Research Output

2020

A kinetic mechanism for enhanced selectivity of membrane transport

Bisignano, P., Lee, M. A., George, A., Zuckerman, D. M., Grabe, M. & Rosenberg, J. M., Jul 2020, In : PLoS computational biology. 16, 7, e1007789.

Research output: Contribution to journalArticle

Open Access

Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4

Coleman, D. J., Sampson, D. A., Sehrawat, A., Kumaraswamy, A., Sun, D., Wang, Y., Schwartzman, J., Urrutia, J., Lee, A. R., Coleman, I. M., Nelson, P. S., Dong, X., Morrissey, C., Corey, E., Xia, Z., Yates, J. A. & Alumkal, J. J., Jun 2020, In : Neoplasia (United States). 22, 6, p. 253-262 10 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

A multitask multiple kernel learning formulation for discriminating early- and late-stage cancers

Rahimi, A. & Gönen, M., Jun 1 2020, In : Bioinformatics (Oxford, England). 36, 12, p. 3766-3772 7 p.

Research output: Contribution to journalArticle

1 Scopus citations

An artificial intelligence decision support system for the management of type 1 diabetes

Tyler, N. S., Mosquera-Lopez, C. M., Wilson, L. M., Dodier, R. H., Branigan, D. L., Gabo, V. B., Guillot, F. H., Hilts, W. W., El Youssef, J., Castle, J. R. & Jacobs, P. G., Jul 1 2020, In : Nature Metabolism. 2, 7, p. 612-619 8 p.

Research output: Contribution to journalArticle

Androgen receptor-binding sites are highly mutated in prostate cancer

Morova, T., McNeill, D. R., Lallous, N., Gönen, M., Dalal, K., Wilson, D. M., Gürsoy, A., Keskin, Ö. & Lack, N. A., Dec 1 2020, In : Nature communications. 11, 1, 832.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

A phase II single-arm study of pembrolizumab with enzalutamide in men with metastatic castration-resistant prostate cancer progressing on enzalutamide alone

Graff, J. N., Beer, T. M., Alumkal, J. J., Slottke, R. E., Redmond, W. L., Thomas, G. V., Thompson, R. F., Wood, M. A., Koguchi, Y., Chen, Y., Latour, E., Bergan, R. C., Drake, C. G. & Moran, A. E., Jul 2 2020, In : Journal for immunotherapy of cancer. 8, 2, e00642.

Research output: Contribution to journalArticle

Open Access

A prospective prediction tool for understanding Crimean–Congo haemorrhagic fever dynamics in Turkey

Ak, Ergönül & Gönen, M., Jan 2020, In : Clinical Microbiology and Infection. 26, 1, p. 123.e1-123.e7

Research output: Contribution to journalArticle

1 Scopus citations

Artificial intelligence in decision support systems for type 1 diabetes

Tyler, N. S. & Jacobs, P. G., Jun 1 2020, In : Sensors (Switzerland). 20, 11, 3214.

Research output: Contribution to journalReview article

Open Access

Assessment of neonatal, cord, and adult platelet granule trafficking and secretion

Ngo, A. T. P., Sheriff, J., Rocheleau, A. D., Bucher, M., Jones, K. R., Sepp, A. L. I., Malone, L. E., Zigomalas, A., Maloyan, A., Bahou, W. F., Bluestein, D., McCarty, O. J. T. & Haley, K. M., Jan 2 2020, In : Platelets. 31, 1, p. 68-78 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms

George, A., Bisignano, P., Rosenberg, J. M., Grabe, M. & Zuckerman, D. M., Jul 2020, In : PLoS computational biology. 16, 7, e1007884.

Research output: Contribution to journalArticle

Open Access

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms (Scientific Data, (2020), 7, 1, (136), 10.1038/s41597-020-0477-8)

Ostaszewski, M., Mazein, A., Gillespie, M. E., Kuperstein, I., Niarakis, A., Hermjakob, H., Pico, A. R., Willighagen, E. L., Evelo, C. T., Hasenauer, J., Schreiber, F., Dräger, A., Demir, E., Wolkenhauer, O., Furlong, L. I., Barillot, E., Dopazo, J., Orta-Resendiz, A., Messina, F., Valencia, A. & 5 others, Funahashi, A., Kitano, H., Auffray, C., Balling, R. & Schneider, R., Dec 1 2020, In : Scientific Data. 7, 1, 247.

