Whiting School of Engineering

Research Output

2016

Incremental scene understanding on dense SLAM

Li, C., Xiao, H., Tateno, K., Tombari, F., Navab, N. & Hager, G. D., Nov 28 2016, IROS 2016 - 2016 IEEE/RSJ International Conference on Intelligent Robots and Systems. Institute of Electrical and Electronics Engineers Inc., p. 574-581 8 p. 7759111. (IEEE International Conference on Intelligent Robots and Systems; vol. 2016-November).

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

Individual estimates of age at detectable amyloid onset for risk factor assessment

Bilgel, M., An, Y., Zhou, Y., Wong, D. F., Prince, J. L., Ferrucci, L. & Resnick, S. M., 2016, (Accepted/In press) In : Alzheimer's and Dementia.

Research output: Contribution to journalArticle

Integrative analysis using coupled latent variable models for individualizing prognoses

Schulam, P. & Saria, S., Dec 1 2016, In : Journal of Machine Learning Research. 17, p. 1-35 35 p.

Research output: Contribution to journalArticle

Intensity inhomogeneity correction of macular OCT using N3 and retinal flatspace

Lang, A., Carass, A., Jedynak, B. M., Solomon, S., Calabresi, P. & Prince, J. L., Jun 15 2016, 2016 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2016 - Proceedings. IEEE Computer Society, Vol. 2016-June. p. 197-200 4 p. 7493243

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

Interplay of the physical microenvironment, contact guidance, and intracellular signaling in cell decision making

Paul, C. D., Shea, D. J., Mahoney, M. R., Chai, A., Laney, V., Hung, W. C. & Konstantopoulos, K., Jun 2016, In : FASEB Journal. 30, 6, p. 2161-2170 10 p.

Research output: Contribution to journalArticle

Investigation of bias in continuous medical image label fusion

Xing, F., Prince, J. L. & Landman, B. A., Jun 1 2016, In : PLoS One. 11, 6, e0155862.

Research output: Contribution to journalArticle

Landmark based shape analysis for cerebellar ataxia classification and cerebellar atrophy pattern visualization

Yang, Z., Abulnaga, S. M., Carass, A., Kansal, K., Jedynak, B. M., Onyike, C. U., Ying, S. H. & Prince, J. L., 2016, Medical Imaging 2016: Image Processing. SPIE, Vol. 9784. 97840P

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

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

DeKosky, B. J., Lungu, O. I., Park, D., Johnson, E. L., Charab, W., Chrysostomou, C., Kuroda, D., Ellington, A. D., Ippolito, G. C., Gray, J. J. & Georgiou, G., May 10 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 19, p. E2636-E2645

Research output: Contribution to journalArticle

Learning (predictive) risk scores in the presence of censoring due to interventions

Dyagilev, K. & Saria, S., Mar 1 2016, In : Machine Learning. 102, 3, p. 323-348 26 p.

Research output: Contribution to journalArticle

Learning convolutional action primitives for fine-grained action recognition

Lea, C., Vidal, R. & Hager, G., Jun 8 2016, 2016 IEEE International Conference on Robotics and Automation, ICRA 2016. Institute of Electrical and Electronics Engineers Inc., Vol. 2016-June. p. 1642-1649 8 p. 7487305

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

Local 3D matrix confinement determines division axis through cell shape

He, L., Chen, W., Wu, P. H., Jimenez, A., Wong, B. S., San, A., Konstantopoulos, K. & Wirtz, D., Jan 1 2016, In : Oncotarget. 7, 6, p. 6994-7011 18 p.

Research output: Contribution to journalArticle

Mechanism of FGF receptor dimerization and activation

Sarabipour, S. & Hristova, K., Jan 4 2016, In : Nature communications. 7, 10262.

Research output: Contribution to journalArticle

Mechanoaccumulative Elements of the Mammalian Actin Cytoskeleton

Schiffhauer, ES. S., Luo, T., Mohan, K., Srivastava, V., Qian, X., Griffis, ER. R., Iglesias, PA. A. & Robinson, DN. N., Jan 1 2016, In : Current Biology. 26, 11, p. 1473-1479 7 p.

Research output: Contribution to journalArticle

Medical robotics and computer-integrated surgery

Taylor, R. H., Menciassi, A., Fichtinger, G., Fiorini, P. & Dario, P., Jan 1 2016, Springer Handbook of Robotics. Springer International Publishing, p. 1657-1683 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Message from the general chair and program chairs

Bajcsy, R., Hager, G., Ma, Y., Ikeuchi, K., Schnörr, C., Sivic, J. & Vidal, R., Feb 17 2016, In : Unknown Journal. 11-18-December-2015, p. xxxvi-xxxvii 7410361.

