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Items: 1 to 20 of 71

1.

Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling.

Hill SM, Nesser NK, Johnson-Camacho K, Jeffress M, Johnson A, Boniface C, Spencer SE, Lu Y, Heiser LM, Lawrence Y, Pande NT, Korkola JE, Gray JW, Mills GB, Mukherjee S, Spellman PT.

Cell Syst. 2016 Dec 19. pii: S2405-4712(16)30408-2. doi: 10.1016/j.cels.2016.11.013. [Epub ahead of print]

2.

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 EF, Creighton CJ, Li F, Shea M, Nardone A, De Angelis C, Heiser LM, Anur P, Wang N, Grasso CS, Spellman PT, Griffith OL, Tsimelzon A, Gutierrez C, Huang S, Edwards DP, Trivedi MV, Rimawi MF, Lopez-Terrada D, Hilsenbeck SG, Gray JW, Brown M, Osborne CK, Schiff R.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):E6600-E6609.

PMID:
27791031
3.

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

Hu Z, Mao JH, Curtis C, Huang G, Gu S, Heiser L, Lenburg ME, Korkola JE, Bayani N, Samarajiwa S, Seoane JA, A Dane M, Esch A, Feiler HS, Wang NJ, Hardwicke MA, Laquerre S, Jackson J, W Wood K, Weber B, Spellman PT, Aparicio S, Wooster R, Caldas C, Gray JW.

Breast Cancer Res. 2016 Jul 1;18(1):70. doi: 10.1186/s13058-016-0728-y.

4.

Identification of shared TCR sequences from T cells in human breast cancer using emulsion RT-PCR.

Munson DJ, Egelston CA, Chiotti KE, Parra ZE, Bruno TC, Moore BL, Nakano TA, Simons DL, Jimenez G, Yim JH, Rozanov DV, Falta MT, Fontenot AP, Reynolds PR, Leach SM, Borges VF, Kappler JW, Spellman PT, Lee PP, Slansky JE.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):8272-7. doi: 10.1073/pnas.1606994113.

5.

Patient-specific factors influence somatic variation patterns in von Hippel-Lindau disease renal tumours.

Fei SS, Mitchell AD, Heskett MB, Vocke CD, Ricketts CJ, Peto M, Wang NJ, Sönmez K, Linehan WM, Spellman PT.

Nat Commun. 2016 May 13;7:11588. doi: 10.1038/ncomms11588.

6.

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

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium., Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.

Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773.

7.

ARTIK-52 induces replication-dependent DNA damage and p53 activation exclusively in cells of prostate and breast cancer origin.

Fleyshman D, Cheney P, Ströse A, Mudambi S, Safina A, Commane M, Purmal A, Morgan K, Wang NJ, Gray J, Spellman PT, Issaeva N, Gurova K.

Cell Cycle. 2016;15(3):455-70. doi: 10.1080/15384101.2015.1127478.

8.

Src and STAT3 inhibitors synergize to promote tumor inhibition in renal cell carcinoma.

Lue HW, Cole B, Rao SA, Podolak J, Van Gaest A, King C, Eide CA, Wilmot B, Xue C, Spellman PT, Heiser LM, Tyner JW, Thomas GV.

Oncotarget. 2015 Dec 29;6(42):44675-87. doi: 10.18632/oncotarget.5971.

9.

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Cancer Genome Atlas Research Network., Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AA, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho TH, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni HV, Drummond JA, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R.

N Engl J Med. 2016 Jan 14;374(2):135-45. doi: 10.1056/NEJMoa1505917.

10.

Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease.

Butler TM, Johnson-Camacho K, Peto M, Wang NJ, Macey TA, Korkola JE, Koppie TM, Corless CL, Gray JW, Spellman PT.

PLoS One. 2015 Aug 28;10(8):e0136407. doi: 10.1371/journal.pone.0136407.

11.

Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination.

Sanborn JZ, Chung J, Purdom E, Wang NJ, Kakavand H, Wilmott JS, Butler T, Thompson JF, Mann GJ, Haydu LE, Saw RP, Busam KJ, Lo RS, Collisson EA, Hur JS, Spellman PT, Cleaver JE, Gray JW, Huh N, Murali R, Scolyer RA, Bastian BC, Cho RJ.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):10995-1000. doi: 10.1073/pnas.1508074112.