Research output: Contribution to journalComment/debate

Open Access

A workflow for visualizing human cancer biopsies using large-format electron microscopy

Riesterer, J. L., López, C. S., Stempinski, E. S., Williams, M., Loftis, K., Stoltz, K., Thibault, G., Lanicault, C., Williams, T. & Gray, J. W., 2020, Methods in Cell Biology. Tran, P. (ed.). Academic Press Inc., p. 163-181 19 p. (Methods in Cell Biology; vol. 158).

Research output: Chapter in Book/Report/Conference proceedingChapter

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Ostaszewski, M., Mazein, A., Gillespie, M. E., Kuperstein, I., Niarakis, A., Hermjakob, H., Pico, A. R., Willighagen, E. L., Evelo, C. T., Hasenauer, J., Schreiber, F., Dräger, A., Demir, E., Wolkenhauer, O., Furlong, L. I., Barillot, E., Dopazo, J., Orta-Resendiz, A., Messina, F., Valencia, A. & 5 others, Funahashi, A., Kitano, H., Auffray, C., Balling, R. & Schneider, R., Dec 1 2020, In : Scientific Data. 7, 1, 136.

Research output: Contribution to journalComment/debate

Open Access
1 Scopus citations
3 Scopus citations

Deregulating MYC in a model of HER2+ breast cancer mimics human intertumoral heterogeneity

Risom, T., Wang, X., Liang, J., Zhang, X., Pelz, C., Campbell, L. G., Eng, J., Chin, K., Farrington, C., Narla, G., Langer, E. M., Sun, X. X., Su, Y., Daniel, C. J., Dai, M. S., Löhr, C. V. & Sears, R. C., Jan 2 2020, In : Journal of Clinical Investigation. 130, 1, p. 231-246 16 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Development and implementation of the SUM breast cancer cell line functional genomics knowledge base

Ethier, S. P., Guest, S. T., Garrett-Mayer, E., Armeson, K., Wilson, R. C., Duchinski, K., Couch, D., Gray, J. W. & Kappler, C., Dec 1 2020, In : npj Breast Cancer. 6, 1, 30.

Research output: Contribution to journalArticle

Open Access

EmrE reminds us to expect the unexpected in membrane transport

Grabe, M., Zuckerman, D. M. & Rosenberg, J. M., Jan 6 2020, In : The Journal of general physiology. 152, 1

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Evaluation of the Antihemostatic and Antithrombotic Effects of Lowering Coagulation Factor VII Levels in a Non-human Primate

Wallisch, M., Olson, S. R., Crosby, J., Johnson, J., Murray, S. F., Shatzel, J. J., Tucker, E., McCarty, O., Hinds, M. T., Monia, B. P. & Gruber, A., Jun 1 2020, In : Cellular and Molecular Bioengineering. 13, 3, p. 179-187 9 p.

Research output: Contribution to journalArticle

Evaluation of the Effect of Crosslinking Method of Poly(Vinyl Alcohol) Hydrogels on Thrombogenicity

Bates, N. M., Puy, C., Jurney, P. L., McCarty, O. J. T. & Hinds, M. T., Aug 1 2020, In : Cardiovascular Engineering and Technology. 11, 4, p. 448-455 8 p.

Research output: Contribution to journalArticle

Fluorescence image-guided surgery: A perspective on contrast agent development

Barth, C. W. & Gibbs, S. L., Jan 1 2020, Molecular-Guided Surgery: Molecules, Devices, and Applications VI. Gioux, S., Gibbs, S. L. & Pogue, B. W. (eds.). SPIE, 112220J. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11222).

