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2016

Therapeutic siRNA for drug-resistant HER2-positive breast cancer

Gu, S., Hu, Z., Ngamcherdtrakul, W., Castro, D. J., Morry, J., Reda, M. M., Gray, J. W. & Yantasee, W., Mar 22 2016, In : Oncotarget. 7, 12, p. 14727-14741 15 p.

Research output: Contribution to journalArticle

14 Scopus citations

Thrombosis in cancer: Research priorities identified by a national cancer institute/national heart, lung, and blood institute strategic working group

Key, N. S., Khorana, A. A., Mackman, N., McCarty, O. J. T., White, G. C., Francis, C. W., McCrae, K. R., Palumbo, J. S., Raskob, G. E., Chan, A. T. & Sood, A. K., Jul 1 2016, In : Cancer Research. 76, 13, p. 3671-3675 5 p.

Research output: Contribution to journalArticle

17 Scopus citations

Tumor-derived cell lines as molecular models of cancer pharmacogenomics

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

Research output: Contribution to journalArticle

77 Scopus citations

Ultrasensitive proteomic quantitation of cellular signaling by digitized nanoparticle-protein counting

Jacob, T., Agarwal, A., Ramunno-Johnson, D., O'Hare, T., Gonen, M., Tyner, J., Druker, B. & Vu, T. T., Jun 20 2016, In : Scientific Reports. 6, 28163.

Research output: Contribution to journalArticle

3 Scopus citations

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

Donovan, R. M., Tapia, J. J., Sullivan, D. P., Faeder, J. R., Murphy, R. F., Dittrich, M. & Zuckerman, D. M., Feb 2016, In : PLoS computational biology. 12, 2, e1004611.

Research output: Contribution to journalArticle

Open Access
10 Scopus citations

Visualization of chicken embryo heart motion

Phan, L., Rugonyi, S. & Grimm, C., Sep 22 2016, (Accepted/In press) In : Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization. p. 1-15 15 p.

Research output: Contribution to journalArticle

2015

Activated factor XI increases the procoagulant activity of the extrinsic pathway by inactivating tissue factor pathway inhibitor

Puy, C., Tucker, E. I., Matafonov, A., Cheng, Q., Zientek, K. D., Gailani, D., Gruber, A. & McCarty, O. J. T., Jan 1 2015, In : Blood. 125, 9, p. 1488-1496 9 p.

Research output: Contribution to journalArticle

29 Scopus citations

Analysis of 4D myocardial wall motion during early stages of chick heart development

Midgett, M. & Rugonyi, S., Jan 1 2015, In : Methods in Molecular Biology. 1299, p. 191-212 22 p.

Research output: Contribution to journalArticle

A network-based model of oncogenic collaboration for prediction of drug sensitivity

Laderas, T. G., Heiser, L. & Sonmez, M. K., 2015, In : Frontiers in Genetics. 6, DEC, 00341.

Research output: Contribution to journalArticle

4 Scopus citations

Aortic outflow occlusion predicts rupture of abdominal aortic aneurysm

Crawford, J. D., Chivukula, V. K., Haller, S., Vatakhah, N., Bohannan, C. J., Moneta, G. G., Rugonyi, S. & Azarbal, A., Nov 25 2015, (Accepted/In press) In : Journal of Vascular Surgery.

Research output: Contribution to journalArticle

8 Scopus citations

A physical sciences network characterization of circulating tumor cell aggregate transport

King, M. R., Phillips, K. G., Mitrugno, A., Lee, T. R., de Guillebon, A. M. E., Chandrasekaran, S., McGuire, M. J., Carr, R. T., Baker-Groberg, S. M., Rigg, R. A., Kolatkar, A., Luttgen, M., Bethel, K., Kuhn, P., Decuzzi, P. & McCarty, O. J. T., May 15 2015, In : American Journal of Physiology - Cell Physiology. 308, 10, p. C792-C802

Research output: Contribution to journalArticle

23 Scopus citations

Application of circularly polarized light for non-invasive diagnosis of cancerous tissues and turbid tissue-like scattering media

Kunnen, B., Macdonald, C., Doronin, A., Jacques, S., Eccles, M. & Meglinski, I., Apr 1 2015, In : Journal of Biophotonics. 8, 4, p. 317-323 7 p.

