Albert Einstein College of Medicine

Research Output 1960 2020

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Conference contribution
2019

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

Li, L., Shemetov, A., Hu, P., Shcherbakova, D., Shi, J., Yao, J., Verkhusha, 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

Photoacoustic effect
Tomography
Pulse code modulation
tomography
Infrared radiation
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., Vol. 2018-July. p. 690-693 4 p. 8512338

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

Metabolomics
Osteosarcoma
Support vector machines
X-Rays
X rays

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

Tumors
Microscopic examination
Cells
Modulation
Imaging techniques
2017
2 Citations (Scopus)

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

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

Osteosarcoma
Metabolomics
Learning systems
Support vector machines
Logistics
1 Citation (Scopus)

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

Crosslinking
Microscopic examination
Signal processing
Cells

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

Radiotherapy
Toxicity
Genes
Genome
Prostatic Neoplasms

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

Lighting
Microscopy
Microscopic examination
illumination
microscopy
2016
1 Citation (Scopus)

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

phytochrome
Fluorescence
Cells
Phytochrome
Infrared radiation

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

Butt, L., Entenberg, D. R., Hemachandra, L. P. M., Strohmayer, M., Keely, P., Aguirre-Ghiso, J., Condeelis, J. S. & Castracane, J., 2016, Microfluidics, BioMEMS, and Medical Microsystems XIV. SPIE, Vol. 9705. 97051A

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

Microfluidics
Cells
Equipment and Supplies
Lab-On-A-Chip Devices
Microchannels
21 Citations (Scopus)

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

Transcription
Technology
Imaging techniques
Biochemical Phenomena
Stochastic Processes

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., 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

Prioritization
Logistic Regression
Logistics
Genes
Gene

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

Yao, J., Kaberniuk, A., Li, L., Shcherbakova, D., Zhang, R., Wang, L., Li, G., Verkhusha, V. & Wanga, L. V., 2016, Photons Plus Ultrasound: Imaging and Sensing 2016. SPIE, Vol. 9708. 97082U

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

phytochrome
Phytochrome
Photoacoustic effect
Tomography
tomography

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

Pathogens
Assays
Semantics
Data warehouses
Data mining
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., 2015, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9320. 932017

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

Tumor Microenvironment
Tumors
tumors
mechanical properties
Equipment and Supplies
8 Citations (Scopus)

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

Super-resolution
Microscope
Microscopes
High Speed
Camera
1 Citation (Scopus)

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

sleep
Tonsillectomy
anatomy
respiration
Obstructive Sleep Apnea
1 Citation (Scopus)

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

Niazi, M. K. K., Weiser, D. A., Pawel, B. R. & Gurcan, M. N., 2015, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9420. 942008

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

refractories
Eosine Yellowish-(YS)
Neuroblastoma
image analysis
Refractory materials
3 Citations (Scopus)

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, International IEEE/EMBS Conference on Neural Engineering, NER. IEEE Computer Society, Vol. 2015-July. p. 308-311 4 p. 7146621

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

Chemical activation
Electroencephalography
Neuroimaging
Brain computer interface
2 Citations (Scopus)

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., 2015, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9417. 94172J

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

sleep
Palatine Tonsil
respiration
Obstructive Sleep Apnea
Oropharynx
3 Citations (Scopus)

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., 2015, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9416. 94161K

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

Single photon emission computed tomography
ground truth
Single-Photon Emission-Computed Tomography
tomography
Imaging techniques
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., 2014, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9038. 903802

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

adipose tissues
Abdominal Fat
Clustering algorithms
Magnetic resonance imaging
Cluster Analysis
1 Citation (Scopus)

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., 2014, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9038. 90380Z

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

Magnetic resonance imaging
Seeds
preprocessing
nonuniformity
seeds
11 Citations (Scopus)

Extracting latent structure from multiple interacting neural populations

Semedo, J. D., Zandvakili, A., Kohn, A., Machens, C. K. & Yu, B. M., 2014, Advances in Neural Information Processing Systems. January ed. Neural information processing systems foundation, Vol. 4. p. 2942-2950 9 p.