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

1 Scopus citations

Fluorescent imaging technologies for in situ measurement of drug target engagement and cell signaling pathways

McMahon, N. P., Solanki, A., Jones, J., Kwon, S., Chang, Y. H., Chin, K., Nederlof, M. A., Gray, J. W. & Gibbs, S. L., Jan 1 2020, Visualizing and Quantifying Drug Distribution in Tissue IV. Chan, K. F. & Evans, C. L. (eds.). SPIE, 112190O. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11219).

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

Fucoidan functionalization on poly(vinyl alcohol) hydrogels for improved endothelialization and hemocompatibility

Yao, Y., Zaw, A. M., Anderson, D. E. J., Hinds, M. T. & Yim, E. K. F., Aug 2020, In : Biomaterials. 249, 120011.

Research output: Contribution to journalArticle

2 Scopus citations

High-dimensional multiplexed immunohistochemical characterization of immune contexture in human cancers

Banik, G., Betts, C. B., Liudahl, S. M., Sivagnanam, S., Kawashima, R., Cotechini, T., Larson, W., Goecks, J., Pai, S. I., Clayburgh, D. R., Tsujikawa, T. & Coussens, L. M., 2020, Methods in Enzymology. Galluzzi, L. & Rudqvist, N-P. (eds.). Academic Press Inc., p. 1-20 20 p. (Methods in Enzymology; vol. 635).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

In Regard to Wallner et al

Kang, J., Thompson, R. F., Fuller, C. D., Camphausen, K. A., Gabriel, P. E. & Thomas, C. R., Jan 1 2020, In : International Journal of Radiation Oncology Biology Physics. 106, 1, p. 217-218 2 p.

Research output: Contribution to journalLetter

Open Access
1 Scopus citations

Intracellular paired agent imaging enables improved evaluation of tyrosine kinase inhibitor target engagement

Solanki, A., Wang, L., Korber, J., McMahon, N., Tichauer, K., Samkoe, K. S. & Gibbs, S. L., Jan 1 2020, Visualizing and Quantifying Drug Distribution in Tissue IV. Chan, K. F. & Evans, C. L. (eds.). SPIE, 112190F. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11219).

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

In vivo nerve-specificity of rhodamines and Si-rhodamines

Montano, A. R., Wang, L. G., Barth, C. W., Shams, N. A., Kumarapeli, K. A. S. U. & Gibbs, S. L., Jan 1 2020, Molecular-Guided Surgery: Molecules, Devices, and Applications VI. Gioux, S., Gibbs, S. L. & Pogue, B. W. (eds.). SPIE, 112220I. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11222).

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

1 Scopus citations

Measuring glucose at the site of insulin delivery with a redox-mediated sensor

Jacobs, P. G., Tyler, N. S., Vanderwerf, S. M., Mosquera-Lopez, C., Seidl, T., Cargill, R., Branigan, D., Ramsey, K., Morris, K., Benware, S., Ward, W. K. & Castle, J. R., Oct 1 2020, In : Biosensors and Bioelectronics. 165, 112221.

Research output: Contribution to journalArticle

Miniaturized Single Cell Imaging for Developing Immuno-Oncology Combinational Therapies

Jacob, T., Malla, P. & Vu, T., Jan 1 2020, Methods in Pharmacology and Toxicology. Humana Press Inc., p. 157-165 9 p. (Methods in Pharmacology and Toxicology).

Research output: Chapter in Book/Report/Conference proceedingChapter

National Cancer Institute Workshop on Artificial Intelligence in Radiation Oncology: Training the Next Generation

Kang, J., Thompson, R. F., Aneja, S., Lehman, C., Trister, A., Zou, J., Obcemea, C. & El Naqa, I., 2020, (Accepted/In press) In : Practical Radiation Oncology.

Research output: Contribution to journalArticle

Open Access

Near-infrared nerve-binding fluorophores for buried nerve tissue imaging

Wang, L. G., Barth, C. W., Kitts, C. H., Mebrat, M. D., Montaño, A. R., House, B. J., McCoy, M. E., Antaris, A. L., Galvis, S. N., McDowall, I., Sorger, J. M. & Gibbs, S. L., May 6 2020, In : Science translational medicine. 12, 542

Research output: Contribution to journalArticle

Noninvasive in vivo mapping of intracellular signaling proteins using a pairing of targeted and untargeted fluorescently labeled small molecule kinase inhibitors

Tichauer, K. M., Wang, L., Solanki, A., Korber, J. R., Gibbs, S. L. & Samkoe, K. S., Jan 1 2020, Visualizing and Quantifying Drug Distribution in Tissue IV. Chan, K. F. & Evans, C. L. (eds.). SPIE, 112190K. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11219).

