Research Output

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Review article
2020

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
2019

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. F., Dec 2019, In : Hematology/Oncology Clinics of North America. 33, 6, p. 1095-1104 10 p.

Research output: Contribution to journalReview article

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

Proteomics advances for precision therapy in ovarian cancer

Labrie, M., Kendsersky, N. D., Ma, H., Campbell, L., Eng, J., Chin, K. & Mills, G. B., Oct 3 2019, In : Expert Review of Proteomics. 16, 10, p. 841-850 10 p.

Research output: Contribution to journalReview article

siRNA therapeutics for breast cancer: recent efforts in targeting metastasis, drug resistance, and immune evasion

Ngamcherdtrakul, W. & Yantasee, W., Dec 2019, In : Translational Research. 214, p. 105-120 16 p.

Research output: Contribution to journalReview article

1 Scopus citations

Systems biology approaches to measure and model phenotypic heterogeneity in cancer

Meyer, A. S. & Heiser, L. M., Oct 2019, In : Current Opinion in Systems Biology. 17, p. 35-40 6 p.

Research output: Contribution to journalReview article

Open Access
2 Scopus citations

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

Rougny, A., Touré, V., Moodie, S., Balaur, I., Czauderna, T., Borlinghaus, H., Dogrusoz, U., Mazein, A., Dräger, A., Blinov, M. L., Villéger, A., Haw, R., Demir, E., Mi, H., Sorokin, A., Schreiber, F. & Luna, A., Jun 13 2019, In : Journal of integrative bioinformatics. 16, 2

Research output: Contribution to journalReview article

Open Access
3 Scopus citations
2018

Carpe low-dose aspirin: the new anti-cancer face of an old anti-platelet drug

Mitrugno, A., Sylman, J. L., Rigg, R. A., Tassi Yunga, S., Shatzel, J. J., Williams, C. D. & McCarty, O., Nov 17 2018, In : Platelets. 29, 8, p. 773-778 6 p.

Research output: Contribution to journalReview article

4 Scopus citations

Cloud computing for genomic data analysis and collaboration

Langmead, B. & Nellore, A., Apr 1 2018, In : Nature Reviews Genetics. 19, 4, p. 208-219 12 p.

Research output: Contribution to journalReview article

44 Scopus citations

Influence of blood flow on cardiac development

Courchaine, K., Rykiel, G. & Rugonyi, S., Sep 1 2018, In : Progress in Biophysics and Molecular Biology. 137, p. 95-110 16 p.

Research output: Contribution to journalReview article

3 Scopus citations

Platelet Mechanotransduction

Hansen, C. E., Qiu, Y., McCarty, O. & Lam, W. A., Jun 4 2018, In : Annual Review of Biomedical Engineering. 20, p. 253-275 23 p.

Research output: Contribution to journalReview article

7 Scopus citations
1 Scopus citations

The predictive value of inflammation-related peripheral blood measurements in cancer staging and prognosis

Sylman, J. L., Mitrugno, A., Atallah, M., Tormoen, G. W., Shatzel, J. J., Yunga, S. T., Wagner, T. H., Leppert, J. T., Mallick, P. & McCarty, O., Mar 21 2018, In : Frontiers in Oncology. 8, MAR, 78.

Research output: Contribution to journalReview article

8 Scopus citations
2017

Best practices for managing large CryoEM facilities

Alewijnse, B., Ashton, A. W., Chambers, M. G., Chen, S., Cheng, A., Ebrahim, M., Eng, E. T., Hagen, W. J. H., Koster, A. J., López, C. S., Lukoyanova, N., Ortega, J., Renault, L., Reyntjens, S., Rice, W. J., Scapin, G., Schrijver, R., Siebert, A., Stagg, S. M., Grum-Tokars, V. & 6 others, Wright, E. R., Wu, S., Yu, Z., Zhou, Z. H., Carragher, B. & Potter, C. S., Sep 2017, In : Journal of Structural Biology. 199, 3, p. 225-236 12 p.

