Whiting School of Engineering

Research Output

2015

A Probabilistic Graphical Model for Individualizing Prognosis in Chronic, Complex Diseases

Schulam, P. & Saria, S., Jan 1 2015, In : AMIA ... Annual Symposium proceedings. AMIA Symposium. 2015, p. 143-144 2 p.

Research output: Contribution to journalArticle

Arioc: High-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Wilton, R., Budavari, T., Langmead, B., Wheelan, S. J., Salzberg, S. L. & Szalay, A. S., 2015, In : PeerJ. 2015, 3, e808.

Research output: Contribution to journalArticle

A study of crowdsourced segment-level surgical skill assessment using pairwise rankings

Malpani, A., Vedula, S. S., Chen, C. C. G. & Hager, G. D., Sep 13 2015, In : International Journal of Computer Assisted Radiology and Surgery. 10, 9, p. 1435-1447 13 p.

Research output: Contribution to journalArticle

A targeted real-time early warning score (TREWScore) for septic shock

Henry, K. E., Hager, D. N., Pronovost, P. J. & Saria, S., Aug 5 2015, In : Science translational medicine. 7, 299, 299ra122.

Research output: Contribution to journalArticle

Augmented reality and cone beam CT guidance for transoral robotic surgery

Liu, W. P., Richmon, J. D., Sorger, J. M., Azizian, M. & Taylor, R. H., Sep 21 2015, In : Journal of Robotic Surgery. 9, 3, p. 223-233 11 p.

Research output: Contribution to journalArticle

Automated objective surgical skill assessment in the operating room from unstructured tool motion in septoplasty

Ahmidi, N., Poddar, P., Jones, J. D., Vedula, S. S., Ishii, L., Hager, G. D. & Ishii, M., Jun 1 2015, In : International Journal of Computer Assisted Radiology and Surgery. 10, 6, p. 981-991 11 p.

Research output: Contribution to journalArticle

Automatic segmentation of microcystic macular edema in OCT

Lang, A., Carass, A., Swingle, E. K., Al-Louzi, O., Bhargava, P., Saidha, S., Ying, H., Calabresi, P. A. & Prince, J. L., Jan 1 2015, In : Biomedical Optics Express. 6, 1, p. 155-169 15 p.

Research output: Contribution to journalArticle

Ballgown bridges the gap between transcriptome assembly and expression analysis

Frazee, A. C., Pertea, G., Jaffe, A. E., Langmead, B., Salzberg, S. L. & Leek, J. T., Feb 2015, In : Nature biotechnology. 33, 3, p. 243-246 4 p.

Research output: Contribution to journalLetter

Beyond spatial pooling: Fine-grained representation learning in multiple domains

Li, C., Reiter, A. & Hager, G. D., Oct 14 2015, IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2015. IEEE Computer Society, p. 4913-4922 10 p. 7299125. (Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition; vol. 07-12-June-2015).

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

B-mode ultrasound pose recovery via surgical fiducial segmentation and tracking

Asoni, A., Ketcha, M., Kuo, N., Chen, L., Boctor, E., Coon, D. & Prince, J. L., Jan 1 2015, Medical Imaging 2015: Image-Guided Procedures, Robotic Interventions, and Modeling. Webster, R. J. & Yaniv, Z. R. (eds.). SPIE, 94152C. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9415).

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

By activating matrix metalloproteinase-7, shear stress promotes chondrosarcoma cell motility, invasion and lung colonization

Guan, P. P., Yu, X., Guo, J. J., Wang, Y., Wang, T., Li, J. Y., Konstantopoulos, K., Wang, Z. Y. & Wang, P., Jan 1 2015, In : Oncotarget. 6, 11, p. 9140-9159 20 p.

Research output: Contribution to journalArticle

Open Access

By suppressing the expression of anterior pharynx-defective-1α and -1β and inhibiting the aggregation of β-amyloid protein, magnesium ions inhibit the cognitive decline of amyloid precursor protein/presenilin 1 transgenic mice

Yu, X., Guan, P. P., Guo, J. W., Wang, Y., Cao, L. L., Xu, G. B., Konstantopoulos, K., Wang, Z. Y. & Wang, P., Dec 1 2015, In : FASEB Journal. 29, 12, p. 5044-5058 15 p.

Research output: Contribution to journalArticle

Cell shape regulation through mechanosensory feedback control

Mohan, K., Luo, T., Robinson, D. & Iglesias, P. A., Aug 6 2015, In : Journal of the Royal Society Interface. 12, 109, 20150512.

