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2016

Colocalization of neutrophils, extracellular DNA and coagulation factors during NETosis: Development and utility of an immunofluorescence-based microscopy platform

Healy, L. D., Puy, C., Itakura, A., Chu, T., Robinson, D. K., Bylund, A., Phillips, K. G., Gardiner, E. E. & McCarty, O. J. T., Aug 1 2016, In : Journal of Immunological Methods. 435, p. 77-84 8 p.

Research output: Contribution to journalArticle

11 Scopus citations

Current development of targeted oligonucleotide-based cancer therapies: Perspective on HER2-positive breast cancer treatment

Ngamcherdtrakul, W., Castro, D. J., Gu, S., Morry, J., Reda, M., Gray, J. & Yantasee, W., Apr 1 2016, In : Cancer Treatment Reviews. 45, p. 19-29 11 p.

Research output: Contribution to journalArticle

9 Scopus citations

Design and calibration of a digital Fourier holographic microscope for particle sizing via goniometry and optical scatter imaging in transmission

Rossi, V. M. & Jacques, S., Jun 13 2016, In : Optics Express. 24, 12, p. 12788-12802 15 p.

Research output: Contribution to journalArticle

2 Scopus citations

Dimensional analysis and scaling relevant to flow models of thrombus formation: Communication from the SSC of the ISTH

For the subcommittee on biorheology, Mar 1 2016, In : Journal of Thrombosis and Haemostasis. 14, 3, p. 619-622 4 p.

Research output: Contribution to journalArticle

16 Scopus citations

DREAMTools: A Python package for scoring collaborative challenges

Cokelaer, T., Bansal, M., Bare, C., Bilal, E., Bot, B. M., Chaibub Neto, E., Eduati, F., de la Fuente, A., Gonen, M., Hill, S. M., Hoff, B., Karr, J. R., Küffner, R., Menden, M. P., Meyer, P., Norel, R., Pratap, A., Prill, R. J., Weirauch, M. T., Costello, J. C. & 2 others, Stolovitzky, G. & Saez-Rodriguez, J., 2016, In : F1000Research. 4, 1030.

Research output: Contribution to journalArticle

6 Scopus citations

Dynamics of Blood Flow and Thrombus Formation in a Multi-Bypass Microfluidic Ladder Network

Zilberman-Rudenko, J., Sylman, J. L., Lakshmanan, H. H. S., McCarty, O. & Maddala, J., Oct 20 2016, (Accepted/In press) In : Cellular and Molecular Bioengineering. p. 1-14 14 p.

Research output: Contribution to journalArticle

17 Scopus citations

Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg2+ Titration Analysis for HIV-1 Ribonuclease H Domain

Karki, I., Christen, M. T., Spiriti, J., Slack, R. L., Oda, M., Kanaori, K., Zuckerman, D. & Ishima, R., Dec 15 2016, In : Journal of Physical Chemistry B. 120, 49, p. 12420-12431 12 p.

Research output: Contribution to journalArticle

3 Scopus citations

Factor XI deficiency alters the cytokine response and activation of contact proteases during polymicrobial sepsis in mice

Bane, C. E., Ivanov, I., Matafonov, A., Boyd, K. L., Cheng, Q., Sherwood, E. R., Tucker, E., Smiley, S. T., McCarty, O., Gruber, A. & Gailani, D., Apr 1 2016, In : PLoS One. 11, 4, e0152968.

Research output: Contribution to journalArticle

25 Scopus citations

FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer

Fu, X., Jeselsohn, R., Pereira, R., Hollingsworth, E. F., Creighton, C. J., Li, F., Shea, M., Nardone, A., De Angelis, C., Heiser, L. M., Anur, P., Wang, N., Grasso, C. S., Spellman, P. T., Griffith, O. L., Tsimelzon, A., Gutierrez, C., Huang, S., Edwards, D. P., Trivedi, M. V. & 7 others, Rimawi, M. F., Lopez-Terrada, D., Hilsenbeck, S. G., Gray, J. W., Brown, M., Osborne, C. K. & Schiff, R., Oct 25 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 43, p. E6600-E6609

Research output: Contribution to journalArticle

43 Scopus citations

Functional oncogene signatures guide rationally designed combination therapies to synergistically induce breast cancer cell death

Guest, S. T., Kratche, Z. R., Irish, J. C., Wilson, R. C., Haddad, R., Gray, J. W., Garrett-Mayer, E. & Ethier, S. P., Jan 1 2016, In : Oncotarget. 7, 24, p. 36138-36153 16 p.

