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A Central role for RAF→MEK→ERK signaling in the genesis of pancreatic ductal adenocarcinoma

Collisson, E. A., Trejo, C. L., Silva, J. M., Gu, S., Korkola, J. E., Heiser, L. M., Charles, R. P., Rabinovich, B. A., Hann, B., Dankort, D., Spellman, P. T., Phillips, W. A., Gray, J. W. & McMahon, M., Aug 2012, In : Cancer discovery. 2, 8, p. 685-693 9 p.

Research output: Contribution to journalArticle

146 Scopus citations

A community computational challenge to predict the activity of pairs of compounds

Cellworks Group & NCI DREAM Community, Dec 1 2014, In : Nature biotechnology. 32, 12, p. 1213-1222 10 p.

Research output: Contribution to journalArticle

119 Scopus citations

A community effort to assess and improve drug sensitivity prediction algorithms

NCI DREAM Community, Dec 1 2014, In : Nature biotechnology. 32, 12, p. 1202-1212 11 p.

Research output: Contribution to journalArticle

283 Scopus citations

Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes

Rahman, M., MacNeil, S. M., Jenkins, D. F., Shrestha, G., Wyatt, S. R., McQuerry, J. A., Piccolo, S. R., Heiser, L. M., Gray, J. W., Johnson, W. E. & Bild, A. H., Apr 26 2017, In : Genome Medicine. 9, 1, 40.

Research output: Contribution to journalArticle

5 Scopus citations

Analysis of K-Ras interactions by biotin ligase tagging

Ritchie, C., Mack, A., Harper, L., Alfadhli, A., Stork, P. J. S., Nan, X. & Barklis, E., Jul 1 2017, In : Cancer Genomics and Proteomics. 14, 4, p. 225-239 15 p.

Research output: Contribution to journalArticle

1 Scopus citations

Analysis of molecular inversion probe performance for allele copy number determination

Wang, Y., Moorhead, M., Karlin-Neumann, G., Wang, N. J., Ireland, J., Lin, S., Chen, C., Heiser, L. M., Chin, K., Esserman, L., Gray, J. W., Spellman, P. T. & Faham, M., Nov 20 2007, In : Genome biology. 8, 11, R246.

Research output: Contribution to journalArticle

50 Scopus citations

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

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

Research output: Contribution to journalArticle

4 Scopus citations

A new model for binding of kinesin 13 to curved microtubule protofilaments

Mulder, A. M., Glavis-Bloom, A., Moores, C. A., Wagenbach, M., Carragher, B., Wordeman, L. & Milligan, R. A., Apr 6 2009, In : Journal of Cell Biology. 185, 1, p. 51-57 7 p.

Research output: Contribution to journalArticle

32 Scopus citations

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

Appion: An integrated, database-driven pipeline to facilitate EM image processing

Lander, G. C., Stagg, S. M., Voss, N. R., Cheng, A., Fellmann, D., Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P. W., Lyumkis, D., Potter, C. S. & Carragher, B., Apr 1 2009, In : Journal of Structural Biology. 166, 1, p. 95-102 8 p.

Research output: Contribution to journalArticle

438 Scopus citations

A robust prognostic signature for hormone-positive node-negative breast cancer

Griffith, O. L., Pepin, F., Enache, O. M., Heiser, L. M., Collisson, E. A., Spellman, P. T. & Gray, J. W., Oct 11 2013, In : Genome Medicine. 5, 10, 92.

Research output: Contribution to journalArticle

11 Scopus citations

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

Assessment of roles for the rho-specific guanine nucleotide dissociation inhibitor Ly-GDI in platelet function: A spatial systems approach

Ngo, A. T. P., Thierheimer, M. L. D., Babur, O., Rocheleau, A. D., Huang, T., Pang, J., Rigg, R. A., Mitrugno, A., Theodorescu, D., Burchard, J., Nan, X., Demir, E., McCarty, O. & Aslan, J., Apr 7 2017, In : American Journal of Physiology - Cell Physiology. 312, 4, p. C527-C536

Research output: Contribution to journalArticle

9 Scopus citations

A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047

Kuo, W. L., Das, D., Ziyad, S., Bhattacharya, S., Gibb, W. J., Heiser, L. M., Sadanandam, A., Fontenay, G. V., Hu, Z., Wang, N., Bayani, N., Feiler, H. S., Neve, R. M., Wyrobek, A. J., Spellman, P. T., Marton, L. J. & Gray, J. W., Dec 14 2009, In : BMC Medicine. 7, 77.