Research output: Contribution to journalReview article

10 Scopus citations

Circulating-tumor DNA as an early detection and diagnostic tool

Butler, T. M., Spellman, P. & Gray, J., Feb 1 2017, In : Current Opinion in Genetics and Development. 42, p. 14-21 8 p.

Research output: Contribution to journalReview article

28 Scopus citations

Ibrutinib-associated bleeding: pathogenesis, management and risk reduction strategies

Shatzel, J. J., Olson, S. R., Tao, D. L., McCarty, O., Danilov, A. & Deloughery, T., May 1 2017, In : Journal of Thrombosis and Haemostasis. 15, 5, p. 835-847 13 p.

Research output: Contribution to journalReview article

51 Scopus citations

Oxidative stress in cancer and fibrosis: Opportunity for therapeutic intervention with antioxidant compounds, enzymes, and nanoparticles

Morry, J., Ngamcherdtrakul, W. & Yantasee, W., Apr 1 2017, In : Redox Biology. 11, p. 240-253 14 p.

Research output: Contribution to journalReview article

97 Scopus citations

Path-sampling strategies for simulating rare events in biomolecular systems

Chong, L. T., Saglam, A. S. & Zuckerman, D., Apr 1 2017, In : Current Opinion in Structural Biology. 43, p. 88-94 7 p.

Research output: Contribution to journalReview article

19 Scopus citations

Utility of microfluidic devices to study the platelet–endothelium interface

Zilberman-Rudenko, J., Sylman, J. L., Garland, K. S., Puy, C., Wong, A. D., Searson, P. C. & McCarty, O., Jul 4 2017, In : Platelets. 28, 5, p. 449-456 8 p.

Research output: Contribution to journalReview article

2 Scopus citations

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software

Zuckerman, D. M. & Chong, L. T., May 22 2017, In : Annual Review of Biophysics. 46, p. 43-57 15 p.

Research output: Contribution to journalReview article

37 Scopus citations
2016

Factor XI as a Therapeutic Target

Gailani, D. & Gruber, A., Jul 1 2016, In : Arteriosclerosis, thrombosis, and vascular biology. 36, 7, p. 1316-1322 7 p.

Research output: Contribution to journalReview article

31 Scopus citations

Nonadjunctive use of continuous glucose monitoring for diabetes treatment decisions

Castle, J. & Jacobs, P., 2016, In : Journal of diabetes science and technology. 10, 5, p. 1169-1173 5 p.

Research output: Contribution to journalReview article

32 Scopus citations

Tumor-derived cell lines as molecular models of cancer pharmacogenomics

Goodspeed, A., Heiser, L. M., Gray, J. W. & Costello, J. C., Jan 2016, In : Molecular Cancer Research. 14, 1, p. 3-13 11 p.

Research output: Contribution to journalReview article

82 Scopus citations
2015

Factor XI and contact activation as targets for antithrombotic therapy

Gailani, D., Bane, C. E. & Gruber, A., Aug 1 2015, In : Journal of Thrombosis and Haemostasis. 13, 8, p. 1383-1395 13 p.

Research output: Contribution to journalReview article

63 Scopus citations

Quantum dots for quantitative imaging: from single molecules to tissue

Vu, T. Q., Lam, W. Y., Hatch, E. W. & Lidke, D. S., Apr 1 2015, In : Cell and tissue research. 360, 1, p. 71-86 16 p.

Research output: Contribution to journalReview article

48 Scopus citations

Ubiquitous real-world sensing and audiology-based health informatics

Jacobs, P. G. & Kaye, J. A., Oct 1 2015, In : Journal of the American Academy of Audiology. 26, 9, p. 777-783 7 p.

Research output: Contribution to journalReview article

4 Scopus citations
2014

Can glucose be monitored accurately at the site of subcutaneous insulin delivery?

Ward, W. K., Castle, J. R., Jacobs, P. G. & Cargill, R. S., May 2014, In : Journal of Diabetes Science and Technology. 8, 3, p. 568-574 7 p.

