Research Output

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Comment/debate
1989

Erratum

Lucas, J. N., Tenjin, T., Straume, T., Pinkel, D., Moore, D., Litt, M. & Gray, J. W., Jan 1 1989, In : International Journal of Radiation Biology. 56, 2, p. 201 1 p.

Research output: Contribution to journalComment/debate

23 Scopus citations
1996

Erratum: Melanin granule model for laser-induced thermal damage in the retina (Bulletin of Mathematical Biology (1996) 58 (513-553)

Thompson, C. R., Gerstman, B. S., Jacques, S. L. & Rogers, M. E., Jan 1 1996, In : Bulletin of Mathematical Biology. 58, 4, p. 809-810 2 p.

Research output: Contribution to journalComment/debate

1 Scopus citations
1998

Cell migration: Regulation of force on extracellular-matrix-integrin complexes

Sheetz, M. P., Felsenfeld, D. P. & Galbraith, C. G., Feb 1998, In : Trends in Cell Biology. 8, 2, p. 51-54 4 p.

Research output: Contribution to journalComment/debate

341 Scopus citations

Erratum: (Proceedings of Laser-Tissue Interaction IX (26-28 January 1998))

Jacques, S. L. & Katzir, A., Dec 1 1998, In : Proceedings of SPIE - The International Society for Optical Engineering. 3254, 1 p.

Research output: Contribution to journalComment/debate

2001

Erratum: Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas (Journal of Vascular Technology (2001) 29 (459-464))

Hodgson, G., Hager, J. H., Volik, S., Hariono, S., Wernick, M., Moore, D., Nowak, N., Albertson, D. G., Pinkel, D., Collins, C., Hanahan, D. & Gray, J. W., Dec 1 2001, In : Nature genetics. 29, 4, 1 p.

Research output: Contribution to journalComment/debate

6 Scopus citations
2002

Erratum: (Laser Tissue Interaction XIII: Photochemical, Photothermal, and Photomechanical (20-23 January 2002))

Jacques, S. L., Duncan, D., Kirkpatrick, S. J. & Kriete, A., Jan 1 2002, In : Proceedings of SPIE - The International Society for Optical Engineering. 4617, p. 294-296 3 p.

Research output: Contribution to journalComment/debate

2004

Erratum: Single-ensemble nonequilibrium path-sampling estimates of free energy differences (Journal of Chemical Physics) (2004) 120 (10876))

Ytreberg, F. M. & Zuckerman, D. M., Sep 8 2004, In : Journal of Chemical Physics. 121, 10, p. 5022-5023 2 p.

Research output: Contribution to journalComment/debate

5 Scopus citations
2006

Bladder cancer outcome and subtype classification by gene expression

Blaveri, E., Simko, J. P., Korkola, J. E., Brewer, J. L., Baehner, F., Mehta, K., Devries, S., Koppie, T., Pejavar, S., Carroll, P. & Waldman, F. M., Apr 1 2006, In : Journal of Urology. 175, 4, 1 p.

Research output: Contribution to journalComment/debate

2007

Erratum: Minimal regulation of platelet activity by PECAM-1 (Platelets (February 2007) 18:1 (56-67))

Dhanjal, T. S., Ross, E. A., Auger, J. M., Mccarty, O. J. T., Hughes, C. E., Senis, Y. A., Buckley, C. D. & Watson, S. P., Mar 1 2007, In : Platelets. 18, 2, 1 p.

Research output: Contribution to journalComment/debate

Erratum: Minimal regulation of platelet activity by PECAM-1 (Platelets (2007) 18:1 (56-67))

Dhanjal, T. S., Ross, E. A., Auger, J. M., Mccarty, O. J. T., Hughes, C. E., Senis, Y. A., Buckley, C. D. & Watson, S. P., Sep 1 2007, In : Platelets. 18, 6, 1 p.

