Albert Einstein College of Medicine

Research Output 1960 2018

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Conference contribution
2017

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: ResearchConference 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: ResearchConference contribution

Radiotherapy
Genome
Forests
Toxicity
Genes

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: ResearchConference contribution

Lighting
Microscopy
illumination
microscopy
Microscopic examination
2016

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

Yang, Z., Shcherbakova, D. M., Verkhusha, V. 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: ResearchConference contribution

Fluorescence
Cells
Infrared radiation
Proteins
proteins

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. 2016 Microfluidics, BioMEMS, and Medical Microsystems XIV. SPIE, Vol. 9705, 97051A

Research output: ResearchConference contribution

Microfluidics
Equipment and Supplies
In Vitro Techniques
Cells
cells
14 Citations

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: ResearchConference contribution

Technology
Transcription
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. 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: ResearchConference contribution

Prioritization
Logistic Regression
Gene
Logistics
Genes

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. 2016 Photons Plus Ultrasound: Imaging and Sensing 2016. SPIE, Vol. 9708, 97082U

Research output: ResearchConference contribution

Phytochrome
Photoacoustic effect
Tomography
Infrared radiation
Imaging techniques

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: ResearchConference contribution

Pathogens
Assays
Semantics
Systems Biology
Data warehouses
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: ResearchConference contribution

tumors
mechanical properties
cells
Tumor Microenvironment
Equipment and Supplies
4 Citations

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: ResearchConference contribution

Super-resolution
Microscope
High Speed
Camera
Imaging

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: ResearchConference contribution

Tonsillectomy
Obstructive Sleep Apnea
Anatomy
sleep
anatomy

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: ResearchConference contribution

refractories
image analysis
cancer
predictions
Neuroblastoma
3 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 International IEEE/EMBS Conference on Neural Engineering, NER. IEEE Computer Society, Vol. 2015-July, p. 308-311 4 p. 7146621

Research output: ResearchConference contribution

Chemical activation
Electroencephalography
Neuroimaging
Brain computer interface
1 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. 2015 Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9417, 94172J

Research output: ResearchConference contribution

Palatine Tonsil
Obstructive Sleep Apnea
sleep
respiration
Sleep
2 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. 2015 Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9416, 94161K

Research output: ResearchConference contribution

ground truth
tomography
evaluation
photons
Single photon emission computed tomography
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: ResearchConference contribution

Clustering algorithms
Magnetic resonance imaging
Tissue
Water
Abdominal Fat
1 Citations

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: ResearchConference contribution

Magnetic resonance imaging
Seeds
preprocessing
nonuniformity
seeds
6 Citations

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: ResearchConference 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: ResearchConference contribution

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

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: ResearchConference contribution

Adiposity
Anatomy
Magnetic resonance imaging
anatomy
Body Regions
6 Citations

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: ResearchConference contribution

Methylation
Statistical methods
Tissue
Genes
DNA Methylation
2 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. 2013 Advances in Experimental Medicine and Biology. Vol. 765, p. 287-292 6 p. (Advances in Experimental Medicine and Biology; vol. 765)

Research output: ResearchConference contribution

Meconium
Near-Infrared Spectroscopy
Premature Infants
Oxygen
Light
1 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. 2013 Proceedings of SPIE - The International Society for Optical Engineering. Vol. 8615, 86150C

Research output: ResearchConference contribution

BioMEMS
Tumors
Cells
Metastasis
Cell
2 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. 2013 Proceedings of SPIE - The International Society for Optical Engineering. Vol. 8670, 86702S

Research output: ResearchConference contribution

Ovary
Pediatrics
Sleep
Object
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: ResearchConference contribution

Genes
Nucleotides
Assays
Proteins
Methylation

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: ResearchConference contribution

test
inhabitant
inhabitants
social participation
video
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: ResearchConference contribution

Biosensors
MEMS
Monitoring
Acoustic impedance
Quartz crystal microbalances

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: ResearchConference contribution

pathology
lesions
spectroscopy
Pathology
Spectroscopy

In vivo spectroscopy of cervical tissue

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

Research output: ResearchConference contribution

pathology
lesions
spectroscopy
Spectrum Analysis
Pathology
11 Citations

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: ResearchConference 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. V. & Wang, L. V. 2012 Progress in Biomedical Optics and Imaging - Proceedings of SPIE. Vol. 8223, 82233A

Research output: ResearchConference contribution

Photoacoustic effect
Tumors
Infrared radiation
Imaging techniques
Proteins

Probing the tumor microenvironment: Collection and induction

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

Research output: ResearchConference contribution

Tumor
Proof by induction
induction
tumors
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: ResearchConference contribution

organs
radioactive isotopes
therapy
simulation
Single-Photon Emission-Computed Tomography
1 Citations

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: ResearchConference contribution

Biological Science Disciplines
Genome
Technology
Genes
Throughput
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: ResearchConference contribution

Tumors
Cells
Electrodes
tumors
cancer
1 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. 2011 Proceedings of SPIE - The International Society for Optical Engineering. Vol. 7929, 79290A

Research output: ResearchConference contribution

Cancer
Path
Cell
Hydrogel
Cells
2 Citations

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: ResearchConference contribution

Electroencephalography
Motion Perception
1 Citations

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: ResearchConference 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: ResearchConference contribution

Visualization
Transmission electron microscopy
Freezing
Substitution reactions
Endothelial cells
4 Citations

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: ResearchConference 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: ResearchConference contribution

2 Citations

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: ResearchConference contribution

Polysaccharides
Sugars
Glycosyltransferases
Fucose
Amino Acids

Study of cells attachment using impedance spectroscopy technique

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

Research output: ResearchConference 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: ResearchConference contribution

2010
7 Citations

Characterization of endothelial cells using electrochemical impedance spectroscopy

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

Research output: ResearchConference contribution

Endothelial cells
Electrochemical impedance spectroscopy
Cell culture
Substrates
Acoustic impedance

Constructing binary decision trees for predicting Deep Venous Thrombosis

Nwosisi, C., Cha, S. H., An, Y. J., Tappert, C. C. & Lipsitz, E. 2010 ICSTE 2010 - 2010 2nd International Conference on Software Technology and Engineering, Proceedings. Vol. 1, 5608901

Research output: ResearchConference contribution

Decision trees
Blood
Genetic algorithms
2 Citations

Device for in-vivo study of the tumor microenvironment

Raja, W. K., Gligorijevic, B., Padgen, M. R., Eggers, D., Condeelis, J. & Castracane, J. 2010 Progress in Biomedical Optics and Imaging - Proceedings of SPIE. Vol. 7593, 75930H

Research output: ResearchConference contribution

Tumors
tumors
Tumor Microenvironment
Equipment and Supplies
Electrodes
7 Citations

Emulsion based selection of T7 promoters of varying activity

Davidson, E. A., Van Blarcom, T., Levy, M. & Ellington, A. D. 2010 Pacific Symposium on Biocomputing 2010, PSB 2010. p. 433-443 11 p.

Research output: ResearchConference contribution

Transcription
Emulsions
In Vitro Techniques
Biological systems
RNA

Modulation of the conformation of cytochrome C oxidase from Paracoccus denitrificans by active-site mutations

Rousseau, D. L., Ji, H., Egawa, T., Das, T., Puustinin, A., Wikström, M. & Yeh, S. R. 2010 AIP Conference Proceedings. Vol. 1267, p. 27-28 2 p.

Research output: ResearchConference contribution