Research Output

2020

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

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

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

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., Jan 1 2020, (Accepted/In press) Methods in Cell Biology. Academic Press Inc., (Methods in Cell Biology).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 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
1 Scopus citations

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

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. I., McCarty, O. J. T., Hinds, M. T., Monia, B. P. & Gruber, A., Jan 1 2020, (Accepted/In press) In : Cellular and Molecular Bioengineering.

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

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

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

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

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

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

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

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

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

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., Jan 1 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

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
1 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

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
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., Widbiller, M., Lococo, P. M., Diogenes, A. & Bertassoni, L., Dec 1 2019, In : Scientific Reports. 9, 1, 10860.

Research output: Contribution to journalArticle

Open Access

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

3 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., Mar 7 2019, In : Blood. 133, 10, p. 1152-1163 12 p.

Research output: Contribution to journalArticle

12 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

Annot: A Django-based sample, reagent, and experiment metadata tracking system

Bucher, E., Claunch, C. J., Hee, D., Smith, R. L., Devlin, K., Thompson, W., Korkola, J. E. & Heiser, L. M., Nov 1 2019, In : BMC bioinformatics. 20, 1, 542.

Research output: Contribution to journalArticle

Open Access

A non-circulating pool of factor XI associated with glycosaminoglycans in mice

Mohammed, B. M., Cheng, Q., Matafonov, A., Verhamme, I. M., Emsley, J., McCrae, K. R., McCarty, O., Gruber, A. & Gailani, D., Jan 1 2019, In : Journal of Thrombosis and Haemostasis.

Research output: Contribution to journalArticle

4 Scopus citations

Antithrombotic Strategies After Bioprosthetic Aortic Valve Replacement: A Systematic Review

Papak, J. N., Chiovaro, J. C., Noelck, N., Healy, L. D., Freeman, M., Quin, J. A., Paynter, R., Low, A., Kondo, K., McCarty, O. J. T. & Kansagara, D., May 2019, In : Annals of Thoracic Surgery. 107, 5, p. 1571-1581 11 p.

Research output: Contribution to journalReview article

3 Scopus citations

Artificial Intelligence in Radiation Oncology

Deig, C. R., Kanwar, A. & Thompson, R., Jan 1 2019, (Accepted/In press) In : Hematology/Oncology Clinics of North America.

Research output: Contribution to journalReview article

Assessment of human pancreas cancer tissue and precursor lesions via a fluorophore with inherent PDAC selectivity

Munhenzva, I. R., Barth, C. W., Sibrian-Vazquez, M., Wang, L. G., Escobedo, J. O., Gibbs, S. & Strongin, R. M., Jan 1 2019, In : Methods.

Research output: Contribution to journalArticle

2 Scopus citations

A statistical virtual patient population for the glucoregulatory system in type 1 diabetes with integrated exercise model

Resalat, N., El Youssef, J., Tyler, N., Castle, J. & Jacobs, P., Jan 1 2019, In : PloS one. 14, 7, e0217301.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

BET bromodomain inhibition blocks the function of a critical AR-independent master regulator network in lethal prostate cancer

Coleman, D. J., Gao, L., King, C. J., Schwartzman, J., Urrutia, J., Sehrawat, A., Tayou, J., Balter, A., Burchard, J., Chiotti, K. E., Derrick, D. S., Sun, D., Xia, Z., Heiser, L. & Alumkal, J., Jan 1 2019, In : Oncogene.

Research output: Contribution to journalArticle

4 Scopus citations

Biomimetic modification of poly(vinyl alcohol): Encouraging endothelialization and preventing thrombosis with antiplatelet monotherapy

Anderson, D. E. J., Truong, K. P., Hagen, M. W., Yim, E. K. F. & Hinds, M., Jan 1 2019, (Accepted/In press) In : Acta Biomaterialia.

Research output: Contribution to journalArticle

5 Scopus citations

Bleeding TAPs out

Ngo, A. T. P., Aslan, J. E. & McCarty, O. J. T., Feb 1 2019, In : Journal of Thrombosis and Haemostasis. 17, 2, p. 247-249 3 p.