Research output: Contribution to journalArticle

Changes in Aβ biomarkers and associations with APOE genotype in 2 longitudinal cohorts

Resnick, S. M., Bilgel, M., Moghekar, A., An, Y., Cai, Q., Wang, M. C., Thambisetty, M., Prince, J. L., Zhou, Y., Soldan, A., Wong, D. F., O'Brien, R. J., Ferrucci, L. & Albert, M. S., Jan 1 2015, In : Neurobiology of Aging. 36, 8, p. 2333-2339 7 p.

Research output: Contribution to journalArticle

Characterization of Membrane Protein Interactions in Plasma Membrane Derived Vesicles with Quantitative Imaging Förster Resonance Energy Transfer

Sarabipour, S., Del Piccolo, N. & Hristova, K., Aug 5 2015, In : Accounts of chemical research. 48, 8, p. 2262-2269 8 p.

Research output: Contribution to journalArticle

Characterization of Monobody Scaffold Interactions with Ligand via Force Spectroscopy and Steered Molecular Dynamics

Cheung, L. S. L., Shea, D. J., Nicholes, N., Date, A., Ostermeier, M. & Konstantopoulos, K., Feb 4 2015, In : Scientific reports. 5, 8247.

Research output: Contribution to journalArticle

Clustering longitudinal clinical marker trajectories from electronic health data: Applications to phenotyping and endotype discovery

Schulam, P., Wigley, F. & Saria, S., Jun 1 2015, Proceedings of the 29th AAAI Conference on Artificial Intelligence, AAAI 2015 and the 27th Innovative Applications of Artificial Intelligence Conference, IAAI 2015. AI Access Foundation, p. 2956-2964 9 p. (Proceedings of the National Conference on Artificial Intelligence; vol. 4).

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

Collective cancer cell invasion induced by coordinated contractile stresses

Valencia, A. M. J., Wu, P. H., Yogurtcu, O. N., Rao, P., DiGiacomo, J., Godet, I., He, L., Lee, M. H., Gilkes, D., Sun, S. X. & Wirtz, D., 2015, In : Oncotarget. 6, 41, p. 43438-43451 14 p.

Research output: Contribution to journalArticle

Comparison of optimization strategy and similarity metric in atlas-to-subject registration using statistical deformation model

Otake, Y., Murphy, R. J., Grupp, R. B., Sato, Y., Taylor, R. H. & Armand, M., Jan 1 2015, Medical Imaging 2015: Image-Guided Procedures, Robotic Interventions, and Modeling. Webster, R. J. & Yaniv, Z. R. (eds.). SPIE, 94150Q. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9415).

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

Computational modeling of membrane proteins

Koehler Leman, J., Ulmschneider, M. B. & Gray, J. J., Jan 1 2015, In : Proteins: Structure, Function and Bioinformatics. 83, 1, p. 1-24 24 p.

Research output: Contribution to journalArticle

COX-2 dependent regulation of mechanotransduction in human breast cancer cells

Yoon, A. R., Stasinopoulos, I., Kim, J. H., Yong, H. M., Kilic, O., Wirtz, D., Bhujwalla, Z. M. & An, S. S., Mar 1 2015, In : Cancer Biology and Therapy. 16, 3, p. 430-437 8 p.

Research output: Contribution to journalArticle

Creating a data science platform for developing complication risk models for personalized treatment planning in radiation oncology

Marungo, F., Robertson, S., Quon, H., Rhee, J., Paisley, H., Taylor, R. H. & McNutt, T., Mar 26 2015, Proceedings of the 48th Annual Hawaii International Conference on System Sciences, HICSS 2015. Sprague, R. H. & Bui, T. X. (eds.). IEEE Computer Society, p. 3132-3140 9 p. 7070193. (Proceedings of the Annual Hawaii International Conference on System Sciences; vol. 2015-March).

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

Cytoskeletal tension induces the polarized architecture of the nucleus

Kim, D. H. & Wirtz, D., Apr 1 2015, In : Biomaterials. 48, p. 161-172 12 p.

Research output: Contribution to journalArticle

Deformation field correction for spatial normalization of PET images

Bilgel, M., Carass, A., Resnick, S. M., Wong, D. F. & Prince, J. L., Oct 1 2015, In : NeuroImage. 119, p. 152-163 12 p.

Research output: Contribution to journalArticle

Development of a biomechanical guidance system for periacetabular osteotomy

Murphy, R. J., Armiger, R. S., Lepistö, J., Mears, S. C., Taylor, R. H. & Armand, M., Apr 1 2015, In : International Journal of Computer Assisted Radiology and Surgery. 10, 4, p. 497-508 12 p.

