Our Alumni Publications

ChooseEric AlonzoMinna BalbasNeha BhagwatRobert BowmanEmily CaseyJames DowdleWeiran FengKinisha GalaNicholas GauthierTheresa GeigerJohn HallidayJens C. HamannKaren HunterEllen HukkelhovenJenny KaroCatherine A. KonopackiMarta KovatchevaShefali KrishnaIsabel LamLindsay M. LaFave (Saunders)Chong LuoAnna Sophia McKenneyDanilo G. MacalinaoJohn MaciejowskiJames MahaffeyDan MarksArmine MatevossianGregory MazoYvonne Gruber MicaAlexandria MillerJustine MillerPrashant MonianSemanti MukherjeeBrandon NemiebokaMoriah Heller NissanJennifer NnoliOakley OlsonJoseph PucellaNeel ShahBerenice Ortiz ThompsonCindy PuenteSadia RahmanLeili RanJessica Rios-EstevesPiero SanfilippoAlison K. SpencerDimiter TassevLy VuWilliam WalkowiczElizabeth WasmuthShannon YuLei WeiYilong Zou

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Eric Alonzo

Alonzo E, Sant’angelo D. (2011) Development of PLZF-expressing innate T cells. Curr Opin Immunol, 23, 220-227.

Gordon S, Carty S, Kim J, Zou T, Smith-Garvin J, Alonzo E, Haimm E, Sant’Angelo D, Koretzky G, Reiner S, Jordan M. (2011) Requirements for eomesodermin and promyelocytic leukemia zinc finger in the development of innate-like CD8+ T cells. J Immunol, 186, 4573-4578. 

Amrani Y, Gill J, Matevossian A, Alonzo E, Yang C, Shieh J, Moore M, Park C, Sant’Angelo D, Denzin L. (2011) The Paf oncogene is essential for hematopoietic stem cell function and development. J Exp Med, 208, 1757-1765.

Alonzo E, Gottschalk R, Das J, Egawa T, Hobbs R, Pandolfi P, Pereira P, Nichols K, Koretzky G, Jordan M, Sant’Angelo D. (2010) Development of promyelocytic zinc finger and ThPOK-expressing innate gamma delta T cells is controlled by strength of TCR signaling and Id3. J Immunol, 184, 1268-1279. 

Kovalovsky D, Alonzo E, Uche O, Eidson M, Nichols K, Sant’Angelo D. (2010) PLZF Induces the Spontaneous Acquisition of Memory/Effector Functions in T Cells Independently of NKT Cell-Related Signals. J Immunol, 184, 6746-6755.

Kim H, Alonzo E, Dorothee G, Pollard J, Sant’Angelo D. (2010) Selective depletion of eosinophils or neutrophils in mice impacts the efficiency of apoptotic cell clearance in the thymus. PLoS One, 5, 1-15.

Kovalovsky D, Uche O, Eladad S, Hobbs R, Woelsung Y, Alonzo E, Chua K, Eidson M, Kim H, Im J, Pandolfi P, Sant’Angelo D. (2008) The BTB-zinc finger transcriptional regulator PLZF controls the development of invariant natural killer T cell effector functions. Nat Immunol, 9, 1055-1064.

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Minna Balbas

Balbas MD, Burgess MR, Murali R, Wongvipat J, Skaggs BJ, Mundel P, Weins A, Sawyers CL. (2014) MAGI-2 scaffold protein is critical for kidney barrier function. Proc Natl Acad Sci U S A., 111, 14876-81. PMCID: PMC4205655.

Arora V, Schenkein E, Murali R, Subudhi S, Wongvipat J, Balbas M, Shah N, Cai L, Efstathiou E, Logothetis C, Cheng D, Sawyers C. (2013) Glucocorticoid receptor confers resistance to antiandrogens by bypassing androgen receptor blockade. Cell, 155, 1309-1322.

Balbas M, Evans M, Hosfield D, Wongvipat J, Arora V, Watson P, Chen Y, Greene G, Shen Y, Sawyers C. (2013) Overcoming mutation-based resistance to antiandrogens with rational drug design. Elife, 2, 1-21.

Watson P, Chen Y, Balbas M, Wongvipat J, Socci N, Viale A, Kim K, Sawyers C. (2010) Constitutively active androgen receptor splice variants expressed in castration-resistant prostate cancer require full-length androgen receptor. Proc Natl Acad Sci U S A, 107, 16759-16765.

Shah NP, Kasap C, Weier C, Balbas M, Nicoll JM, Bleickardt E, Nicaise C, Sawyers CL. (2008) Transient potent BCR-ABL inhibition is sufficient to commit chronic myeloid leukemia cells irreversibly to apoptosis. Cancer Cell  14, 485-93.

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Neha Bhagwat

Kleppe M, Kwak M, Koppikar P, Riester M, Keller M, Bastian L, Hricik T, Bhagwat N, McKenney AS, Papalexi E, Abdel-Wahab O, Rampal R, Marubayashi S, Chen JJ, Romanet V, Fridman JS, Bromberg J, Teruya-Feldstein J, Murakami M, Radimerski T, Michor F, Fan R, Levine RL. (2015) JAK-STAT pathway activation in malignant and nonmalignant cells contributes to MPN pathogenesis and therapeutic response. Cancer discovery, 5, 316-31. PMCID: PMC4355105.

Kucine N, Marubayashi S, Bhagwat N, Papalexi E, Koppikar P, Sanchez Martin M, Dong L, Tallman MS, Paietta E, Wang K, He J, Lipson D, Stephens P, Miller V, Rowe JM, Teruya-Feldstein J, Mullighan CG, Ferrando AA, Krivtsov A, Armstrong S, Leung L, Ochiana SO, Chiosis G, Levine RL, Kleppe . (2015)  Tumor-specific HSP90 inhibition as a therapeutic approach in JAK-mutant acute lymphoblastic leukemias. Blood, 126, 2479-83. PMCID: PMC4661170.

Grundschober E, Hoelbl-Kovacic A, Bhagwat N, Kovacic B, Scheicher R, Eckelhart E, Kollmann K, Keller M, Grebien F, Wagner KU, Levine RL, Sexl V. (2014) Acceleration of Bcr-Abl+ leukemia induced by deletion of JAK2. Leukemia, 28, 1918-22. PMCID: PMC4158830.

Meyer SC, Keller MD, Woods BA, LaFave LM, Bastian L, Kleppe M, Bhagwat N, Marubayashi S, Levine RL. (2014)  Genetic studies reveal an unexpected negative regulatory role for Jak2 in thrombopoiesis. Blood, 124, 2280-4. PMCID: PMC4183987.

Bhagwat N, Koppikar P, Keller M, Marubayashi S, Shank K, Rampal R, Qi J, Kleppe M, Patel H, Shah S, Taldone T, Bradner J, Chiosis G, Levine R. (2014) Improved targeting of JAK2 leads to increased therapeutic efficacy in myeloproliferative neoplasms. Blood, 123, 2075-2083.

Murphy A, Bijl N, Yvan-Charvet L, Welch C, Bhagwat N, Reheman A, Wang Y, Shaw J, Levine R, Ni H, Tall A, Wang N. (2013) Cholesterol efflux in megakaryocyte progenitors suppresses platelet production and thrombocytosis. Nat Med, 19, 586-594. 

Gautier E, Westerterp M, Bhagwat N, Cremers S, Shih A, Abdel-Wahab O, Lütjohann D, Randolph G, Levine R, Tall A, Tvan-Charvet L. (2013) HDL and Glut1 inhibition reverse a hypermetabolic state in mouse models of myeloproliferative disorders. J Exp Med, 210, 339-353.

Bhagwat N, Levine R, Koppikar P. (2013) Sensitivity and resistance of JAK2 inhibitors to myeloproliferative neoplasms. Int J Hematol, 97, 695-702.

Koppikar P, Bhagwat N, Kilpivaara O, Manshouri T, Adli M, Hricik T, Liu F, Saunders L, Mullally A, Abdel-Wahab O, Leung L, Weinstein A, Marubayashi S, Goel A, Gönen M, Estrov Z, Ebert B, Chiosis G, Nimer S, Bernstein B, Verstovsek S, Levine R. (2012) Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy. Nature, 489, 155-159.

Andraos R, Qian Z, Bonenfant D, Rubert J, Vangrevelinghe E, Scheufler C, Marque F, Régnier C, De Pover A, Ryckelynck H, Bhagwat N, Koppikar P, Goel A, Wyder L, Tavares G, Baffert F, Pissot-Soldermann C, Manley P, Gaul C, Voshol H, Levine R, Sellers W, Hofmann F, Radimerski T. (2012) Modulation of activation-loop phosphorylation by JAK inhibitors is binding more dependent. Cancer Discov, 2, 512-523.

Marubayashi S, Koppikar P, Taydone T, Abdel-Wahab O, West N, Bhagwat N, Caldas-Lopes R, Ross K, Gönen M, Gozman A, Ahn, J, Rodina A, Ouerfelli O, Yang G, Hedvat C, Bradner J, Chiosis G, Levine R. (2010) HSP90 is a therapeutic target in JAK2-dependent myeloproliferative neoplasms in mice and humans. J Clin Invest, 120, 3578-3593.

Figueroa M, Abdel-Wahab O, Lu C, Ward P, Patel J, Shih A, Li Y, Bhagwat N, Vasanthakumar A, Fernandez H, Tallman M, Sun Z, Wolniak K, Peeters J, Liu W, Chloe S, Fantin V, Paietta E, Löwenberg B, Licht J, Godley L, Delwel R, Valk P, Thompson C, Levine R, Melnick A. (2010) Leukemia IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell, 18, 553-567.

Bhagwat N, Levine R. (2010) Metabolic syndromes and malignant transformation: where the twain shall meet. Sci Transl Med, 2, 1-3.

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Robert Bowman

Sansone P, Berishaj M, Rajasekhar VK, Ceccarelli C, Chang Q, Strillacci A, Savini C, Shapiro L, Bowman R, Mastroleo C, De Carolis S, Daly L, Benito-Martin A, Perna F, Fabbri N, Healey JH, Spisni E, Cricca M, Lyden D, Bonafé M, Bromberg J. (2017) Evolution of cancer stem-like cells in endocrine-resistant metastatic breast cancers is mediated by stromal microvesicles. Cancer Res. [Epub ahead of print]

Bowman RL, Wang Q, Carro A, Verhaak RG, Squatrito M. (2017) GlioVis data portal for visualization and analysis of brain tumor expression datasets. Neuro Oncol. 19, 139-141. PMCID: PMC5193031 [Available on 2018-01-01]

Kim IS, Heilmann S, Kansler ER, Zhang Y, Zimmer M, Ratnakumar K, Bowman RL, Simon-Vermot T, Fennell M, Garippa R, Lu L, Lee W, Hollmann T, Xavier JB, White RM. (2017) Microenvironment-derived factors driving metastatic plasticity in melanoma. Nat Commun. 8, 14343. PMCID: PMC5309794

Akkari L, Gocheva V, Quick ML, Kester JC, Spencer AK, Garfall AL, Bowman RL, Joyce JA. (2016) Combined deletion of cathepsin protease family members reveals compensatory mechanisms in cancer. Genes Dev., 30, 220-32. PMCID: PMC4719311.

Alidori S, Bowman RL, Yarilin D, Romin Y, Barlas A, Mulvey JJ, Fujisawa S, Xu K, Ruggiero A, Riabov V, Thorek DL, Ulmert HD, Brea EJ, Behling K, Kzhyshkowska J, Manova-Todorova K, Scheinberg DA, McDevitt MR. (2016) Deconvoluting hepatic processing of carbon nanotubes. Nat Commun.  7,12343. PMCID: PMC4974572

Bowman RL, Klemm F, Akkari L, Pyonteck SM, Sevenich L, Quail DF, Dhara S, Simpson K, Gardner EE, Iacobuzio-Donahue CA, Brennan CW, Tabar V, Gutin PH, Joyce JA. (2016) Macrophage Ontogeny Underlies Differences in Tumor-Specific Education in Brain Malignancies. Cell Rep. 17, 2445-2459.