Research output: Contribution to journalComment/debate

Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis

Vedanayagam, J., Chatila, W. K., Aksoy, B. A., Majumdar, S., Skanderup, A. J., Demir, E., Schultz, N., Sander, C. & Lai, E. C., Dec 1 2019, In : Nature communications. 10, 1, 3682.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Career enrichment opportunities at the scientific frontier in radiation oncology

Thompson, R. F., Fuller, C. D., Berman, A. T., Aneja, S. & Thomas, C. R., Jan 1 2019, In : JCO Clinical Cancer Informatics. 3

Research output: Contribution to journalEditorial

Circulating tumor DNA dynamics using patient-customized assays are associated with outcome in neoadjuvantly treated breast cancer

Butler, T. M., Boniface, C. T., Johnson-Camacho, K., Tabatabaei, S., Melendez, D., Kelley, T., Gray, J., Corless, C. L. & Spellman, P. T., Jan 1 2019, In : Cold Spring Harbor Molecular Case Studies. 5, 2, a003772.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation

Weng, T., Ko, J., Masamha, C. P., Xia, Z., Xiang, Y., Chen, N. Y., Molina, J. G., Collum, S., Mertens, T. C., Luo, F., Philip, K., Davies, J., Huang, J., Wilson, C., Thandavarayan, R. A., Bruckner, B. A., Jyothula, S. S. K., Volcik, K. A., Li, L., Han, L. & 5 others, Li, W., Assassi, S., Karmouty-Quintana, H., Wagner, E. J. & Blackburn, M. R., May 1 2019, In : Journal of Clinical Investigation. 129, 5, p. 1984-1999 16 p.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

cmIF: A Python Library for Scalable Multiplex Imaging Pipelines

Eng, J., Bucher, E., Gray, E., Campbell, L. G., Thibault, G., Heiser, L., Gibbs, S., Gray, J. W., Chin, K. & Chang, Y. H., Jan 1 2019, Mathematical and Computational Oncology - 1st International Symposium, ISMCO 2019, Proceedings. Bebis, G., Benos, T., Chen, K., Jahn, K. & Lima, E. (eds.). Springer, p. 37-43 7 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11826 LNCS).

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

1 Scopus citations

Computational Estimation of Microsecond to Second Atomistic Folding Times

Adhikari, U., Mostofian, B., Copperman, J., Subramanian, S. R., Petersen, A. A. & Zuckerman, D. M., Apr 24 2019, In : Journal of the American Chemical Society. 141, 16, p. 6519-6526 8 p.

Research output: Contribution to journalArticle

4 Scopus citations

Contact Activation Inhibitor and Factor XI Antibody, AB023, Produces Safe, Dose-Dependent Anticoagulation in a Phase 1 First-In-Human Trial

Lorentz, C. U., Verbout, N. G., Wallisch, M., Hagen, M. W., Shatzel, J. J., Olson, S. R., Puy, C., Hinds, M., McCarty, O., Gailani, D., Gruber, A. & Tucker, E., Apr 1 2019, In : Arteriosclerosis, thrombosis, and vascular biology. 39, 4, p. 799-809 11 p.

Research output: Contribution to journalArticle

Open Access

Contact system sends defensins to the rescue

Healy, L. D. & McCarty, O., Jan 31 2019, In : Blood. 133, 5, p. 385-386 2 p.

Research output: Contribution to journalReview article

Correlating thrombus constituents of surface-modified vascular graft materials to luminal volume using microct to better quantify clinical functionality

Anderson, D. E. J., Gupta, A. & Hinds, M., Jan 1 2019, Society for Biomaterials Annual Meeting and Exposition 2019: The Pinnacle of Biomaterials Innovation and Excellence - Transactions of the 42nd Annual Meeting. Society for Biomaterials, 1 p. (Transactions of the Annual Meeting of the Society for Biomaterials and the Annual International Biomaterials Symposium; vol. 40).

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

Design and evaluation of a non-contact bed-mounted sensing device for automated in-home detection of obstructive sleep apnea: A pilot study

Mosquera-Lopez, C., Leitschuh, J., Condon, J., Hagen, C. C., Rajhbeharrysingh, U., Hanks, C. & Jacobs, P. G., Sep 2019, In : Biosensors. 9, 3, 90.

Research output: Contribution to journalArticle

Open Access