Research output: Contribution to journalArticle

Direct ultrasound to video registration using photoacoustic markers from a single image pose

Cheng, A., Guo, X., Kang, H. J., Choti, M. A., Kang, J. U., Taylor, R. H. & Boctor, E. M., Jan 1 2015, Advanced Biomedical and Clinical Diagnostic and Surgical Guidance Systems XIII. Vo-Dinh, T., Mahadevan-Jansen, A. & Grundfest, W. S. (eds.). SPIE, 93130X. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9313).

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

Dissecting an Online Intervention for Cancer Survivors: Four Exploratory Analyses of Internet Engagement and Its Effects on Health Status and Health Behaviors

Chen, Z., Koh, P. W., Ritter, P. L., Lorig, K., Bantum, E. OC. & Saria, S., Feb 17 2015, In : Health Education and Behavior. 42, 1, p. 32-45 14 p.

Research output: Contribution to journalArticle

Distinct kinetic and mechanical properties govern mucin 16- and podocalyxin-mediated tumor cell adhesion to E- and L-selectin in shear f low

Shea, D. J., Wirtz, D., Stebe, K. J. & Konstantopoulos, K., 2015, In : Oncotarget. 6, 28, p. 24842-24855 14 p.

Research output: Contribution to journalArticle

Effect of thanatophoric dysplasia type i mutations on FGFR3 dimerization

Del Piccolo, N., Placone, J. & Hristova, K., Jan 20 2015, In : Biophysical journal. 108, 2, p. 272-278 7 p.

Research output: Contribution to journalArticle

Effect of white matter lesions on manual dexterity in healthy middle-aged persons

Nyquist, P. A., Yanek, L. R., Bilgel, M., Cuzzocreo, J. L., Becker, L. C., Chevalier-Davis, K., Yousem, D., Prince, J., Kral, B. G., Vaidya, D. & Becker, D. M., May 12 2015, In : Neurology. 84, 19, p. 1920-1926 7 p.

Research output: Contribution to journalArticle

Effects of micro-vibratory modulation during robot-assisted membrane peeling

Gonenc, B., Gehlbach, P., Taylor, R. H. & Iordachita, I., Dec 11 2015, IROS Hamburg 2015 - Conference Digest: IEEE/RSJ International Conference on Intelligent Robots and Systems. Institute of Electrical and Electronics Engineers Inc., p. 3811-3816 6 p. 7353912. (IEEE International Conference on Intelligent Robots and Systems; vol. 2015-December).

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

EphA2 receptor unliganded dimers suppress EphA2 pro-tumorigenic signaling

Singh, D. R., Ahmed, F., King, C., Gupta, N., Salotto, M., Pasquale, E. B. & Hristova, K., Nov 6 2015, In : Journal of Biological Chemistry. 290, 45, p. 27271-27279 9 p.

Research output: Contribution to journalArticle

Evolution of cellular morpho-phenotypes in cancer metastasis

Wu, P. H., Phillip, J. M., Khatau, S. B., Chen, W. C., Stirman, J., Rosseel, S., Tschudi, K., Van Patten, J., Wong, M., Gupta, S., Baras, A. S., Leek, J. T., Maitra, A. & Wirtz, D., Dec 17 2015, In : Scientific reports. 5, 18437.

Research output: Contribution to journalArticle

FBG-based sensorized light pipe for robotic intraocular illumination facilitates bimanual retinal microsurgery

Horise, Y., He, X., Gehlbach, P., Taylor, R. & Iordachita, I., Nov 4 2015, 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015. Institute of Electrical and Electronics Engineers Inc., p. 13-16 4 p. 7318249. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS; vol. 2015-November).

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

FGFR3 unliganded dimer stabilization by the juxtamembrane domain

Sarabipour, S. & Hristova, K., Jan 1 2015, In : Journal of molecular biology. 427, 8, p. 1705-1714 10 p.

Research output: Contribution to journalArticle

Five-dimensional ultrasound system for soft tissue visualization

Deshmukh, N. P., Caban, J. J., Taylor, R. H., Hager, G. D. & Boctor, E. M., Dec 1 2015, In : International Journal of Computer Assisted Radiology and Surgery. 10, 12, p. 1927-1939 13 p.

Research output: Contribution to journalArticle

Fluid shear promotes chondrosarcoma cell invasion by activating matrix metalloproteinase 12 via IGF-2 and VEGF signaling pathways

Wang, P., Chen, S. H., Hung, W. C., Paul, C., Zhu, F., Guan, P. P., Huso, D. L., Kontrogianni-Konstantopoulos, A. & Konstantopoulos, K., Aug 27 2015, In : Oncogene. 34, 35, p. 4558-4569 12 p.