Sansone P, Ceccarelli C, Berishaj M, Chang Q, Rajasekhar VK, Perna F, Bowman RL, Vidone M, Daly L, Nnoli J, Santini D, Taffurelli M, Shih NN, Feldman M, Mao JJ, Colameco C, Chen J, DeMichele A, Fabbri N, Healey JH, Cricca M, Gasparre G, Lyden D, Bonafé M, Bromberg J. (2016)  Self-renewal of CD133(hi) cells by IL6/Notch3 signalling regulates endocrine resistance in metastatic breast cancer.  Nat Commun., 7, 10442. PMCID: PMC4748123.

Yan D, Wang HW, Bowman RL, Joyce JA. (2016) STAT3 and STAT6 Signaling Pathways Synergize to Promote Cathepsin Secretion from Macrophages via IRE1α Activation. Cell Rep. 16, 2914-27

Quail DF, Bowman RL, Akkari L, Quick ML, Schuhmacher AJ, Huse JT, Holland EC, Sutton JC, Joyce JA. (2016)  The tumor microenvironment underlies acquired resistance to CSF-1R inhibition in gliomas. Science, 352, aad3018.

Sevenich L, Bowman R, Mason S, Quail D, Rapaport F, Elie B, Brogi E, Brastianos P, Hahn W, Holsinger L, Massagué J, Leslie C, Joyce J. (2014) Analysis of tumour- and stroma-supplied proteolytic networks reveals a brain-metastasis-promoting role for cathepsin S. Nat Cell Biol., 16, 876-88. PMCID: PMC4249762.

Bowman R, Joyce J. (2014) Therapeutic targeting of tumor-associated macrophages and microglia in glioblastoma. Immunotherapy, 6, 663-666.

Pyonteck S, Akkari L, Schuhmacher A, Bowman R, Sevenich L, Quail D, Olson O, Quick M, Huse J, Teijeiro V, Setty M, Leslie C, Oei Y, Pedraza A, Zhang J, Brennan C, Sutton J, Holland E, Daniel D, and Joyce J. (2013) CSF-1R inhibition alters macrophage polarization and blocks glioma progression. Nat Med. 19, 1264-1272. PMCID: PMC38440724.

Miller J, Ganat Y, Kishinevsky S, Bowman R, Liu B, Tu E, Mandal P, Vera E, Shim J, Kriks S, Taldone T, Fusaki N, Tomishima M, Krainc D, Milner T, Rossi D, and Studer L. (2013) Human iPSC-Based Modeling of Late-Onset Disease via Progerin-Induced Aging. Cell Stem Cell, 13, 691-705.

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Emily Casey

Casey E, Bournazos S, Mo G, Mondello P, Tan KS, Ravetch JV, Scheinberg DA. (2018). A new mouse expressing human Fcγ receptors to better predict therapeutic efficacy of human anti-cancer antibodies. Leukemia. 32, 547-549. PMCID: PMC5803448

Thorek DL, Watson PA, Lee SG, Ku AT, Bournazos S, Braun K, Kim K, Sjöström K, Doran MG, Lamminmäki U, Santos E, Veach D, Turkekul M, Casey E, Lewis JS, Abou DS, van Voss MR, Scardino PT, Strand SE, Alpaugh ML, Scher HI, Lilja H, Larson SM, Ulmert D. (2016) Internalization of secreted antigen-targeted antibodies by the neonatal Fc receptor for precision imaging of the androgen receptor axis. Sci Transl Med. 8, 367ra167.

Dubrovsky L, Brea EJ, Pankov D, Casey E, Dao T, Liu C, Scheinberg DA. (2016) Mechanisms of leukemia resistance to antibody dependent cellular cytotoxicity. Oncoimmunology 5, e1211221. PMCID: PMC5048777 [Available on 2017-08-03]

Chang AY, Gejman RS, Brea EJ, Oh CY, Mathias MD, Pankov D, Casey E, Dao T, Scheinberg DA. (2016). Opportunities and challenges for TCR mimic antibodies in cancer therapy. Expert Opin Biol Ther. 16, 979-87. PMCID: PMC4936943 [Available on 2017-08-01]

Dubrovsky L, Dao T, Gejman RS, Brea EJ, Chang AY, Oh CY, Casey E, Pankov D, Scheinberg DA. (2015) T cell receptor mimic antibodies for cancer therapy. Oncoimmunology 5, e1049803. PMCID: PMC4760335

Veomett, N.,  Dao, T., Liu, H., Xiang, J., Pankov, D., Dubrovsky, L., Whitten, J., Park, S., Korontsvit, T., Zakhaleva, V., Casey, E., Curcio, M., Kharas, M., O’Reilly, R., Liu, C., and  Scheinberg, D. (2014) Therapeutic Efficacy of an Fc-Enhanced TCR-Like Antibody to the Intracellular WT1 Oncoprotein.  Clin Cancer Res, 20, OF1-OF11. PMID: 24850840.

Dao, T., Yan, S., Veomett, N., Pankov, D., Zhou, L., Korontzvit, T., Scott, A., Whitten, J., Maslak, P., Casey, E., Tan, T., Liu, H., Zakhaleva, V., Curcio, M., Doubrovina, E., O’Reilly, R., Liu, C., and Scheinberg, D. (2013) Targeting the intracellular WT1 oncogene product with a therapeutic human antibody.  Sci Transl Med, 5, 1-11. PMID: 23486779; PMCID: PMC3963696.

Mulvey, J., Villa, C., McDevitt, M., Escorcia, F., Casey, E., and Scheinberg, D. (2013) Self-assembly of carbon nanotubes and antibodies on tumours for targeted amplified delivery.  Nat Nanotechnol, 8, 763-771. PMID: 24077028; PMCID: PMC3798027.

Villa, C., Dao, T., Ahearn, I., Fehrenbacher, N., Casey, E., Rey, D., Korontsvit, T., Zakhaleva, V., Batt, C., Philips, M., and Scheinberg, D. (2011)  Single-walled carbon nanotubes deliver peptide antigen into dendritic cells and enhance IgG responses to tumor-associated antigens.  ACS Nano, 5, 5300-5311. PMID: 21682329; PMCID: PMC3143710.

Han L, Witmer PD, Casey E, Valle D, Sukumar S. (2007) DNA methylation regulates MicroRNA expression. (2007) Cancer Biol Ther., 6, 1284-8.

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James Dowdle

Liu H, Dowdle JA, Khurshid S, Sullivan NJ, Bertos N, Rambani K, Mair M, Daniel P, Wheeler E, Tang X, Toth K, Lause M, Harrigan ME, Eiring K, Sullivan C, Sullivan MJ, Chang SW, Srivastava S, Conway JS, Kladney R, McElroy J, Bae S, Lu Y, Tofigh A, Saleh SMI, Fernandez SA, Parvin JD, Coppola V, Macrae ER, Majumder S, Shapiro CL, Yee LD, Ramaswamy B, Hallett M, Ostrowski MC, Park M, Chamberlin HM, Leone G. (2017) Discovery of Stromal Regulatory Networks that Suppress Ras-Sensitized Epithelial Cell Proliferation. Dev. Cell, 41, 392-407.

Dowdle J, Mehta M, Kass E, Vuong B, Inagaki A, Egli D, Jasin M, Keeney S. (2013) Mouse BAZ1A (ACF1) Is Dispensable for Double-Strand Break Repair but Is Essential for Averting Improper Gene Expression During Spermatogenesis. PLoS Genet, 9, 1-21.

Roig I, Dowdle J, Toth A, de Rooij D, Jasin M, Keeney S. (2010) Mouse TRIP13/PCH2 Is Required for Recombination and Normal Higher-Order Chromosome Structure during Meiosis. PLoS Genet, 6, 1-19.

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Weiran Feng

Chen CC, Feng W, Lim PX, Kass EM, Jasin M. (2018) Homology-Directed Repair and the Role of BRCA1, BRCA2, and Related Proteins in Genome Integrity and Cancer. Annu Rev Cancer Biol. 2, 313-336. PMCID: PMC619349.

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Kinisha Gala

Gala K, Li Q, Sinha A, Razavi P, Dorso M, Sanchez-Vega F, Chung YR, Hendrickson R, Hsieh J, Berger M, Schultz N, Pastore A, Abdel-Wahab O, Chandarlapaty S. (2018) KMT2C mediates the estrogen dependence of breast cancer through regulation of ERα enhancer function. Oncogene. [Epub ahead of print]

Gala, K. and Chandarlapaty, S. (2014)  Molecular pathways: HER3 targeted therapy.  Clin Cancer Res, 20, 1410-1416. PMCID: PMC3977203.

Toy, W., Shen, Y., Won, H., Green, B., Sakr, R., Will, M., Li, Z., Gala, K., Fanning, S., King, T., Hudis, C., Chen, D., Taran, T., Hortobagyi, G., Greene, G., Berger, M., Baselga, J., and Chandarlapaty, S. (2013)  ESR1 ligand-binding domain mutations in hormone- resistant breast cancer.  Nat Genet, 45, 1439-1445. PMCID: PMC3903423.

Scaglione BJ, Salerno E, Gala K, Pan M, Langer JA, Mostowski HS, Bauer S, Marti G, Li Y, Tsiagbe VK, Raveche ES. (2009) Regulatory T cells as central regulators of both autoimmunity and B cell malignancy in New Zealand Black mice. J Autoimmun., 32, 14-23.

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Nicholas Gauthier

Gauthier NP, Reznik E, Gao J, Sumer SO, Schultz N, Sander C, Miller ML. (2016) MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. Nucleic Acids Res., 44, D986-91. PMCID: PMC4702822.

Miller ML, Reznik E, Gauthier NP, Aksoy BA, Korkut A, Gao J, Ciriello G, Schultz N, Sander C. (2015) Pan-Cancer Analysis of Mutation Hotspots in Protein Domains. Cell Syst., 1, 197-209.

Liu Y, Raheja R, Yeh N, Ciznadija D, Pedraza A, Ozawa T, Hukkelhoven E, Erdjument-Bromage H, Tempst P, Gauthier N, Brennan C, Hollan E, Koff A. (2014) TRIM3, a tumor suppressor linked to regulation of p21 (Waf1/Cip1.). Oncogene, 33, 308-315.

Gauthier N, Soufi B, Walkowicz W, Pedicord V, Mavrakis K, Macek B, Gin D, Sander C, Miller M. (2013) Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environment. Nat Methods, 10, 768-773.

Molinelli E, Korkut A, Wang W, Miller M, Gauthier N, Jing X, Kaushik P, He Q, Mills G, Solit D, Pratilas C, Weigt M, Braunstein A, Pagnani A, Zecchina R, Sander C. (2013) Perturbation biology: inferring signaling networks in cellular systems. PLoS Comput Biol, 9, 1-23.

Gauthier N, Jensen L, Wernersson R, Brunak S, Jensen T. (2010) Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Res., 38, D669-D702.

Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ, Brunak S, Jensen TS. (2008) Cyclebase.org—a comprehensive multi-organism online databse of cell-cycle experiments. Necleic Acids Res., 36, D854-9.

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Theresa Geiger

O’Sullivan TE, Geary CD, Weizman OE, Geiger TL, Rapp M, Dorn GW, Overholtzer M, Sun JC. (2016) Atg5 Is Essential for the Development and Survival of Innate Lymphocytes. Cell Rep, 15, 1910-9. PMCID: PMC4889506.

Geiger TL, Sun JC. (2016) Development and Maturation of Natural Killer Cells.  Curr Opin Immunol., 39, 82-9. PMCID: PMC4801705.

