Research Output 1978 2020

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2014
52 Citations (Scopus)

Coupling 3D Monte Carlo light transport in optically heterogeneous tissues to photoacoustic signal generation

Jacques, S., Dec 1 2014, In : Photoacoustics. 2, 4, p. 137-142 6 p.

Research output: Contribution to journalArticle

Acoustics
blood vessels
Blood Vessels
Light
acoustics
136 Citations (Scopus)

CUL4A induces epithelial-mesenchymal transition and promotes cancer metastasis by regulating ZEB1 expression

Wang, Y., Wen, M., Kwon, Y., Xu, Y., Liu, Y., Zhang, P., He, X., Wang, Q., Huang, Y., Jen, K. Y., Labarge, M. A., You, L., Kogan, S. C., Gray, J., Mao, J. H. & Wei, G., Jan 15 2014, In : Cancer Research. 74, 2, p. 520-531 12 p.

Research output: Contribution to journalArticle

Epithelial-Mesenchymal Transition
Breast Neoplasms
Neoplasm Metastasis
Neoplasms
Carcinogenesis
5 Citations (Scopus)

CXCR7 expression disrupts endothelial cell homeostasis and causes ligand-dependent invasion

Totonchy, J. E., Clepper, L., Phillips, K. G., McCarty, O. & Moses, A., 2014, In : Cell Adhesion and Migration. 8, 2, p. 165-176 12 p.

Research output: Contribution to journalArticle

Homeostasis
Endothelial Cells
Ligands
Blood Vessels
CD31 Antigens
28 Citations (Scopus)

Detecting cancer by monitoring circulating tumor DNA.

Spellman, P. & Gray, J., 2014, In : Nature Medicine. 20, 5, p. 474-475 2 p.

Research output: Contribution to journalArticle

Neoplasm DNA
Tumor Biomarkers
Non-Small Cell Lung Carcinoma
DNA
Neoplasms
7 Citations (Scopus)

Development of a method to quantify platelet adhesion and aggregation under static conditions

Baker-Groberg, S. M., Cianchetti, F. A., Phillips, K. G. & McCarty, O., 2014, In : Cellular and Molecular Bioengineering. 7, 2, p. 285-290 6 p.

Research output: Contribution to journalArticle

Platelets
Adhesion
Platelet Aggregation
Aggregation
Quantify
10 Citations (Scopus)

Do breast cancer cell lines provide a relevant model of the patient tumor methylome?

Cope, L. M., Fackler, M. J., Lopez-Bujanda, Z., Wolff, A. C., Visvanathan, K., Gray, J., Sukumar, S. & Umbricht, C. B., Aug 26 2014, In : PLoS One. 9, 8, e105545.

Research output: Contribution to journalArticle

breast neoplasms
Tumors
Cells
cell lines
Breast Neoplasms
10 Citations (Scopus)

Endocytic trafficking of laminin is controlled by dystroglycan and is disrupted in cancers

Leonoudakis, D., Huang, G., Akhavan, A., Fata, J. E., Singh, M., Gray, J. & Muschler, J., 2014, In : Journal of Cell Science. 127, 22, p. 4894-4903 10 p.

Research output: Contribution to journalArticle

Dystroglycans
Laminin
Neoplasms
Basement Membrane
Laminin Receptors
24 Citations (Scopus)

Endothelial outgrowth cells: Function and performance in vascular grafts

Glynn, J. J. & Hinds, M., Aug 1 2014, In : Tissue Engineering - Part B: Reviews. 20, 4, p. 294-303 10 p.

Research output: Contribution to journalArticle

Grafts
Blood Vessels
Endothelial Cells
Transplants
Endothelium
15 Citations (Scopus)

Engineering an endothelialized vascular graft: A rational approach to study design in a non-human primate model

Anderson, D. E. J., Glynn, J. J., Song, H. & Hinds, M., Dec 19 2014, In : PLoS One. 9, 12, e115163.

Research output: Contribution to journalArticle

blood vessels
Grafts
Primates
endothelial cells
Blood Vessels

Erratam: Tri-modal confocal mosaics detect residual invasive squamous cell carcinoma in Mohs surgical excisions (Journal of Biomedical Optics (2012) 17:6 (066018))

Gareau, D., Bar, A., Snaveley, N., Lee, K., Chen, N., Swanson, N., Simpson, E. & Jacques, S., Feb 2014, In : Journal of Biomedical Optics. 19, 2, 029801.

