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Alumni Publications

Our Alumni Publications

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Jennifer E. (Nnoli) Adeleye

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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Nicholas M. Adams

Weizman OE, Song E, Adams NM, Hildreth AD, Riggan L, Krishna C, Aguilar OA, Leslie CS, Carlyle JR, Sun JC, O’Sullivan TE; (2019) Mouse cytomegalovirus-experienced ILC1s acquire a memory response dependent on the viral glycoprotein m12. Nat Immunol. 20, 1004-1011. PMCID:PMC6697419.

Adams NM, Geary CD, Santosa EK, Lumaquin D, Le Luduec JB, Sottile R, van der Ploeg K, Hsu J, Whitlock BM, Jackson BT, Weizman OE, Huse M, Hsu KC, Sun JC. (2019) Cytomegalovirus Infection Drives Avidity Selection of Natural Killer Cells. Immunity. pii: S1074-7613(19)30189-X. [Epub ahead of print].

Dong H, Adams NM, Xu Y, Cao J, Allan DSJ, Carlyle JR, Chen X, Sun JC, Glimcher LH; (2019) The IRE1 endoplasmic reticulum stress sensor activates natural killer cell immunity in part by regulating c-Myc. Nat Immunol. PMCID: PMC6588410 [Available on 2019-11-13].

Adams NM, Sun JC; (2018) Spatial and temporal coordination of antiviral responses by group 1 ILCs. Immunol Rev. 286, 23-36. PMCID: PMC6178831 [Available on 2019-11-01].

Seelige R, Saddawi-Konefka R, Adams NM, Picarda G, Sun JC, Benedict CA, Bui JD; (2018) Interleukin-17D and Nrf2 mediate initial innate immune cell recruitment and restrict MCMV infection. Sci Rep. 8, 13670. PMCID: PMC6135835.

Geary CD, Krishna C, Lau CM, Adams NM, Gearty SV, Pritykin Y, Thomsen AR, Leslie CS, Sun JC; (2018) Non-redundant ISGF3 Components Promote NK Cell Survival in an Auto-regulatory Manner during Viral Infection. Cell Rep. 24, 1949-1957. PMCID:PMC6153266.

Lau CM, Adams NM, Geary CD, Weizman OE, Rapp M, Pritykin Y, Leslie CS, Sun JC; (2018) Epigenetic control of innate and adaptive immune memory. Nat Immunol. 19, 963-972. PMCID: PMC6225771.

Adams NM, Lau CM, Fan X, Rapp M, Geary CD, Weizman OE, Diaz-Salazar C, Sun JC. (2018) Transcription Factor IRF8 Orchestrates the Adaptive Natural Killer Cell Response. Immunity pii: S1074-7613(18)30187-0. [Epub ahead of print]

Rapp M, Lau CM, Adams NM, Weizman OE, O’Sullivan TE, Geary CD, Sun JC; Core-binding factor ß and Runx transcription factors promote adaptive natural killer cell responses.; Science immunology; 2017; 2(18);

Weizman OE, Adams NM, Schuster IS, Krishna C, Pritykin Y, Lau C, Degli-Esposti MA, Leslie CS, Sun JC, O’Sullivan TE; ILC1 Confer Early Host Protection at Initial Sites of Viral Infection.; Cell; 2017; 171(4):795-808.e12;

O’Sullivan TE, Rapp M, Fan X, Weizman OE, Bhardwaj P, Adams NM, Walzer T, Dannenberg AJ, Sun JC. (2016) Adipose-resident group 1 innate lymphoid cells promote obesity-associated insulin resistance. Immunity, 45, 428-41. PMCID: PMC5004886.

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 [Available on 2017-10-15]

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Steven K. Albanese

Minuesa G, Albanese SK, Xie W, Kazansky Y, Worroll D, Chow A, Schurer A, Park SM, Rotsides CZ, Taggart J, Rizzi A, Naden LN, Chou T, Gourkanti S, Cappel D, Passarelli MC, Fairchild L, Adura C, Glickman JF, Schulman J, Famulare C, Patel M, Eibl JK, Ross GM, Bhattacharya S, Tan DS, Leslie CS, Beuming T, Patel DJ, Goldgur Y, Chodera JD, Kharas MG; (2019) Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia. Nat Commun. 10, 2691. PMCID:PMC6584500.