Research output: Contribution to journalReview article

8 Scopus citations

Endothelial outgrowth cells: Function and performance in vascular grafts

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

Research output: Contribution to journalReview article

26 Scopus citations

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. T. & McCarty, O. J. T., Mar 2014, In : Cellular and Molecular Bioengineering. 7, 1, p. 1-14 14 p.

Research output: Contribution to journalReview article

10 Scopus citations

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. W. & Chen, F. F., 2014, In : Theranostics. 4, 9, p. 872-892 21 p.

Research output: Contribution to journalReview article

117 Scopus citations

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

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

Research output: Contribution to journalReview article

22 Scopus citations
2013

Optical properties of biological tissues: A review

Jacques, S. L., Jun 7 2013, In : Physics in Medicine and Biology. 58, 11, p. R37-R61

Research output: Contribution to journalReview article

1524 Scopus citations

Rho GTPases in platelet function

Aslan, J. E. & Mccarty, O. J. T., Jan 1 2013, In : Journal of Thrombosis and Haemostasis. 11, 1, p. 35-46 12 p.

Research output: Contribution to journalReview article

84 Scopus citations

The cancer genome atlas pan-cancer analysis project

Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Sander, C., Stuart, J. M., Chang, K., Creighton, C. J., Davis, C., Donehower, L., Drummond, J., Wheeler, D., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chu, A., Chuah, E. & 316 others, Chun, H. J. E., Dhalla, N., Guin, R., Hirst, M., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Robertson, A. G., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Varhol, R. J., Beroukhim, R., Bhatt, A. S., Brooks, A. N., Cherniack, A. D., Freeman, S. S., Gabriel, S. B., Helman, E., Jung, J., Meyerson, M., Ojesina, A. I., Pedamallu, C. S., Saksena, G., Schumacher, S. E., Tabak, B., Zack, T., Lander, E. S., Bristow, C. A., Hadjipanayis, A., Haseley, P., Kucherlapati, R., Lee, S., Lee, E., Luquette, L. J., Mahadeshwar, H. S., Pantazi, A., Parfenov, M., Park, P. J., Protopopov, A., Ren, X., Santoso, N., Seidman, J., Seth, S., Song, X., Tang, J., Xi, R., Xu, A. W., Yang, L., Zeng, D., Auman, J. T., Balu, S., Buda, E., Fan, C., Hoadley, K. A., Jones, C. D., Meng, S., Mieczkowski, P. A., Parker, J. S., Perou, C. M., Roach, J., Shi, Y., Silva, G. O., Tan, D., Veluvolu, U., Waring, S., Wilkerson, M. D., Wu, J., Zhao, W., Bodenheimer, T., Hayes, D. N., Hoyle, A. P., Jeffreys, S. R., Mose, L. E., Simons, J. V., Soloway, M. G., Baylin, S. B., Berman, B. P., Bootwalla, M. S., Danilova, L., Herman, J. G., Hinoue, T., Laird, P. W., Rhie, S. K., Shen, H., Triche, T., Weisenberger, D. J., Carter, S. L., Cibulskis, K., Chin, L., Zhang, J., Sougnez, C., Wang, M., Getz, G., Dinh, H., Doddapaneni, H. V., Gibbs, R., Gunaratne, P., Han, Y., Kalra, D., Kovar, C., Lewis, L., Morgan, M., Morton, D., Muzny, D., Reid, J., Xi, L., Cho, J., Dicara, D., Frazer, S., Gehlenborg, N., Heiman, D. I., Kim, J., Lawrence, M. S., Lin, P., Liu, Y., Noble, M. S., Stojanov, P., Voet, D., Zhang, H., Zou, L., Stewart, C., Bernard, B., Bressler, R., Eakin, A., Iype, L., Knijnenburg, T., Kramer, R., Kreisberg, R., Leinonen, K., Lin, J., Liu, Y., Miller, M., Reynolds, S. M., Rovira, H., Shmulevich, I., Thorsson, V., Yang, D., Zhang, W., Amin, S., Wu, C. J., Wu, C. C., Akbani, R., Aldape, K., Baggerly, K. A., Broom, B., Casasent, T. D., Cleland, J., Dodda, D., Edgerton, M., Han, L., Herbrich, S. M., Ju, Z., Kim, H., Lerner, S., Li, J., Liang, H., Liu, W., Lorenzi, P. L., Lu, Y., Melott, J., Nguyen, L., Su, X., Verhaak, R., Wang, W., Wong, A., Yang, Y., Yao, J., Yao, R., Yoshihara, K., Yuan, Y., Yung, A. K., Zhang, N., Zheng, S., Ryan, M., Kane, D. W., Aksoy, B. A., Ciriello, G., Dresdner, G., Gao, J., Gross, B., Jacobsen, A., Kahles, A., Ladanyi, M., Lee, W., Lehmann, K. V., Miller, M. L., Ramirez, R., Rätsch, G., Reva, B., Schultz, N., Senbabaoglu, Y., Shen, R., Sinha, R., Sumer, S. O., Sun, Y., Taylor, B. S., Weinhold, N., Fei, S., Spellman, P., Benz, C., Carlin, D., Cline, M., Craft, B., Goldman, M., Haussler, D., Ma, S., Ng, S., Paull, E., Radenbaugh, A., Salama, S., Sokolov, A., Swatloski, T., Uzunangelov, V., Waltman, P., Yau, C., Zhu, J., Hamilton, S. R., Abbott, S., Abbott, R., Dees, N. D., Delehaunty, K., Ding, L., Dooling, D. J., Eldred, J. M., Fronick, C. C., Fulton, R., Fulton, L. L., Kalicki-Veizer, J., Kanchi, K. L., Kandoth, C., Koboldt, D. C., Larson, D. E., Ley, T. J., Lin, L., Lu, C., Magrini, V. J., Mardis, E. R., McLellan, M. D., McMichael, J. F., Miller, C. A., O'Laughlin, M., Pohl, C., Schmidt, H., Smith, S. M., Walker, J., Wallis, J. W., Wendl, M. C., Wilson, R. K., Wylie, T., Zhang, Q., Burton, R., Jensen, M. A., Kahn, A., Pihl, T., Pot, D., Wan, Y., Levine, D. A., Black, A. D., Bowen, J., Frick, J., Gastier-Foster, J. M., Harper, H. A., Helsel, C., Leraas, K. M., Lichtenberg, T. M., McAllister, C., Ramirez, N. C., Sharpe, S., Wise, L., Zmuda, E., Chanock, S. J., Davidsen, T., Demchok, J. A., Eley, G., Felau, I., Sheth, M., Sofia, H., Staudt, L., Tarnuzzer, R., Wang, Z., Yang, L., Zhang, J., Omberg, L., Margolin, A., Raphael, B. J., Vandin, F., Wu, H. T., Leiserson, M. D. M., Benz, S. C., Vaske, C. J., Noushmehr, H., Wolf, D., Veer, L. V. T., Anastassiou, D., Yang, T. H. O., Lopez-Bigas, N., Gonzalez-Perez, A., Tamborero, D., Xia, Z., Li, W., Cho, D. Y., Przytycka, T., Hamilton, M., McGuire, S., Nelander, S., Johansson, P., Jörnsten, R. & Kling, T., Oct 1 2013, In : Nature genetics. 45, 10, p. 1113-1120 8 p.

Research output: Contribution to journalReview article

2239 Scopus citations
2012

Omics and therapy - A basis for precision medicine

Garay, J. P. & Gray, J. W., Apr 2012, In : Molecular Oncology. 6, 2, p. 128-139 12 p.

Research output: Contribution to journalReview article

30 Scopus citations

What are we learning from the cancer genome?

Collisson, E. A., Cho, R. J. & Gray, J. W., Nov 1 2012, In : Nature Reviews Clinical Oncology. 9, 11, p. 621-630 10 p.