Research output: Contribution to journalArticle

1 Scopus citations

Functional proteomics identifies miRNAs to target a p27/Myc/phospho-Rb signature in breast and ovarian cancer

Seviour, E. G., Sehgal, V., Lu, Y., Luo, Z., Moss, T., Zhang, F., Hill, S. M., Liu, W., Maiti, S. N., Cooper, L., Azencot, R., Lopez-Berestein, G., Rodriguez-Aguayo, C., Roopaimoole, R., Pecot, C., Sood, A. K., Mukherjee, S., Gray, J., Mills, G. & Ram, P. T., Feb 11 2016, In : Oncogene. 35, 6, p. 691-701 11 p.

Research output: Contribution to journalArticle

26 Scopus citations

Gait velocity estimation using time-interleaved between consecutive passive IR Sensor Activations

Rana, R., Austin, D., Jacobs, P., Karunanithi, M. & Kaye, J., Aug 1 2016, In : IEEE Sensors Journal. 16, 16, p. 6351-6358 8 p., 7486123.

Research output: Contribution to journalArticle

7 Scopus citations

Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer

Hu, Z., Mao, J. H., Curtis, C., Huang, G., Gu, S., Heiser, L., Lenburg, M. E., Korkola, J. E., Bayani, N., Samarajiwa, S., Seoane, J. A., Dane, M., Esch, A., Feiler, H. S., Wang, N. J., Hardwicke, M. A., Laquerre, S., Jackson, J., Wood, K., Weber, B. & 5 others, Spellman, P. T., Aparicio, S., Wooster, R., Caldas, C. & Gray, J. W., Jul 1 2016, In : Breast Cancer Research. 18, 1, 70.

Research output: Contribution to journalArticle

6 Scopus citations

Heat shock protein 70 regulates platelet integrin activation, granule secretion and aggregation

Rigg, R. A., Healy, L. D., Nowak, M. S., Mallet, J., Thierheimer, M. L. D., Pang, J., McCarty, O. J. T. & Aslan, J. E., Apr 1 2016, In : American Journal of Physiology - Cell Physiology. 310, 7, p. C568-C575

Research output: Contribution to journalArticle

12 Scopus citations

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

Nellore, A., Jaffe, A. E., Fortin, J. P., Alquicira-Hern�ndez, J., Collado-Torres, L., Wang, S., Phillips, R. A., Karbhari, N., Hansen, K. D., Langmead, B. & Leek, J. T., Dec 30 2016, In : Genome biology. 17, 1, 266.

Research output: Contribution to journalArticle

35 Scopus citations

IL-10 and integrin signaling pathways are associated with head and neck cancer progression

Bornstein, S., Schmidt, M., Choonoo, G., Levin, T., Gray, J., Thomas, C., Wong, M. & McWeeney, S., Jan 8 2016, In : BMC Genomics. 17, 1, 38.

Research output: Contribution to journalArticle

25 Scopus citations

Inferring causal molecular networks: Empirical assessment through a community-based effort

Hill, S. M., Heiser, L. M., Cokelaer, T., Linger, M., Nesser, N. K., Carlin, D. E., Zhang, Y., Sokolov, A., Paull, E. O., Wong, C. K., Graim, K., Bivol, A., Wang, H., Zhu, F., Afsari, B., Danilova, L. V., Favorov, A. V., Lee, W. S., Taylor, D., Hu, C. W. & 115 others, Long, B. L., Noren, D. P., Bisberg, A. J., Mills, G. B., Gray, J. W., Kellen, M., Norman, T., Friend, S., Qutub, A. A., Fertig, E. J., Guan, Y., Song, M., Stuart, J. M., Spellman, P. T., Koeppl, H., Stolovitzky, G., Saez-Rodriguez, J., Mukherjee, S., Al-Ouran, R., Anton, B., Arodz, T., Sichani, O. A., Bagheri, N., Berlow, N., Bohler, A., Bonet, J., Bonneau, R., Budak, G., Bunescu, R., Caglar, M., Cai, B., Cai, C., Carlon, A., Chen, L., Ciaccio, M. F., Cooper, G., Coort, S., Creighton, C. J., Daneshmand, S. M. H., De La Fuente, A., Di Camillo, B., Dutta-Moscato, J., Emmett, K., Evelo, C., Fassia, M. K. H., Finotello, F., Finkle, J. D., Gao, X., Garcia-Garcia, J., Ghosh, S., Giaretta, A., Großeholz, R., Guinney, J., Hafemeister, C., Hahn, O., Haider, S., Hase, T., Hodgson, J., Hoff, B., Hsu, C. H., Hu, Y., Huang, X., Jalili, M., Jiang, X., Kacprowski, T., Kaderali, L., Kang, M., Kannan, V., Kikuchi, K., Kim, D. C., Kitano, H., Knapp, B., Komatsoulis, G., Krämer, A., Kursa, M. B., Kutmon, M., Li, Y., Liang, X., Liu, Z., Liu, Y., Lu, S., Lu, X., Manfrini, M., Matos, M. R. A., Meerzaman, D., Min, W., Müller, C. L., Neapolitan, R. E., Oliva, B., Opiyo, S. O., Pal, R., Palinkas, A., Planas-Iglesias, J., Poglayen, D., Sambo, F., Sanavia, T., Sharifi-Zarchi, A., Slawek, J., Streck, A., Strunz, S., Tegnér, J., Thobe, K., Toffolo, G. M., Trifoglio, E., Unger, M., Wan, Q., Welch, L., Wu, J. J., Xue, A. Y., Yamanaka, R., Yan, C., Zairis, S., Zengerling, M., Zenil, H. & Zi, Z., Mar 30 2016, In : Nature Methods. 13, 4, p. 310-322 13 p.

