Albert Einstein College of Medicine

Research Output

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2019

In vivo photoacoustic multi-contrast imaging and detection of protein interactions using a small near-infrared photochromic protein

Li, L., Shemetov, A. A., Hu, P., Shcherbakova, D. M., Shi, J., Yao, J., Verkhusha, V. V. & Wang, L. V., Jan 1 2019, Photons Plus Ultrasound: Imaging and Sensing 2019. Oraevsky, A. A. & Wang, L. V. (eds.). SPIE, 1087818. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10878).

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

Real-Time Thermoacoustic Imaging and Thermometry during Focused Microwave Heating in Multilayer Breast Phantom

Karunakaran, C., Saraswat, S., Tak, J., Zhao, H., Xin, H. & Witte, R. S., Oct 2019, 2019 IEEE International Ultrasonics Symposium, IUS 2019. IEEE Computer Society, p. 536-539 4 p. 8925833. (IEEE International Ultrasonics Symposium, IUS; vol. 2019-October).

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

Thermoacoustic Image-Guided Focused Microwave Therapy for Enhanced Breast Cancer Treatment

Saraswat, S., Karunakaran, C. P., Tak, J., Zhao, H., Ahmad, W., Witte, R. S. & Xin, H., Jun 2019, 2019 IEEE MTT-S International Microwave Symposium, IMS 2019. Institute of Electrical and Electronics Engineers Inc., p. 220-223 4 p. 8701116. (IEEE MTT-S International Microwave Symposium Digest; vol. 2019-June).

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

2018

Osteosarcoma Patients Classification Using Plain X-Rays and Metabolomic Data

Shen, R., Li, Z., Zhang, L., Hua, Y., Mao, M., Li, Z., Cai, Z., Qiu, Y., Gryak, J. & Najarian, K., Oct 26 2018, 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2018. Institute of Electrical and Electronics Engineers Inc., p. 690-693 4 p. 8512338. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS; vol. 2018-July).

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

Real-time imaging of invadopodia in tumor microenvironment context

Bergman, A. & Gligorijevic, B., Jan 1 2018, Microscopy Histopathology and Analytics, MICROSCOPY 2018. OSA - The Optical Society, Vol. Part F89-MICROSCOPY 2018.

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

2017

Classifying osteosarcoma patients using machine learning approaches

Li, Z., Soroushmehr, S. M. R., Hua, Y., Mao, M., Qiu, Y. & Najarian, K., Sep 13 2017, 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Smarter Technology for a Healthier World, EMBC 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 82-85 4 p. 8036768. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

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

4 Scopus citations

Integrating live-cell fluorescent microscopy and signal processing to discover the relationship of invadopodia digging cycles with extracellular matrix crosslinking ratio

Pourfarhangi, K. E., Bergman, A. & Gligorijevic, B., Feb 7 2017, 2016 IEEE Signal Processing in Medicine and Biology Symposium, SPMB 2016 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 7846865

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

1 Scopus citations

Objective assessment of depressive symptoms with machine learning and wearable sensors data

Ghandeharioun, A., Fedor, S., Sangermano, L., Ionescu, D., Alpert, J., Dale, C., Sontag, D. & Picard, R., Jul 2 2017, 2017 7th International Conference on Affective Computing and Intelligent Interaction, ACII 2017. Institute of Electrical and Electronics Engineers Inc., p. 325-332 8 p. (2017 7th International Conference on Affective Computing and Intelligent Interaction, ACII 2017; vol. 2018-January).

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

10 Scopus citations

Preconditioned random forest regression: Application to genome-wide study for radiotherapy toxicity prediction

Lee, S., Ostrer, H., Kerns, S., Deasy, J. O., Rosenstein, B. & Oh, J. H., Aug 20 2017, ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, 1 p.

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

Structured illumination microscopy as a diagnostic tool for nephrotic disease

Nylk, J., Pullman, J. M., Campbell, E. C., Gunn-Moore, F. J., Prystowsky, M. B. & Dholakia, K., 2017, Advanced Biomedical and Clinical Diagnostic and Surgical Guidance Systems XV. SPIE, Vol. 10054. 1005417

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

2016

Developing a time-resolved flow cytometer for fluorescence lifetime measurements of near-infrared fluorescent proteins

Yang, Z., Shcherbakova, D., Verkhusha, V. & Houston, J. P., Dec 16 2016, 2016 Conference on Lasers and Electro-Optics, CLEO 2016. Institute of Electrical and Electronics Engineers Inc., 7789260

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

1 Scopus citations

Development of microfluidic-based cell collection devices for in vitro and in vivo use

Butt, L., Entenberg, D., Hemachandra, L. P. M., Strohmayer, M., Keely, P., Aguirre-Ghiso, J., Condeelis, J. S. & Castracane, J., Jan 1 2016, Microfluidics, BioMEMS, and Medical Microsystems XIV. Becker, H. & Gray, B. L. (eds.). SPIE, 97051A. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9705).