Cortez VS, Cervantes-Barragan L, Robinette ML, Bando JK, Wang Y, Geiger TL, Gilfillan S, Fuchs A, Vivier E, Sun JC, Cella M, Colonna M. Transforming Growth Factor-β Signaling Guides the Differentiation of Innate Lymphoid Cells in Salivary Glands. (2016) Immunity, 44, 1127-39.

Geiger TL, Abt MC, Gasteiger G, Firth MA, O’Connor MH, Geary CD, O’Sullivan TE, van den Brink MR, Pamer EG, Hanash AM, Sun JC. (2014)  Nfil3 is crucial for development of innate lymphoid cells and host protection against intestinal pathogens. J Exp Med., 211, 1723-31. PMCID: PMC4144732.

Curran M, Geiger T, Montalvo W, Kim M, Reiner S, Al-Shamkhani A, Sun J, and Allison J. (2013) Systemic 4-1BB activation induces a novel T cell phenotype driven by high expression of Eomesodermin.  J Exp Med, 210, 743-755. PMCID: PMC3620352.

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John Halliday

Halliday J, Helmy K, Pattwell SS, Pitter KL, LaPlant Q, Ozawa T, Holland EC. (2014) In vivo radiation response of proneural glioma characterized by protective p53 transcriptional program and proneural-mesenchymal shift. Proc Natl Acad Sci U S A., 111, 5248-53. PMCID: PMC3986190.

Pietras A, Katz A, Ekström E, Wee B, Halliday J, Pitter K, Werbeck J, Amankulor N, Huse J, Holland E. (2014) Osteopontin-CD44 Signaling in the Glioma Perivascular Niche Enhances Cancer Stem Cell Phenotypes and Promotes Aggressive Tumor Growth. Cell Stem Cell, 14, 357-369.

Huse JT, Edgar M, Halliday J, Mikolaenko I, Lavi E, Rosenblum MK. (2013) Multinodular and vacuolating neuronal tumors of the cerebrum: 10 cases of a distinctive seizure-associated lesion. Brain Pathol. 23, 515-24.

Helmy K, Halliday J, Fomchenko E, Setty M, Pitter K, Hafemeister C, Holland E. (2012) Identification of global alteration of translational regulation in glioma in vivo. PLoS One 7, e46965. PMCID: PMC3463531

Halliday J, Holland E. (2011) Connective tissue growth factor and the parallels between brain injury and brain tumors. J Natl Cancer Inst, 103, 1141-1143.

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Jens C. Hamann

Hawk MA, Gorsuch CL, Fagan P, Lee C, Kim SE, Hamann JC, Mason JA, Weigel KJ, Tsegaye MA, Shen L, Shuff S, Zuo J, Hu S, Jiang L, Chapman S, Leevy WM, DeBerardinis RJ, Overholtzer M, Schafer ZT. (2018) RIPK1-mediated induction of mitophagy compromises the viability of extracellular-matrix-detached cells. Nat Cell Biol. 20, 272-284.

Hamann JC, Overholtzer M. (2017) Entosis enables a population response to starvation. Oncotarget 8, 57934-57935. PMCID: PMC5601622

Hamann JC, Surcel A, Chen R, Teragawa C, Albeck JG, Robinson DN, Overholtzer M. (2017) Entosis Is Induced by Glucose Starvation. Cell Rep. 20, 201-210. PMCID: PMC5559205

Hamann J, Overholtzer M. (2017) Killing me softly: microparticles target deformable cells.Cell Res.26, 637-8. PMCID: PMC4897184 [Available on 2017-06-01]

Durgan J, Tseng YY, Hamann JC, Domart MC, Collinson L, Hall A, Overholtzer M, Florey O. (2017) Mitosis can drive cell cannibalism through entosis. Elife 6, pii: e27134. PMCID: PMC5505699

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Karen Hunter

Akkari L, Gocheva V, Kester JC, Hunter KE, Quick ML, Sevenich L, Wang HW, Peters C, Tang LH, Klimstra DS, Reinheckel T, Joyce JA. (2014) Distinct functions of macrophage-derived and cancer cell-derived cathepsin Z combine to promote tumor malignancy via interactions with the extracellular matrix. Genes Dev., 28, 2134-50. PMCID: PMC4180975.

Hunter K, Palermo C, Kester J, Simpson K, Li J, Tang L, Klimstra D, Vlodavsky I, Joyce J. (2014) Heparanase promotes lymphangiogenesis and tumor invasion in pancreatic neuroendocrine tumors. Oncogene, 3, 1799-1808.

Hunter K, Quick M, Sadanandam A, Hanahan D, Joyce J. (2013) Identification and characterization of poorly differentiated invasive carcinomas in a mouse model of pancreatic neuroendocrine tumorigenesis. PLoS One, 8, 1-11.

Pyonteck S, Gadea B, Wang H, Gocheva V, Hunter K, Tang L, Joyce J. (2012) Deficiency of the macrophage growth factor CSF-1 disrupts pancreatic neuroendocrine tumor development. Oncogene, 31, 1459-1467.

Gocheva V, Wang H, Gadea B, Shree T, Hunter K, Garfall A, Berman T, Joyce J. (2010) IL-4 induces cathepsin protease activity in tumor-associated macrophages to promote cancer growth and invasion. Genes Dev, 24, 241-255.

Williams BR, Prabhu VR, Hunter KE, Glazier CM, Whittaker CA, Housman DE, Amon A. (2008) Aneuploidy affects proliferation and spontaneous immortalization in mammalian cells. Science. 322, 703-9. PMCID: PMC2701511

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Ellen Hukkelhoven

Gong Y, Zack TI, Morris LG, Lin K, Hukkelhoven E, Raheja R, Tan IL, Turcan S, Veeriah S, Meng S, Viale A, Schumacher SE, Palmedo P, Beroukhim R, Chan TA. (2014) Pan-cancer genetic analysis identifies PARK2 as a master regulator of G1/S cyclins. Nat Genet. 46, 588-94. PMCID: PMC4251771

Raheja R, Liu Y, Hukkelhoven E, Yeh N, Koff A. (2014) The ability of TRIM3 to induce growth arrest depends on RING-dependent E3 ligase activity. Biochem J, 458, 537-545.

Liu Y, Raheja R, Yeh N, Ciznadija D, Pedraza A, Ozawa T, Hukkelhoven E, Erdjument-Bromage H, Tempst P, Gauthier N, Brennan C, Holland E, Koff A. (2014) TRIM3, a tumor suppressor linked to regulation of p21 (Waf1/Cip1). Oncogene, 33, 308-315.

Hukkelhoven E, Liu Y, Yeh N, Ciznadija D, Blain S, Koff A. (2012) Tyrosine phosphorylation of the p21 cyclin-dependent kinase inhibitor facilitates the development of proneural glioma. J Biol Chem, 287, 38523-38530.

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Jenny Karo

Adams NM, O’Sullivan TE, Geary CD, Karo JM, Amezquita RA, Joshi NS, Kaech SM, Sun JC. (2016) NK Cell Responses Redefine Immunological Memory. J Immunol. 197, 2963-2970. PMCID: PMC5108457

Karo JM, Sun JC. (2015) Novel molecular mechanism for generating NK-cell fitness and memory. Eur J Immunol., 45, 1906-15. PMCID: PMC4561546.

Karo JM, Schatz DG, Sun JC. (2014) The RAG recombinase dictates functional heterogeneity and cellular fitness in natural killer cells. Cell, 159, 94-107. PMCID: PMC4371485.

Zawislak CL, Beaulieu AM, Loeb GB, Karo J, Canner D, Bezman NA, Lanier LL, Rudensky AY, Sun JC. (2013)  Stage-specific regulation of natural killer cell homeostasis and response against viral infection by microRNA-155. Proc Natl Acad Sci U S A, 110, 6967-72. PMCID: PMC3637707.

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Catherine A. Konopacki

Azizi E, Carr AJ, Plitas G, Cornish AE, Konopacki C, Prabhakaran S, Nainys J, Wu K, Kiseliovas V, Setty M, Choi K, Fromme RM, Dao P, McKenney PT, Wasti RC, Kadaveru K, Mazutis L, Rudensky AY, Pe’er D. (2018) Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment. Cell, pii: S0092-8674(18)30723-2. PMID: 29961579 [Epub ahead of print] 

Levine AG, Hemmers S, Baptista AP, Schizas M, Faire MB, Moltedo B, Konopacki C, Schmidt-Supprian M, Germain RN, Treuting PM, Rudensky AY. (2017)Suppression of lethal autoimmunity by regulatory T cells with a single TCR specificity. J Exp Med. 214, 609-622. PMCID: PMC5339675 [Available on 2017-09-06]

Plitas G, Konopacki C, Wu K, Bos PD, Morrow M, Putintseva EV, Chudakov DM, Rudensky. (2016)  AYRegulatory T Cells Exhibit Distinct Features in Human Breast Cancer. Immunity 45, 1122-1134. PMCID: PMC5134901 [Available on 2017-11-15]

Konopacki C, Plitas G, Rudensky A. (2015) Reigning in regulatory T-cell function. Nat Biotechnol. 33, 718-9.

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Marta Kovatcheva

Kovatcheva M, Klein ME, Tap WD, Koff A. (2017) Mechanistic understanding of the role of ATRX in senescence provides new insight for combinatorial therapies with CDK4 inhibitors. Mol Cell Oncol. 5, e1384882. PMCID: PMC5791849. [Available on 2018-11-07]

Klein ME, Kovatcheva M, Davis LE, Tap WD, Koff A. (2018) CDK4/6 Inhibitors: The Mechanism of Action May Not Be as Simple as Once Thought. Cancer Cell. [Epub ahead of print]

Kovatcheva M, Liao W, Klein ME, Robine N, Geiger H, Crago AM, Dickson MA, Tap WD, Singer S, Koff A. (2017) ATRX is a regulator of therapy induced senescence in human cells. Nat Commun. 8, 386. PMCID: PMC5577318

Kovatcheva M, Liu DD, Dickson MA, Klein ME, O’Connor R, Wilder FO, Socci ND, Tap WD, Schwartz GK, Singer S, Crago AM, Koff A. (2015) MDM2 turnover and expression of ATRX determine the choice between quiescence and senescence in response to CDK4 inhibition. Oncotarget, 6, 8226-43. PMCID: PMC4480747.

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Shefali Krishna

Zaritsky A, Tseng YY, Rabadán MA, Krishna S, Overholtzer M, Danuser G, Hall A. (2017) Diverse roles of guanine nucleotide exchange factors in regulating collective cell migration. J Cell Biol. 216, 1543-1556. PMCID: PMC5461017 [Available on 2017-12-05]

Krishna S, Overholtzer M. (2016) Germ Cells Get by with a Little Cannibalistic Help from Their Friends. Dev Cell. 39, 631-633.

Krishna S, Overholtzer M. (2016) Mechanisms and consequences of entosis. Cell Mol Life Sci, 73, 2379-86. PMCID: PMC4889469 [Available on 2017-06-01]

Krishna S, Palm W, Lee Y, Yang W, Bandyopadhyay U, Xu H, Florey O, Thompson CB, Overholtzer M. (2016). PIKfyve Regulates Vacuole Maturation and Nutrient Recovery following Engulfment.  Dev Cell, 38, 536-47.

Krishna S, Overholtzer M. (2014) Milk makes lysosomes lethal. Nat Cell Biol, 16, 1029-31.

Krajcovic, M., Krishna, S., Akkari, L., Joyce, J., and Overholtzer, M. (2013) mTOR regulates phagosome and entotic vacuole fission.  Mol Biol Cell, 24, 3736-3745. PMID: 24088573; PMCID: PMC3842999.

Krishna S, Low IC, Pervaiz S. (2011)  Regulation of mitochondrial metabolism: yet another facet in the biology of the oncoprotein Bcl-2. Biochem J., 435, 545-51.