Hauser K, Negron C, Albanese SK, Ray S, Steinbrecher T, Abel R, Chodera JD, Wang L. (2018) Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations. Commun Biol 1, pii: 70. PMCID: PMC6110136

Albanese SK, Parton DL, Işık M, Rodríguez-Laureano L, Hanson SM, Behr JM, Gradia S, Jeans C, Levinson NM, Seeliger MA, Chodera JD; (2018) An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression. Biochemistry 57, 4675-4689. PMCID: PMC6081246 [Available on 2019-08-07].

Intlekofer AM, Shih AH, Wang B, Nazir A, Rustenburg AS, Albanese SK, Patel M, Famulare C, Correa FM, Takemoto N, Durani V, Liu H, Taylor J, Farnoud N, Papaemmanuil E, Cross JR, Tallman MS, Arcila ME, Roshal M, Petsko GA, Wu B, Choe S, Konteatis ZD, Biller SA, Chodera JD, Thompson CB, Levine RL, Stein EM. (2018) Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations. Nature 559, 125-129.

Ruff EF, Muretta JM, Thompson AR, Lake EW, Cyphers S, Albanese SK, Hanson SM, Behr JM, Thomas DD, Chodera JD, Levinson NM. (2018) A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation. Elife 7, e32766.

Xu J, Pham CG, Albanese SK, Dong Y, Oyama T, Lee CH, Rodrik-Outmezguine V, Yao Z, Han S, Chen D, Parton DL, Chodera JD, Rosen N, Cheng EH, Hsieh JJ. (2016) Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin. J Clin Invest, pii: 86120.

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Eric S. 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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Scott J. Callahan

Callahan SJ, Tepan S, Zhang YM, Lindsay H, Burger A, Campbell NR, Kim IS, Hollmann TJ, Studer L, Mosimann C, White RM. (2018) Cancer modeling by Transgene Electroporation in Adult Zebrafish (TEAZ). Dis Model Mech. pii: dmm.034561 PMID: 30061297 [Epub ahead of print]

Zhang YM, Zimmer MA, Guardia T, Callahan SJ, Mondal C, Di Martino J, Takagi T, Fennell M, Garippa R, Campbell NR, Bravo-Cordero JJ, White RM. (2018) Distant Insulin Signaling Regulates Vertebrate Pigmentation through the Sheddase Bace2. Dev Cell. pii: S1534-5807(18)30357-5 [Epub ahead of print]

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

Callahan SJ, Morgan RD, Jain R, Townson SA, Wilson GG, Roberts RJ, Aggarwal AK. (2011) Crystallization and preliminary crystallographic analysis of the type IIL restriction enzyme MmeI in complex with DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun., 67, 1262-5. PMCID: PMC3212378.

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Emily C. 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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Ivan J. Cohen

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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

Feng W, Jasin M. (2018) Homologous Recombination and Replication Fork Protection: BRCA2 and More! Cold Spring Harb Symp Quant Biol. pii: 035006.

Feng W, Jasin M. (2017) BRCA2 suppresses replication stress-induced mitotic and G1 abnormalities through homologous recombination. Nat Commun. 8, 525. PMCID: PMC5597640

Vanoli F, Tomishima M, Feng W, Lamribet K, Babin L, Brunet E, Jasin M. (2017) CRISPR-Cas9-guided oncogenic chromosomal translocations with conditional fusion protein expression in human mesenchymal cells. Proc Natl Acad Sci U S A. 114, 3696-3701. PMCID: PMC5389291 [Available on 2017-10-04]

Prakash R, Zhang Y, Feng W, Jasin M. (2015)  Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins. Cold Spring Harb Perspect Biol.,  7, a016600. PMCID: PMC4382744.

Reviews

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., in press. https://www.annualreviews.org/doi/full/10.1146/annurev-cancerbio-030617-050502

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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. 

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 Paul 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 L. 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.

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

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. PMID: 23547098; PMCID: PMC3620352.

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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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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

Lee Y, Hamann JC, Pellegrino M, Durgan J, Domart MC, Collinson LM, Haynes CM, Florey O, Overholtzer M. (2019) Entosis Controls a Developmental Cell Clearance in C. elegans. Cell Rep. 26, 3212-3220.