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

Imaging transcription: Past, present, and future

Coleman, R. A., Liu, Z., Darzacq, X., Tjian, R., Singer, O. H. & Lionnet, T., 2016, 21st Century Genetics Genes at Work, 2015. Cold Spring Harbor Laboratory Press, Vol. 80. p. 1-8 8 p. (Cold Spring Harbor Symposia on Quantitative Biology; vol. 80).

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

23 Scopus citations

Prioritization of schizophrenia risk genes by a network-regularized logistic regression method

Zhang, W., Lin, J. R., Nogales-Cadenas, R., Zhang, Q., Cai, Y. & Zhang, Z. D., 2016, Bioinformatics and Biomedical Engineering - 4th International Conference, IWBBIO 2016, Proceedings. Springer Verlag, Vol. 9656. p. 434-445 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9656).

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

Reversibly switchable photoacoustic tomography using a genetically encoded near-infrared phytochrome

Yao, J., Kaberniuk, A. A., Li, L., Shcherbakova, D. M., Zhang, R., Wang, L., Li, G., Verkhusha, V. V. & Wanga, L. V., Jan 1 2016, Photons Plus Ultrasound: Imaging and Sensing 2016. Oraevsky, A. A. & Wang, L. V. (eds.). SPIE, 97082U. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9708).

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

Understanding the Systems Biology of Pathogen Virulence Using Semantic Methodologies

Rhee, D., Shieh, K., Sullivan, J., Micklem, G., Kim, K. & Golden, A., Mar 22 2016, Proceedings - 2016 IEEE 10th International Conference on Semantic Computing, ICSC 2016. Institute of Electrical and Electronics Engineers Inc., p. 314-320 7 p. 7439354

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

2015

A bioMEMS device for the study of mechanical properties of cells

Sanders, J. M., Butt, L., Clark, A., Williams, J., Padgen, M., Leung, E., Keely, P., Condeelis, J. S., Aguirre-Ghiso, J. & Castracane, J., Jan 1 2015, Microfluidics, BioMEMS, and Medical Microsystems XIII. Becker, H. & Gray, B. L. (eds.). SPIE, 932017. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9320).

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

A three-camera imaging microscope for high-speed single-molecule tracking and super-resolution imaging in living cells

English, B. P. & Singer, R. H., 2015, Proceedings of SPIE - The International Society for Optical Engineering. SPIE, Vol. 9550. 955008

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

10 Scopus citations

Automatic anatomy recognition in post-tonsillectomy MR images of obese children with OSAS

Tong, Y., Udupa, J. K., Odhner, D., Sin, S. & Arens, R., 2015, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9414. 94140Z

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

1 Scopus citations

Characterizing primary refractory neuroblastoma: Prediction of outcome by microscopic image analysis

Niazi, M. K. K., Weiser, D. A., Pawel, B. R. & Gurcan, M. N., Jan 1 2015, Medical Imaging 2015: Digital Pathology. Gurcan, M. N. & Madabhushi, A. (eds.). SPIE, 942008. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9420).

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

1 Scopus citations

Investigating the temporal dynamics of auditory cortical activation to silent lipreading

Crosse, M. J., Elshafei, H. A., Foxe, J. J. & Lalor, E. C., Jul 1 2015, 2015 7th International IEEE/EMBS Conference on Neural Engineering, NER 2015. IEEE Computer Society, p. 308-311 4 p. 7146621. (International IEEE/EMBS Conference on Neural Engineering, NER; vol. 2015-July).

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

4 Scopus citations

Lens Biology and Biochemistry

Hejtmancik, J. F., Riazuddin, S. A., McGreal, R., Liu, W., Cvekl, A. & Shiels, A., Jan 1 2015, Molecular Biology of Eye Disease, 2015. Nickerson, J. M. & Hejtmancik, J. F. (eds.). Elsevier B.V., p. 169-201 33 p. (Progress in Molecular Biology and Translational Science; vol. 134).

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

19 Scopus citations

Lens Development and Crystallin Gene Expression

Cvekl, A., McGreal, R. & Liu, W., Jan 1 2015, Molecular Biology of Eye Disease, 2015. Nickerson, J. M. & Hejtmancik, J. F. (eds.). Elsevier B.V., p. 129-167 39 p. (Progress in Molecular Biology and Translational Science; vol. 134).

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

16 Scopus citations

MR image analytics to characterize upper airway architecture in children with OSAS

Tong, Y., Udupa, J. K., Torigian, D. A., Matsumoto, M. M. S., Sin, S. & Arens, R., Jan 1 2015, Medical Imaging 2015: Biomedical Applications in Molecular, Structural, and Functional Imaging. Gimi, B. & Molthen, R. C. (eds.). SPIE, 94172J. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9417).