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Isabel Lam

Lam I, Mohibullah N, Keeney S. (2017) Sequencing Spo11 Oligonucleotides for Mapping Meiotic DNA Double-Strand Breaks in Yeast. Methods Mol Biol. 1471, 51-98.

Lam I, Keeney S. (2015) Non-paradoxical evolutionary stability of the meiotic recombination initiation landscape in yeasts. Science, 350, 932–937. PMCID: PMC4656144.

Vincenten N, Kuhl LM, Lam I, Oke A, Kerr A, Hochwagen A, Fung J, Keeney S, Vader G, Marston AL. (2015) The kinetochore prevents centromere-proximal crossover recombination during meiosis. eLife, 4, e10850. PMCID: PMC4749563.

Lam I, Keeney S. (2014) Mechanism and regulation of meiotic recombination initiation. In: Heyer, Hunter, and Kowalczykowski, editors. Cold Spring Harb Perspect Biol., 7, a016634. PMCID: PMC4292169.

Chi P, Kwon Y, Visnapuu M, Lam I, Santa Maria S, Zheng X, Epshtein A, Greene E, Sung P, Klein H. (2011). Analyses of the yeast Rad51 recombinase A265V mutant reveal different in vivo roles of Swi2-like factors. Nucleic Acids Res, 39, 6511-6522. PMCID: PMC3159464.

Thacker D, Lam I, Knop M, Keeney S. (2011) Exploiting Spore-Autonomous Fluorescent Protein Expression to Quantify Meiotic Chromosome Behaviors in Saccharomyces cerevisiae. Genetics, 189, 423-439. PMCID: PMC3189805.

Siaud N, Barbera M, Egashira A, Lam I, Christ N, Schlacher K, Xia B, Jasin M. (2011) Plasticity of BRCA2 function in homologous recombination: genetic interactions of the PALB2 and DNA binding domains. PLoS Genet, 7, 1-12. PMCID: PMC3240595.

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Lindsay M. LaFave (Saunders)

LaFave LM, Béguelin W, Koche R, Teater M, Spitzer B, Chramiec A, Papalexi E, Keller MD, Hricik T, Konstantinoff K, Micol JB, Durham B, Knutson SK, Campbell JE, Blum G, Shi X, Doud EH, Krivtsov AV, Chung YR, Khodos I, de Stanchina E, Ouerfelli O, Adusumilli PS, Thomas PM, Kelleher NL, Luo M, Keilhack H, Abdel-Wahab O, Melnick A, Armstrong SA, Levine RL. (2016) Reply to “Uveal melanoma cells are resistant to EZH2 inhibition regardless of BAP1 status”. Nat Med. 22, 578-9.

LaFave LM, Levine RL. (2016)  Targeting a regulator of protein homeostasis in myeloproliferative neoplasms. Nat Med., 22, 20-1.

LaFave LM, Béguelin W, Koche R, Teater M, Spitzer B, Chramiec A, Papalexi E, Keller MD, Hricik T, Konstantinoff K, Micol JB, Durham B, Knutson SK, Campbell JE, Blum G, Shi X, Doud EH, Krivtsov AV, Chung YR, Khodos I, de Stanchina E, Ouerfelli O, Adusumilli PS, Thomas PM, Kelleher NL, Luo M, Keilhack H, Abdel-Wahab O, Melnick A, Armstrong SA, Levine RL. (2015)  Loss of BAP1 function leads to EZH2-dependent transformation. Nat Med., 21, 1344-9. PMCID: PMC4636469.

Meyer SC, Keller MD, Woods BA, LaFave LM, Bastian L, Kleppe M, Bhagwat N, Marubayashi S, Levine RL. (2014)  Genetic studies reveal an unexpected negative regulatory role for Jak2 in thrombopoiesis. Blood, 124, 2280-4. PMCID: PMC4183987.

Abdel-Wahab O, Gao J, Adli M, Dey A, Trimarchi T, Chung Y, Kuscu C, Hricik T, Ndiaye-Lobry D, LaFave L, Koche R, Shih A, Guryanova O, Kim E, Li S, Pandey S, Shin J, Telis L, Liu J, Bhatt P, Monette S, Zhao X, Mason C, Park C, Bernstein B, Aifantis I, Levine R. (2013) Deletion of Asxl1 results in myelodysplasia and sever developmental defects in vivo. J Exp Med, 210, 2641-2659. PMCID: PMC3832937.

LaFave L, Levine R. (2013) Mining the epigenetic landscape in ALL. Nat Genet, 45, 1269-1270.

Abdel-Wahab O, Adli M, LaFave L, Gao J, Hricik T, Shih A, Pandey S, Patel J, Chung Y, Koche R, Perna F, Zhao X, Taylor J, Park C, Carroll M, Melnick A, Nimer S, Jaffe J, Aifantis I, Bernstein B, Levine R. (2012) ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell, 22, 180-193. PMCID: PMC3422511.

Koppikar P, Bhagwat N, Kilpivaara O, Manshouri T, Adli M, Hricik T, Liu F, Saunders L, Mullally A, Abdel-Wahab O, Leung L, Weinstein A, Marubayashi S, Goel A, Gönen M, Estrov Z, Ebert B, Chiosis G, Nimer S, Berstein B, Verstovsek S, Levine R. (2012) Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy. Nature, 489, 155-159. PMCID: PMC3991463.

LaFave L, Levine R. (2012) JAK2 the future: therapeutic strategies for JAK-dependent malignancies. Trends Pharmacol Sci, 33, 574-582.

Dey A, Seshasayee D, Noubade R, French D, Liu J, Chaurushiya M, Kirkpatrick D, Pham V, Lill J, Bakalarski C, Wu J, Phu L, Katavolos P, LaFave L, Abdel-Wahab O, Modrusan Z, Seshagiri S, Dong K, Lin Z, Balazs M, Suriben R, Newton K, Hymowitz S, Garcia-Manero G, Martin F, Levine R, Dixit V. (2012) Loss of the tumor suppressor BAP1 causes myeloid transformation. Science, 337, 1541-1546.

Dawson M, Bannister A, Saunders L, Wahab O, Liu F, Nimer S, Levine R, Göttgens B, Kouzarides T, Green A. (2011) Nuclear JAK2. Blood, 118, 6987-6988.

Brenner JC, Graham MP, Kumar B, Saunders LM, Kupfer R, Lyons RH, Bradford CR, Carey TE. (2010) Genotyping of 73 UM-SCC head and neck squamous cell carcinoma cell lines. Head Neck, 32, 417-26. PMCID: PMC3292176

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Chong Luo

Dadi S, Chhangawala S, Whitlock BM, Franklin RA, Luo CT, Oh SA, Toure A, Pritykin Y, Huse M, Leslie CS, Li MO. (2016) Cancer Immunosurveillance by Tissue-Resident Innate Lymphoid Cells and Innate-like T Cells. Cell, 164, 365-77. PMCID: PMC4733424.

Luo CT, Liao W, Dadi S, Toure A, Li MO. (2016) Graded Foxo1 activity in Treg cells differentiates tumour immunity from spontaneous autoimmunity. Nature, 529, 532-6.

Pucella JN, Yen WF, Kim MV, van der Veeken J, Luo CT, Socci ND, Naito Y, Li MO, Iwai N, Chaudhuri J. (2015) miR-182 is largely dispensable for adaptive immunity: lack of correlation between expression and function. J Immunol., 2015, 194, 2635-42. PMCID: PMC4355037

Luo C, Li M. (2013) Transcriptional control of regulatory T cell development and function. Trends Immunol, 34, 531-539.

Ouyang W, Liao W, Luo C, Yin N, Huse M, Kim M, Peng M, Chan P, Ma Q, Mo Y, Meijer D, Zhao K, Rudensky A, Atwal G, Zhang M, Li M. (2012) Novel Foxo1-dependent transcriptional programs control T(reg) cell function.  Nature, 491, 554-559. PMCID: PMC3771531.

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Anna Sophia McKenney

Hobbs GS, Hanasoge Somasundara AV, Kleppe M, Litvin R, Arcila M, Ahn J, McKenney AS, Knapp K, Ptashkin R, Weinstein H, Heinemann MH, Francis J, Chanel S, Berman E, Mauro M, Tallman MS, Heaney ML, Levine RL, Rampal RK. (2018) Hsp90 inhibition disrupts JAK-STAT signaling and leads to reductions in splenomegaly in patients with myeloproliferative neoplasms. Haematologica. 103, e5-e9. PMCID: PMC5777196

McKenney AS, Lau AN, Somasundara AVH, Spitzer B, Intlekofer AM, Ahn J, Shank K, Rapaport FT, Patel MA, Papalexi E, Shih AH, Chiu A, Freinkman E, Akbay EA, Steadman M, Nagaraja R, Yen K, Teruya-Feldstein J, Wong KK, Rampal R, Heiden MGV, Thompson CB, Levine RL. (2018) JAK2/IDH-mutant-driven myeloproliferative neoplasm is sensitive to combined targeted inhibition. J Clin Invest. 128, 789-804. PMCID: PMC5785272 [PMID: 29355841]                                                                      

Guryanova OA, Shank K, Spitzer B, Luciani L, Koche RP, Garrett-Bakelman FE, Ganzel C, Durham BH, Mohanty A, Hoermann G, Rivera SA, Chramiec AG, Pronier E, Bastian L, Keller MD, Tovbin D, Loizou E, Weinstein AR, Gonzalez AR, Lieu YK, Rowe JM, Pastore F, McKenney AS, Krivtsov AV, Sperr WR, Cross JR, Mason CE, Tallman MS, Arcila ME, Abdel-Wahab O, Armstrong SA, Kubicek S, Staber PB, Gönen M, Paietta EM, Melnick AM, Nimer S, Mukherjee S, Levine RL. (2016) DNMT3A mutations promote anthracycline resistance in acute myeloid leukemia via impaired nucleosome remodeling. Nat Med. 22:1488-1495. PMCID: PMC5359771 [Available on 2017-06-01]

Kleppe M, Kwak M, Koppikar P, Riester M, Keller M, Bastian L, Hricik T, Bhagwat N, McKenney AS, Papalexi E, Abdel-Wahab O, Rampal R, Marubayashi S, Chen  JJ, Romanet V, Fridman JS, Bromberg J, Teruya-Feldstein J, Murakami M, Radimerski T, Michor F, Fan R, Levine RL. (2015) JAK-STAT pathway activation in malignant and nonmalignant cells contributes to MPN pathogenesis and therapeutic response. Cancer Discov., 5, 316-31. PMCID: PMC4355105.

Meyer SC, Keller MD, Chiu S, Koppikar P, Guryanova OA, Rapaport F, Xu K, Manova K, Pankov D, O’Reilly RJ, Kleppe M, McKenney AS, Shih AH, Shank K, Ahn J, Papalexi E, Spitzer B, Socci N, Viale A, Mandon E, Ebel N, Andraos R, Rubert J, Dammassa E, Romanet V, Dölemeyer A, Zender M, Heinlein M, Rampal R, Weinberg RS, Hoffman R, Sellers WR, Hofmann F, Murakami M, Baffert F, Gaul C, Radimerski T, Levine RL. (2015) CHZ868, a Type II JAK2 Inhibitor, Reverses Type I JAK Inhibitor Persistence and Demonstrates Efficacy in Myeloproliferative Neoplasms. Cancer Cell, 28, 15-28. PMCID: PMC4503933.

Rampal R, Ahn J, Abdel-Wahab O, Nahas M, Wang K, Lipson D, Otto GA, Yelensky R, Hricik T, McKenney AS, Chiosis G, Chung YR, Pandey S, van den Brink MR, Armstrong SA, Dogan A, Intlekofer A, Manshouri T, Park CY, Verstovsek S, Rapaport F, Stephens PJ, Miller VA, Levine RL. (2014) Genomic and functional analysis of leukemic transformation of myeloproliferative neoplasms. Proc Natl Acad Sci U S A, 111, E5401-10. PMCID: PMC4273376.