Research output: Contribution to journalArticle

97 Scopus citations

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

Salomonis, N., Dexheimer, P. J., Omberg, L., Schroll, R., Bush, S., Huo, J., Schriml, L., Ho Sui, S., Keddache, M., Mayhew, C., Shanmukhappa, S. K., Wells, J., Daily, K., Hubler, S., Wang, Y., Zambidis, E., Margolin, A., Hide, W., Hatzopoulos, A. K., Malik, P. & 3 others, Cancelas, J. A., Aronow, B. J. & Lutzko, C., Jul 12 2016, In : Stem Cell Reports. 7, 1, p. 110-125 16 p.

Research output: Contribution to journalArticle

38 Scopus citations

In vivo assessment of two endothelialization approaches on bioprosthetic valves for the treatment of chronic deep venous insufficiency

Glynn, J. J., Jones, C. M., Anderson, D. E. J., Pavcnik, D. & Hinds, M. T., Nov 1 2016, In : Journal of Biomedical Materials Research - Part B Applied Biomaterials. 104, 8, p. 1610-1621 12 p.

Research output: Contribution to journalArticle

5 Scopus citations

KDM5 lysine demethylases are involved in maintenance of 3′UTR length

Blair, L. P., Liu, Z., Labitigan, R. L. D., Wu, L., Zheng, D., Xia, Z., Pearson, E. L., Nazeer, F. I., Cao, J., Lang, S. M., Rines, R. J., Mackintosh, S. G., Moore, C. L., Li, W., Tian, B., Tackett, A. J. & Yan, Q., Nov 1 2016, In : Science advances. 2, 11, e1501662.

Research output: Contribution to journalArticle

10 Scopus citations

Longitudinal Relationship between Loneliness and Social Isolation in Older Adults: Results from the Cardiovascular Health Study

Petersen, J., Kaye, J., Jacobs, P., Quinones, A., Dodge, H., Arnold, A. & Thielke, S., Aug 1 2016, In : Journal of Aging and Health. 28, 5, p. 775-795 21 p.

Research output: Contribution to journalArticle

9 Scopus citations

Mechanism of NMDA Receptor Inhibition and Activation

Zhu, S., Stein, R. A., Yoshioka, C., Lee, C. H., Goehring, A., McHaourab, H. S. & Gouaux, E., Apr 21 2016, In : Cell. 165, 3, p. 704-714 11 p.

Research output: Contribution to journalArticle

90 Scopus citations

Methodology for quantitative characterization of fluorophore photoswitching to predict superresolution microscopy image quality

Bittel, A. M., Nickerson, A., Saldivar, I. S., Dolman, N. J., Nan, X. & Gibbs, S., Jul 14 2016, In : Scientific Reports. 6, 29687.

Research output: Contribution to journalArticle

9 Scopus citations

Minimal basilar membrane motion in low-frequency hearing

Warren, R. L., Ramamoorthy, S., Ciganovic, N., Zhang, Y., Wilson, T. M., Petrie, T., Wang, R. K., Jacques, S. L., Reichenbach, T., Nuttall, A. L. & Fridberger, A., Jul 26 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 30, p. E4304-E4310

Research output: Contribution to journalArticle

19 Scopus citations

Minimally invasive surgical method to detect sound processing in the cochlear apex by optical coherence tomography

Ramamoorthy, S., Zhang, Y., Petrie, T., Fridberger, A., Ren, T., Wang, R., Jacques, S. L. & Nuttall, A. L., Feb 1 2016, In : Journal of biomedical optics. 21, 2, 025003.