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

2 Scopus citations

Objective evaluation of reconstruction methods for quantitative SPECT imaging in the absence of ground truth

Jha, A. K., Song, N., Caffo, B. & Frey, E. C., Jan 1 2015, Medical Imaging 2015: Image Perception, Observer Performance, and Technology Assessment. Mello-Thoms, C. R., Kupinski, M. A. & Mello-Thoms, C. R. (eds.). SPIE, 94161K. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9416).

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

3 Scopus citations
2014

Abdominal adipose tissue quantification on water-suppressed and non-water-suppressed MRI at 3T using semi-automated FCM clustering algorithm

Valaparla, S. K., Peng, Q., Gao, F. & Clarke, G. D., Jan 1 2014, Medical Imaging 2014: Biomedical Applications in Molecular, Structural, and Functional Imaging. SPIE, 903802. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9038).

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

A novel non-registration based segmentation approach of 4D dynamic upper airway MR images: Minimally interactive fuzzy connectedness

Tong, Y., Udupa, J. K., Odhner, D., Sin, S., Wagshul, M. E. & Arens, R., Jan 1 2014, Medical Imaging 2014: Biomedical Applications in Molecular, Structural, and Functional Imaging. SPIE, 90380Z. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9038).

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

1 Scopus citations

Using SAGA and the open science grid to search for aptamers

Shieh, K., Broin, P. Ó., Rhee, D., Levy, M. & Golden, A., Jan 1 2014, Proceedings of the XSEDE 2014 Conference: Engaging Communities. Association for Computing Machinery, 27. (ACM International Conference Proceeding Series).

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

2013

Abdominal adiposity quantification at MRI via fuzzy model-based anatomy recognition

Tong, Y., Udupa, J. K., Odhner, D., Sin, S. & Arens, R., Jun 3 2013, Medical Imaging 2013: Biomedical Applications in Molecular, Structural, and Functional Imaging. 86721R. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8672).

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

5 Scopus citations

Atomic-level modeling of organic electrolytes in lithium-ion batteries

Ferguson, G. & Curtiss, L. A., Jun 3 2013, Applications of Molecular Modeling to Challenges in Clean Energy. American Chemical Society, p. 217-233 17 p. (ACS Symposium Series; vol. 1133).

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

5 Scopus citations

Meconium and transitional stools may cause interference with near-infrared spectroscopy measurements of intestinal oxygen saturation in preterm infants

Thompson, A., Benni, P., Seyhan, S. & Ehrenkranz, R., Jan 1 2013, Oxygen Transport to Tissue XXXIV. Welch, W. J., Bruley, D. F., Palm, F. & Harrison, H. (eds.). p. 287-292 6 p. (Advances in Experimental Medicine and Biology; vol. 765).

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

6 Scopus citations

Optimized release matrices for use in a BioMEMS device to study metastasis

Clark, A., Williams, J., Padgen, M., Keely, P., Condeelis, J. & Castracane, J., May 29 2013, Microfluidics, BioMEMS, and Medical Microsystems XI. 86150C. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 8615).

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

1 Scopus citations

Recognition of upper airway and surrounding structures at MRI in pediatric PCOS and OSAS

Tong, Y., Udupa, J. K., Odhner, D., Sin, S. & Arens, R., Jun 5 2013, Medical Imaging 2013: Computer-Aided Diagnosis. 86702S. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 8670).

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

4 Scopus citations

Spring through the gateway - Deploying genomic workflows with XSEDE

Rhee, D., Hargitai, J., Brent Calder, R., Broin, P. Ó., Shieh, K. & Golden, A., Aug 26 2013, Proceedings of the XSEDE 2013 Conference: Gateway to Discovery. 30. (ACM International Conference Proceeding Series).

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

The influence of spatial organization of the home on inhabitant activity

Bafna, S. & Chambers, E. C., 2013, 2013 International Space Syntax Symposium. Sejong University Press

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

1 Scopus citations
2012

High sensitivity MEMS biosensor for monitoring cell attachment

Liu, F., Li, F., Spray, D. C., Nordin, A. N. & Voiculescu, I., Dec 1 2012, ASME 2012 International Mechanical Engineering Congress and Exposition, IMECE 2012. PARTS A AND B ed. p. 67-71 5 p. (ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE); vol. 9, no. PARTS A AND B).

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

In vivo spectroscopy of cervical tissue

Mourant, J. R., Marina, O. C. & Smith, H. O., Dec 1 2012, Digital Holography and Three-Dimensional Imaging, DH 2012. p. JM3A.23 (Digital Holography and Three-Dimensional Imaging, DH 2012).