Research output: Contribution to journalArticle

cancer
optics
Biomedical optics
Epithelial Cells
21 Citations (Scopus)

Exact reconstruction of gene regulatory networks using compressive sensing

Chang, Y. H., Gray, J. & Tomlin, C. J., 2014, In : BMC Bioinformatics. 15, p. 400 1 p.

Research output: Contribution to journalArticle

Compressive Sensing
Gene Regulatory Networks
Gene Regulatory Network
Genes
Connectivity
33 Citations (Scopus)

Extraction of optical properties and prediction of light distribution in rat brain tissue

Azimipour, M., Baumgartner, R., Liu, Y., Jacques, S., Eliceiri, K. & Pashaie, R., 2014, In : Journal of Biomedical Optics. 19, 7, 075001.

Research output: Contribution to journalArticle

rats
brain
Rats
Brain
Optical properties
114 Citations (Scopus)

Factor XII inhibition reduces thrombus formation in a primate thrombosis model

Matafonov, A., Leung, P. Y., Gailani, A. E., Grach, S. L., Puy, C., Cheng, Q., Sun, M. F., McCarty, O., Tucker, E., Kataoka, H., Renné, T., Morrissey, J. H., Gruber, A. & Gailani, D., Mar 13 2014, In : Blood. 123, 11, p. 1739-1746 8 p.

Research output: Contribution to journalArticle

Factor XII
Primates
Thrombosis
Factor XI
Fibrin
22 Citations (Scopus)

Filtering of acoustic signals within the hearing organ

Ramamoorthy, S., Zha, D., Chen, F., Jacques, S., Wang, R., Choudhury, N., Nuttall, A. & Fridberger, A., 2014, In : Journal of Neuroscience. 34, 27, p. 9051-9058 8 p.

Research output: Contribution to journalArticle

Inner Auditory Hair Cells
Outer Auditory Hair Cells
Acoustics
Hearing
Vibration
14 Citations (Scopus)

Flow-dependent thrombin and fibrin generation in vitro: Opportunities for standardization: Communication from SSC of the ISTH

Neeves, K. B., McCarty, O., Reininger, A. J., Sugimoto, M. & King, M. R., Mar 2014, In : Journal of Thrombosis and Haemostasis. 12, 3, p. 418-420 3 p.

Research output: Contribution to journalArticle

International Cooperation
Medical Societies
Thromboplastin
Blood Coagulation
Fibrin
18 Citations (Scopus)

Heterogeneous intracellular trafficking dynamics of brain-derived neurotrophic factor complexes in the neuronal soma revealed by single quantum dot tracking

Vermehren-Schmaedick, A., Krueger, W., Jacob, T., Ramunno-Johnson, D., Balkowiec, A., Lidke, K. A. & Vu, T. T., Apr 14 2014, In : PLoS One. 9, 4, e95113.

Research output: Contribution to journalArticle

quantum dots
Quantum Dots
neurotrophins
Brain-Derived Neurotrophic Factor
Carisoprodol
8 Citations (Scopus)

Identification of gene regulation patterns underlying both oestrogen- and tamoxifen-stimulated cell growth through global gene expression profiling in breast cancer cells

Fan, P., Cunliffe, H. E., Griffith, O. L., Agboke, F. A., Ramos, P., Gray, J. & Jordan, V. C., 2014, In : European Journal of Cancer. 50, 16, p. 2877-2886 10 p.

Research output: Contribution to journalArticle

Gene Expression Profiling
Tamoxifen
Estrogens
Breast Neoplasms
Growth
22 Citations (Scopus)

Immobilization of Actively Thromboresistant Assemblies on Sterile Blood-Contacting Surfaces

Qu, Z., Krishnamurthy, V., Haller, C. A., Dorr, B. M., Marzec, U. M., Hurst, S., Hinds, M., Hanson, S. R., Liu, D. R. & Chaikof, E. L., Jan 2014, In : Advanced healthcare materials. 3, 1, p. 30-35 6 p.