Research output: Contribution to journalComment/debate

Erratum to "Fast neural network surrogates for very high dimensional physics-based models in computational oceanography" [Neural Netw. 20 (4) (2007) 462-478] (DOI:10.1016/j.neunet.2007.04.023)

van der Merwe, R., Leen, T. K., Lu, Z., Frolov, S. & Baptista, A. M., Aug 1 2007, In : Neural Networks. 20, 6, p. 761-762 2 p.

Research output: Contribution to journalComment/debate

1 Scopus citations
2009

ChiBE: Interactive visualization and manipulation of BioPAX pathway models

Babur, O., Dogrusoz, U., Demir, E. & Sander, C., Dec 9 2009, In : Bioinformatics. 26, 3, p. 429-431 3 p.

Research output: Contribution to journalComment/debate

27 Scopus citations

Erratum: Imaging of glioma tumor with endogenous fluorescence tomography (Journal of Biomedical Optics (2009) 14 (030501))

Kepshire, D. S., Gibbs-Strauss, S. L., O'Hara, J. A., Hutchins, M., Mincu, N., Leblond, F., Khayat, M., Dehghani, H., Srinivasan, S. & Pogue, B. W., Dec 1 2009, In : Journal of biomedical optics. 14, 3, 039802.

Research output: Contribution to journalComment/debate

3 Scopus citations

Erratum: The systems biology graphical notation (Nature Biotechnology (2009) 27 (735-741))

Le Novère, N., 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., Sep 1 2009, In : Nature biotechnology. 27, 9, 1 p.

Research output: Contribution to journalComment/debate

2 Scopus citations
2010

Erratum: Review of neurosurgical fluorescence imaging methodologies (IEEE Journal on Selected Topics in Quantum Electronics (2010) 16: 3 (493-505))

Pogue, B. W., Gibbs-Strauss, S., Valdés, P. A., Samkoe, K., Roberts, D. W. & Paulsen, K. D., Nov 1 2010, In : IEEE Journal on Selected Topics in Quantum Electronics. 16, 6, 1 p., 5640636.

Research output: Contribution to journalComment/debate

1 Scopus citations

Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942)

Demir, E., 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., Splendiani, A. & 69 others, 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., Dec 1 2010, In : Nature biotechnology. 28, 12, 1 p.

Research output: Contribution to journalComment/debate

3 Scopus citations

Nanotechnology research: Applications in nutritional sciences (Journal of Nutrition (2010) 140, (119-124))

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., May 1 2010, In : Journal of Nutrition. 140, 5, 1 p.

Research output: Contribution to journalComment/debate

Platelet polyphosphate: An endogenous activator of coagulation factor XII

Mackman, N. & Gruber, A., May 2010, In : Journal of Thrombosis and Haemostasis. 8, 5, p. 865-867 3 p.

Research output: Contribution to journalComment/debate

18 Scopus citations
2011

Erratum: Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI (Integrative Biology (2011) 3 (910-921) DOI:10.1039/C1IB00043H)

Nabavizadeh, N., Klifa, C., Newitt, D., Lu, Y., Chen, Y. Y., Hsu, H., Fisher, C., Tokuyasu, T., Olshen, A. B., Spellman, P., Gray, J. W., Hylton, N. & Park, C. C., Dec 2011, In : Integrative Biology. 3, 12, 1 p.

Research output: Contribution to journalComment/debate

Erratum: Optical fiber probe spectroscopy for laparoscopic monitoring of tissue oxygenation during esophagectomies (J. Biomed. Opt (2010) 14 (061712))

Gareau, D. S., Truffer, F., Perry, K. A., Pham, T. H., Kristian Enestvedt, C., Dolan, J. P., Hunter, J. G. & Jacques, S. L., Mar 1 2011, In : Journal of biomedical optics. 16, 3, 039801.

Research output: Contribution to journalComment/debate

Size matters

Gruber, A. & Tucker, E. I., Dec 15 2011, In : Blood. 118, 25, p. 6481-6482 2 p.