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

Neurons
Brain
Population dynamics
Statistical methods

Using SAGA and the open science grid to search for aptamers

Shieh, K., Broin, P. Ó., Rhee, D., Levy, M. & Golden, A., 2014, ACM International Conference Proceeding Series. Association for Computing Machinery, 27

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

Application programming interfaces (API)
RNA
Ligands
Oligonucleotides
Interfaces (computer)
2013
5 Citations (Scopus)

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

Tong, Y., Udupa, J. K., Odhner, D., Sin, S. & Arens, R., 2013, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. Vol. 8672. 86721R

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

anatomy
Adiposity
Magnetic resonance imaging
Anatomy
Body Regions
14 Citations (Scopus)

A powerful statistical method for identifying differentially methylated markers in complex diseases

Ahn, S. & Wang, T., 2013, 18th Pacific Symposium on Biocomputing, PSB 2013. World Scientific Publishing Co. Pte Ltd, p. 69-79 11 p.

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

Methylation
Statistical methods
Tissue
DNA Methylation
Epigenomics
6 Citations (Scopus)

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

Thompson, A. M., Benni, P., Seyhan, S. & Ehrenkranz, R., 2013, Advances in Experimental Medicine and Biology. Vol. 765. p. 287-292 6 p. (Advances in Experimental Medicine and Biology; vol. 765).

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

Meconium
Near infrared spectroscopy
Near-Infrared Spectroscopy
Premature Infants
Oxygen
1 Citation (Scopus)

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

Clark, A., Williams, J., Padgen, M., Keely, P., Condeelis, J. S. & Castracane, J., 2013, Proceedings of SPIE - The International Society for Optical Engineering. Vol. 8615. 86150C

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

BioMEMS
Metastasis
metastasis
Tumors
Hydrogel
4 Citations (Scopus)

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., 2013, Proceedings of SPIE - The International Society for Optical Engineering. Vol. 8670. 86702S

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

sleep
ovaries
Ovary
Pediatrics
Sleep

Spring through the gateway - Deploying genomic workflows with XSEDE

Rhee, D., Hargitai, J., Brent Calder, R., Broin, P. Ó., Shieh, K. & Golden, A., 2013, ACM International Conference Proceeding Series. 30

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

Genes
Nucleotides
Assays
Proteins
Methylation
1 Citation (Scopus)

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

inhabitants
social participation
inhabitant
test
rooms
2012

High sensitivity MEMS biosensor for monitoring cell attachment

Liu, F., Li, F., Spray, D. C., Nordin, A. N. & Voiculescu, I., 2012, ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE). PARTS A AND B ed. Vol. 9. p. 67-71 5 p.

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

Biosensors
MEMS
Acoustic impedance
Monitoring
Quartz crystal microbalances

In vivo spectroscopy of cervical tissue

Mourant, J. R., Marina, O. C. & Smith, H. O., 2012, Biomedical Optics, BIOMED 2012.

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

pathology
lesions
Spectrum Analysis
Pathology
spectroscopy

In vivo spectroscopy of cervical tissue

Mourant, J. R., Marina, O. C. & Smith, H. O., 2012, Digital Holography and Three-Dimensional Imaging, DH 2012.

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

pathology
Pathology
lesions
Spectroscopy
Tissue

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., 2012, Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. p. 1542-1545 4 p. 6346236

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

Neuroimaging
Walking
Brain
Imaging techniques
Evoked Potentials

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

Krumholz, A., Filonov, G. S., Xia, J., Yao, J., Verkhusha, V. & Wang, L. V., 2012, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. Vol. 8223. 82233A

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

Photoacoustic effect
Tumors
tumors
Infrared radiation
proteins

Probing the tumor microenvironment: Collection and induction

Williams, J. K., Padgen, M. R., Wang, Y., Entenberg, D. R., Gertler, F., Condeelis, J. S. & Castracane, J., 2012, Proceedings of SPIE - The International Society for Optical Engineering. Vol. 8251. 825105

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

Tumors
Tumor
Proof by induction
induction
tumors

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., 2012, IEEE Nuclear Science Symposium Conference Record. p. 2938-2941 4 p. 6551671

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

Single-Photon Emission-Computed Tomography
Radioisotopes
organs
radioactive isotopes
therapy
1 Citation (Scopus)

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., 2012, Studies in Health Technology and Informatics. Vol. 175. p. 182-191 10 p.