Research output: Contribution to journalArticle

Grafts
Immobilization
Thrombomodulin
Blood
Transplants
11 Citations (Scopus)

Improving the efficiency of abdominal aortic aneurysm wall stress computations

Zelaya, J. E., Goenezen, S., Dargon, P. T., Azarbal, A. & Rugonyi, S., Jul 9 2014, In : PLoS One. 9, 7, e101353.

Research output: Contribution to journalArticle

aneurysm
Abdominal Aortic Aneurysm
Aneurysm
Rupture
Abdominal Aorta
11 Citations (Scopus)

Joint estimation of multiple related biological networks

Oates, C. J., Korkola, J., Gray, J. & Mukherjee, S., Sep 1 2014, In : Annals of Applied Statistics. 8, 3, p. 1892-1919 28 p.

Research output: Contribution to journalArticle

Biological Networks
Graphical Models
Molecular biology
Bayesian networks
Exchangeability
9 Citations (Scopus)

Measurement science in the circulatory system

Jones, C. M., Baker-Groberg, S. M., Cianchetti, F. A., Glynn, J. J., Healy, L. D., Lam, W. Y., Nelson, J. W., Parrish, D. C., Phillips, K. G., Scott-Drechsel, D. E., Tagge, I. J., Zelaya, J. E., Hinds, M. & McCarty, O., 2014, In : Cellular and Molecular Bioengineering. 7, 1, p. 1-14 14 p.

Research output: Contribution to journalArticle

Cardiovascular System
Measurement Techniques
Molecular Dynamics Simulation
Blood Proteins
Blood Cells
19 Citations (Scopus)

Molecular imaging: From bench to clinic

Wáng, Y. X. J., Choi, Y., Chen, Z., Laurent, S. & Gibbs, S., Dec 29 2014, In : BioMed Research International. 2014, 357258.

Research output: Contribution to journalArticle

Molecular imaging
Animals
626 Citations (Scopus)

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

Hoadley, K. A., Yau, C., Wolf, D. M., Cherniack, A. D., Tamborero, D., Ng, S., Leiserson, M. D. M., Niu, B., McLellan, M. D., Uzunangelov, V., Zhang, J., Kandoth, C., Akbani, R., Shen, H., Omberg, L., Chu, A., Margolin, A., Van'T Veer, L. J., Lopez-Bigas, N., Laird, P. W. & 12 others, Raphael, B. J., Ding, L., Robertson, A. G., Byers, L. A., Mills, G., Weinstein, J. N., Van Waes, C., Chen, Z., Collisson, E. A., Benz, C. C., Perou, C. M. & Xia, Z., Aug 14 2014, In : Cell. 158, 4, p. 929-944 16 p.

Research output: Contribution to journalArticle

Tissue
Urinary Bladder Neoplasms
Neoplasms
Genes
Data Mining
104 Citations (Scopus)

Nanoparticle-mediated systemic delivery of siRNA for treatment of cancers and viral infections

Draz, M. S., Fang, B. A., Zhang, P., Hu, Z., Gu, S., Weng, K. C., Gray, J. & Chen, F. F., 2014, In : Theranostics. 4, 9, p. 872-892 21 p.

Research output: Contribution to journalArticle

Virus Diseases
Nanoparticles
Small Interfering RNA
Metal Nanoparticles
Neoplasms
19 Citations (Scopus)

Neonatal platelets: Mediators of primary hemostasis in the developing hemostatic system

Haley, K., Recht, M. & McCarty, O., 2014, In : Pediatric Research. 76, 3, p. 230-237 8 p.

Research output: Contribution to journalArticle

Hemostatics
Hemostasis
Blood Platelets
Platelet Transfusion
Fetal Blood
14 Citations (Scopus)

Network signatures of nuclear and cytoplasmic density alterations in a model of pre and postmetastatic colorectal cancer

Damania, D., Subramanian, H., Backman, V., Anderson, E., Wong, M., McCarty, O. & Phillips, K. G., Jan 2014, In : Journal of Biomedical Optics. 19, 1, 016016.