Research output: Contribution to journalComment/debate

1 Scopus citations
2013

A controlled study of the effectiveness of an adaptive closed-loop algorithm to minimize corticosteroidinduced stress hyperglycemia in type 1 diabetes

El Castle, J., Youssef, J. R., Branigan, D. L., Massoud, R. G., Breen, M. E., Jacobs, P. G., Bequette, B. W. & Ward, W. K., Jun 1 2013, In : Diabetes Technology and Therapeutics. 15, SUPPL.1, p. S30-S31

Research output: Contribution to journalComment/debate

Erratum: Optical properties of biological tissues: A review (Physics in Medicine and Biology (2013) 58)

Jacques, S. L., Jul 21 2013, In : Physics in Medicine and Biology. 58, 14, p. 5007-5008 2 p.

Research output: Contribution to journalComment/debate

104 Scopus citations
2014

Erratam: Tri-modal confocal mosaics detect residual invasive squamous cell carcinoma in Mohs surgical excisions (Journal of Biomedical Optics (2012) 17:6 (066018))

Gareau, D., Bar, A., Snaveley, N., Lee, K., Chen, N., Swanson, N., Simpson, E. & Jacques, S., Feb 1 2014, In : Journal of biomedical optics. 19, 2, 029801.

Research output: Contribution to journalComment/debate

Erratum: Novel oral detoxification of mercury, cadmium, and lead with thiol-modified nanoporous silica (ACS Applied Materials and Interfaces (2014) 6:8 DOI: 10.1021/am5007707)

Sangvanich, T., Morry, J., Fox, C., Ngamcherdtrakul, W., Goodyear, S., Castro, D., Fryxell, G. E., Addleman, R. S., Summers, A. O. & Yantasee, W., Dec 10 2014, In : ACS Applied Materials and Interfaces. 6, 23, 1 p.

Research output: Contribution to journalComment/debate

1 Scopus citations
2015

Erratum: "quantitative analysis of transcranial and intraparenchymal light penetration in human cadaver brain tissue" (Lasers in Surgery and Medicine (2015) 47(4):312-322)

Tedford, C. E., Delapp, S., Jacques, S. & Anders, J., Jul 1 2015, In : Lasers in Surgery and Medicine. 47, 5, 1 p.

Research output: Contribution to journalComment/debate

Open Access
1 Scopus citations

Erratum to Modeling precision treatment of breast cancer [Genome Biology, 14, (2013), R110]

Daemen, A., Griffith, O. L., Heiser, L. M., Wang, N. J., Enache, O. M., Sanborn, Z., Pepin, F., Durinck, S., Korkola, J. E., Griffith, M., Hur, J. S., Huh, N., Chung, J., Cope, L., Fackler, M. J., Umbricht, C., Sukumar, S., Seth, P., Sukhatme, V. P., Jakkula, L. R. & 7 others, Lu, Y., Mills, G. B., Cho, R. J., Collisson, E. A., van't Veer, L. J., Spellman, P. T. & Gray, J. W., May 12 2015, In : Genome biology. 16, 1, 95.

Research output: Contribution to journalComment/debate

2 Scopus citations
2016

Erratum: Functional proteomics identifies miRNAs to target a p27/Myc/phospho-Rb signature in breast and ovarian cancer (Oncogene (2016) 35 (691-701) DOI:10.1038/onc.2014.469)

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. V., Sood, A. K., Mukherjee, S., Gray, J. W., Mills, G. B. & Ram, P. T., Feb 11 2016, In : Oncogene. 35, 6, p. 801 1 p.

Research output: Contribution to journalComment/debate

3 Scopus citations

Erratum to Dermal delivery of HSP47 siRNA with NOX4-modulating mesoporous silica-based nanoparticles for treating fibrosis [Biomaterials, 66, (2015), 41-52] DOI:10.1016/j.biomaterials.2015.07.005

Morry, J., Ngamcherdtrakul, W., Gu, S., Goodyear, S. M., Castro, D. J., Reda, M. M., Sangvanich, T. & Yantasee, W., Jan 2016, In : Biomaterials. 74, 1 p.