McKenney AS, Levine RL. (2013) Isocitrate dehydrogenase mutations in leukemia. J Clin Invest.,  123, 3672-7. PMCID: PMC3754251.

Russ JB, McKenney AS, Patel AB. (2013) An identity crisis: the need for core competencies in undergraduate medical education. Med Educ Online, 18, 1-2. PMCID: PMC3641287.

Francis ER, Goodsmith N, Michelow M, Kulkarni A, McKenney AS, Kishore SP, Bertelsen N, Fein O, Balsari S, Lemery J, Fitzgerald D, Johnson W, Finkel ML. (2012) The global health curriculum of Weill Cornell Medical College: how one school developed a global health program. Acad Med., 87, 1296-302.

Tetenbaum-Novatt J, Hough LE, Mironska R, McKenney AS, Rout MP. (2012) Nucleocytoplasmic transport: a role for nonspecific competition in karyopherin-nucleoporin interactions. Mol Cell Proteomics, 11, 31-46. PMCID: PMC3418842.

Barzilla JE, McKenney AS, Cowan AE, Durst CA, Grande-Allen KJ. (2010) Design and validation of a novel splashing bioreactor system for use in mitral valve organ culture. Ann Biomed Eng., 38, 3280-94. PMCID: PMC4412843.

Jovanovic-Talisman T, Tetenbaum-Novatt J, McKenney AS, Zilman A, Peters R, Rout MP, Chait BT. (2009)  Artificial nanopores that mimic the transport selectivity of the nuclear pore complex. Nature, 457, 1023-7. PMCID: PMC2764719.

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Danilo G. Macalinao

Boire A, Zou Y, Shieh J, Macalinao DG, Pentsova E, Massagué J. (2017) Complement Component 3 Adapts the Cerebrospinal Fluid for Leptomeningeal Metastasis. Cell 168, 1101-1113.

Malladi S, Macalinao DG, Jin X, He L, Basnet H, Zou Y, de Stanchina E, Massagué J. (2016) Metastatic Latency and Immune Evasion through Autocrine Inhibition of WNT. Cell, 165, 45-60. PMCID: PMC4808520.

Cross SH, Macalinao DG, McKie L, Rose L, Kearney AL, Rainger J, Thaung C, Keighren M, Jadeja S, West K, Kneeland SC, Smith RS, Howell GR, Young F, Robertson M, van T’ Hof R, John SW, Jackson IJ. (2014). A dominant-negative mutation of mouse Lmx1b causes glaucoma and is semi-lethal via LDB1-mediated dimerization. PLoS Genet., 10, e1004359. PMCID: PMC4014447.

Howell GR, MacNicoll KH, Braine CE, Soto I, Macalinao DG, Sousa GL, John SW. (2014). Combinatorial targeting of early pathways profoundly inhibits neurodegeneration in a mouse model of glaucoma. Neurobiol Dis., 71, 44-52. PMCID: PMC4319373.

Reinholdt LG, Howell GR, Czechanski AM, Macalinao DG, Macnicoll KH, Lin CS, Donahue LR, John SW. (2012). Generating Embryonic Stem Cells from the Inbred Mouse Strain DBA/2J, a Model of Glaucoma and Other Complex Diseases. PLoS One. 7, e50081. PMCID: PMC3507949.

Howell GR, Soto I, Zhu X, Ryan M, Macalinao DG, Sousa GL, Caddle LB, MacNicoll KH, Barbay JM, Porciatti V, Anderson MG, Smith RS, Clark AF, Libby RT, John SW. (2012). Radiation treatment inhibits monocyte entry into the optic nerve head and prevents neuronal damage in a mouse model of glaucoma. J Clin Invest., 122, 1246-61. PMCID: PMC3314470.

Nair KS, Hmani-Aifa M, Ali Z, Kearney AL, Ben Salem S, Macalinao DG, Cosma IM, Bouassida W, Hakim B, Benzina Z, Soto I, Söderkvist P, Howell GR, Smith RS, Ayadi H, John SW. (2011). Alteration of the serine protease PRSS56 causes angle-closure glaucoma in mice and posterior microphthalmia in humans and mice. Nat Genet., 43, 579-84. PMCID: PMC4388060.

Howell GR, Macalinao DG, Sousa GL, Walden M, Soto I, Kneeland SC, Barbay JM, King BL, Marchant JK, Hibbs M, Stevens B, Barres BA, Clark AF, Libby RT, John SW. (2011). Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma. J Clin Invest., 121, 1429-44. PMCID: PMC3069778.

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John Maciejowski

Maciejowski J, Drechsler H, Grundner-Culemann K, Ballister ER, Rodriguez-Rodriguez JA, Rodriguez-Bravo V, Jones MJK, Foley E, Lampson MA, Daub H, McAinsh AD, Jallepalli PV. (2017) Mps1 Regulates Kinetochore-Microtubule Attachment Stability via the Ska Complex to Ensure Error-Free Chromosome Segregation. Dev Cell. 41, 143-156. PMCID: PMC5477644.

Rodriguez-Bravo V, Maciejowski J, Corona J, Buch H, Collin P, Kanemaki M, Shah J, Jallepalli P. (2014) Nuclear pores protect genome integrity by assembling a premitotic and mad1-dependent anaphase inhibitor. Cell, 156, 1017-1031.

Paschal C, Maciejowski J, Jallepalli P. (2012) A stringent requirement for Plk1 T210 phosphorylation during K-fiber assembly and chromosome congression. Chromosoma, 121, 565-572.

Maciejowski J, George K, Terret M, Zhang C, Shokat K, Jallepalli P. (2010) Mps1 directs the assembly of Cdc20 inhibitory complexes during interphase and mitosis to control M phase timing and spindle checkpoint signaling. J Cell Biol, 190, 89-100.

Burkard M, Maciejowski J, Rodriguez-Bravo V, Repka M, Lowery D, Clauser K, Zhang C, Shokat K, Carr S, Yaffe M, Jallepalli P. (2009) Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells. PLoS Biol, 7, 1-16.

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James Mahaffey

Mahaffey J, Grego-Bessa J, Liem K, Anderson K. (2013) Cofilin and Vangl2 cooperate in the initiation of planar cell polarity in the mouse embryo. Development, 140, 1262-1271. 

Qian L, Mahaffey J, Alcorn H, Anderson K. (2011) Tissue-specific roles of Axin2 in the inhibition and activation of Wnt signaling in the mouse embryo. Proc Natl Acad Sci U S A, 108, 8692-8697. 

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Dan Marks

Marks DH, Thomas R, Chin Y, Shah R, Khoo C, Benezra R. (2017) Mad2 overexpression uncovers a critical role for TRIP13 in mitotic exit. Cell Rep. 19, 1832-1845. PMCID: PMC5526606.

Russell JR, Huang J, Anand P, Kucera K, Sandoval AG, Dantzler KW, Hickman D, Jee J, Kimovec FM, Koppstein D, Marks DH, Mittermiller PA, Núñez SJ, Santiago M, Townes MA, Vishnevetsky M, Williams NE, Vargas MP, Boulanger LA, Bascom-Slack C, Strobel SA. (2011) Biodegradation of polyester polyurethane by endophytic fungi. Appl Environ Microbiol 77, 6076-84. PMCID: PMC3165411

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Armine Matevossian

Matevossian A, Resh MD. (2015) Hedgehog Acyltransferase as a target in estrogen receptor positive, HER2 amplified, and tamoxifen resistant breast cancer cells. Mol Cancer, 14, 72 [Epub ahead of print]  

Matevossian A, Resh MD. (2015) Membrane topology of hedgehog acyltransferase. J Biol Chem., 290, 2235-43. PMCID: PMC4303674.

Petrova E, Matevossian A, Resh M. (2014) Hedgehog acyltransferase as a target in pancreatic ductal adenocarcinoma. Oncogene, 1-6.

Callier P, Calvel P, Matevossian A, Makrythanasis P, Bernard P, Kurosaka H, Vannier A, Thauvin-Robinet C, Borel C, Mazaud-Guittot S, Rolland A, Desdoits-Lethimonier C, Guipponi M, Zimmermann C, Stévant I, Kuhne F, Conne B, Santoni F, Lambert S, Huet F, Mugneret F, Jaruzelska J, Faivre L, Wilhelm D, Jégou B, Trainor P, Resh M, Antonarakis S, Nef S. (2014) Loss of function mutation in the palmitoyl-transferase HHAT leads to syndromic 46, XY disorder of sex development by impeding Hedgehog protein palmitoylation and signaling. PLoS Genet, 10, 1-12. PMCID: PMC4006744.

Amrani Y, Gill J, Matevossian A, Alonzo E, Yang C, Shieh J, Moore M, Park C, Sant-Angelo D, Denzin L. (2011) The Paf oncogene is essential for hematopoietic stem cell function and development. J Exp Med, 208, 1757-1765. PMCID: PMC3171089.

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Gregory Mazo

Yang TT, Chong WM, Wang WJ, Mazo G, Tanos B, Chen Z, Tran TMN, Chen YD, Weng RR, Huang CE, Jane WN, Tsou MB, Liao JC (2018) Super-resolution architecture of mammalian centriole distal appendages reveals distinct blade and matrix functional components. Nat Commun. 9, 2023. PMCID: PMC5964178

Mazo G, Soplop N, Wang WJ, Uryu K, Tsou MB.(2016) Spatial Control of Primary Ciliogenesis by Subdistal Appendages Alters Sensation-Associated Properties of Cilia. Dev Cell. 39, 424-437. PMCID: PMC5125554 [Available on 2017-11-21]

Fong CS, Mazo G, Das T, Goodman J, Kim M, O’Rourke BP, Izquierdo D, Tsou MF.(2016) 53BP1 and USP28 mediate p53-dependent cell cycle arrest in response to centrosome loss and prolonged mitosis. Elife 5.   PMCID: PMC4946878

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Yvonne Gruber Mica

Fattahi F, Steinbeck JA, Kriks S, Tchieu J, Zimmer B, Kishinevsky S, Zeltner N, Mica Y, El-Nachef W, Zhao H, de Stanchina E, Gershon MD, Grikscheit TC, Chen S, Studer L. (2016) Deriving human ENS lineages for cell therapy and drug discovery in Hirschsprung disease. Nature. 531, 105-9. PMCID: PMC4846424

Callahan SJ, Mica Y, Studer L. (2016)  Feeder-free Derivation of Melanocytes from Human Pluripotent Stem Cells. J Vis Exp., 109.

Chambers S, Mica Y, Lee G, Studer L, Tomishima M. (2013) Dual-SMAD Inhibition/WNT Activation-Based Methods to Induce Neural Crest and Derivatives from Human Pluripotent Stem Cells. Methods Mol Biol. 

Mica Y, Lee G, Chambers S, Tomishima M, Studer L. (2013) Modeling Neural Crest Induction, Melanocyte Specification, and Disease-Related Pigmentation Defects in hESCs and Patient-Specific iPSCs. Cell Rep, 3, 1140-1152.

Chambers S, Qi Y, Mica Y, Lee G, Zhang X, Niu L, Bilsland J, Cao L, Stevens E, Whiting P, Shi S, Studer L. (2012) Combined small-molecule inhibition accelerates developmental timing and converts human pluripotent stem cells into nociceptors. Nat Biotechnol, 30, 715-720.

Chambers S, Mica Y, Studer L, Tomishima M. (2011) Converting human pluripotent stem cells to neural tissue and neurons to model neurodegeneration. Methods Mol Biol, 793, 87-97. 

Papapetrou E, Tomishima M, Chambers S, Mica Y, Reed E, Menon J, Tabar V, Mo Q, Studer L, Sadelain M. (2009) Stoichiometric and temporal requirements of Oct4, Sox2, Klf4, and c-Myc expression for efficient human iPSC induction and differentiation. Proc Natl Acad Sci U S A, 106, 12759-12764.