Research output: Contribution to journalArticle

8 Scopus citations

Monte Carlo modeling of photon propagation reveals highly scattering coral tissue

Wangpraseurt, D., Jacques, S., Petrie, T. & Kühl, M., Sep 21 2016, In : Frontiers in Plant Science. 7, September, 1404.

Research output: Contribution to journalArticle

14 Scopus citations

Multiplexed imaging reveals heterogeneity of PI3K/MAPK network signaling in breast lesions of known PIK3CA genotype

Jacob, T., Gray, J., Troxell, M. & Vu, T. T., Oct 1 2016, In : Breast Cancer Research and Treatment. 159, 3, p. 575-583 9 p.

Research output: Contribution to journalArticle

4 Scopus citations

Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1

Giudice, J., Xia, Z., Li, W. & Cooper, T. A., Oct 19 2016, In : Scientific Reports. 6, 35550.

Research output: Contribution to journalArticle

6 Scopus citations

New insight into the role of MMP14 in metabolic balance

Mori, H., Bhat, R., Bruni-Cardoso, A., Chen, E. I., Jorgens, D. M., Coutinho, K., Louie, K., Bowen, B. B., Inman, J. L., Tecca, V., Lee, S. J., Becker-Weimann, S., Northen, T., Seiki, M., Borowsky, A. D., Auer, M. & Bissell, M. J., Jan 1 2016, In : PeerJ. 2016, 7, e2142.

Research output: Contribution to journalArticle

6 Scopus citations

Oral administration of Bruton's tyrosine kinase inhibitors impairs GPVI-mediated platelet function

Rigg, R. A., Aslan, J., Healy, L. D., Wallisch, M., Thierheimer, M. L. D., Loren, C. P., Pang, J., Hinds, M., Gruber, A. & McCarty, O., Mar 1 2016, In : American Journal of Physiology - Cell Physiology. 310, 5, p. C373-C380

Research output: Contribution to journalArticle

31 Scopus citations

PEG-lipid micelles enable cholesterol efflux in Niemann-Pick Type C1 disease-based lysosomal storage disorder

Brown, A., Patel, S., Ward, C., Lorenz, A., Ortiz, M., DuRoss, A., Wieghardt, F., Esch, A., Otten, E. G., Heiser, L. M., Korolchuk, V. I., Sun, C., Sarkar, S. & Sahay, G., Aug 30 2016, In : Scientific Reports. 6, 31750.

Research output: Contribution to journalArticle

13 Scopus citations

PI3 Kinase Pathway Mutations in Human Cancers

Gray, J., Dec 1 2016, In : JAMA oncology. 2, 12, p. 1543-1544 2 p.

Research output: Contribution to journalArticle

4 Scopus citations

Platelet-derived short-chain polyphosphates enhance the inactivation of tissue factor pathway inhibitor by activated coagulation factor XI

Puy, C., Tucker, E., Ivanov, I. S., Gailani, D., Smith, S. A., Morrissey, J. H., Gruber, A. & McCarty, O., Oct 1 2016, In : PLoS One. 11, 10, e0165172.

Research output: Contribution to journalArticle

10 Scopus citations

Polarized light imaging specifies the anisotropy of light scattering in the superficial layer of a tissue

Jacques, S., Roussel, S. & Samatham, R., Jul 1 2016, In : Journal of Biomedical Optics. 21, 7, 071115.

Research output: Contribution to journalArticle

8 Scopus citations

Primer for image informatics in personalized medicine

Chang, Y. H., Foley, P., Azimi, V., Borkar, R. & Lefman, J., 2016, In : Unknown Journal. 159, p. 58-65 8 p.

Research output: Contribution to journalArticle

2 Scopus citations

Profiling Esterases in Mycobacterium tuberculosis Using Far-Red Fluorogenic Substrates

Tallman, K. R., Levine, S. R. & Beatty, K., Jul 15 2016, In : ACS Chemical Biology. 11, 7, p. 1810-1815 6 p.

Research output: Contribution to journalArticle

15 Scopus citations

Prothrombotic skeletal muscle myosin directly enhances prothrombin activation by binding factors Xa and Va

Deguchi, H., Sinha, R. K., Marchese, P., Ruggeri, Z. M., Zilberman-Rudenko, J., McCarty, O., Cohen, M. J. & Griffin, J. H., Oct 6 2016, In : Blood. 128, 14, p. 1870-1878 9 p.