Research output: Contribution to journalArticle

104 Scopus citations

A Quick Guide for Building a Successful Bioinformatics Community

Budd, A., Corpas, M., Brazas, M. D., Fuller, J. C., Goecks, J., Mulder, N. J., Michaut, M., Ouellette, B. F. F., Pawlik, A. & Blomberg, N., Jan 1 2015, In : PLoS computational biology. 11, 2, e1003972.

Research output: Contribution to journalArticle

15 Scopus citations

A store-and-forward tele-audiology solution to promote efficient screenings for ototoxicity during cisplatin cancer treatment

Dille, M. F., McMillan, G. P., Helt, W. J., Konrad-Martin, D. & Jacobs, P., Oct 1 2015, In : Journal of the American Academy of Audiology. 26, 9, p. 750-760 11 p.

Research output: Contribution to journalArticle

5 Scopus citations

Blood flow through the embryonic heart outflow tract during cardiac looping in HH13-HH18 chicken embryos

Midgett, M., Chivukula, V. K., Dorn, C., Wallace, S. & Rugonyi, S., Oct 6 2015, In : Journal of the Royal Society Interface. 12, 111, 20150652.

Research output: Contribution to journalArticle

13 Scopus citations

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

Chen, K., Chen, Z., Wu, D., Zhang, L., Lin, X., Su, J., Rodriguez, B., Xi, Y., Xia, Z., Chen, X., Shi, X., Wang, Q. & Li, W., Sep 29 2015, In : Nature genetics. 47, 10, p. 1149-1157 9 p.

Research output: Contribution to journalArticle

105 Scopus citations

Building new computational models to support health behavior change and maintenance: new opportunities in behavioral research

Spruijt-Metz, D., Hekler, E., Saranummi, N., Intille, S., Korhonen, I., Nilsen, W., Rivera, D. E., Spring, B., Michie, S., Asch, D. A., Sanna, A., Salcedo, V. T., Kukakfa, R. & Pavel, M., Sep 17 2015, In : Translational behavioral medicine. 5, 3, p. 335-346 12 p.

Research output: Contribution to journalArticle

77 Scopus citations

Cationic polymer modified mesoporous silica nanoparticles for targeted siRNA delivery to HER2+ breast cancer

Ngamcherdtrakul, W., Morry, J., Gu, S., Castro, D. J., Goodyear, S. M., Sangvanich, T., Reda, M. M., Lee, R., Mihelic, S. A., Beckman, B. L., Hu, Z., Gray, J. W. & Yantasee, W., May 13 2015, In : Advanced Functional Materials. 25, 18, p. 2646-2659 14 p.

Research output: Contribution to journalArticle

95 Scopus citations

Charge and hydrophobicity effects of NIR fluorophores on bone-specific imaging

Bao, K., Nasr, K. A., Hyun, H., Lee, J. H., Gravier, J., Gibbs, S. L. & Choi, H. S., Jan 1 2015, In : Theranostics. 5, 6, p. 609-617 9 p.

Research output: Contribution to journalArticle

18 Scopus citations

Circular polarization memory in polydisperse scattering media

Macdonald, C. M., Jacques, S. L. & Meglinski, I. V., Mar 16 2015, In : Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 91, 3, 033204.

Research output: Contribution to journalArticle

20 Scopus citations

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

Ewing, A. D., Houlahan, K. E., Hu, Y., Ellrott, K., Caloian, C., Yamaguchi, T. N., Bare, J. C., P'Ng, C., Waggott, D., Sabelnykova, V. Y., Kellen, M. R., Norman, T. C., Haussler, D., Friend, S. H., Stolovitzky, G., Margolin, A. A., Stuart, J. M. & Boutros, P. C., Jun 30 2015, In : Nature Methods. 12, 7, p. 623-630 8 p.