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

Biological Science Disciplines
Computing Methodologies
Genes
Throughput
Genome
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., 2011, Proceedings of SPIE - The International Society for Optical Engineering. Vol. 7929. 792905

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

Tumors
Tumor
Cancer
tumors
cancer
1 Citation (Scopus)

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. S. & Castracane, J., 2011, Proceedings of SPIE - The International Society for Optical Engineering. Vol. 7929. 79290A

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

Hydrogel
Hydrogels
Cancer
BioMEMS
cancer
2 Citations (Scopus)

Electrophysiological source analysis of passive self-motion

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

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

Electroencephalography
Motion Perception
1 Citation (Scopus)

Immune system modulation with LOFU and HIFU treatment of prostate cancer

Guha, C., Huagang, Z., Chen, W., Carlosn, R. & Sanghvi, N. T., 2011, AIP Conference Proceedings. Vol. 1359. p. 277-282 6 p.

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

immune systems
tumors
cancer
modulation
energy

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., 2011, 2011 IEEE 37th Annual Northeast Bioengineering Conference, NEBEC 2011. 5778556

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

Freezing
Visualization
Transmission electron microscopy
Substitution reactions
Endothelial cells

Motion P3 demonstrates neural nature of motion ERPs

Nolan, H., Butler, J. S., Whelan, R., Foxe, J. J., Bulthoff, H. H. & Reilly, R. B., 2011, Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. p. 3884-3887 4 p. 6090965

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

Enterprise resource planning
Data recording
Motion Perception
Artifacts
Reproduction

Piconewton level loading and sub-cellular deformation of bone cells using a novel stokesian fluid stimulus probe (SFSP)

Wu, D., Ganatos, P., Weinbaum, S. & Spray, D. C., 2011, ASME 2011 Summer Bioengineering Conference, SBC 2011. PARTS A AND B ed. p. 501-502 2 p.

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

Bone
Fluids
3 Citations (Scopus)

Roles for N- and O-glycans in early mouse development

Williams, S. A. & Stanley, P., 2011, Advances in Experimental Medicine and Biology. Vol. 705. p. 397-410 14 p. (Advances in Experimental Medicine and Biology; vol. 705).

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

Polysaccharides
Sugars
Glycosyltransferases
Fucose
Glycosylation

Study of cells attachment using impedance spectroscopy technique

Nordin, A. N., Arifuzzaman, S. M., Mel, M., Spray, D. C. & Voiculescu, I., 2011, ASME 2011 International Mechanical Engineering Congress and Exposition, IMECE 2011. Vol. 2. p. 931-935 5 p.

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

Endothelial cells
Cell culture
Cells
Spectroscopy
Fibroblasts

The roles of HS and its glypican-1 core protein in flow-induced endothelial NOS activation and cell remodeling

Ebong, E. E., Spray, D. C. & Tarbell, J. M., 2011, ASME 2011 Summer Bioengineering Conference, SBC 2011. PARTS A AND B ed. p. 321-322 2 p.

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

Chemical activation
Proteins
2010
7 Citations (Scopus)

Characterization of endothelial cells using electrochemical impedance spectroscopy

Liu, F., Arifuzzaman, S. M., Nordin, A. N., Spray, D. C. & Voiculescu, I., 2010, IEEE Asia-Pacific Conference on Circuits and Systems, Proceedings, APCCAS. p. 252-255 4 p. 5774824

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

Endothelial cells
Electrochemical impedance spectroscopy
Cell culture
Acoustic impedance
Substrates