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

Oligonucleotide conjugated antibodies permit highly multiplexed immunofluorescence for future use in clinical histopathology

Mcmahon, N. P., Jones, J. A., Kwon, S., Chin, K., Nederlof, M. A., Gray, J. W. & Gibbs, S. L., May 1 2020, In : Journal of biomedical optics. 25, 5, 056004.

Research output: Contribution to journalArticle

Open Access

One-Pot Covalent Grafting of Gelatin on Poly(Vinyl Alcohol) Hydrogel to Enhance Endothelialization and Hemocompatibility for Synthetic Vascular Graft Applications

Rizwan, M., Yao, Y., Gorbet, M. B., Tse, J. W., Anderson, D. E. J., Hinds, M. T. & Yim, E. K. F., Jan 21 2020, In : ACS Applied Bio Materials. 3, 1, p. 693-703 11 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

Rodchenkov, I., Babur, O., Luna, A., Aksoy, B. A., Wong, J. V., Fong, D., Franz, M., Siper, M. C., Cheung, M., Wrana, M., Mistry, H., Mosier, L., Dlin, J., Wen, Q., O'Callaghan, C., Li, W., Elder, G., Smith, P. T., Dallago, C., Cerami, E. & 5 others, Gross, B., Dogrusoz, U., Demir, E., Bader, G. D. & Sander, C., Jan 8 2020, In : Nucleic acids research. 48, D1, p. D489-D497

Research output: Contribution to journalArticle

Open Access
7 Scopus citations

Predicting primary site of secondary liver cancer with a neural estimator of metastatic origin

Schau, G. F., Burlingame, E. A., Thibault, G., Anekpuritanang, T., Wang, Y., Gray, J. W., Corless, C. & Chang, Y. H., Jan 1 2020, In : Journal of Medical Imaging. 7, 1, 012706.

Research output: Contribution to journalArticle

Probing the spatiotemporal dynamics of Ras-associated membrane nanodomains with high-throughput single particle tracking via photoactivated localization microscopy (spt-PALM)

Lee, Y., Tao, K., Phelps, C., Huang, T., Mostofian, B., Zuckerman, D. & Nan, X., Jan 1 2020, High-Speed Biomedical Imaging and Spectroscopy V. Tsia, K. K. & Goda, K. (eds.). SPIE, 112500N. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11250).

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

Quantification of fluorophore distribution and therapeutic response in matched in vivo and ex vivo pancreatic cancer model systems

Solanki, A., King, D., Thibault, G., Wang, L. & Gibbs, S. L., 2020, In : PloS one. 15, 2, e0229407.

Research output: Contribution to journalArticle

Open Access

RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging

Chang, Y. H., Chin, K., Thibault, G., Eng, J., Burlingame, E. & Gray, J. W., Dec 1 2020, In : Communications Biology. 3, 1, 111.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Simultaneous detection of rnas and proteins with subcellular resolution

Kwon, S., Chin, K. & Nederlof, M., 2020, Methods in Molecular Biology. Humana Press Inc., p. 59-73 15 p. (Methods in Molecular Biology; vol. 2161).

Research output: Chapter in Book/Report/Conference proceedingChapter

Targeting MerTK Enhances Adaptive Immune Responses After Radiation Therapy

Tormoen, G. W., Blair, T. C., Bambina, S., Kramer, G., Baird, J., Rahmani, R., Holland, J. M., McCarty, O. J. T., Baine, M. J., Verma, V., Nabavizadeh, N., Gough, M. J. & Crittenden, M., Sep 1 2020, In : International Journal of Radiation Oncology Biology Physics. 108, 1, p. 93-103 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

TGFβ signaling is critical for maintenance of the tendon cell fate

Tan, G. K., Pryce, B. A., Stabio, A., Brigande, J. V., Wang, C., Xia, Z., Tufa, S. F., Keene, D. R. & Schweitzer, R., Jan 2020, In : eLife. 9, e52695.