Research output: Contribution to journalArticle

120 Scopus citations

Critical Behavior of Subcellular Density Organization During Neutrophil Activation and Migration

Baker-Groberg, S. M., Phillips, K. G., Healy, L. D., Itakura, A., Porter, J. E., Newton, P. K., Nan, X. & McCarty, O. J. T., Dec 1 2015, In : Cellular and Molecular Bioengineering. 8, 4, p. 543-552 10 p.

Research output: Contribution to journalArticle

1 Scopus citations

Crosslinking decreases the hemocompatibility of decellularized, porcine small intestinal submucosa

Glynn, J. J., Polsin, E. G. & Hinds, M. T., Mar 1 2015, In : Acta Biomaterialia. 14, p. 96-103 8 p.

Research output: Contribution to journalArticle

14 Scopus citations

Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites

Nishi, H., Demir, E. & Panchenko, A. R., Jan 30 2015, In : Journal of molecular biology. 427, 2, p. 511-520 10 p.

Research output: Contribution to journalArticle

22 Scopus citations

Current and Future Challenges in Point-of-Care Technologies: A Paradigm-Shift in Affordable Global Healthcare with Personalized and Preventive Medicine

Dhawan, A. P., Heetderks, W. J., Pavel, M., Acharya, S., Akay, M., Mairal, A., Wheeler, B., Dacso, C. C., Sunder, T., Lovell, N., Gerber, M., Shah, M., Senthilvel, S. G., Wang, M. D. & Bhargava, B., 2015, In : IEEE Journal of Translational Engineering in Health and Medicine. 3, 2800110.

Research output: Contribution to journalArticle

26 Scopus citations

Data detailing the platelet acetyl-lysine proteome

Aslan, J. E., David, L. L. & McCarty, O. J. T., Dec 1 2015, In : Data in Brief. 5, p. 368-371 4 p.

Research output: Contribution to journalArticle

1 Scopus citations

Decoupling of the PI3K pathway via mutation necessitates combinatorial treatment in HER2+ breast cancer

Korkola, J. E., Collisson, E. A., Heiser, L., Oates, C., Bayani, N., Itani, S., Esch, A., Thompson, W., Griffith, O. L., Wang, N. J., Kuo, W. L., Cooper, B., Billig, J., Ziyad, S., Hung, J. L., Feiler, H., Lu, Y., Mills, G. B., Spellman, P. T., Tomlin, C. & 3 others, Mukherjee, S., Gray, J. W. & Jakkula, L., Jul 16 2015, In : PloS one. 10, 7, e0133219.

Research output: Contribution to journalArticle

11 Scopus citations

Dermal delivery of HSP47 siRNA with NOX4-modulating mesoporous silica-based nanoparticles for treating fibrosis

Morry, J., Ngamcherdtrakul, W., Gu, S., Goodyear, S. M., Castro, D. J., Reda, M. M., Sangvanich, T. & Yantasee, W., Oct 1 2015, In : Biomaterials. 66, p. 41-52 12 p.

Research output: Contribution to journalArticle

29 Scopus citations

Development and evaluation of a standardized method and atlas for contouring primary and permanent dentition

Fang, P., Batra, S., Hollander, A. B., Lin, A., Hill-Kayser, C. E., Levin, L. M., Mupparapu, M. & Thompson, R. F., Sep 1 2015, In : Dentomaxillofacial Radiology. 44, 7, 20150034.

Research output: Contribution to journalArticle

Development and validation of a gene-based model for outcome prediction in germ cell tumors using a combined genomic and expression profiling approach

Korkola, J., Heck, S., Olshen, A. B., Feldman, D. R., Reuter, V. E., Houldsworth, J., Bosl, G. J. & Chaganti, R. S. K., Dec 1 2015, In : PLoS One. 10, 12, e0142846.

Research output: Contribution to journalArticle

8 Scopus citations

Disentangling multidimensional spatio-temporal data into their common and aberrant responses

Chang, Y. H., Korkola, J., Amin, D. N., Moasser, M. M., Carmena, J. M., Gray, J. W. & Tomlin, C. J., Apr 22 2015, In : PloS one. 10, 4, e0121607.