Hamann JC, Kim SE, Overholtzer M. (2019) Methods for the Study of Entotic Cell Death. Methods Mol Biol. 1880, 447-454.

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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Yun-Han Huang

Su J, Morgani SM, David CJ, Wang Q, Er EE, Huang YH, Basnet H, Zou Y, Shu W, Soni RK, Hendrickson RC, Hadjantonakis AK, Massague J. (2020) TGF-β orchestrates fibrogenic and developmental EMTs via the RAS effector RREB1. Nature. 578.

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.

Cohen LJ, Kang HS, Chu J, Huang YH, Gordon EA, Reddy BV, Ternei MA, Craig JW, Brady SF. (2015) Brady Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist. Proc Natl Acad Sci U S A, 112, E4825-34. PMCID: PMC4568208.

Colucci PG, Kostandy P, Shrauner WR, Arleo E, Fuortes M, Griffin AS, Huang YH, Juluru K, Tsiouris AJ. (2015) Tsiouris Development and utilization of a web-based application as a robust radiology teaching tool (radstax) for medical student anatomy teaching. Acad Radiol., 22, 247-55. PMCID: PMC4750394.

Vyas S, Chesarone-Cataldo M, Todorova T, Huang YH, Chang P. (2013) A systematic analysis of the PARP protein family identifies new functions critical for cell physiology. Nat Commun., 4, 2240. PMCID: PMC3756671.

Huang YH. (2013) Gene patents: a broken incentives system. J Relig Health, 52, 1079-84. PMCID: PMC3819421.

Huang YH, Hu J, Chen F, Lecomte N, Basnet H, David CJ, Witkin MD, Allen PJ, Leach SD, Hollmann TJ, Iacobuzio-Donahue CA, Massague J. (2019) ID1 mediates escape from TGF-β tumor suppression in pancreatic cancer. Cancer Discov. pii: CD-19-05294 [Epub ahead of print]

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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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Karen Hunter Cohn

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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Mehmet Erman Karasu

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Jenny M. Karo Leeds

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) A novel molecular mechanism for generating NK-cell fitness and memory. Eur J Immunol. doi: 10.1002/eji.201445339. [Epub ahead of print]

Zawislak, C., Beaulieu, A., Loeb, G., Karo, J., Canner, D., Bezman, N., Lanier, L., Rudensky, A., and Sun, J. (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, 6967-6972. PMID: 23572582; PMCID: PMC3637707.

Karo, J., Schatz, D., and Sun, J. (2014) The RAG recombinase dictates functional heterogeneity and cellular fitness in natural killer cells. Cell. 2014 Sep 25;159(1):94-107. doi: 10.1016/j.cell.2014.08.026.

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Edward Kastenhuber

Loizou E, Banito A, Livshits G, Ho YJ, Koche RP, Sanchez-Rivera FJ, Mayle A, Chen CC, Kinalis S, Bagger FO, Kastenhuber ER, Durham BH, Lowe SW. (2019) A gain-of-function p53 mutant oncogene promotes cell fate plasticity and myeloid leukemia through the pluripotency factor Foxh1. Cancer Discov. pii: CD-18-1391.

Dinh TA, Jewell ML, Kanke M, Francisco A, Sritharan R, Turnham RE, Lee S, Kastenhuber ER, Wauthier E, Guy CD, Yeung RS, Lowe SW, Reid LM, Scott JD, Diehl AM, Sethupathy P. (2019) MicroRNA-375 Suppresses the Growth and Invasion of Fibrolamellar Carcinoma. Cell Mol Gastroenterol Hepatol. 7, 803-817. PMC6468197.

Moon SH, Huang CH, Houlihan SL, Regunath K, Freed-Pastor WA, Morris JP, Tschaharganeh DF, Kastenhuber ER, Barsotti AM, Culp-Hill R, Xue W, Ho YJ, Baslan T, Li X, Mayle A, de Stanchina E, Zender L, Tong DR, D’Alessandro A, Lowe SW, Prives C. (2019) p53 Represses the Mevalonate Pathway to Mediate Tumor Suppression. Cell. 176, 564-580. PMCID: PMC6483089.