Research output: Contribution to journalArticle

Microscopic examination
cancer
Cells
signatures
compartments
10 Citations (Scopus)
Mobile Applications
Rural Health Services
Audiology
United States Department of Veterans Affairs
Hearing Aids
28 Citations (Scopus)

Novel oral detoxification of mercury, cadmium, and lead with thiol-modified nanoporous silica

Sangvanich, T., Morry, J., Fox, C., Ngamcherdtrakul, W., Goodyear, S., Castro, D., Fryxell, G. E., Addleman, R. S., Summers, A. O. & Yantasee, W., Apr 23 2014, In : ACS Applied Materials and Interfaces. 6, 8, p. 5483-5493 11 p.

Research output: Contribution to journalArticle

Detoxification
Mercury (metal)
Heavy Metals
Mercury
Cadmium
40 Citations (Scopus)

Overcoming endocrine resistance due to reduced PTEN levels in estrogen receptor-positive breast cancer by co-targeting mammalian target of rapamycin, protein kinase B, or mitogen-activated protein kinase kinase

Fu, X., Creighton, C. J., Biswal, N. C., Kumar, V., Shea, M., Herrera, S., Contreras, A., Gutierrez, C., Wang, T., Nanda, S., Giuliano, M., Morrison, G., Nardone, A., Karlin, K. L., Westbrook, T. F., Heiser, L., Anur, P., Spellman, P., Guichard, S. M., Smith, P. D. & 10 others, Davies, B. R., Klinowska, T., Lee, A. V., Mills, G., Rimawi, M. F., Hilsenbeck, S. G., Gray, J., Joshi, A., Osborne, C. K. & Schiff, R., Sep 11 2014, In : Breast Cancer Research. 16, 5, 430.

Research output: Contribution to journalArticle

TOR Serine-Threonine Kinases
Proto-Oncogene Proteins c-akt
Mitogen-Activated Protein Kinase Kinases
Phosphatidylinositol 3-Kinase
Phosphoric Monoester Hydrolases
42 Citations (Scopus)

Photoactivated localization microscopy with Bimolecular Fluorescence Complementation (BiFC-PALM) for nanoscale imaging of protein-protein interactions in cells

Nickerson, A., Huang, T., Lin, L. J. & Nan, X., Jun 25 2014, In : PLoS One. 9, 6, e100589.

Research output: Contribution to journalArticle

protein-protein interactions
Cell Communication
Microscopy
microscopy
Microscopic examination
16 Citations (Scopus)

Physical biology in cancer. 2. The physical biology of circulating tumor cells

Phillips, K. G., Kuhn, P. & McCarty, O., Jan 15 2014, In : American Journal of Physiology - Cell Physiology. 306, 2

Research output: Contribution to journalArticle

Circulating Neoplastic Cells
Neoplasms
Cell Separation
Neoplasm Metastasis

Preface

Mendelsohn, J., Gray, J., Howley, P. M., Israel, M. A. & Thompson, C. B., Mar 2014, In : Unknown Journal.

Research output: Contribution to journalArticle

8 Citations (Scopus)
Interference Microscopy
Optical microscopy
Microscopy
Microscopic examination
Microscopes
46 Citations (Scopus)

Reconciliation of classification systems defining molecular subtypes of colorectal cancer: Interrelationships and clinical implications

Sadanandam, A., Wang, X., De Sousa E Melo, F., Gray, J., Vermeulen, L., Hanahan, D. & Medema, J. P., Feb 1 2014, In : Cell Cycle. 13, 3, p. 353-357 5 p.

Research output: Contribution to journalArticle

Colorectal Neoplasms
Gene Expression
Therapeutics
4 Citations (Scopus)

Reply to Colorectal cancer classification based on gene expression is not associated with FOLFIRI response

Sadanandam, A., Gray, J. & Hanahan, D., Nov 1 2014, In : Nature Medicine. 20, 11, p. 1231-1232 2 p.

Research output: Contribution to journalArticle

Gene expression
5 Citations (Scopus)

RRE-dependent HIV-1 Env RNA effects on Gag protein expression, assembly and release

Lopez, C., Sloan, R., Cylinder, I., Kozak, S. L., Kabat, D. & Barklis, E., 2014, In : Virology. 462-463, 1, p. 126-134 9 p.

Research output: Contribution to journalArticle

env Genes
gag Gene Products
HIV-1
RNA
Messenger RNA
65 Citations (Scopus)

Sensory reweighting dynamics in human postural control

Assländer, L. & Peterka, R. B., May 1 2014, In : Journal of Neurophysiology. 111, 9, p. 1852-1864 13 p.