Research output: Contribution to journalArticle

1 Scopus citations

Effect of Ionizing Radiation on the Physical Biology of Head and Neck Squamous Cell Carcinoma Cells

Baker-Groberg, S. M., Bornstein, S., Zilberman-Rudenko, J., Schmidt, M., Tormoen, G. W., Kernan, C., Thomas, C. R., Wong, M. H., Phillips, K. G. & McCarty, O. J. T., Sep 21 2015, In : Cellular and Molecular Bioengineering. 8, 3, p. 517-525 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

Effect of repeated glucagon doses on hepatic glycogen in type 1 Diabetes: Implications for a bihormonal Closed-Loop system

Castle, J., El Youssef, J., Bakhtiani, P. A., Cai, Y., Stobbe, J. M., Branigan, D., Ramsey, K., Jacobs, P., Reddy, R., Woods, M. & Ward, W. K., Nov 1 2015, In : Diabetes Care. 38, 11, p. 2115-2119 5 p.

Research output: Contribution to journalArticle

17 Scopus citations
4 Scopus citations

Entropy and enthalpy for triggering cutaneous erythema

Jacques, S. L. & Walsh, J. T., Jul 25 2015, In : Journal of Innovative Optical Health Sciences. 8, 4, 1550026.

Research output: Contribution to journalArticle

Excess of heme induces tissue factor-dependent activation of coagulation in mice

Sparkenbaugh, E. M., Chantrathammachart, P., Wang, S., Jonas, W., Kirchhofer, D., Gailani, D., Gruber, A., Kasthuri, R., Key, N. S., Mackman, N. & Pawlinski, R., Jan 1 2015, In : Haematologica. 100, 3, p. 308-313 6 p.

Research output: Contribution to journalArticle

30 Scopus citations

Exome sequencing of cell-free DNA from metastatic cancer patients identifies clinically actionable mutations distinct from primary disease

Butler, T. M., Johnson-Camacho, K., Peto, M., Wang, N. J., Macey, T. A., Korkola, J. E., Koppie, T. M., Corless, C. L., Gray, J. W. & Spellman, P. T., Aug 28 2015, In : PloS one. 10, 8, e0136407.

Research output: Contribution to journalArticle

61 Scopus citations

Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway

Shain, A. H., Garrido, M., Botton, T., Talevich, E., Yeh, I., Sanborn, J. Z., Chung, J., Wang, N. J., Kakavand, H., Mann, G. J., Thompson, J. F., Wiesner, T., Roy, R., Olshen, A. B., Gagnon, A., Gray, J. W., Huh, N., Hur, J. S., Busam, K. J., Scolyer, R. A. & 3 others, Cho, R. J., Murali, R. & Bastian, B. C., Sep 29 2015, In : Nature genetics. 47, 10, p. 1194-1199 6 p.

Research output: Contribution to journalArticle

101 Scopus citations

Fabrication of a flexible amperometric glucose sensor using additive processes

Du, X., Durgan, C. J., Matthews, D. J., Motley, J. R., Tan, X., Pholsena, K., Árnadoóttir, L., Castle, J. R., Jacobs, P. G., Cargill, R. S., Ward, W. K., Conley, J. F. & Herman, G. S., Jan 1 2015, In : ECS Journal of Solid State Science and Technology. 4, 4, p. P3069-P3074

Research output: Contribution to journalArticle

17 Scopus citations

Factors affecting the success of glucagon delivered during an automated closed-loop system in type 1 diabetes

Bakhtiani, P. A., El Youssef, J., Duell, A. K., Branigan, D. L., Jacobs, P. G., Lasarev, M. R., Castle, J. R. & Ward, W. K., Jan 1 2015, In : Journal of Diabetes and Its Complications. 29, 1, p. 93-98 6 p.

Research output: Contribution to journalArticle

13 Scopus citations

Far-red fluorogenic probes for esterase and lipase detection

Tallman, K. R. & Beatty, K. E., 2015, In : ChemBioChem. 16, 1, p. 70-75 6 p.