Research output: Contribution to journalArticle

Force-based puncture detection and active position holding for assisted retinal vein cannulation

Gonenc, B., Tran, N., Riviere, C. N., Gehlbach, P., Taylor, R. H. & Iordachita, I., Oct 9 2015, 2015 IEEE International Conference on Multisensor Fusion and lntegration for Intelligent Systems, MFI 2015. Institute of Electrical and Electronics Engineers Inc., p. 322-327 6 p. 7295828. (IEEE International Conference on Multisensor Fusion and Integration for Intelligent Systems; vol. 2015-October).

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

Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to hirschsprung disease liability

Jiang, Q., Arnold, S., Heanue, T., Kilambi, K. P., Doan, B., Kapoor, A., Ling, A. Y., Sosa, M. X., Guy, M., Jiang, Q., Burzynski, G., West, K., Bessling, S., Griseri, P., Amiel, J., Fernandez, R. M., Verheij, J. B. G. M., Hofstra, R. M. W., Borrego, S., Lyonnet, S. & 5 others, Ceccherini, I., Gray, J. J., Pachnis, V., McCallion, A. S. & Chakravarti, A., Apr 2 2015, In : American journal of human genetics. 96, 4, p. 581-596 16 p.

Research output: Contribution to journalArticle

Generalized iterative most likely oriented-point (G-IMLOP) registration

Billings, S. & Taylor, R., Aug 5 2015, In : International Journal of Computer Assisted Radiology and Surgery. 10, 8, p. 1213-1226 14 p.

Research output: Contribution to journalArticle

Geometric deformable models

Bai, Y., Han, X. & Prince, J. L., Jan 1 2015, Handbook of Biomedical Imaging: Methodologies and Clinical Research. Springer US, p. 83-104 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

HER2 missense mutations have distinct effects on oncogenic signaling and migration

Zabransky, D. J., Yankaskas, C. L., Cochran, R. L., Wong, H. Y., Croessmann, S., Chu, D., Kavuri, S. M., Brewer, M. R., Marc Rosen, D., Brian Dalton, W., Cimino-Mathews, A., Cravero, K., Button, B., Kyker-Snowman, K., Cidado, J., Erlanger, B., Parsons, H. A., Manto, K. M., Bose, R., Lauring, J. & 3 others, Arteaga, C. L., Konstantopoulos, K. & Park, B. H., Nov 10 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 45, p. E6205-E6214

Research output: Contribution to journalArticle

Open Access

Hierarchical Sparse and Collaborative Low-Rank representation for emotion recognition

Xiang, X., Dao, M., Hager, G. D. & Tran, T. D., Aug 4 2015, 2015 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2015 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 3811-3815 5 p. 7178684. (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings; vol. 2015-August).

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

HISAT: A fast spliced aligner with low memory requirements

Kim, D., Langmead, B. & Salzberg, S. L., Mar 31 2015, In : Nature Methods. 12, 4, p. 357-360 4 p.

Research output: Contribution to journalArticle

Impaired IKs channel activation by Ca2+-dependent PKC shows correlation with emotion/arousal-triggered events in LQT1

O-Uchi, J., Rice, J. J., Ruwald, M. H., Parks, X. X., Ronzier, E., Moss, A. J., Zareba, W. & Lopes, C. M., Feb 1 2015, In : Journal of Molecular and Cellular Cardiology. 79, p. 203-211 9 p.

Research output: Contribution to journalArticle

Inhibition of Spleen Tyrosine Kinase Potentiates Paclitaxel-Induced Cytotoxicity in Ovarian Cancer Cells by Stabilizing Microtubules

Yu, Y., Gaillard, S., Phillip, J. M., Huang, T. C., Pinto, S. M., Tessarollo, N. G., Zhang, Z., Pandey, A., Wirtz, D., Ayhan, A., Davidson, B., Wang, T. L. & Shih, I. M., Jul 13 2015, In : Cancer cell. 28, 1, p. 82-96 15 p.

Research output: Contribution to journalArticle

Intelligent surgical robots with situational awareness: From good to great surgeons

Simaan, N., Taylor, R. H. & Choset, H., Sep 1 2015, Mechanical Engineering, 137, 9, p. 3-6 4 p.

Research output: Contribution to specialist publicationArticle

Interfacial Mineral-Peptide Properties of a Mineral Binding Peptide from Osteonectin and Bone-like Apatite

Matlahov, I., Iline-Vul, T., Abayev, M., Lee, E. M. Y., Nadav-Tsubery, M., Keinan-Adamsky, K., Gray, J. J. & Goobes, G., Aug 25 2015, In : Chemistry of Materials. 27, 16, p. 5562-5569 8 p.

Research output: Contribution to journalArticle