Zafra MP, Schatoff EM, Katti A, Foronda M, Breinig M, Schweitzer AY, Simon A, Han T, Goswami S, Montgomery E, Thibado J, Kastenhuber ER, Sánchez-Rivera FJ, Shi J, Vakoc CR, Lowe SW, Tschaharganeh DF, Dow LE. (2018) Optimized base editors enable efficient editing in cells, organoids and mice. Nat Biotechnol. doi: 10.1038/nbt.4194. [Epub ahead of print].

Kastenhuber ER, Lalazar G, Houlihan SL, Tschaharganeh DF, Baslan T, Chen CC, Requena D, Tian S, Bosbach B, Wilkinson JE, Simon SM, Lowe SW. (2017) DNAJB1-PRKACA fusion kinase interacts with β-catenin and the liver regenerative response to drive fibrolamellar hepatocellular carcinoma. Proc Natl Acad Sci U S A 114, 13076-13084. PMCID: PMC5740683.

Kastenhuber ER, Lowe SW. (2017) Putting p53 in Context. Cell 170, 1062-1078.

Shirole NH, Pal D, Kastenhuber ER, Senturk S, Boroda J, Pisterzi P, Miller M, Munoz G, Anderluh M, Ladanyi M, Lowe SW, Sordella R. (2017) TP53 exon-6 truncating mutations produce separation of function isoforms with pro-tumorigenic functions. Elife 6. PMCID: PMC5287711

Liu Y, Chen C, Xu Z, Scuoppo C, Rillahan CD, Gao J, Spitzer B, Bosbach B, Kastenhuber ER, Baslan T, Ackermann S, Cheng L, Wang Q, Niu T, Schultz N, Levine RL, Mills AA, Lowe SW. (2016)  Deletions linked to TP53 loss drive cancer through p53-independent mechanisms. Nature,  531, 471-5.

Ebbesen SH, Scaltriti M, Bialucha CU, Morse N, Kastenhuber ER, Wen HY, Dow LE, Baselga J, Lowe SW. (2016) Pten loss promotes MAPK pathway dependency in HER2/neu breast carcinomas. Proc Natl Acad Sci U S A, pii: 201523693. PMCID: PMC4801318.

Dow LE, Fisher J, O’Rourke KP, Muley A, Kastenhuber ER, Livshits G, Tschaharganeh DF, Socci ND, Lowe SW. (2015)  Inducible in vivo genome editing with CRISPR-Cas9. Nat Biotechnol., 33, 390-4. PMCID: PMC4390466.

Lito, P., Saborowski, A., Yue, J., Solomon, M., Josephm E., Gadal, S., Saborowski, M., Kastenhuber, E., Fellmann, C., Ohara, K., Morikami, K., Miura, T., Lukacs, C., Ishii, N., Lowe, S., and Rosen, N. (2014)  Disruption of CRAF-Mediated MEK Activation Is Required for Effective MEK Inhibition in KRAS Mutant Tumors, Cancer Cell, 25, 697-710. PMID: 24746704; PMCID: PMC4049532.

Tschaharganeh DF, Xue W, Calvisi DF, Evert M, Michurina TV, Dow LE, Banito A, Katz SF, Kastenhuber ER, Weissmueller S, Huang CH, Lechel A, Andersen JB, Capper D, Zender L, Longerich T, Enikolopov G, Lowe SW. (2014)  p53-dependent Nestin regulation links tumor suppression to cellular plasticity in liver cancer. Cell,  158, 579-92. PMCID: PMC4221237.

Kastenhuber ER, Huse JT, Berman SH, Pedraza A, Zhang J, Suehara Y, Viale A, Cavatore M, Heguy A, Szerlip N, Ladanyi M, Brennan CW. (2014) Quantitative assessment of intragenic receptor tyrosine kinase deletions in primary glioblastomas: their prevalence and molecular correlates. Acta Neuropathol., 127, 747-59. PMCID: PMC3984672.

Kannan K, Inagaki A, Silber J, Gorovets D, Zhang J, Kastenhuber ER, Heguy A, Petrini JH, Chan TA, Huse JT. (2012) Whole-exome sequencing identifies ATRX mutation as a key molecular determinant in lower-grade glioma. Oncotarget, 3, 1194-203. PMCID: PMC3717947.

 Gorovets D, Kannan K, Shen R, Kastenhuber ER, Islamdoust N, Campos C, Pentsova E, Heguy A, Jhanwar SC, Mellinghoff IK, Chan TA, Huse JT. (2012) IDH mutation and neuroglial developmental features define clinically distinct subclasses of lower grade diffuse astrocytic glioma. Clin Cancer Res., 18, 2490-501.