Research output: Contribution to journalComment/debate

2017

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

Griffith, M., Spies, N. C., Krysiak, K., McMichael, J. F., Coffman, A. C., Danos, A. M., Ainscough, B. J., Ramirez, C. A., Rieke, D. T., Kujan, L., Barnell, E. K., Wagner, A. H., Skidmore, Z. L., Wollam, A., Liu, C. J., Jones, M. R., Bilski, R. L., Lesurf, R., Feng, Y. Y., Shah, N. M. & 25 others, Bonakdar, M., Trani, L., Matlock, M., Ramu, A., Campbell, K. M., Spies, G. C., Graubert, A. P., Gangavarapu, K., Eldred, J. M., Larson, D. E., Walker, J. R., Good, B. M., Wu, C., Su, A. I., Dienstmann, R., Margolin, A. A., Tamborero, D., Lopez-Bigas, N., Jones, S. J. M., Bose, R., Spencer, D. H., Wartman, L. D., Wilson, R. K., Mardis, E. R. & Griffith, O. L., Jan 31 2017, In : Nature genetics. 49, 2, p. 170-174 5 p.

Research output: Contribution to journalComment/debate

132 Scopus citations

Correction: Decoupling of the PI3K pathway via mutation necessitates combinatorial treatment in HER2+ breast cancer (PLoS ONE (2015) 10:7 (e0133219) DOI: 10.1371/journal.pone.0133219)

Korkola, J. E., Collisson, E. A., Heiser, L. M., 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., Jakkula, L., Feiler, H., Lu, Y., Mills, G. B., Spellman, P. T. & 3 others, Tomlin, C., Mukherjee, S. & Gray, J. W., Oct 1 2017, In : PLoS One. 12, 10, e0186551.

Research output: Contribution to journalComment/debate

Erratum: Correction: Human mutations in integrator complex subunits link transcriptome integrity to brain development (PLoS genetics (2017) 13 5 (e1006809))

Oegema, R., Baillat, D., Schot, R., van Unen, L. M., Brooks, A., Kia, S. K., Hoogeboom, A. J. M., Xia, Z., Li, W., Cesaroni, M., Lequin, M. H., van Slegtenhorst, M., Dobyns, W. B., de Coo, I. F. M., van den Berg, D., Verheijen, F. W., Kremer, A., van der Spek, P. J., Heijsman, D., Wagner, E. J. & 2 others, Fornerod, M. & Mancini, G. M. S., Aug 1 2017, In : PLoS genetics. 13, 8, p. e1006923

Research output: Contribution to journalComment/debate

Open Access
1 Scopus citations

Erratum to: "Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer", [Breast Cancer Research, 19, (2017) (17)] DOI: 10.1186/s13058-017-0809-6

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. A., Esch, A., Feiler, H. S., Wang, N. J., Hardwicke, M. A., Laquerre, S., Jackson, J., Wood, K. W., Weber, B. & 5 others, Spellman, P. T., Aparicio, S., Wooster, R., Caldas, C. & Gray, J. W., Feb 9 2017, In : Breast Cancer Research. 19, 1, 17.

Research output: Contribution to journalComment/debate

Ticagrelor breaks up the tumor-platelet party

Mitrugno, A. & McCarty, O., Sep 7 2017, In : Blood. 130, 10, p. 1177-1178 2 p.

Research output: Contribution to journalComment/debate

4 Scopus citations
2018

Corrigendum: Potential role of the glycolytic oscillator in acute hypoxia in tumors (Physics in Medicine and Biology (2015) 60 (9215) DOI: 10.1088/0031-9155/60/24/9215)

Che Fru, L., Adamson, E. B., Campos, D. D., Fain, S. B., Jacques, S. L., Van Der Kogel, A. J., Nickel, K. P., Song, C., Kimple, R. J. & Kissick, M. W., Jun 27 2018, In : Physics in Medicine and Biology. 63, 13, 139501.

Research output: Contribution to journalComment/debate

1 Scopus citations
14 Scopus citations

Erratum: Cloud computing for genomic data analysis and collaboration (Nature reviews. Genetics (2018) 19 4 (208-219))

Langmead, B. & Nellore, A., May 1 2018, In : Nature reviews. Genetics. 19, 5, 1 p.