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

In vivo spectroscopy of cervical tissue

Mourant, J. R., Marina, O. C. & Smith, H. O., Dec 1 2012, Biomedical Optics, BIOMED 2012. p. JM3A.23 (Biomedical Optics, BIOMED 2012).

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

Mobile brain/body imaging (MoBI): High-density electrical mapping of inhibitory processes during walking

De Sanctis, P., Butler, J. S., Green, J. M., Snyder, A. C. & Foxe, J. J., Dec 14 2012, 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012. p. 1542-1545 4 p. 6346236. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

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

17 Scopus citations

Photoacoustic imaging of the near-infrared fluorescent protein iRFP in vivo

Krumholz, A., Filonov, G. S., Xia, J., Yao, J., Verkhusha, V. V. & Wang, L. V., Apr 9 2012, Photons Plus Ultrasound: Imaging and Sensing 2012. 82233A. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8223).

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

Probing the tumor microenvironment: Collection and induction

Williams, J. K., Padgen, M. R., Wang, Y., Entenberg, D., Gertler, F., Condeelis, J. S. & Castracane, J., Apr 2 2012, Microfluidics, BioMEMS, and Medical Microsystems X. 825105. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 8251).

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

Quantum dots induce charge-specific amyloid-like fibrillation of insulin at physiological conditions

Sukhanova, A., Poly, S., Shemetov, A. & Nabiev, I. R., Dec 1 2012, Nanosystems in Engineering and Medicine. 85485F. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8548).

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

5 Scopus citations

The effect of non-rigid misregistration in sequential quantitative SPECT for targeted radionuclide therapy - A simulation study

Mok, G. S. P., Ao, E. C. I., Song, N. & Frey, E. C., Dec 1 2012, 2012 IEEE Nuclear Science Symposium and Medical Imaging Conference Record, NSS/MIC 2012. p. 2938-2941 4 p. 6551671. (IEEE Nuclear Science Symposium Conference Record).

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

The Einstein Genome Gateway using WASP - A high throughput multi-layered life sciences portal for XSEDE

Golden, A., McLellan, A. S., Dubin, R. A., Jing, Q., Broin, P. Ó., Moskowitz, D., Zhang, Z., Suzuki, M., Hargitai, J., Calder, R. B. & Greally, J. M., Jan 1 2012, HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences. IOS Press, p. 182-191 10 p. (Studies in Health Technology and Informatics; vol. 175).

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

1 Scopus citations
2011

Complementary approaches to investigating cancer cell dynamics in the tumor microenvironment

Padgen, M. R., Raja, W. K., Gligorijevic, B., Williams, J. K., Condeelis, J. S. & Castracane, J., Jun 9 2011, Microfluidics, BioMEMS, and Medical Microsystems IX. 792905. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 7929).

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

Cryptanalysis and improvement of a concurrent signature scheme based on identity

Zhang, Z. & Xu, S., Sep 12 2011, ICSESS 2011 - Proceedings: 2011 IEEE 2nd International Conference on Software Engineering and Service Science. p. 453-456 4 p. 5982351. (ICSESS 2011 - Proceedings: 2011 IEEE 2nd International Conference on Software Engineering and Service Science).

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

1 Scopus citations

Development path and current status of the NANIVID: A new device for cancer cell studies

Raja, W. K., Padgen, M. R., Williams, J. K., Wyckoff, J., Condeelis, J. & Castracane, J., Jun 9 2011, Microfluidics, BioMEMS, and Medical Microsystems IX. 79290A. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 7929).

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

1 Scopus citations

Electrophysiological source analysis of passive self-motion

Nolan, H., Butler, J. S., Whelan, R., Foxe, J. J., Bulthoff, H. H. & Reilly, R. B., Jul 20 2011, 2011 5th International IEEE/EMBS Conference on Neural Engineering, NER 2011. p. 53-56 4 p. 5910487. (2011 5th International IEEE/EMBS Conference on Neural Engineering, NER 2011).

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

2 Scopus citations

Immune system modulation with LOFU and HIFU treatment of prostate cancer

Guha, C., Huagang, Z., Chen, W., Carlosn, R. & Sanghvi, N. T., Oct 13 2011, 10th International Symposium on Therapeutic Ultrasound, ISTU 2010. p. 277-282 6 p. (AIP Conference Proceedings; vol. 1359).

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

1 Scopus citations

Life-like preservation and TEM visualization of the glycocalyx reveals that it is substantial in vitro

Ebong, E. E., Macaluso, F. P., Spray, D. C. & Tarbell, J. M., Jun 16 2011, 2011 IEEE 37th Annual Northeast Bioengineering Conference, NEBEC 2011. 5778556. (2011 IEEE 37th Annual Northeast Bioengineering Conference, NEBEC 2011).

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