Research output: Contribution to journalEditorial

Message from the General Chair and Program Chairs

Bajcsy, R., Hager, G., Ma, Y., Ikeuchi, K., Schnörr, C., Sivic, J. & Vidal, R., Feb 11 2016, In : Unknown Journal. 2016-February, p. xvii-xviii 7406354.

Research output: Contribution to journalArticle

MIND Demons: Symmetric Diffeomorphic Deformable Registration of MR and CT for Image-Guided Spine Surgery

Reaungamornrat, S., De Silva, T., Uneri, A., Vogt, S., Kleinszig, G., Khanna, A. J., Wolinsky, J. P., Prince, J. L. & Siewerdsen, J. H., Nov 1 2016, In : IEEE Transactions on Medical Imaging. 35, 11, p. 2413-2424 12 p., 7484313.

Research output: Contribution to journalArticle

MIND Demons for MR-to-CT deformable image registration in image-guided spine surgery

Reaungamornrat, S., De Silva, T., Uneri, A., Wolinsky, J. P., Khanna, A. J., Kleinszig, G., Vogt, S., Prince, J. L. & Siewerdsen, J. H., Jan 1 2016, Medical Imaging 2016: Image-Guided Procedures, Robotic Interventions, and Modeling. Webster, R. J. & Yaniv, Z. R. (eds.). SPIE, 97860H. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9786).

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

MMSET/WHSC1 enhances DNA damage repair leading to an increase in resistance to chemotherapeutic agents

Shah, M. Y., Martinez-Garcia, E., Phillip, J. M., Chambliss, A. B., Popovic, R., Ezponda, T., Small, E. C., Will, C., Phillip, M. P., Neri, P., Bahlis, N. J., Wirtz, D. & Licht, J. D., Nov 10 2016, In : Oncogene. 35, 45, p. 5905-5915 11 p.

Research output: Contribution to journalArticle

Modeling excitable dynamics of chemotactic networks

Bhattacharya, S. & Iglesias, P. A., 2016, Methods in Molecular Biology. Humana Press Inc., Vol. 1407. p. 397-415 19 p. (Methods in Molecular Biology; vol. 1407).

Research output: Chapter in Book/Report/Conference proceedingChapter

Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35

Marze, N. A., Jeliazkov, J. R., Roy Burman, S. S., Boyken, S. E., Dimaio, F. & Gray, J. J., 2016, (Accepted/In press) In : Proteins: Structure, Function and Genetics.

Research output: Contribution to journalArticle

Pain, cognition and quality of life associate with structural measures of brain volume loss in multiple sclerosis

Fritz, N. E., Roy, S., Keller, J., Prince, J. L., Calabresi, P. & Zackowski, K. M., Oct 14 2016, In : NeuroRehabilitation. 39, 4, p. 535-544 10 p.

Research output: Contribution to journalArticle

Pathogenic Cysteine Removal Mutations in FGFR Extracellular Domains Stabilize Receptor Dimers and Perturb the TM Dimer Structure

Sarabipour, S. & Hristova, K. A., Oct 9 2016, In : Journal of Molecular Biology. 428, 20, p. 3903-3910 8 p.

Research output: Contribution to journalArticle

Peptide-based strategies for enhanced cell uptake, transcellular transport, and circulation: Mechanisms and challenges

Komin, A., Russell, L. M., Hristova, K. A. & Searson, P. C., Apr 5 2016, (Accepted/In press) In : Advanced Drug Delivery Reviews.

Research output: Contribution to journalArticle

Performance evaluation of MIND demons deformable registration of MR and CT images in spinal interventions

Reaungamornrat, S., De Silva, T., Uneri, A., Goerres, J., Jacobson, M., Ketcha, M., Vogt, S., Kleinszig, G., Khanna, A. J., Wolinsky, J. P., Prince, J. L. & Siewerdsen, J. H., Nov 3 2016, In : Physics in Medicine and Biology. 61, 23, p. 8276-8297 22 p.