Research output: Contribution to journalArticle

25 Scopus citations

ATM Suppresses SATB1-Induced Malignant Progression in Breast Epithelial Cells

Ordinario, E., Han, H. J., Furuta, S., Heiser, L. M., Jakkula, L. R., Rodier, F., Spellman, P. T., Campisi, J., Gray, J. W., Bissell, M. J., Kohwi, Y. & Kohwi-Shigematsu, T., Dec 10 2012, In : PloS one. 7, 12, e51786.

Research output: Contribution to journalArticle

17 Scopus citations

A Toolbox for ab initio 3-D reconstructions in single-particle electron microscopy

Voss, N. R., Lyumkis, D., Cheng, A., Lau, P. W., Mulder, A., Lander, G. C., Brignole, E. J., Fellmann, D., Irving, C., Jacovetty, E. L., Leung, A., Pulokas, J., Quispe, J. D., Winkler, H., Yoshioka, C., Carragher, B. & Potter, C. S., Mar 1 2010, In : Journal of Structural Biology. 169, 3, p. 389-398 10 p.

Research output: Contribution to journalArticle

36 Scopus citations

Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition

Mirzoeva, O. K., Das, D., Heiser, L. M., Bhattacharya, S., Siwak, D., Gendelman, R., Bayani, N., Wang, N. J., Neve, R. M., Guan, Y., Hu, Z., Knight, Z., Feiler, H. S., Gascard, P., Parvin, B., Spellman, P. T., Shokat, K. M., Wyrobek, A. J., Bissell, M. J., McCormick, F. & 4 others, Kuo, W. L., Mills, G. B., Gray, J. W. & Korn, W. M., Jan 15 2009, In : Cancer Research. 69, 2, p. 565-572 8 p.

Research output: Contribution to journalArticle

274 Scopus citations

Bayesian Inference of Signaling Network Topology in a Cancer Cell Line

Hill, S. M., Lu, Y., Molina, J., Heiser, L. M., Spellman, P. T., Speed, T. P., Gray, J. W., Mills, G. B. & Mukherjee, S., Nov 2012, In : Bioinformatics. 28, 21, p. 2804-2810 7 p.

Research output: Contribution to journalArticle

64 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. M. & Alumkal, J. J., Jul 11 2019, In : Oncogene. 38, 28, p. 5658-5669 12 p.

Research output: Contribution to journalArticle

5 Scopus citations

CARS microscopy lights up lipids in living cells

Nan, X., Yang, W. Y. & Xie, X. S., Aug 1 2004, In : Biophotonics International. 11, 8, p. 44-47 4 p.

Research output: Contribution to journalArticle

22 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

100 Scopus citations

Cellular androgen content influences enzalutamide agonism of F877L mutant androgen receptor

Coleman, D. J., Van Hook, K., King, C. J., Schwartzman, J., Lisac, R., Urrutia, J., Sehrawat, A., Woodward, J., Wang, N., Gulati, R., Thomas, G. V., Beer, T. M., Gleave, M., Korkola, J. E., Gao, L., Heiser, L. M. & Alumkal, J. J., 2016, In : Oncotarget. 7, 26, p. 40690 1 p.

Research output: Contribution to journalArticle

7 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., 2015, In : Theranostics. 5, 6, p. 609-617 9 p.

Research output: Contribution to journalArticle

19 Scopus citations

Chemically assembled single-wall carbon nanotubes and their electrochemistry

Diao, P., Liu, Z., Wu, B., Nan, X., Zhang, J. & Wei, Z., Oct 18 2002, In : ChemPhysChem. 3, 10, p. 898-991 94 p.