Research output: Contribution to journalArticle

Proprioception
Torque
Cues
Healthy Volunteers
32 Citations (Scopus)

Sleep habits in mild cognitive impairment

Hayes, T. L., Riley, T., Mattek, N., Pavel, M. & Kaye, J., 2014, In : Alzheimer Disease and Associated Disorders. 28, 2, p. 145-150 6 p.

Research output: Contribution to journalArticle

Habits
Sleep
Self Report
Volunteers
Independent Living
12 Citations (Scopus)

Stance width changes how sensory feedback is used for multisegmental balance control

Goodworth, A. D., Mellodge, P. & Peterka, R. B., Aug 1 2014, In : Journal of Neurophysiology. 112, 3, p. 525-542 18 p.

Research output: Contribution to journalArticle

Sensory Feedback
Cues
Proprioception
Therapeutics
12 Citations (Scopus)

The role of the contact pathway in thrombus propagation

Gruber, A., 2014, In : Thrombosis Research. 133, SUPPL. 1

Research output: Contribution to journalArticle

Factor XII
Factor XIIa
Thrombin
Thrombosis
Hemostasis
8 Citations (Scopus)

Thrombin mutant W215A/E217A treatment improves neurological outcome and attenuates central nervous system damage in experimental autoimmune encephalomyelitis

Verbout, N. G., Yu, X., Healy, L. D., Phillips, K. G., Tucker, E., Gruber, A., McCarty, O. & Offner, H., 2014, In : Metabolic Brain Disease. 30, 1, p. 57-65 9 p.

Research output: Contribution to journalArticle

Autoimmune Experimental Encephalomyelitis
Neurology
Protein C
Thrombin
Multiple Sclerosis
8 Citations (Scopus)

Thrombotic responses of endothelial outgrowth cells to protein-coated surfaces

Anderson, D. E. J., McKenna, K., Glynn, J. J., Marzec, U., Hanson, S. R. & Hinds, M., Feb 24 2014, In : Cells Tissues Organs. 199, 4, p. 238-248 11 p.

Research output: Contribution to journalArticle

Membrane Proteins
Collagen
Endothelial Cells
Fibronectins
Transplants
44 Citations (Scopus)

Transcription Restores DNA Repair to Heterochromatin, Determining Regional Mutation Rates in Cancer Genomes

Zheng, C., Wang, N. J., Chung, J., Moslehi, H., Sanborn, J. Z., Hur, J. S., Collisson, E. A., Vemula, S. S., Naujokas, A., Chiotti, K. E., Cheng, J. B., Fassihi, H., Blumberg, A. J., Bailey, C. V., Fudem, G. M., Mihm, F. G., Cunningham, B. B., Neuhaus, I. M., Liao, W., Oh, D. H. & 10 others, Cleaver, J. E., LeBoit, P. E., Costello, J. F., Lehmann, A. R., Gray, J., Spellman, P., Arron, S. T., Huh, N., Purdom, E. & Cho, R. J., Nov 20 2014, In : Cell Reports. 9, 4, p. 1228-1234 7 p.

Research output: Contribution to journalArticle

Heterochromatin
Mutation Rate
Transcription
DNA Repair
Repair
53 Citations (Scopus)

Validating and calibrating the Nintendo Wii balance board to derive reliable center of pressure measures

Leach, J. M., Mancini, M., Peterka, R. B., Hayes, T. L. & Horak, F., 2014, In : Sensors (Basel, Switzerland). 14, 10, p. 18244-18267 24 p.

Research output: Contribution to journalArticle

center of pressure
calibrating
Pressure
Equipment and Supplies
Pendulums
2013
33 Citations (Scopus)

Accelerating 3B single-molecule super-resolution microscopy with cloud computing

Hu, Y. S., Nan, X., Sengupta, P., Lippincott-Schwartz, J. & Cang, H., Feb 2013, In : Nature Methods. 10, 2, p. 96-97 2 p.