Research output: Contribution to journalArticle

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Lensink, M. F., Velankar, S., Kryshtafovych, A., Huang, S. Y., Schneidman-Duhovny, D., Sali, A., Segura, J., Fernandez-Fuentes, N., Viswanath, S., Elber, R., Grudinin, S., Popov, P., Neveu, E., Lee, H., Baek, M., Park, S., Heo, L., Lee, G. R., Seok, C., Qin, S. & 82 others, Zhou, H. X., Ritchie, D. W., Maigret, B., Devignes, M. D., Ghoorah, A., Torchala, M., Chaleil, R. A. G., Bates, P. A., Ben-Zeev, E., Eisenstein, M., Negi, S. S., Weng, Z., Vreven, T., Pierce, B. G., Borrman, T. M., Yu, J., Ochsenbein, F., Guerois, R., Vangone, A., Rodrigues, J. P. G. L. M., Van Zundert, G., Nellen, M., Xue, L., Karaca, E., Melquiond, A. S. J., Visscher, K., Kastritis, P. L., Bonvin, A. M. J. J., Xu, X., Qiu, L., Yan, C., Li, J., Ma, Z., Cheng, J., Zou, X., Shen, Y., Peterson, L. X., Kim, H. R., Roy, A., Han, X., Esquivel-Rodriguez, J., Kihara, D., Yu, X., Bruce, N. J., Fuller, J. C., Wade, R. C., Anishchenko, I., Kundrotas, P. J., Vakser, I. A., Imai, K., Yamada, K., Oda, T., Nakamura, T., Tomii, K., Pallara, C., Romero-Durana, M., Jiménez-García, B., Moal, I. H., Férnandez-Recio, J., Joung, J. Y., Kim, J. Y., Joo, K., Lee, J., Kozakov, D., Vajda, S., Mottarella, S., Hall, D. R., Beglov, D., Mamonov, A., Xia, B., Bohnuud, T., Del Carpio, C. A., Ichiishi, E., Marze, N., Kuroda, D., Roy Burman, S. S., Gray, J. J., Chermak, E., Cavallo, L., Oliva, R., Tovchigrechko, A. & Wodak, S. J., Jan 1 2016, In : Proteins: Structure, Function and Bioinformatics. 84, p. 323-348 26 p.

Research output: Contribution to journalArticle

Preface

Tsaftaris, S. A., Gooya, A., Frangi, A. F. & Prince, J. L., 2016, In : Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9968 LNCS, p. V-VI

Research output: Contribution to journalEditorial

Process monitoring in the intensive care unit: Assessing patient mobility through activity analysis with a non-invasive mobility sensor

Reiter, A., Ma, A., Rawat, N., Shrock, C. & Saria, S., 2016, Medical Image Computing and Computer-Assisted Intervention - MICCAI 2016 - 19th International Conference, Proceedings. Springer Verlag, Vol. 9900 LNCS. p. 482-490 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9900 LNCS).

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

Progress toward robotic surgery of the lateral skull base: Integration of a dexterous continuum manipulator and flexible ring curette

Gao, A., Carey, J. P., Murphy, R. J., Iordachita, I., Taylor, R. H. & Armand, M., Jun 8 2016, 2016 IEEE International Conference on Robotics and Automation, ICRA 2016. Institute of Electrical and Electronics Engineers Inc., p. 4429-4435 7 p. 7487642. (Proceedings - IEEE International Conference on Robotics and Automation; vol. 2016-June).

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

Pushing the Backbone in Protein-Protein Docking

Kuroda, D. & Gray, J. J., Oct 4 2016, In : Structure. 24, 10, p. 1821-1829 9 p.

Research output: Contribution to journalArticle

Quality assurance using outlier detection on an automatic segmentation method for the cerebellar peduncles

Li, K., Ye, C., Yang, Z., Carass, A., Ying, S. H. & Prince, J. L., 2016, Medical Imaging 2016: Image Processing. SPIE, Vol. 9784. 97841H

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

Query-by-example surgical activity detection

Gao, Y., Vedula, S. S., Lee, G. I., Lee, M. R., Khudanpur, S. & Hager, G., Apr 12 2016, (Accepted/In press) In : International journal of computer assisted radiology and surgery. p. 1-10 10 p.

Research output: Contribution to journalArticle

Rail-dbGaP: Analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

Nellore, A., Wilks, C., Hansen, K. D., Leek, J. T. & Langmead, B., Aug 15 2016, In : Bioinformatics. 32, 16, p. 2551-2553 3 p.

Research output: Contribution to journalArticle

Recognizing surgical activities with recurrent neural networks

Dipietro, R., Lea, C., Malpani, A., Ahmidi, N., Vedula, S. S., Lee, G. I., Lee, M. R. & Hager, G., 2016, Medical Image Computing and Computer-Assisted Intervention - MICCAI 2016 - 19th International Conference, Proceedings. Springer Verlag, Vol. 9900 LNCS. p. 551-558 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9900 LNCS).