Research output: Contribution to journalArticle

103 Scopus citations

Combating subclonal evolution of resistant cancer phenotypes

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., Dec 1 2017, In : Nature communications. 8, 1, 1231.

Research output: Contribution to journalArticle

32 Scopus citations

Comparing implementations of magnetic-resonance-guided fluorescence molecular tomography for diagnostic classification of brain tumors

Davis, S. C., Samkoe, K. S., O'Hara, J. A., Gibbs-Strauss, S. L., Paulsen, K. D. & Pogue, B. W., Sep 2010, In : Journal of biomedical optics. 15, 5, 051602.

Research output: Contribution to journalArticle

29 Scopus citations

Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling

Hill, S. M., Nesser, N. K., Johnson-Camacho, K., Jeffress, M., Johnson, A., Boniface, C., Spencer, S. E. F., Lu, Y., Heiser, L. M., Lawrence, Y., Pande, N. T., Korkola, J. E., Gray, J. W., Mills, G. B., Mukherjee, S. & Spellman, P. T., Jan 25 2017, In : Cell Systems. 4, 1, p. 73-83.e10

Research output: Contribution to journalArticle

12 Scopus citations

Copy Number Gain of hsa-miR-569 at 3q26.2 Leads to Loss of TP53INP1 and Aggressiveness of Epithelial Cancers

Chaluvally-Raghavan, P., Zhang, F., Pradeep, S., Hamilton, M. P., Zhao, X., Rupaimoole, R., Moss, T., Lu, Y., Yu, S., Pecot, C. V., Aure, M. R., Peuget, S., Rodriguez-Aguayo, C., Han, H. D., Zhang, D., Venkatanarayan, A., Krohn, M., Kristensen, V. N., Gagea, M., Ram, P. & 11 others, Liu, W., Lopez-Berestein, G., Lorenzi, P. L., Børresen-Dale, A. L., Chin, K., Gray, J., Dusetti, N. J., McGuire, S. E., Flores, E. R., Sood, A. K. & Mills, G. B., Dec 8 2014, In : Cancer Cell. 26, 6, p. 863-879 17 p.

Research output: Contribution to journalArticle

31 Scopus citations

Corollary discharge and spatial updating: When the brain is split, is space still unified?

Colby, C. L., Berman, R. A., Heiser, L. M. & Saunders, R. C., Oct 24 2005, In : Progress in Brain Research. 149, p. 187-205 19 p.

Research output: Contribution to journalArticle

23 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

Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: The IRES functions as an RNA-based translation factor

Spahn, C. M. T., Jan, E., Mulder, A., Grassucci, R. A., Sarnow, P. & Frank, J., Aug 20 2004, In : Cell. 118, 4, p. 465-475 11 p.

Research output: Contribution to journalArticle

200 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

Diagnostic detection of diffuse glioma tumors in vivo with molecular fluorescent probe-based transmission spectroscopy

Gibbs-Strauss, S. L., O'Hara, J. A., Srinivasan, S., Hoopes, P. J., Hasan, T. & Pogue, B. W., 2009, In : Medical Physics. 36, 3, p. 974-983 10 p.

Research output: Contribution to journalArticle

9 Scopus citations

Diagnostic performance of receptor-specific surgical specimen staining correlates with receptor expression level

Schaefer, J. M., Barth, C. W., Davis, S. C. & Gibbs, S. L., Feb 1 2019, In : Journal of biomedical optics. 24, 2, 026002.

Research output: Contribution to journalArticle

5 Scopus citations

Differential Roles for the Coagulation Factors XI and XII in Regulating the Physical Biology of Fibrin

Sylman, J. L., Daalkhaijav, U., Zhang, Y., Gray, E. M., Farhang, P. A., Chu, T. T., Zilberman-Rudenko, J., Puy, C., Tucker, E. I., Smith, S. A., Morrissey, J. H., Walker, T. W., Nan, X. L., Gruber, A. & McCarty, O. J. T., May 1 2017, In : Annals of Biomedical Engineering. 45, 5, p. 1328-1340 13 p.