Research output: Contribution to journalArticle

11 Scopus citations

Randomized trial of a dual-hormone artificial pancreas with dosing adjustment during exercise compared with no adjustment and sensor-augmented pump therapy

Jacobs, P., El Youssef, J., Reddy, R., Resalat, N., Branigan, D., Condon, J., Preiser, N., Ramsey, K., Jones, M., Edwards, C., Kuehl, K., Leitschuh, J., Rajhbeharrysingh, U. & Castle, J., 2016, (Accepted/In press) In : Diabetes, Obesity and Metabolism.

Research output: Contribution to journalArticle

57 Scopus citations

Ras dimer formation as a new signaling mechanism and potential cancer therapeutic target

Chen, M., Peters, A., Huang, T. & Nan, X., Mar 1 2016, In : Mini-Reviews in Medicinal Chemistry. 16, 5, p. 391-403 13 p.

Research output: Contribution to journalArticle

21 Scopus citations

Reconstruction of Gene Regulatory Networks Based on Repairing Sparse Low-Rank Matrices

Chang, Y. H., Dobbe, R., Bhushan, P., Gray, J. & Tomlin, C. J., Jul 1 2016, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 13, 4, p. 767-777 11 p., 7182286.

Research output: Contribution to journalArticle

Sensory reweighting dynamics following removal and addition of visual and proprioceptive cues

Assländer, L. & Peterka, R. B., Aug 1 2016, In : Journal of Neurophysiology. 116, 2, p. 272-285 14 p.

Research output: Contribution to journalArticle

21 Scopus citations

Small-Molecule Probes Reveal Esterases with Persistent Activity in Dormant and Reactivating Mycobacterium tuberculosis

Tallman, K. R., Levine, S. R. & Beatty, K., Dec 9 2016, In : ACS Infectious Diseases. 2, 12, p. 936-944 9 p.

Research output: Contribution to journalArticle

20 Scopus citations

Sparse network identifiability via Compressed Sensing

Hayden, D., Chang, Y. H., Goncalves, J. & Tomlin, C. J., 2016, In : Automatica. 68, p. 9-17 9 p.

Research output: Contribution to journalArticle

32 Scopus citations

Synthesis of a far-red fluorophore and its use as an esterase probe in living cells

Levine, S. R. & Beatty, K. E., Jan 31 2016, In : Chemical Communications. 52, 9, p. 1835-1838 4 p.

Research output: Contribution to journalArticle

18 Scopus citations

The Black Bug Myth: Selective photodestruction of pigmented pathogens

Harris, D. M., Jacques, S. & Darveau, R., Sep 1 2016, In : Lasers in Surgery and Medicine. 48, 7, p. 706-714 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

The ErbB2ΔEx16 splice variant is a major oncogenic driver in breast cancer that promotes a pro-metastatic tumor microenvironment

Turpin, J., Ling, C., Crosby, E. J., Hartman, Z. C., Simond, A. M., Chodosh, L. A., Rennhack, J. P., Andrechek, E. R., Ozcelik, J., Hallett, M., Mills, G. B., Cardiff, R. D., Gray, J. W., Griffith, O. L. & Muller, W. J., May 9 2016, (Accepted/In press) In : Oncogene.

Research output: Contribution to journalArticle

20 Scopus citations

The Formation of Microthrombi in Parenchymal Microvessels after Traumatic Brain Injury Is Independent of Coagulation Factor XI

Schwarzmaier, S. M., De Chaumont, C., Balbi, M., Terpolilli, N. A., Kleinschnitz, C., Gruber, A. & Plesnila, N., Sep 1 2016, In : Journal of Neurotrauma. 33, 17, p. 1634-1644 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

Afgan, E., Baker, D., van den Beek, M., Blankenberg, D., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Eberhard, C., Grüning, B., Guerler, A., Hillman-Jackson, J., Von Kuster, G., Rasche, E., Soranzo, N., Turaga, N., Taylor, J., Nekrutenko, A. & Goecks, J., Jul 8 2016, In : Nucleic acids research. 44, W1, p. W3-W10

Research output: Contribution to journalArticle

802 Scopus citations

The hemostatic role of factor XI

Puy, C., Rigg, R. A. & McCarty, O., May 1 2016, In : Thrombosis Research. 141, p. S8-S11

Research output: Contribution to journalArticle

19 Scopus citations

The prothrombotic activity of cancer cells in the circulation

Mitrugno, A., Tormoen, G. W., Kuhn, P. & McCarty, O., Jan 1 2016, In : Blood Reviews. 30, 1, p. 11-19 9 p.

Research output: Contribution to journalArticle

35 Scopus citations