J. L., Sep 1 2017, In : NeuroImage. 158, p. 430-440 11 p.

Research output: Contribution to journalArticle

The effects of palate features and glossectomy surgery on /s/ production

Grimm, D. L., Stone, M., Woo, J., Lee, J., Hwang, J. H., Bedrosian, G. E. & Prince, J. L., Dec 1 2017, In : Journal of Speech, Language, and Hearing Research. 60, 12, p. 3417-3425 9 p.

Research output: Contribution to journalArticle

The robotic ENT microsurgery system: A novel robotic platform for microvascular surgery

Feng, A. L., Razavi, C. R., Lakshminarayanan, P., Ashai, Z., Olds, K., Balicki, M., Gooi, Z., Day, A. T., Taylor, R. H. & Richmon, J. D., 2017, (Accepted/In press) In : Laryngoscope.

Research output: Contribution to journalArticle

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O'Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., Labonte, J. W., Pacella, M. S., Bonneau, R., Bradley, P., Dunbrack, R. L., Das, R., Baker, D., Kuhlman, B., Kortemme, T. & Gray, J. J., Jun 13 2017, In : Journal of Chemical Theory and Computation. 13, 6, p. 3031-3048 18 p.

Research output: Contribution to journalArticle

The SAM domain inhibits EphA2 interactions in the plasma membrane

Singh, D. R., Ahmed, F., Paul, M. D., Gedam, M., Pasquale, E. B. & Hristova, K. A., Jan 1 2017, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1864, 1, p. 31-38 8 p.

Research output: Contribution to journalArticle

The surgical robot challenge

Merrifield, R. & Taylor, R., Jun 1 2017, In : IEEE Robotics and Automation Magazine. 24, 2, p. 22-23 2 p., 7947289.

Research output: Contribution to journalEditorial

The triggering, curving and stopping of excitable waves during cell migration

Bhattacharya, S. & Iglesias, P. A., May 10 2017, 2017 51st Annual Conference on Information Sciences and Systems, CISS 2017. Institute of Electrical and Electronics Engineers Inc., 7926103

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

Towards robot-assisted retinal vein cannulation: A motorized force-sensing microneedle integrated with a handheld micromanipulator

Gonenc, B., Chae, J., Gehlbach, P., Taylor, R. H. & Iordachita, I., Oct 1 2017, In : Sensors (Switzerland). 17, 10, 2195.

Research output: Contribution to journalArticle

Towards topological correct segmentation of macular OCT from cascaded FCNs

He, Y., Carass, A., Yun, Y., Zhao, C., Jedynak, B. M., Solomon, S., Saidha, S., Calabresi, P. & Prince, J. L., 2017, Fetal, Infant and Ophthalmic Medical Image Analysis - International Workshop, FIFI 2017 and 4th International Workshop, OMIA 2017 Held in Conjunction with MICCAI 2017, Proceedings. Springer Verlag, Vol. 10554 LNCS. p. 202-209 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10554 LNCS).

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

Transient Opening of the Mitochondrial Permeability Transition Pore Induces Microdomain Calcium Transients in Astrocyte Processes

Agarwal, A., Wu, P. H., Hughes, E. G., Fukaya, M., Tischfield, M. A., Langseth, A. J., Wirtz, D. & Bergles, D. E., Feb 8 2017, In : Neuron. 93, 3, p. 587-605.e7

Research output: Contribution to journalArticle

Transition state clustering: Unsupervised surgical trajectory segmentation for robot learning

Krishnan, S., Garg, A., Patil, S., Lea, C., Hager, G., Abbeel, P. & Goldberg, K., Dec 1 2017, In : International Journal of Robotics Research. 36, 13-14, p. 1595-1618 24 p.

Research output: Contribution to journalArticle

Treatment-response models for counterfactual reasoning with continuous-time, continuous-valued interventions

Soleimani, H., Subbaswamy, A. & Saria, S., 2017, Uncertainty in Artificial Intelligence - Proceedings of the 33rd Conference, UAI 2017. AUAI Press Corvallis

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

Tumour mechanopathology: Cutting the stress out

Gilkes, D. & Wirtz, D., Jan 10 2017, In : Nature Biomedical Engineering. 1, 1, 0012.

Research output: Contribution to journalShort survey

Understanding the FRET signatures of interacting membrane proteins

King, C., Raicu, V. & Hristova, K. A., Mar 31 2017, In : Journal of Biological Chemistry. 292, 13, p. 5291-5310 20 p.

Research output: Contribution to journalArticle

Whole brain parcellation with pathology: Validation on ventriculomegaly patients

Carass, A., Shao, M., Li, X., Dewey, B. E., Blitz, A. M., Roy, S., Pham, D. L., Prince, J. L. & Ellingsen, L. M., 2017, Patch-Based Techniques in Medical Imaging - 3rd International Workshop, Patch-MI 2017 Held in Conjunction with MICCAI 2017, Proceedings. Springer Verlag, Vol. 10530 LNCS. p. 20-28 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10530 LNCS).

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

Whole brain segmentation and labeling from CT using synthetic MR images

Zhao, C., Carass, A., Lee, J., He, Y. & Prince, J. L., Jan 1 2017, Machine Learning in Medical Imaging - 8th International Workshop, MLMI 2017, Held in Conjunction with MICCAI 2017, Proceedings. Springer Verlag, p. 291-298 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10541 LNCS).

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

2016

A Bayesian approach to fiber orientation estimation guided by volumetric tract segmentation

Ye, C. & Prince, J. L., Dec 1 2016, In : Computerized Medical Imaging and Graphics. 54, p. 35-47 13 p.

Research output: Contribution to journalArticle

Accuracy assessment and kinematic calibration of the robotic endoscopic microsurgical system

Feng, L., Wilkening, P., Sevimli, Y., Balicki, M., Olds, K. C. & Taylor, R. H., Oct 13 2016, 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2016. Institute of Electrical and Electronics Engineers Inc., Vol. 2016-October. p. 5091-5094 4 p. 7591872

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