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Alexandria Miller

Vaisey G, Miller AN, Long SB. (2016) Distinct regions that control ion selectivity and calcium-dependent activation in the bestrophin ion channel. Proc Natl Acad Sci U S A. 113, E7399-E7408. PMCID: PMC5127342

Miller A, Long S. (2012) Crystal structure of the human two-pore domain potassium channel K2P1. Science, 335, 432-436.

Alarcón C, Zaromytidou A, Xi Q, Gao S, Yu J, Fujisawa S, Barlas A, Miller A, Manova-Todorova K, Macias M, Sapkota G, Pan D, Massagué J. (2009) Nuclear CDKs drive Smad transcriptional activation and turnover in BMP and TGF-beta pathways. Cell, 139, 757-769. 

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Justine Miller

Miller J, Studer L. (2014) Aging in iPS cells. Aging (Albany NY), 6, 246-7. PMCID: PMC4032792.

Miller J, Ganat Y, Kishinevsky S, Bowman R, Liu B, Tu E, Mandal P, Vera E, Shim J, Kriks S, Taldone T, Fusaki N, Tomishima M, Krainc D, Milner T, Rossi D, Studer L. (2013) Human iPSC-Based Modeling of Late-Onset Disease via Progerin-Induced Again. Cell Stem Cell, 13, 691-705.

Cherry A, Gagne K, McLoughlin E, Baccei A, Gorman B, Hartung O, Miller J, Zhang J, Zon R, Ince T, Neufeld E, Lerou P, Fleming M, Daley G, Agarwal S. (2013) Induced pluripotent stem cells with a mitochondrial DNA deletion. Stem Cells, 31, 1287-1297. PMCID: PMC3692613

Miller J, Schlaeger T. (2011) Generation of induced pluripotent stem cell lines form human fibroblasts via retroviral gene transfer. Methods Mol Biol, 767, 55-65. 

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Prashant Monian

Gao M, Monian P, Pan Q, Zhang W, Xiang J, Jiang X.(2016) Ferroptosis is an autophagic cell death process. Cell Res., 2016, 26, 1021-32. PMCID: PMC5034113

Monian P, Jiang X. (2016) The Cellular Apoptosis Susceptibility Protein (CAS) Promotes Tumor Necrosis Factor-related Apoptosis-inducing Ligand (TRAIL)-induced Apoptosis and Cell Proliferation. J Biol Chem., 291, 2379-88. PMCID: PMC4732220.

Gao M, Monian P, Jiang X. (2015) Metabolism and iron signaling in ferroptotic cell death. Oncotarget, 6, 35145-6.

Gao M, Monian P, Quadri N, Ramasamy R, Jiang X. (2015) Glutaminolysis and Transferrin Regulate Ferroptosis. Mol Cell, 59, 298-308. PMCID: PMC4506736.

Will M, Qin AC, Toy W, Yao Z, Rodrik-Outmezguine V, Schneider C, Huang X, Monian P, Jiang X, de Stanchina E, Baselga J, Liu N, Chandarlapaty S, Rosen N. (2014) Rapid induction of apoptosis by PI3K inhibitors is dependent upon their transient inhibition of RAS-ERK signaling. Cancer Discov.,  4, 334-47. PMCID: PMC4049524.

Monian P, Jiang X. (2012) Clearing the final hurdles to mitochondrial apoptosis: regulation post cytochrome C release. Exp Oncol., 34, 185-91.

Peterson B, Stovall K, Monian P, Franklin JL, Cummings BS. (2008) Alterations in phospholipid and fatty acid lipid profiles in primary neocortical cells during oxidant-induced cell injury.  Chem Biol Interact., 174, 163-76.

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Semanti Mukherjee

Willis J, Mukherjee S, Orlow I, Viale A, Offit K, Kurtz R, Olson S, Klein R. (2014) Genome-wide analysis of the role of copy-number variation in pancreatic cancer risk.  Front Genet, 5, 29. 

Willis J, Olson S, Orlow I, Mukherjee S, McWilliams R, Kurtz R, Klein R. (2012) A replication study and genome-wide scan of single-nucleotide polymorphisms associated with pancreatic cancer risk and overall survival. Clin Cancer Res, 18, 3942-3951. 

Mukherjee S, Simon J, Bayuga S, Ludwig E, Yoo S, Orlow I, Viale A, Offit K, Kurtz R, Olson S, Klein R. (2011) Including additional controls from public databases improves the power of a genome wide association study. Hum Hered, 72, 21-34.

Klein R, Xu X, Mukherjee S, Willis J, Hayes J. (2010) Successes of genome wide association studies. Cell, 142, 350-351. 

Pomerantz JH, Mukherjee S, Palermo AT, Blau HM. (2009) Reprogramming to a muscle fate by fusion recapitulates differentiation. J Cell Sci. 122, 1045-53. PMCID: PMC2720934

Kilpivaara O, Mukherjee S, Schram A, Wadleigh M, Mullally A, Ebert B, Bass A, Marubayashi S, Heguy A, Garcia-Manero G, Kantarjian H, Offit K, Stone R, Gilliland D, Klein R, Levine R. (2009) A germline JAK2 SNP is associated with predisposition to the development of JAK2V617F-positive myeloproliferative neoplasms. Nat Genet, 41, 455-459.

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Brandon Nemieboka

Rao TD, Fernández-Tejada A, Axelrod A, Rosales N, Yan X, Thapi S, Wang A, Park KJ, Nemieboka B, Xiang J, Lewis JS, Olvera N, Levine DA, Danishefsky SJ, Spriggs DR. (2017) Antibodies Against Specific MUC16 Glycosylation Sites Inhibit Ovarian Cancer Growth. ACS Chem Biol. 12, 2085-2096. PMCID: PMC5603915 [Available on 2018-08-18]

Sharma SK, Nemieboka B, Sala E, Lewis JS, Zeglis BM. (2016) Molecular Imaging of Ovarian Cancer. J Nucl Med. 57, 827-33. PMCID: PMC5047520

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Moriah Heller Nissan

Nissan M, Solit B. (2014) Ch. 22: BRAF mutations in human cancer: biologic and therapeutic implications. Molecular Oncology: Causes of Cancer and Targets for Treatment, Eds. Gelmann et al. Cambridge University Press, 272-277.

Nissan MH, Pratilas CA, Jones AM, Ramirez R, Won H, Liu C, Tiwari S, Kong L, Hanrahan AJ, Yao Z, Merghoub T, Ribas A, Chapman PB, Yaeger R, Taylor BS, Schultz N, Berger MF, Rosen N, Solit DB. (2014) Loss of NF1 in cutaneous melanoma is associated with RAS activation and MEK dependence. Cancer Res. 74, 2340-50. PMCID: PMC4005042

Nissan M, Rosen N, Solit D. (2013) ERK pathway inhibitors: how low should we go? Cancer Discov, 3, 719-721.

Nissan M, Solit D. (2011) The “SWOT” of BRAF inhibition in melanoma: RAF inhibitors, MEK inhibitors or both? Curr Oncol Rep, 13, 479-487. 

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Jennifer Nnoli

Sansone P, Ceccarelli C, Berishaj M, Chang Q, Rajasekhar VK, Perna F, Bowman RL, Vidone M, Daly L, Nnoli J, Santini D, Taffurelli M, Shih NN, Feldman M, Mao JJ, Colameco C, Chen J, DeMichele A, Fabbri N, Healey JH, Cricca M, Gasparre G, Lyden D, Bonafé M, Bromberg J. (2016) Self-renewal of CD133(hi) cells by IL6/Notch3 signalling regulates endocrine resistance in metastatic breast cancer. Nat Commun., 7, 10442. PMCID: PMC4748123.

Gholami S, Chen CH, Gao S, Lou E, Fujisawa S, Carson J, Nnoli JE, Chou TC, Bromberg J, Fong Y. (2014) Role of MAPK in oncolytic herpes viral therapy in triple-negative breast cancer. Cancer Gene Ther., 21, 283-9.

Azare J, Doane A, Leslie K, Chang Q, Berishaj M, Nnoli J, Mark K, Al-Ahmadie H, Gerald W, Hassimi M, Viale A, Stracke M, Lyden D, Bromberg J. (2011) Stat3 mediates expression of autotoxin in breast cancer. PLoS, 6, 1-11.

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Oakley Olson

Quail DF, Olson OC, Bhardwaj P, Walsh LA, Akkari L, Quick ML, Chen IC, Wendel N, Ben-Chetrit N, Walker J, Holt PR, Dannenberg AJ, Joyce JA. (2017) Obesity alters the lung myeloid cell landscape to enhance breast cancer metastasis through IL5 and GM-CSF. Nat Cell Biol.19, 974-987.

Prudova A, Gocheva V, Auf dem Keller U, Eckhard U, Olson OC, Akkari L, Butler GS, Fortelny N, Lange PF, Mark JC, Joyce JA, Overall CM. (2016) TAILS N-Terminomics and Proteomics Show Protein Degradation Dominates over Proteolytic Processing by Cathepsins in Pancreatic Tumors. Cell Rep., 16, 1762-73.

Olson OC, Joyce JA. (2015) Cysteine cathepsin proteases: regulators of cancer progression and therapeutic response. Nature reviews. Cancer,  15, 712-29.

Hughes R, Qian BZ, Rowan C, Muthana M, Keklikoglou I, Olson OC, Tazzyman S, Danson S, Addison C, Clemons M, Gonzalez-Angulo AM, Joyce JA, De Palma M, Pollard JW, Lewis CE. (2015)  Perivascular M2 Macrophages Stimulate Tumor Relapse after Chemotherapy. Cancer Res, 75, 3479-91.

Olson O, Joyce J. (2013) A splicing twist on metastasis. Sci Transl Med, 23, 1-3.

Pyonteck S, Akkari L, Schuhmacher A, Bowman R, Sevenich L, Quail D, Olson O, Quick M, Huse J, Teijeiro V, Setty M, Leslie C, Oei Y, Pedraza A, Zhang J, Brennan C, Sutton J, Holland E, Daniel D, Joyce J. (2013) CSF-1R inhibition alters macrophage polarization and blocks glioma progression. Nat Med, 19, 1264-1272. PMCID: PMC3840724.

Olson O, Joyce J. (2013) Microenvironment-mediated resistance to anticancer therapies. Cell Res, 23, 179-181. PMCID: PMC3567818.

Shree T, Olson O, Elie B, Kester J, Garfall A, Simpson K, Bell-McGuinn K, Zabor E, Brogi E, Joyce J. (2011) Macrophages and cathepsin proteases blunt chemotherapeutic response in breast cancer. Genes Dev, 25, 2465-2479. PMCID: PMC3243057.

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Joseph Pucella

Pucella JN, Chaudhuri J. (2017) AID Invited to the G4 Summit. Mol Cell. 67, 355-357.

Yen WF, Chaudhry A, Vaidyanathan B, Yewdell WT, Pucella JN, Sharma R, Liang Y, Li K, Rudensky AY, Chaudhuri J. (2017) BRCT-domain protein BRIT1 influences class switch recombination. Proc Natl Acad Sci U S A pii: 201708211 [Epub ahead of print]. PMCID: PMC5547652 [Available on 2018-02-01]

Pucella JN, Yen WF, Kim MV, van der Veeken J, Socci ND, Naito Y, Li MO, Iwai N, Chaudhuri J. (2015)  miR-182 Is Largely Dispensable for Adaptive Immunity: Lack of Correlation between Expression and Function. J Immunol., 195, 1903.

Vaidyanathan B., Yen, W., Pucella, J.,and Chaudhuri, J. (2014)  AIDing Chromatin and  Transcription-Coupled Orchestration of Immunoglobulin Class-Switch Recombination.  Front Immunol, 5, 1-13. PMID: 24734031; PMCID: PMC3975107.