Research output: Contribution to journalComment/debate

Open Access
7 Scopus citations

Erratum: Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes (Nature communications (2017) 8 1 (1231))

Brady, S. W., McQuerry, J. A., Qiao, Y., Piccolo, S. R., Shrestha, G., Jenkins, D. F., Layer, R. M., Pedersen, B. S., Miller, R. H., Esch, A., Selitsky, S. R., Parker, J. S., Anderson, L. A., Dalley, B. K., Factor, R. E., Reddy, C. B., Boltax, J. P., Li, D. Y., Moos, P. J., Gray, J. W. & 8 others, Heiser, L. M., Buys, S. S., Cohen, A. L., Johnson, W. E., Quinlan, A. R., Marth, G., Werner, T. L. & Bild, A. H., Feb 5 2018, In : Nature communications. 9, 1, 1 p.

Research output: Contribution to journalComment/debate

Practical Computational Reproducibility in the Life Sciences

Grüning, B., Chilton, J., Köster, J., Dale, R., Soranzo, N., van den Beek, M., Goecks, J., Backofen, R., Nekrutenko, A. & Taylor, J., Jun 27 2018, In : Cell Systems. 6, 6, p. 631-635 5 p.

Research output: Contribution to journalComment/debate

15 Scopus citations
2019

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

Erratum: Modeling subdiffusive light scattering by incorporating the tissue phase function and detector numerical aperture (Journal of Biomedical Optics (2017) 22:5 (050501) DOI: 10.1117/1.JBO.22.5.050501)

Post, A. L., Jacques, S., Sterenborg, H. J. C. M., Faber, D. J. & Van Leeuwen, T. G., Jun 30 2019, In : Journal of biomedical optics. 24, 6, 069801.

Research output: Contribution to journalComment/debate

Open Access

Erratum: Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity (Nature (2012) 483 7391 (603-607))

Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., Wilson, C. J., Lehár, J., Kryukov, G. V., Sonkin, D., Reddy, A., Liu, M., Murray, L., Berger, M. F., Monahan, J. E., Morais, P., Meltzer, J., Korejwa, A., Jané-Valbuena, J., Mapa, F. A. & 41 others, Thibault, J., Bric-Furlong, E., Raman, P., Shipway, A., Engels, I. H., Cheng, J., Yu, G. K., Yu, J., Aspesi, P., de Silva, M., Jagtap, K., Jones, M. D., Wang, L., Hatton, C., Palescandolo, E., Gupta, S., Mahan, S., Sougnez, C., Onofrio, R. C., Liefeld, T., MacConaill, L., Winckler, W., Reich, M., Li, N., Mesirov, J. P., Gabriel, S. B., Getz, G., Ardlie, K., Chan, V., Myer, V. E., Weber, B. L., Porter, J., Warmuth, M., Finan, P., Harris, J. L., Meyerson, M., Golub, T. R., Morrissey, M. P., Sellers, W. R., Schlegel, R. & Garraway, L. A., Jan 1 2019, In : Nature. 565, 7738, p. E5-E6

Research output: Contribution to journalComment/debate

3 Scopus citations

Erratum: Correction: FGF2-FGFR1 signaling regulates release of leukemia-protective exosomes from bone marrow stromal cells (eLife (2019) 8 PII: e47174)

Javidi-Sharifi, N., Martinez, J., English, I., Joshi, S. K., Scopim-Ribeiro, R., Viola, S. K., Edwards, D. K., Agarwal, A., Lopez, C., Jorgens, D., Tyner, J. W., Druker, B. J. & Traer, E., Mar 29 2019, In : eLife. 8

Research output: Contribution to journalComment/debate

Open Access

The Potential and Pitfalls of Crowdsourced Algorithm Development in Radiation Oncology

Elhalawani, H., Fuller, C. D. & Thompson, R., Jan 1 2019, In : JAMA Oncology.

Research output: Contribution to journalComment/debate

1 Scopus citations
2020

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