Research output: Contribution to journalArticle

Nanotechnology
Computational Biology
Fluorescent Dyes
Fluorescence Microscopy
Microscopy
471 Citations (Scopus)

A colorectal cancer classification system that associates cellular phenotype and responses to therapy

Sadanandam, A., Lyssiotis, C. A., Homicsko, K., Collisson, E. A., Gibb, W. J., Wullschleger, S., Ostos, L. C. G., Lannon, W. A., Grotzinger, C., Del Rio, M., Lhermitte, B., Olshen, A. B., Wiedenmann, B., Cantley, L. C., Gray, J. & Hanahan, D., May 2013, In : Nature Medicine. 19, 5, p. 619-625 7 p.

Research output: Contribution to journalArticle

Colorectal Neoplasms
Phenotype
Chemotherapy
Disease-Free Survival
Filamins
19 Citations (Scopus)
Pulse Wave Analysis
Pulse
Chickens
Embryonic Structures
Blood Pressure
14 Citations (Scopus)

Analysis of small molecule ligands targeting the HIV-1 matrix protein-RNA binding site

Alfadhli, A., McNett, H., Eccles, J., Tsagli, S., Noviello, C., Sloan, R., Lopez, C., Peyton, D. H. & Barklis, E., Jan 4 2013, In : Journal of Biological Chemistry. 288, 1, p. 666-676 11 p.

Research output: Contribution to journalArticle

RNA
HIV-1
Binding Sites
Ligands
Proteins
68 Citations (Scopus)

Antithrombotic effect of antisense factor xi oligonucleotide treatment in primates

Crosby, J. R., Marzec, U., Revenko, A. S., Zhao, C., Gao, D., Matafonov, A., Gailani, D., MacLeod, A. R., Tucker, E., Gruber, A., Hanson, S. R. & Monia, B. P., Jul 2013, In : Arteriosclerosis, Thrombosis, and Vascular Biology. 33, 7, p. 1670-1678 9 p.

Research output: Contribution to journalArticle

Antisense Oligonucleotides
Oligonucleotides
Primates
Hemostasis
Thrombosis
90 Citations (Scopus)

A physical sciences network characterization of non-tumorigenic and metastatic cells

Agus, D. B., Alexander, J. F., Arap, W., Ashili, S., Aslan, J., Austin, R. H., Backman, V., Bethel, K. J., Bonneau, R., Chen, W. C., Chen-Tanyolac, C., Choi, N. C., Curley, S. A., Dallas, M., Damania, D., Davies, P. C. W., Decuzzi, P., Dickinson, L., Estevez-Salmeron, L., Estrella, V. & 75 others, Ferrari, M., Fischbach, C., Foo, J., Fraley, S. I., Frantz, C., Fuhrmann, A., Gascard, P., Gatenby, R. A., Geng, Y., Gerecht, S., Gillies, R. J., Godin, B., Grady, W. M., Greenfield, A., Hemphill, C., Hempstead, B. L., Hielscher, A., Hillis, W. D., Holland, E. C., Ibrahim-Hashim, A., Jacks, T., Johnson, R. H., Joo, A., Katz, J. E., Kelbauskas, L., Kesselman, C., King, M. R., Konstantopoulos, K., Kraning-Rush, C. M., Kuhn, P., Kung, K., Kwee, B., Lakins, J. N., Lambert, G., Liao, D., Licht, J. D., Liphardt, J. T., Liu, L., Lloyd, M. C., Lyubimova, A., Mallick, P., Marko, J., McCarty, O., Meldrum, D. R., Michor, F., Mumenthaler, S. M., Nandakumar, V., O'Halloran, T. V., Oh, S., Pasqualini, R., Paszek, M. J., Philips, K. G., Poultney, C. S., Rana, K., Reinhart-King, C. A., Ros, R., Semenza, G. L., Senechal, P., Shuler, M. L., Srinivasan, S., Staunton, J. R., Stypula, Y., Subramanian, H., Tlsty, T. D., Tormoen, G. W., Tseng, Y., Van Oudenaarden, A., Verbridge, S. S., Wan, J. C., Weaver, V. M., Widom, J., Will, C., Wirtz, D., Wojtkowiak, J. & Wu, P. H., 2013, In : Scientific Reports. 3, 1449.

Research output: Contribution to journalArticle

Natural Science Disciplines
Neoplasm Metastasis
Cell Line
Mechanics
Proteomics