Research output: Contribution to journalReview article

33 Scopus citations
2011

Chemical strategies for tagging and imaging the proteome

Beatty, K. E., Aug 1 2011, In : Molecular BioSystems. 7, 8, p. 2360-2367 8 p.

Research output: Contribution to journalReview article

17 Scopus citations

Multiple kernel learning algorithms

Gönen, M. & Alpaydin, E., Jul 1 2011, In : Journal of Machine Learning Research. 12, p. 2211-2268 58 p.

Research output: Contribution to journalReview article

1094 Scopus citations

'Omic approaches to preventing or managing metastatic breast cancer

Griffith, O. L. & Gray, J. W., Dec 8 2011, In : Breast Cancer Research. 13, 6, 230.

Research output: Contribution to journalReview article

14 Scopus citations

Super-resolution microscopy for nanosensing

Galbraith, J. A. & Galbraith, C. G., May 1 2011, In : Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology. 3, 3, p. 247-255 9 p.

Research output: Contribution to journalReview article

5 Scopus citations
2010

Anti-Hebbian spike-timing-dependent plasticity and adaptive sensory processing

Roberts, P. D. & Leen, T. K., Dec 1 2010, In : Frontiers in Computational Neuroscience. 4

Research output: Contribution to journalReview article

16 Scopus citations

Breast cancer genomes - form and function

Korkola, J. & Gray, J. W., Feb 1 2010, In : Current Opinion in Genetics and Development. 20, 1, p. 4-14 11 p.

Research output: Contribution to journalReview article

39 Scopus citations

Cell-matrix interactions in mammary gland development and breast cancer.

Muschler, J. & Streuli, C. H., Oct 1 2010, In : Cold Spring Harbor Perspectives in Biology. 2, 10, p. a003202

Research output: Contribution to journalReview article

Open Access
86 Scopus citations

Epigenetic basis for fetal origins of age-related disease

Thompson, R. F. & Einstein, F. H., Mar 1 2010, In : Journal of Women's Health. 19, 3, p. 581-587 7 p.

Research output: Contribution to journalReview article

32 Scopus citations

Nanotechnology research: Applications in nutritional sciences

Srinivas, P. R., Philbert, M., Vu, T. Q., Huang, Q., Kokini, J. L., Saos, E., Chen, H., Peterson, C. M., Friedl, K. E., McDade-Ngutter, C., Hubbard, V., Starke-Reed, P., Miller, N., Betz, J. M., Dwyer, J., Milner, J. & Ross, S. A., Jan 1 2010, In : Journal of Nutrition. 140, 1, p. 119-124 6 p.

Research output: Contribution to journalReview article

60 Scopus citations

The BioPAX community standard for pathway data sharing

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I. & 70 others, Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, Ö., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., Van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K. H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novère, N. L., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. & Bader, G. D., Sep 1 2010, In : Nature biotechnology. 28, 9, p. 935-942 8 p.

Research output: Contribution to journalReview article

399 Scopus citations
2009

Molecular events in germ cell tumours: Linking chromosome-12 gain, acquisition of pluripotency and response to cisplatin

Korkola, J. E., Houldsworth, J., Bosl, G. J. & Chaganti, R. S. K., Nov 1 2009, In : BJU international. 104, 9 B, p. 1334-1338 5 p.

Research output: Contribution to journalReview article

20 Scopus citations

The Systems Biology Graphical Notation

Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villéger, A., Boyd, S. E., Calzone, L., Courtot, M. & 19 others, Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K. & Kitano, H., Aug 1 2009, In : Nature biotechnology. 27, 8, p. 735-741 7 p.

Research output: Contribution to journalReview article

515 Scopus citations
2008

Percutaneous management of chronic deep venous reflux: Review of experimental work and early clinical experience with bioprosthetic valve

Pavcnik, D., Uchida, B., Kaufman, J., Hinds, M., Keller, F. S. & Rösch, J., May 5 2008, In : Vascular Medicine. 13, 1, p. 75-84 10 p.

Research output: Contribution to journalReview article

41 Scopus citations