Morris LG, Taylor BS, Bivona TG, Gong Y, Eng S, Brennan CW, Kaufman A, Kastenhuber ER, Banuchi VE, Singh B, Heguy A, Viale A, Mellinghoff IK, Huse J, Ganly I, Chan TA. (2011)  Genomic dissection of the epidermal growth factor receptor (EGFR)/PI3K pathway reveals frequent deletion of the EGFR phosphatase PTPRS in head and neck cancers. Proc Natl Acad Sci U S A, 108, 19024-9. PMCID: PMC3223475.

Huse JT, Nafa K, Shukla N, Kastenhuber ER, Lavi E, Hedvat CV, Ladanyi M, Rosenblum MK. (2011) High frequency of IDH-1 mutation links glioneuronal tumors with neuropil-like islands to diffuse astrocytomas. Acta Neuropathol., 122, 367-9. PMCID: PMC3170121.

Palaskas N, Larson SM, Schultz N, Komisopoulou E, Wong J, Rohle D, Campos C, Yannuzzi N, Osborne JR, Linkov I, Kastenhuber ER, Taschereau R, Plaisier SB, Tran C, Heguy A, Wu H, Sander C, Phelps ME, Brennan C, Port E, Huse JT, Graeber TG, Mellinghoff IK. (2011) 18F-fluorodeoxy-glucose positron emission tomography marks MYC-overexpressing human basal-like breast cancers. Cancer Res., 71, 5164-74. PMCID: PMC3148325.

Zhu X, Fallert-Junecko BA, Fujita M, Ueda R, Kohanbash G, Kastenhuber ER, McDonald HA, Liu Y, Kalinski P, Reinhart TA, Salazar AM, Okada H. (2010) Poly-ICLC promotes the infiltration of effector T cells into intracranial gliomas via induction of CXCL10 in IFN-alpha and IFN-gamma dependent manners. Cancer Immunol Immunother, 59, 1401-9. PMCID: PMC2893267.

Fujita M, Scheurer ME, Decker SA, McDonald HA, Kohanbash G, Kastenhuber ER, Kato H, Bondy ML, Ohlfest JR, Okada H. (2010) Role of type 1 IFNs in antiglioma immunosurveillance—using mouse studies to guide examination of novel prognostic markers in humans. Clin Cancer Res., 16, 3409-19. PMCID: PMC2896455.

Ueda R, Fujita M, Zhu X, Sasaki K, Kastenhuber ER, Kohanbash G, McDonald HA, Harper J, Lonning S, Okada H. (2009) Systemic inhibition of transforming growth factor-beta in glioma-bearing mice improves the therapeutic efficacy of glioma-associated antigen peptide vaccines. Clin Cancer Res., 15, 6551-9. PMCID: PMC2783346.

Ueda R, Kohanbash G, Sasaki K, Fujita M, Zhu X, Kastenhuber ER, McDonald HA, Potter DM, Hamilton RL, Lotze MT, Khan SA, Sobol RW, Okada H. (2009) Dicer-regulated microRNAs 222 and 339 promote resistance of cancer cells to cytotoxic T-lymphocytes by down-regulation of ICAM-1. Proc Natl Acad Sci U S A, 106, 10746-51. PMCID: PMC2705554.

Okada H, Kohanbash G, Zhu X, Kastenhuber ER, Hoji A, Ueda R, Fujita M. (2009) Immunotherapeutic approaches for glioma. Crit Rev Immunol., 29, 1-42. PMCID: PMC2713019.

Fujita M, Zhu X, Ueda R, Sasaki K, Kohanbash G, Kastenhuber ER, McDonald HA, Gibson GA, Watkins SC, Muthuswamy R, Kalinski P, Okada H. (2009) Effective immunotherapy against murine gliomas using type 1 polarizing dendritic cells—significant roles of CXCL10. Cancer Res., 69, 1587-95.

 

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James W. Keith, Jr.