12.

Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer.

Korkola JE, Collisson EA, Heiser L, Oates C, Bayani N, Itani S, Esch A, Thompson W, Griffith OL, Wang NJ, Kuo WL, Cooper B, Billig J, Ziyad S, Hung JL, Jakkula L, Feiler H, Lu Y, Mills GB, Spellman PT, Tomlin C, Mukherjee S, Gray JW.

PLoS One. 2015 Jul 16;10(7):e0133219. doi: 10.1371/journal.pone.0133219.

13.

Functionally defined therapeutic targets in diffuse intrinsic pontine glioma.

Grasso CS, Tang Y, Truffaux N, Berlow NE, Liu L, Debily MA, Quist MJ, Davis LE, Huang EC, Woo PJ, Ponnuswami A, Chen S, Johung TB, Sun W, Kogiso M, Du Y, Qi L, Huang Y, Hütt-Cabezas M, Warren KE, Le Dret L, Meltzer PS, Mao H, Quezado M, van Vuurden DG, Abraham J, Fouladi M, Svalina MN, Wang N, Hawkins C, Nazarian J, Alonso MM, Raabe EH, Hulleman E, Spellman PT, Li XN, Keller C, Pal R, Grill J, Monje M.

Nat Med. 2015 Jul;21(7):827. doi: 10.1038/nm0715-827a. No abstract available.

PMID:
26151328
14.

Erratum to: Modeling precision treatment of breast cancer.

Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson EA, Van't Veer LJ, Spellman PT, Gray JW.

Genome Biol. 2015 May 12;16:95. doi: 10.1186/s13059-015-0658-5.

15.

Functionally defined therapeutic targets in diffuse intrinsic pontine glioma.

Grasso CS, Tang Y, Truffaux N, Berlow NE, Liu L, Debily MA, Quist MJ, Davis LE, Huang EC, Woo PJ, Ponnuswami A, Chen S, Johung TB, Sun W, Kogiso M, Du Y, Qi L, Huang Y, Hütt-Cabezas M, Warren KE, Le Dret L, Meltzer PS, Mao H, Quezado M, van Vuurden DG, Abraham J, Fouladi M, Svalina MN, Wang N, Hawkins C, Nazarian J, Alonso MM, Raabe EH, Hulleman E, Spellman PT, Li XN, Keller C, Pal R, Grill J, Monje M.

Nat Med. 2015 Jun;21(6):555-9. doi: 10.1038/nm.3855. Erratum in: Nat Med. 2015 Jul;21(7):827.

16.

Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes.

Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS, Collisson EA, Vemula SS, Naujokas A, Chiotti KE, Cheng JB, Fassihi H, Blumberg AJ, Bailey CV, Fudem GM, Mihm FG, Cunningham BB, Neuhaus IM, Liao W, Oh DH, Cleaver JE, LeBoit PE, Costello JF, Lehmann AR, Gray JW, Spellman PT, Arron ST, Huh N, Purdom E, Cho RJ.

Cell Rep. 2014 Nov 20;9(4):1228-34. doi: 10.1016/j.celrep.2014.10.031.

17.

Detecting cancer by monitoring circulating tumor DNA.

Spellman PT, Gray JW.

Nat Med. 2014 May;20(5):474-5. doi: 10.1038/nm.3564. No abstract available.

PMID:
24804754
18.

Global optimization of somatic variant identification in cancer genomes with a global community challenge.

Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM.

Nat Genet. 2014 Apr;46(4):318-9. doi: 10.1038/ng.2932. No abstract available.

19.

Characterization of tissue histopathology via predictive sparse decomposition and spatial pyramid matching.

Chang H, Nayak N, Spellman PT, Parvin B.

Med Image Comput Comput Assist Interv. 2013;16(Pt 2):91-8.

20.

Integrated analysis of germline and somatic variants in ovarian cancer.

Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L.

Nat Commun. 2014;5:3156. doi: 10.1038/ncomms4156.

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