Vuong, B., Herrick-Reynolds, K., Vaidyanathan, B., Pucella, J., Ucher, A., Donghia, N., Gu, X., Nicolas, L., Nowak, U., Rahman, N., Strout, M., Mills, K., Stavnezer, J., and Chaudhuri, J. (2013) A DNA break- and phosphorylation-dependent positive feedback loop promotes immunoglobulin class-switch recombination. Nat Immunol, 14, 1183-1189. PMID: 24097111; PMCID: PMC4005274.

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Neel Shah

Bose R, Karthaus WR, Armenia J, Abida W, Iaquinta PJ, Zhang Z, Wongvipat J, Wasmuth EV, Shah N, Sullivan PS, Doran MG, Wang P, Patruno A, Zhao Y, International SU2C/PCF Prostate Cancer Dream Team, Zheng D, Schultz N, Sawyers CL. (2017) ERF mutations reveal a balance of ETS factors controlling prostate oncogenesis. Nature 546, 671-675. PMCID: PMC5576182 [Available on 2018-06-29]

Shah N, Wang P, Wongvipat J, Karthaus WR, Abida W, Armenia J, Rockowitz S, Drier Y, Bernstein BE, Long HW, Freedman ML, Arora VK, Zheng D, Sawyers CL. (2017) Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer. Elife 6, pii: e27861. PMCID: PMC5593504

Mu P, Zhang Z, Benelli M, Karthaus WR, Hoover E, Chen CC, Wongvipat J, Ku SY, Gao D, Cao Z, Shah N, Adams EJ, Abida W, Watson PA, Prandi D, Huang CH, de Stanchina E, Lowe SW, Ellis L, Beltran H, Rubin MA, Goodrich DW, Demichelis F, Sawyers CL. (2017) SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer. Science 355, 84-88. PMCID: PMC5247742 [Available on 2017-04-06]

Caley MP, King H, Shah N, Wang K, Rodriguez-Teja M, Gronau JH, Waxman J, Sturge J. (2016)  Tumor-associated Endo180 requires stromal-derived LOX to promote metastatic prostate cancer cell migration on human ECM surfaces. Clin Exp Metastasis, 33, 151-65. PMCID: PMC4761374.

Arora, V., Schenkein, E., Murali, R., Subudhi, S., Wongvipat, J., Balbas, M., Shah, N., Cai, L., Efstathiou, E., Logothetis, C., Zheng, D., and Sawyers, C. (2013)  Glucocorticoid receptor confers resistance to antiandrogens by bypassing androgen receptor blockade. Cell, 155, 1309-1322. PMID: 24315100; PMCID: PMC3932525.

Polkinghorn, W., Parker, J., Lee, M., Kass, E., Spratt, D., Iaquinta, P., Arora, V., Yen, W., Cai, L., Zheng, D., Carver, B., Chen, Y., Watson, P., Shah, N., Fujisawa, S., Goglia, A., Gopalan, A., Hieronymus, H., Wongvipat, J., Scardino, P., Zelefsky, M., Jasin, M., Chaudhuri, J., Powell, S., and Sawyers, C. (2013)  Androgen receptor signaling regulates DNA repair in prostate cancers. Cancer Discov, 3, 1245-1253. PMID: 24027196; PMCID: PMC3888815.

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Berenice Ortiz Thompson

Ortiz B, White R, Wu W, Chan T. (2014) Deletion of PTPRD and Cdkn2a cooperate to accelerate tumorigenesis Oncotarget. Oncotarget, 5, 6976-82.

Ortiz B, Fabius A, Wu W, Pedraza A, Brennan C, Schultz N, Pitter K, Bromberg J, Huse J, Holland E, Chan T. (2014) Loss of the tyrosine phosphatase PTPRD leads to aberrant STAT3 activation and promotes gliomagenesis. Proc Natl Acad Sci U S A, 111, 8149-9154. PMCID: PMC4050622.

Carta G, Murru E, Cordeddu L, Ortiz B, Giordano E, Belury MA, Quadro L, Banni S. (2014) Metabolic interactions between vitamin A and conjugated linoleic acid. Nutrients. 6, 1262-1272. PMCID: PMC3967192.

Meehan M, Parthasarathi L, Moran N, Jefferies C, Foley N, Lazzari E, Murphy D, Ryan J, Ortiz B, Fabius A, Chan T, Stallings R. (2012) Protein tyrosine phosphatase receptor delta actas as a neuroblastoma tumor suppressor by destabilizing the aurora kinase A oncogene. Mol Cancer, 11, 1-9. PMCID: PMC3395855.

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Cindy Puente

Puente C, Hendrickson RC, Jiang X. (2016) Nutrient-regulated Phosphorylation of ATG13 Inhibits Starvation-induced Autophagy. J Biol Chem., 291, 6026-35. PMCID: PMC4786734.

Gammoh N, Fraser J, Puente C, Syred HM, Kang H, Ozawa T, Lam D, Acosta JC, Finch AJ, Holland E, Jiang X. (2016) Suppression of autophagy impedes glioblastoma development and induces senescence. Autophagy. 12, 1431-9. PMCID: PMC5082770 [Available on 2017-06-15]

Wong P, Puente C, Ganley I, Jiang X. (2013) The ULK1 complex: sensing nutrient signals for autophagy activation. Autophagy, 9, 124-137. PMCID: PMC3552878.

Gammoh N, Lam D, Puente C, Ganley I, Marks P, Jiang X. (2012) Role of autophagy in histone deacetylase inhibitor-induced apoptotic and nonapoptotic cell death. Proc Natl Acad Sci, 109, 6561-6565. PMCID: PMC3340088.

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Sadia Rahman

Rahman S, Jones MJ, Jallepalli PV. (2015) Cohesin recruits the Esco1 acetyltransferase genome wide to repress transcription and promote cohesion in somatic cells. Proc Natl Acad Sci U S A, 112, 11270-5. PMCID: PMC4568707.

Cremona CA, Sarangi P, Yang Y, Hang LE, Rahman S, Zhao X. (2012) Extensive DNA damage-induced sumoylation contributes to replication and repair and acts in addition to the mec1 checkpoint. Mol Cell. 45, 422-32. PMCID: PMC3340930

Terret M, Sherwood R, Rahman S, Qin J, Jallepalli P. (2009) Cohesin acetylation speeds the replication fork. Nature, 462, 231-234. 

Gao S, Alarcón C, Sapkota G, Rahman S, Chen P, Goerner N, Macias M, Erdjument-Bromage H, Tempst P, Massagué J. (2009) Ubiquitin ligase Nedd4L targets activated Smad2/3 to limit TGF-beta signaling. Mol Cell, 36, 457-468.

Burgess RC, Rahman S, Lisby M, Rothstein R, Zhao X. (2007) The Slx5-Slx8 complex affects sumoylation of DNA repair proteins and negatively regulates recombination. Mol Cell Biol. 27, 6153-62. PMCID: PMC1952148 [PMID: 17591698]

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Leili Ran

Lu C, Jain SU, Hoelper D, Bechet D, Molden RC, Ran L, Murphy D, Venneti S, Hameed M, Pawel BR, Wunder JS, Dickson BC, Lundgren SM, Jani KS, De Jay N, Papillon-Cavanagh S, Andrulis IL, Sawyer SL, Grynspan D, Turcotte RE, Nadaf J, Fahiminiyah S, Muir TW, Majewski J, Thompson CB, Chi P, Garcia BA, Allis CD, Jabado N, Lewis PW. (2016) Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape. Science. 352, 844-849. PMCID: PMC4928577

Wiesner T, Lee W, Obenauf AC, Ran L, Murali R, Zhang QF, Wong EW, Hu W, Scott SN, Shah RH, Landa I, Button J, Lailler N, Sboner A, Gao D, Murphy DA, Cao Z, Shukla S, Hollmann TJ, Wang L, Borsu L, Merghoub T, Schwartz GK, Postow MA, Ariyan CE, Fagin JA, Zheng D, Ladanyi M, Busam KJ, Berger MF, Chen Y, Chi P. (2015) Alternative transcription initiation leads to expression of a novel ALK isoform in cancer. Nature,  526, 453-7. PMCID: PMC4807020.

Ran L, Sirota I, Cao Z, Murphy D, Chen Y, Shukla S, Xie Y, Kaufmann MC, Gao D, Zhu S, Rossi F, Wongvipat J, Taguchi T, Tap WD, Mellinghoff IK, Besmer P, Antonescu CR, Chen Y, Chi P. (2015) Combined inhibition of MAP kinase and KIT signaling synergistically destabilizes ETV1 and suppresses GIST tumor growth. Cancer Discov.,  5, 304-15. PMCID: PMC4355391.

Sheth A, Escobar-Alvarez S, Gardner J, Ran L, Heaney ML, Scheinberg DA. (2014) Inhibition of human mitochondrial peptide deformylase causes apoptosis in c-myc-overexpressing hematopoietic cancers.  Cell Death Dis., 5, e1152. PMCID: PMC3973238.

Gao D, Vela I, Sboner A, Iaquinta PJ, Karthaus WR, Gopalan A, Dowling C, Wanjala JN, Undvall EA, Arora VK, Wongvipat J, Kossai M, Ramazanoglu S, Barboza LP, Di W, Cao Z, Zhang QF, Sirota I, Ran L, MacDonald TY, Beltran H, Mosquera JM, Touijer KA, Scardino PT, Laudone VP, Curtis KR, Rathkopf DE, Morris MJ, Danila DC, Slovin SF, Solomon SB, Eastham JA, Chi P, Carver B, Rubin MA, Scher HI, Clevers H, Sawyers CL, Chen Y. (2014)  Organoid cultures derived from patients with advanced prostate cancer. Cell, 159, 176-87. PMCID: PMC4237931.

Lee W, Teckie S, Wiesner T, Ran L, Prieto Granada CN, Lin M, Zhu S, Cao Z, Liang Y, Sboner A, Tap WD, Fletcher JA, Huberman KH, Qin LX, Viale A, Singer S, Zheng D, Berger MF, Chen Y, Antonescu CR, Chi P. (2014) PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors. Nat Genet., 46, 1227-32. PMCID: PMC4249650.

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Jessica Rios-Esteves

Rios-Esteves J, Haugen B, Res M. (2014) Identification of Key Residues and Regions Important for Porcupine-mediated Wnt Acylation. J Biol Chem, 289, 17009-17019. PMCID: PMC4059143.

Petrova E, Rios-Esteves J, Ouerfelli O, Glickman J, Resh M. (2013) Inhibitors of Hedgehog acyltransferase block Sonic Hedgehog signaling. Nat Chem Biol, 9, 247-249. PMCID: PMC3604071.

Rios-Esteves J, Resh M. (2013) Stearoyl CoA desaturase is required to produce active, lipid-modified Wnt proteins. Cell Rep, 4, 1072-1081. PMCID: PMC3845236.

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Piero Sanfilippo

Sanfilippo P, Wen J, Lai EC. (2017) Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species. Genome Biol. 18, 229. PMCID: PMC5707805

Lin CJ, Wen J, Bejarano F, Hu F, Bortolamiol-Becet D, Kan L, Sanfilippo P, Kondo S, Lai EC. (2017) Characterization of a TUTase/RNase complex required for Drosophila gametogenesis. RNA. 23, 284-296. PMCID: PMC5311484 [Available on 2018-03-01]

Sanfilippo P, Miura P, Lai EC. (2017) Genome-wide profiling of the 3’ ends of polyadenylated RNAs. Methods 126, 86-94. PMCID: PMC5583017 [Available on 2018-08-15]

Sanfilippo P, Smibert P, Duan H, Lai EC. (2016) Neural specificity of the RNA-binding protein Elav is achieved by post-transcriptional repression in non-neural tissues. Development 143, 4474-4485. PMCID: PMC5201049 [Available on 2017-12-01]

Sanfilippo P, Smibert P, Duan H, Lai EC. (2017) Neural specificity of the RNA-binding protein Elav is achieved by post-transcriptional repression in non-neural tissues. Development 144, 1578. PMCID: PMC5201049

Shenker S, Miura P, Sanfilippo P, Lai EC. (2015)  IsoSCM: improved and alternative 3’ UTR annotation using multiple change-point inference. RNA, 21, 14-27. PMCID: PMC4274634.