Keith J, Dong Q, Sorbara MT, Becattini S, Sia JK, Gjonbalaj M, Seok R, Leiner I, Littmann E, Pamer EG. (2020) Impact of antibiotic-resistant bacteria in the mouse intestine on immune activation and Clostridioides difficile infection. Infect Immun, pii: IAI.00362-19. [Epub ahead of print]

Gjonbalaj M, Keith JW, Do MH, Hohl TM, Pamer EG, Becattini S. Antibiotic degradation by commensal microbes shields pathogens.(2020) Infect Immun., pii: IAI.00012-20 [Epub ahead of print]

Keith JW, Pamer EG. (2018) Enlisting commensal microbes to resist antibiotic-resistant pathogens. J Exp Med, pii: jem.20180399. [Epub ahead of print]

Bakst RL, Xiong H, Chen CH, Deborde S, Lyubchik A, Zhou Y, He S, McNamara W, Lee SY, Olson OC, Leiner IM, Marcadis AR, Keith JW, Al-Ahmadie HA, Katabi N, Gil Z, Vakiani E, Joyce JA, Pamer E, Wong RJ. (2017) Inflammatory Monocytes Promote Perineural Invasion via CCL2-Mediated Recruitment and Cathepsin B Expression. Cancer Res. 77, 6400-6414. PMCID: PMC5831809 [Available on 2018-11-15]

Xiong H, Keith JW, Samilo DW, Carter RA, Leiner IM, Pamer EG. (2016) Innate Lymphocyte/Ly6Chi Monocyte Crosstalk Promotes Klebsiella Pneumoniae Clearance. Cell, pii: S0092-8674, 30273-2.

Abt MC, Buffie CG, Sušac B, Becattini S, Carter RA, Leiner I, Keith JW, Artis D, Osborne LC, Pamer EG. (2016) TLR-7 activation enhances IL-22-mediated colonization resistance against vancomycin-resistant enterococcus. Sci Transl Med., 8, 327ra25.

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Mary E. Klein Dooley

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. pii: S1535-6108(18)30128-4 [Epub ahead of print]

Klein ME, Dickson MA, Antonescu C, Qin LX, Dooley SJ, Barlas A, Manova K, Schwartz GK, Crago AM, Singer S, Koff A, Tap WD. (2018) PDLIM7 and CDH18 regulate the turnover of MDM2 during CDK4/6 inhibitor therapy-induced senescence. Oncogene. [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, 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]

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.

Tula-Sanchez AA, Havas AP, Alonge PJ, Klein ME, Doctor SR, Pinkston W, Glinsmann-Gibson BJ, Rimsza LM, Smith CL. (2013) A model of sensitivity and resistance to histone deacetylase inhibitors in diffuse large B cell lymphoma: Role of cyclin-dependent kinase inhibitors.  Cancer Biol Ther., 14, 949-61. PMCID: PMC3926892.

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Catherine Konopacki

Konopacki C, Pritykin Y, Rubtsov Y, Leslie CS, Rudensky AY. (2019) Transcription factor Foxp1 regulates Foxp3 chromatin binding and coordinates regulatory T cell function. Nat Immunol. 20, 232-242.

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.

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

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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Nicholas F. Kuhn

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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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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. PMID: 21558173; 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. PMID: 21840861; 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. PMID: 22194698; PMCID: PMC3240595.

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Qing Li

Li QV, Rosen BP, Huangfu D. (2019) Decoding pluripotency: Genetic screens to interrogate the acquisition, maintenance, and exit of pluripotency. Wiley Interdiscip Rev Syst Biol Med. e1464.

Lee K, Cho H, Rickert RW, Li QV, Pulecio J, Leslie CS, Huangfu D. (2019) FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation. Cell Rep. 28, 382-393. PMCID: PMC6636862.

Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh CL, Yang D, Crespo M, Shukla A, Xiang Q, Dündar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massagué J, Garippa R, Evans T, Beer MA, Huangfu D. (2019) Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation. Nat Genet. 51, 999-1010.