Research output: Contribution to journalArticle

17 Scopus citations

GATA2 regulates Wnt signaling to promote primitive red blood cell fate

Mimoto, M. S., Kwon, S., Green, Y. S., Goldman, D. & Christian, J. L., Nov 1 2015, In : Developmental Biology. 407, 1, p. 1-11 11 p.

Research output: Contribution to journalArticle

6 Scopus citations

Genome-wide perturbations by miRNAs map onto functional cellular pathways, identifying regulators of chromatin modifiers

Moss, T. J., Luo, Z., Seviour, E. G., Sehgal, V., Lu, Y., Hill, S. M., Rupaimoole, R., Lee, J. S., Rodriguez-Aguayo, C., Lopez-Berestein, G., Sood, A. K., Azencott, R., Gray, J., Mukherjee, S., Mills, G. & Ram, P. T., Sep 28 2015, In : npj Systems Biology and Applications. 1, 15001.

Research output: Contribution to journalArticle

2 Scopus citations

Incorporating an exercise detection, grading, and hormone dosing algorithm into the artificial pancreas using accelerometry and heart rate

Jacobs, P., Resalat, N., El Youssef, J., Reddy, R., Branigan, D., Preiser, N., Condon, J. & Castle, J., Nov 1 2015, In : Journal of diabetes science and technology. 9, 6, p. 1175-1184 10 p.

Research output: Contribution to journalArticle

45 Scopus citations

Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency

Kushwaha, R., Jagadish, N., Kustagi, M., Tomishima, M. J., Mendiratta, G., Bansal, M., Kim, H. R., Sumazin, P., Alvarez, M. J., Lefebvre, C., Villagrasa-Gonzalez, P., Viale, A., Korkola, J. E., Houldsworth, J., Feldman, D. R., Bosl, G. J., Califano, A. & Chaganti, R. S. K., Feb 1 2015, In : Stem Cells. 33, 2, p. 367-377 11 p.

Research output: Contribution to journalArticle

14 Scopus citations

In vitro and ex vivo hemocompatibility of off-the-shelf modified poly(vinyl alcohol) vascular grafts

Cutiongco, M. F. A., Anderson, D. E. J., Hinds, M. T. & Yim, E. K. F., Oct 1 2015, In : Acta Biomaterialia. 25, p. 97-108 12 p.

Research output: Contribution to journalArticle

42 Scopus citations

Large-scale drug screens support precision medicine

Gray, J. W. & Mills, G. B., Nov 2015, In : Cancer discovery. 5, 11, p. 1130-1132 3 p.

Research output: Contribution to journalArticle

5 Scopus citations

Long non-coding RNAs control hematopoietic stem cell function

Luo, M., Jeong, M., Sun, D., Park, H. J., Rodriguez, B. A. T., Xia, Z., Yang, L., Zhang, X., Sheng, K., Darlington, G. J., Li, W. & Goodell, M. A., Apr 2 2015, In : Cell Stem Cell. 16, 4, p. 426-438 13 p.

Research output: Contribution to journalArticle

73 Scopus citations

Lysine acetyltransfer supports platelet function

Aslan, J. E., Rigg, R. A., Nowak, M. S., Loren, C. P., Baker-Groberg, S. M., Pang, J., David, L. L. & Mccarty, O. J. T., Oct 1 2015, In : Journal of Thrombosis and Haemostasis. 13, 10, p. 1908-1917 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming

Hirsch, C. L., Akdemir, Z. C., Wang, L., Jayakumaran, G., Trcka, D., Weiss, A., Javier Hernandez, J., Pan, Q., Han, H., Xu, X., Xia, Z., Salinger, A. P., Wilson, M., Vizeacoumar, F., Datti, A., Li, W., Cooney, A. J., Barton, M. C., Blencowe, B. J., Wrana, J. L. & 1 others, Dent, S. Y. R., Jan 1 2015, In : Genes and Development. 29, 8, p. 803-816 14 p.

Research output: Contribution to journalArticle

36 Scopus citations