Research output: Contribution to journalArticle

2 Scopus citations

DIRAS3 (ARHI) Blocks RAS/MAPK Signaling by Binding Directly to RAS and Disrupting RAS Clusters

Sutton, M. N., Lu, Z., Li, Y. C., Zhou, Y., Huang, T., Reger, A. S., Hurwitz, A. M., Palzkill, T., Logsdon, C., Liang, X., Gray, J. W., Nan, X., Hancock, J., Wahl, G. M. & Bast, R. C., Dec 10 2019, In : Cell Reports. 29, 11, p. 3448-3459.e6

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Direct administration of nerve-specific contrast to improve nerve sparing radical prostatectomy

Barth, C. W. & Gibbs, S. L., 2017, In : Theranostics. 7, 3, p. 573-593 21 p.

Research output: Contribution to journalArticle

21 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

Dynamic circuitry for updating spatial representations. I. Behavioral evidence for interhemispheric transfer in the split-brain macaque

Berman, R. A., Heiser, L. M., Saunders, R. C. & Colby, C. L., Nov 1 2005, In : Journal of neurophysiology. 94, 5, p. 3228-3248 21 p.

Research output: Contribution to journalArticle

24 Scopus citations

Dynamic circuitry for updating spatial representations. II. Physiological evidence for interhemispheric transfer in area LIP of the split-brain macaque

Heiser, L. M., Berman, R. A., Saunders, R. C. & Colby, C. L., Nov 1 2005, In : Journal of neurophysiology. 94, 5, p. 3249-3258 10 p.

Research output: Contribution to journalArticle

27 Scopus citations

Dynamic circuitry for updating spatial representations. III. From neurons to behavior

Berman, R. A., Heiser, L. M., Dunn, C. A., Saunders, R. C. & Colby, C. L., Jul 1 2007, In : Journal of neurophysiology. 98, 1, p. 105-121 17 p.

Research output: Contribution to journalArticle

22 Scopus citations

Endocannabinoid metabolism in the absence of fatty acid amide hydrolase (FAAH): Discovery of phosphorylcholine derivatives of N-acyl ethanolamines

Mulder, A. M. & Cravatt, B. F., Sep 26 2006, In : Biochemistry. 45, 38, p. 11267-11277 11 p.

Research output: Contribution to journalArticle

35 Scopus citations

Exact reconstruction of gene regulatory networks using compressive sensing

Chang, Y. H., Gray, J. W. & Tomlin, C. J., Dec 14 2014, In : BMC bioinformatics. 15, 1, 400.

Research output: Contribution to journalArticle

22 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

64 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

103 Scopus citations

Far-Red and Near-Infrared Seminaphthofluorophores for Targeted Pancreatic Cancer Imaging

Wang, L., Barth, C. W., Sibrian-Vazquez, M., Escobedo, J. O., Lowry, M., Muschler, J., Li, H., Gibbs, S. L. & Strongin, R. M., Jan 31 2017, In : ACS Omega. 2, 1, p. 154-163 10 p.

Research output: Contribution to journalArticle

11 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

46 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 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., 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

HER2 reactivation through acquisition of the HER2 L755S mutation as a mechanism of acquired resistance to HER2-targeted therapy in HER2+ breast cancer

Xu, X., De Angelis, C., Burke, K. A., Nardone, A., Hu, H., Qin, L., Veeraraghavan, J., Sethunath, V., Heiser, L., Wang, N., Ng, C. K. Y., Chen, E. S., Renwick, A., Wang, T., Nanda, S., Shea, M., Mitchell, T., Rajendran, M., Waters, I., Zabransky, D. J. & 14 others, Scott, K. L., Gutierrez, C., Nagi, C., Geyer, F. C., Chamness, G. C., Park, B. H., Shaw, C. A., Hilsenbeck, S. G., Rimawi, M. F., Gray, J., Weigelt, B., Reis-Filho, J. S., Osborne, C. K. & Schiff, R., Sep 1 2017, In : Clinical Cancer Research. 23, 17, p. 5123-5134 12 p.

Research output: Contribution to journalArticle

30 Scopus citations