Verma N, Pan H, Doré LC, Shukla A, Li QV, Pelham-Webb B, Teijeiro V, González F, Krivtsov A, Chang CJ, Papapetrou EP, He C, Elemento O, Huangfu D. (2018) TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells. Nat Genet, 50, 83-95. PMCID: PMC5742051 [Available on 2018-06-04]

Shi ZD, Lee K, Yang D, Amin S, Verma N, Li QV, Zhu Z, Soh CL, Kumar R, Evans T, Chen S, Huangfu D. (2017) Genome Editing in hPSCs Reveals GATA6 Haploinsufficiency and a Genetic Interaction with GATA4 in Human Pancreatic Development. Cell Stem Cell [Epub ahead of print]

Wang Q, Zou Y, Nowotschin S, Kim SY, Li QV, Soh CL, Su J, Zhang C, Shu W, Xi Q, Huangfu D, Hadjantonakis AK, Massagué J. (2017) The p53 Family Coordinates Wnt and Nodal Inputs in Mesendodermal Differentiation of Embryonic Stem Cells. Cell Stem Cell 20, 70-86. PMCID: PMC5218926 [Available on 2018-01-05]

Zhu Z, Li QV, Lee K, Rosen BP, González F, Soh CL, Huangfu D. (2016) Genome Editing of Lineage Determinants in Human Pluripotent Stem Cells Reveals Mechanisms of Pancreatic Development and Diabetes. Cell Stem Cell 18, 755-68. PMCID: PMC4892994 [Available on 2017-06-02]

Mercado-Pimentel ME, Onyeagucha BC, Li Q, Pimentel AC, Jandova J, Nelson MA. (2015) The S100P/RAGE signaling pathway regulates expression of microRNA-21 in colon cancer cells. FEBS Lett., 589, 2388-93. PMCID: PMC4582666.

González, F., Zhu, Z., Shi, Z., Lelli, K., Verma, N., Li, Q., and Huangfu, D. (2014)  An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells.  Cell Stem Cell, 15, 1-12. PMID: 24931489.

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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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Danilo G. Macalinao

Basnet H, Tian L, Ganesh K, Huang YH, Macalinao DG, Brogi E, Finley LW, Massagué J. (2019) Flura-seq identifies organ-specific metabolic adaptations during early metastatic colonization. Elife. 8, pii: e43627. PMCID: PMC6440742.

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 P. Mahaffey

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Daniel H. Marks

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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

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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

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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Alexandria N. Miller

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Justine D. 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

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Oakley C. 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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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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Joseph N. Pucella

Yen WF, Sharma R, Cols M, Lau CM, Chaudhry A, Chowdhury P, Yewdell WT, Vaidyanathan B, Sun A, Coffre M, Pucella JN, Chen CC, Jasin M, Sun JC, Rudensky AY, Koralov SB, Chaudhuri J. (2019) Distinct Requirements of CHD4 during B Cell Development and Antibody Response. Cell Rep. 27, 1472-1486.

Pucella JN, Cols M, Yen WF, Xu S, Chaudhuri J. (2019) The B Cell Activation-Induced miR-183 Cluster Plays a Minimal Role in Canonical Primary Humoral Responses. J Immunol. pii: ji1800071.

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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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

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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

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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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Brian H. Santich

Wu Z, Santich BH, Liu H, Liu C, Cheung NV. (2018) Targeting Intracellular Antigens with pMHC-Binding Antibodies: A Phage Display Approach. Methods Mol Biol. 1701, 255-269.

Ahmed M, Lopez-Albaitero A, Pankov D, Santich BH, Liu H, Yan S, Xiang J, Wang P, Hasan AN, Selvakumar A, O’Reilly RJ, Liu C, Cheung NV. (2018) TCR-mimic bispecific antibodies targeting LMP2A show potent activity against EBV malignancies. JCI Insight. 3, pii: 97805. PMCID: PMC5916246 [Epub ahead of print]

Cheng M, Santich BH, Xu H, Ahmed M, Huse M, Cheung NK. (2016) Successful engineering of a highly potent single-chain variable-fragment (scFv) bispecific antibody to target disialoganglioside (GD2) positive tumors. Oncoimmunology 5, 1168557. PMCID: PMC4938304.

Santich BH, Liu H, Liu C, Cheung NK. Generation of TCR-like antibodies using phage display. Methods Mol Biol. 2015;1348:191-204.