Garaulet DL, Castellanos MC, Bejarano F, Sanfilippo P, Tyler DM, Allan DW, Sánchez-Herrero E, Lai EC. (2014)  Homeotic function of Drosophila Bithorax-complex miRNAs mediates fertility by restricting multiple Hox genes and TALE cofactors in the CNS. Dev Cell, 29, 635-48. PMCID: PMC4111139.

Miura P, Sanfilippo P, Shenker S, Lai EC. (2014)  Alternative polyadenylation in the nervous system: to what lengths will 3” UTR extensions take us? Bioessays. 36, 766-77. PMCID: PMC4503322.

Westholm JO, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P, Celniker SE, Graveley BR, Lai EC. (2014) Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation. Cell Rep., 9, 1966-80. PMCID: PMC4279448.

Hayes ET, Wilks JC, Sanfilippo P, Yohannes E, Tate DP, Jones BD, Radmacher MD, BonDurant SS, Slonczewski JL. (2006) Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12. BMC Microbiol., 6, 89. PMCID: PMC1626474.

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Alison K. Spencer

Spencer AK, Schaumberg AJ, Zallen JA. (2017) Scaling of cytoskeletal organization with cell size in Drosophila. Mol Biol Cell. pii: mbc.E16-10-0691. [Epub ahead of print]

Akkari L, Gocheva V, Quick ML, Kester JC, Spencer AK, Garfall AL, Bowman RL, Joyce JA. (2016) Combined deletion of cathepsin protease family members reveals compensatory mechanisms in cancer. Genes Dev.,  30, 220-32. PMCID: PMC4719311.

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Dimiter Tassev

Zhao Q, Ahmed M, Tassev DV, Hasan A, Kuo TY, Guo HF, O’Reilly RJ, Cheung NK. (2015) Affinity maturation of T-cell receptor-like antibodies for Wilms tumor 1 peptide greatly enhances therapeutic potential.  Leukemia.

Cheung N, Guo H, Hu J, Tassev D, Cheung I. (2012) Humanizing murine IgG3 anti-GD2 antibody m3F8 substantially improves antibody-dependent cell-mediated cytotoxicity while retaining targeting in vivo. Oncoimmunology, 1, 477-486.

Tassev D, Cheng M, Cheung N. (2011) Retargeting NK92 cells using an HLA-A2-restricted, EBNA3C-specific chimeric antigen receptor. Cancer Gene Ther, 19, 84-100. 

Tassev D, Cheung N. (2009) Monoclonal Antibody Therapies for Solid Tumors. Expert Opin Biol Ther, 9, 341-353.

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Ly Vu

Taggart J, Ho TC, Amin E, Xu H, Barlowe TS, Perez AR, Durham BH, Tivnan P, Okabe R, Chow A, Vu L, Park SM, Prieto C, Famulare C, Patel M, Lengner CJ, Verma A, Roboz G, Guzman M, Klimek VM, Abdel-Wahab O, Leslie C, Nimer SD, Kharas MG. (2016) MSI2 is required for maintaining activated myelodysplastic syndrome stem cells. Nat Commun., 7, 10739. PMCID: PMC4764878.

Perna F, Vu LP, Themeli M, Kriks S, Hoya-Arias R, Khanin R, Hricik T, Mansilla-Soto J, Papapetrou EP, Levine RL, Studer L, Sadelain M, Nimer SD. (2015) The polycomb group protein L3MBTL1 represses a SMAD5-mediated hematopoietic transcriptional program in human pluripotent stem cells. Stem Cell Reports, 4, 658-69. PMCID: PMC4400644.

Park SM, Gönen M, Vu L, Minuesa G, Tivnan P, Barlowe TS, Taggart J, Lu Y, Deering RP, Hacohen N, Figueroa ME, Paietta E, Fernandez HF, Tallman MS, Melnick A, Levine R, Leslie C, Lengner CJ, Kharas MG. (2015) Musashi2 sustains the mixed-lineage leukemia-driven stem cell regulatory program. J Clin Invest. 125, 1286-98. PMCID: PMC4362230

Vu L, Luciani L, Nimer S. (2013) Histone-modifying enzymes: their role in the pathogenesis of acute leukemia and their therapeutic potential. Int J Hematol, 97, 198-209. 

Vu L, Perna F, Wang L, Voza F, Figueroa M, Tempst P, Erdjument-Bromage H, Gao R, Chen S, Paietta E, Deblasio T, Melnick A, Liu Y, Zhao X, Nimer S. (2013) PRMT4 blocks myeloid differentiation by assembling a methyl-RUNX1-dependent repressor complex. Cell Rep, 5, 1625-1638. 

Moulick K, Ahn J, Zong H, Rodina A, Cerchietti L, Gomes Dagama E, Caldas-Lopes E, Beebe K, Perna F, Hatzi K, Vu L, Zhao X, Zatorska D, Taldone T, Smith-Jones P, Alpaugh M, Gross S, Pillarsetty N, Ku T, Lewis J, Larson S, Levine R, Erdjument-Bromage H, Guzman M, Nimer S, Melnick A, Neckers L, Chiosis G. (2011) Affinity-based proteomics reveal cancer-specific networks coordinated by Hsp90. Nat Chem Biol, 7, 818-826. 

Wang L, Gural A, Sun X, Zhao X, Perna X, Huang G, Hatlen M, Vu L, Liu F, Xu H, Asai T, Xu H, Deblasio T, Menendez S, Voza F, Jiang Y, Cole P, Zhang J, Melnick A, Roeder R, Nimer S. (2011). The leukemogenicity of AML1-ETO is dependent on site-specific lysine acetylation. Science, 333, 765-769.

Wang L, Huang G, Zhao X, Hatlen M, Vu L, Liu F, Nimer S. (2009) Post-translational modifications of Runx1 regulate its activity in the cell. Blood Cells Mol Dis, 43, 30-34.

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William Walkowicz

Fernández-Tejada A, Walkowicz WE, Tan DS, Gin DY. (2017) Semisynthesis of Analogues of the Saponin Immunoadjuvant QS-21. Methods Mol Biol. 1494, 45-71. PMCID: PMC5120590

Walkowicz WE, Fernández-Tejada A, George C, Corzana F, Jiménez-Barbero J, Ragupathi G, Tan DS, Gin DY. (2016) Quillaja Saponin Variants with Central Glycosidic Linkage Modifications Exhibit Distinct Conformations and Adjuvant Activities. Chem Sci, 7, 2371-2380. PMCID: PMC4800320.

Gauthier N, Soufi B, Walkowicz W, Pedicord V, Mavrakis K, Macek B, Gin D, Sander C, Miller M. (2013) Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nat Methods, 10, 768-773. 

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Elizabeth Wasmuth

Bose R, Karthaus WR, Armenia J, Abida W, Iaquinta PJ, Zhang Z, Wongvipat J, Wasmuth EV, Shah N, Sullivan PS, Doran MG, Wang P, Patruno A, Zhao Y, International SU2C/PCF Prostate Cancer Dream Team, Zheng D, Schultz N, Sawyers CL. (2017) ERF mutations reveal a balance of ETS factors controlling prostate oncogenesis. Nature 546, 671-675. PMCID: PMC5576182 [Available on 2018-06-29]

Wasmuth EV, Zinder JC, Zattas D, Das M, Lima CD. (2017) Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase. Elife 6, pii: e29062. PMCID: PMC5553935

Wasmuth EV, Lima CD. (2017) The Rrp6 C-terminal domain binds RNA and activates the nuclear RNA exosome. Nucleic Acids Res. 45, 846-860. PMCID: PMC5314766

Zinder JC, Wasmuth EV, Lima CD. (2016) Nuclear RNA Exosome at 3.1 Å Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3. Mol Cell. 64, 734-745. PMCID: PMC5115963

Wasmuth E, Januszyk K, Lima C. (2014) Structure of an Rrp6-RNA exosome complex bound to polyA RNA. Nature,511, 435-9. PMCID: PMC4310248.

Wasmuth E, Lima C. (2012) Exo- and endoribonucleolytic activities of yeast cytoplasmic and nuclear RNA exosomes are dependent on the noncatalytic core and central channel. Mol Cell, 48, 133-144. PMCID: PMC3472098.

Wasmuth E, Lima C. (2012) Structure and activities of the eukaryotic RNA exosome. Chapter in the book “The Enzymes” 31, 53-75. ISBN: 18746047. Publisher: Elsevier, Editors: Guillaume F. Chanfreau, Fuyuhiko Tamanoi.

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Shannon Yu

Yu S, Baylies M. (2013) Cell biology: Death brings new life to muscle. Nature, 497, 196-197.

Rochlin K, Yu S, Roy S, Baylies M. (2010) Myoblast fusion: when it takes more to make one. Dev Biol, 341, 66-83. 

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Lei Wei

Wei L, Zhao X. (2016). A new MCM modification cycle regulates DNA replication initiation. Nature Structural & Molecular Biology, 23, 209–216.

Bonner JN1 Choi K, Xue X, Torres NP, Szakal B, Wei L, Wan B, Arter M, Matos J, Sung P, Brown GW, Branzei D, Zhao X. (2016) Smc5/6 Mediated Sumoylation of the Sgs1-Top3-Rmi1 Complex Promotes Removal of Recombination Intermediates. Cell Rep., 16, 368-78. PMCID: PMC5051638

Hang LE, Lopez CR, Liu X, Williams JM, Chung I, Wei L, Bertuch AA, Zhao X. (2014). Regulation of Ku-DNA association by Yku70 C-terminal tail and SUMO modification. The Journal of Biological Chemistry, 289, 10308-10317.

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Yilong Zou

Malladi S, Macalinao DG, Jin X, He L, Basnet H, Zou Y, de Stanchina E, Massagué J. (2016) Metastatic Latency and Immune Evasion through Autocrine Inhibition of WNT. Cell, 165, 45-60. PMCID: PMC4808520.

David CJ, Huang YH, Chen M, Su J, Zou Y, Bardeesy N, Iacobuzio-Donahue CA, Massagué J.  (2016) TGF-β Tumor Suppression through a Lethal EMT.  Cell, 164, 1015-30. PMCID: PMC4801341

Obenauf AC, Zou Y, Ji AL, Vanharanta S, Shu W, Shi H, Kong X, Bosenberg MC, Wiesner T, Rosen N, Lo RS, Massagué J. (2015) Therapy-induced tumour secretomes promote resistance and tumour progression. Nature, 520, 368-72. PMCID: PMC4507807

Vanharanta S, Marney C, Shu W, Valiente M, Zou Y, Mele A, Darnell R, and Massagué J. (2014) Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer.  Elife, 3, 1-24.

Morris L, Kaufman A, Gong Y, Ramaswami D, Walsh L, Turcan Ş, Eng S, Kannan K, Zou Y, Peng L, Banuchi V, Paty P, Zeng Z, Vakiani E, Solit D, Singh B, Ganly I, Liau L, Cloughesy T, Mischel P, Mellinghoff I, Chan T. (2013) Recurrent somatic mutation of FAT1 in multiple human cancers leads to aberrant Wnt activation. Nat Genet, 45, 253-261. PMCID:PMC3729040.

Zhang X, Jin X, Malladi S, Zou Y, Wen Y, Brogi E, Smid M, Foekens J, and Massagué J. (2013) Selection of bone metastasis seeds by mesenchymal signals in the primary tumor stroma.  Cell, 154, 1060-1073. PMCID: PMC3974915.

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