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

Robot-assisted retinal vein cannulation with force-based puncture detection: Micron vs. the steady-hand eye robot

Gonenc, B., Tran, N., Gehlbach, P., Taylor, R. H. & Iordachita, I., 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. 5107-5111 5 p. 7591876

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

Segmental spatiotemporal CNNs for fine-grained action segmentation

Lea, C., Reiter, A., Vidal, R. & Hager, G. D., Jan 1 2016, Computer Vision - 14th European Conference, ECCV 2016, Proceedings. Matas, J., Sebe, N., Welling, M. & Leibe, B. (eds.). Springer Verlag, p. 36-52 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9907 LNCS).

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

Segmentation and labeling of the ventricular system in normal pressure hydrocephalus using patch-based tissue classification and multi-atlas labeling

Ellingsen, L. M., Roy, S., Carass, A., Blitz, A. M., Pham, D. L. & Prince, J. L., 2016, Medical Imaging 2016: Image Processing. SPIE, Vol. 9784. 97840G

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

Segmentation of thalamus from MR images via task-driven dictionary learning

Liu, L., Glaister, J., Sun, X., Carass, A., Tran, T. D. & Prince, J. L., 2016, Medical Imaging 2016: Image Processing. SPIE, Vol. 9784. 97843H

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

Semi-autonomous telerobotic assembly over high-latency networks

Bohren, J., Paxton, C., Howarth, R., Hager, G. & Whitcomb, L. L., Apr 12 2016, ACM/IEEE International Conference on Human-Robot Interaction. IEEE Computer Society, Vol. 2016-April. p. 149-156 8 p. 7451746

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

Sensing and estimation

Christensen, H. I. & Hager, G. D., Jan 1 2016, Springer Handbook of Robotics. Springer International Publishing, p. 91-112 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Sensor substitution for video-based action recognition

Rupprecht, C., Lea, C., Tombari, F., Navab, N. & Hager, G., Nov 28 2016, IROS 2016 - 2016 IEEE/RSJ International Conference on Intelligent Robots and Systems. Institute of Electrical and Electronics Engineers Inc., Vol. 2016-November. p. 5230-5237 8 p. 7759769

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

Simultaneous segmentation of retinal surfaces and microcystic macular edema in SDOCT volumes

Antony, B. J., Lang, A., Swingle, E. K., Al-Louzi, O., Carass, A., Solomon, S., Calabresi, P., Saidha, S. & Prince, J. L., 2016, Medical Imaging 2016: Image Processing. SPIE, Vol. 9784. 97841C

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

Structural diversity in the type IV Pili of multidrug-resistant acinetobacter

Piepenbrink, K. H., Lillehoj, E., Harding, C. M., Labonte, J. W., Zuo, X., Rapp, C. A., Munson, R. S., Goldblum, S. E., Feldman, M. F., Gray, J. J. & Sundberg, E. J., Oct 28 2016, In : Journal of Biological Chemistry. 291, 44, p. 22924-22935 12 p.

Research output: Contribution to journalArticle

Structure and variability in human tongue muscle anatomy

Stone, M., Woo, J., Lee, J., Poole, T., Seagraves, A., Chung, M., Kim, E., Murano, E. Z., Prince, J. L. & Blemker, S. S., Mar 30 2016, (Accepted/In press) In : Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization. p. 1-9 9 p.

Research output: Contribution to journalArticle

Surgical fiducial segmentation and tracking for pose estimation based on ultrasound B-mode images

Chen, L., Kuo, N., Aalamifar, F., Narrow, D., O'Brien-Coon, D., Prince, J. L. & Boctor, E., 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. 1244-1247 4 p. 7590931

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

System events: readily accessible features for surgical phase detection

Malpani, A., Lea, C., Chen, C. C. G. & Hager, G., May 13 2016, (Accepted/In press) In : International journal of computer assisted radiology and surgery. p. 1-9 9 p.

Research output: Contribution to journalArticle

Task-Level vs. Segment-Level Quantitative Metrics for Surgical Skill Assessment

Vedula, S. S., Malpani, A., Ahmidi, N., Khudanpur, S., Hager, G. & Chen, C. C. G., May 1 2016, In : Journal of surgical education. 73, 3, p. 482-489 8 p.

Research output: Contribution to journalArticle