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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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Alison K. Spencer

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Dimiter V. Tassev

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Kelsey R. Temprine

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George Vaisey

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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

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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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Lei Wei

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Hannah Wise

Gao J, Chang MT, Johnsen HC, Gao SP, Sylvester BE, Sumer SO, Zhang H, Solit DB, Taylor BS, Schultz N, Sander C. (2017) 3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets. Genome Med. 9, 4. PMCID: PMC5260099

Jordan EJ, Kim HR, Arcila ME, Barron DA, Chakravarty D, Gao J, Chang MT, Ni A, Kundra R, Jonsson P, Jayakumaran G, Gao SP, Johnsen HC, Hanrahan AJ, Zehir A, Rekhtman N, Ginsberg MS, Li BT, Yu H, Paik PK, Drilon A, Hellmann MD, Reales DN, Benayed R, Rusch VW, Kris MG, Chaft JE, Baselga J, Taylor BS, Schultz N, Rudin CM, Hyman DM, Berger MF, Solit DB, Ladanyi M, Riely GJ. (2017) Prospective Comprehensive Molecular Characterization of Lung Adenocarcinomas for Efficient Patient Matching to Approved and Emerging Therapie Cancer Discov. CD-16-1337[Epub ahead of print].

Park H, Heldman N, Rebentrost P, Abbondanza L, Iagatti A, Alessi A, Patrizi B, Salvalaggio M, Bussotti L, Mohseni M, Caruso F, Johnsen HC, Fusco R, Foggi P, Scudo PF, Lloyd S, Belcher AM. (2016) Enhanced energy transport in genetically engineered excitonic networks. Nat Mater., 15, 211-6.

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Brittany A. Woods

Woods B, Chen W, Chiu S, Marinaccio C, Fu C, Gu L, Bulic M, Yang Q, Zouak A, Jia S, Suraneni PK, Xu K, Levine RL, Crispino JD, Wen QJ. (2019) Activation of JAK/STAT signaling in megakaryocytes sustains myeloproliferation in vivo. Clin Cancer Res. pii: clincanres.4089.2018. [Epub ahead of print].

Wang W, Liu W, Fidler T, Wang Y, Tang Y, Woods B, Welch C, Cai B, Silvestre-Roig C, Ai D, Yang YG, Hidalgo A, Soehnlein O, Tabas I, Levine RL, Tall AR, Wang N. (2018) Macrophage Inflammation, Erythrophagocytosis, and Accelerated Atherosclerosis in Jak2 V617F Mice. Circ Res. 123, e35-e47.

Woods BA, Levine RL. (2015) The role of mutations in epigenetic regulators in myeloid malignancies. Immunol Rev., 263, 22-35.

Shih AH, Jiang Y, Meydan C, Shank K, Pandey S, Barreyro L, Antony-Debre I, Viale A, Socci N, Sun Y, Robertson A, Cavatore M, de Stanchina E, Hricik T, Rapaport F, Woods B, Wei C, Hatlen M, Baljevic M, Nimer SD, Tallman M, Paietta E, Cimmino L, Aifantis I, Steidl U, Mason C, Melnick A, Levine RL. (2015) Mutational cooperativity linked to combinatorial epigenetic gain of function in acute myeloid leukemia. Cancer Cell, 27, 502-15. PMCID: PMC4518555.

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.

Beauchamp EM, Woods BA, Dulak AM, Tan L, Xu C, Gray NS, Bass AJ, Wong KK, Meyerson M, Hammerman PS. (2014) Acquired resistance to dasatinib in lung cancer cell lines conferred by DDR2 gatekeeper mutation and NF1 loss. Mol Cancer Ther., 13, 475-82. PMCID: PMC3946067.

Hammerman PS, Sos ML, Ramos AH, Xu C, Dutt A, Zhou W, Brace LE, Woods BA, Lin W, Zhang J, Deng X, Lim SM, Heynck S, Peifer M, Simard JR, Lawrence MS, Onofrio RC, Salvesen HB, Seidel D, Zander T, Heuckmann JM, Soltermann A, Moch H, Koker M, Leenders F, Gabler F, Querings S, Ansén S, Brambilla E, Brambilla C, Lorimier P, Brustugun OT, Helland A, Petersen I, Clement JH, Groen H, Timens W, Sietsma H, Stoelben E, Wolf J, Beer DG, Tsao MS, Hanna M, Hatton C, Eck MJ, Janne PA, Johnson BE, Winckler W, Greulich H, Bass AJ, Cho J, Rauh D, Gray NS, Wong KK, Haura EB, Thomas RK, Meyerson M. (2011) Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer. Cancer Discov., 1, 78-89. PMCID: PMC3274752.

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Raymond Wu

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Yuchen Xie

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Shannon Yu

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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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