Research output: Contribution to journalArticle

Open Access
7 Scopus citations

The Efficacy of Basal Rate and Carbohydrate Ratio Learning Algorithm for Closed-Loop Insulin Delivery (Artificial Pancreas) in Youth with Type 1 Diabetes in a Diabetes Camp

Palisaitis, E., El Fathi, A., Von Oettingen, J. E., Krishnamoorthy, P., Kearney, R., Jacobs, P., Rutkowski, J., Legault, L. & Haidar, A., Mar 2020, In : Diabetes Technology and Therapeutics. 22, 3, p. 185-194 10 p.

Research output: Contribution to journalArticle

3 Scopus citations

The protein C activator AB002 rapidly interrupts thrombus development in baboons

Tucker, E. I., Verbout, N. G., Markway, B. D., Wallisch, M., Lorentz, C. U., Hinds, M. T., Shatzel, J. J., Pelc, L. A., Wood, D. C., McCarty, O. J. T., Di Cera, E. & Gruber, A., Feb 27 2020, In : Blood. 135, 9, p. 689-699 11 p.

Research output: Contribution to journalArticle

Open Access

The Sensor Technology and Rehabilitative Timing (START) Protocol: A Randomized Controlled Trial for the Rehabilitation of Mild Traumatic Brain Injury

Parrington, L., Jehu, D. A., Fino, P. C., Stuart, S., Wilhelm, J., Pettigrew, N., Murchison, C. F., El-Gohary, M., Vanderwalker, J., Pearson, S., Hullar, T., Chesnutt, J. C., Peterka, R. J., Horak, F. B. & King, L. A., Apr 17 2020, In : Physical therapy. 100, 4, p. 687-697 11 p.

Research output: Contribution to journalArticle

Venous Biomechanics of Angioplasty and Stent Placement: Implications of the Poisson Effect

Li, N., Mendoza, F., Rugonyi, S., Farsad, K., Kaufman, J. A., Jahangiri, Y., Uchida, B. T., Bonsignore, C. & Al-Hakim, R., Aug 2020, In : Journal of Vascular and Interventional Radiology. 31, 8, p. 1348-1356 9 p.

Research output: Contribution to journalArticle

2019

3D-Imaging of Whole Neuronal and Vascular Networks of the Human Dental Pulp via CLARITY and Light Sheet Microscopy

França, C. M., Riggers, R., Muschler, J. L., Widbiller, M., Lococo, P. M., Diogenes, A. & Bertassoni, L. E., Dec 1 2019, In : Scientific Reports. 9, 1, 10860.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2 Scopus citations

Adaptive tuning of basal and bolus insulin to reduce postprandial hypoglycemia in a hybrid artificial pancreas

Resalat, N., El Youssef, J., Reddy, R., Castle, J. & Jacobs, P., Aug 1 2019, In : Journal of Process Control. 80, p. 247-254 8 p.

Research output: Contribution to journalArticle

4 Scopus citations

A mechanism for hereditary angioedema with normal C1 inhibitor: An inhibitory regulatory role for the factor XII heavy chain

Ivanov, I., Matafonov, A., Sun, M. F., Mohammed, B. M., Cheng, Q., DIckeson, S. K., Kundu, S., Verhamme, I. M., Gruber, A., McCrae, K. & Gailani, D., 2019, In : Blood. 133, 10, p. 1152-1163 12 p.

Research output: Contribution to journalArticle

14 Scopus citations

A multitask multiple kernel learning algorithm for survival analysis with application to cancer biology

Dereli, O., Oǧuz, C. & Gönen, M., Jan 1 2019, 36th International Conference on Machine Learning, ICML 2019. International Machine Learning Society (IMLS), p. 2844-2853 10 p. (36th International Conference on Machine Learning, ICML 2019; vol. 2019-June).

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