Selected Publications
Baker SJ, Zong H, Monje M. Glial Malignancies. Cold Spring Harb Perspect Biol. a041373. 2025.
Zuckermann M, He C, Andrews J, Bagchi A, Sloan-Henry R, Bianski B, Xie J, Wang Y, Twarog N, Onar-Thomas A, Ernst KJ, Yang L, Li Y, Zhu X, Ocasio JK, Budd KM, Dalton J, Li X, Chepyala D, Zhang J, Xu K, Hover L, Roach JT, Chan KC, Hofmann N, McKinnon PJ, Pfister SM, Shelat AA, Rankovic Z, Freeman BB 3rd, Chiang J, Jones DTW, Tinkle CL, Baker SJ. Capmatinib is an effective treatment for MET-fusion driven pediatric high-grade glioma and synergizes with radiotherapy. Mol Cancer. 23(1):123. 2024.
Ocasio JK, Budd KM, Roach JT, Andrews JM, Baker SJ. Oncohistones and disrupted development in pediatric-type diffuse high-grade glioma. Cancer Metastasis Rev. 42(2):367-388. 2023.
Roberts, HG, Ji S, Picca A, Sanson M, Garcia M, Snuderl M, Schuller U, Picart T, Ducray F, Green AL, Nakano Y, Sturm D, Abdullaev Z, Aldape K, Dang D, Kumar-Sinha C, Wu YM, Robinson D, Vo JN, Chinnaiyan AM, Cartaxo R, Upadhyaya SA, Mody R, Chiang J, Baker S, Solomon D, Venneti S, Pratt D, Waszak SM, Koschmann C. Clinical, genomic, and epigenomic analyses of H3K27M-mutant diffuse midline glioma long-term survivors reveal a distinct group of tumors with MAPK pathways alterations. Acta Neuropathol. 146:849-852. 2023
Rameh V, Vajapeyam S, Ziaei A, Kao P, London WB, Baker SJ, Chiang J, Lucas J, Tinkle CL, Wright KD, Poussaint TY. Correlation between Multiparametric MR Imaging and Molecular Genetics in Pontine Pediatric High-Grade Glioma. AJNR Am J Neuroradiol. 44(7):833-840. 2023.
Xie J, Kuriakose T, Bianski B, Twarog N, Savage E, Xu K, Zhu X, He C, Hansen B, Wang H, High A, Li Y, Rehg JE, Tillman HS, Freeman BB, Rankovic Z, Onar-Thomas A, Fan Y, Wu G, Peng J, Miller S, Baker SJ, Shelat AA, Tinkle CL. ATM inhibition enhances the efficacy of radiation across distinct molecular subgroups of pediatric high-grade glioma. Neuro Oncol. 25(10):1828-1841. 2023.
Keck MK, Sill M, Wittmann A, Joshi P, Stichel D, Beck P, Okonechnikow K, Sievers P, Wefers AK, Roncaroli F, Avula S, McCabe MG, Hayden JT, Wesseling P, Øra I, Nistér M, Kranendonk MEG, Tops BBJ, Zapotocky M, Zamecnik J, Vasiljevic A, Fenouil T, Meyronet D, von Hoff K, Schüller U, Loiseau H, Figarella-Branger D, Kramm CM, Sturm D, Scheie D, Rauramaa T, Pesola J, Gojo J, Haberler C, Brandner S, Jacques T, Sexton Oates A, Saffery R, Koscielniak E, Baker SJ, Yip S, Snuderl M, Ud Din N, Samuel D, Schramm K, Blattner-Johnson M, Selt F, Ecker J, Milde T, von Deimling A, Korshunov A, Perry A, Pfister SM, Sahm F, Solomon DA, Jones DTW. Amplification of the PLAG-family genes-PLAGL1 and PLAGL2-is a key feature of the novel tumor type CNS embryonal tumor with PLAGL amplification. Acta Neuropathol. 145(1):49-69. 2023.
Tsai JW, Cejas P, Wang DK, Patel S, Wu DW, Arounleut P, Wei X, Zhou N, Syamala S, Dubois FPB, Crane A, Pelton K, Vogelzang J, Sousa C, Baguette A, Chen X, Condurat AL, Dixon-Clarke SE, Zhou KN, Lu SD, Gonzalez EM, Chacon MS, Digiacomo JJ, Kumbhani R, Novikov D, Hunter J, Tsoli M, Ziegler DS, Dirksen U, Jager N, Balasubramanian GP, Kramm CM, Nathrath M, Bielack S, Baker SJ, Zhang J, McFarland JM, Getz G, Aguet F, Jabado N, Witt O, Pfister SM, Ligon KL, Hovestadt V, Kleinman CL, Long H, Jones DTW, Bandopadhayay P, Phoenix TN. FOXR2 Is an Epigenetically Regulated Pan-Cancer Oncogene That Activates ETS Transcriptional Circuits. Cancer Res. 82(17):2980-3001. 2022.
Arunachalam S, Szlachta K, Brady SW, Ma X, Ju B, Shaner B, Mulder HL, Easton J, Raphael BJ, Myers M, Tinkle C, Allen SJ, Orr BA, Wetmore CJ, Baker SJ, Zhang J. Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor. Acta Neuropathol Commun. 10(1):80. 2022.
Furth N, Algranati D, Dassa B, Beresh O, Fedyuk V, Morris N, Kasper LH, Jones D, Monje M, Baker SJ, Shema E. H3-K27M-mutant nucleosomes interact with MLL1 to shape the glioma epigenetic landscape. Cell Rep. 39(7):110836. 2022.
Flasch DA, Chen X, Ju B, Li X, Dalton J, Mulder HL, Easton J, Wang L, Baker SJ, Chiang J, Zhang J. Somatic LINE-1 promoter acquisition drives oncogenic FOXR2 activation in pediatric brain tumor. Acta Neuropathol. 143(5):605-607. 2022.
Tinkle CL, Broniscer A, Chiang J, Campagne O, Huang J, Orr BA, Li X, Patay Z, Zhang J, Baker SJ, Merchant TE, Jain V, Onar-Thomas A, Stewart CF, Wetmore C, Gajjar A. Phase I study using crenolanib to target PDGFR kinase in children and young adults with newly diagnosed DIPG or recurrent high-grade glioma, including DIPG. Neurooncol Adv. 3(1):vdab179. 2021.
Sweha SR, Chung C, Natarajan SK, Panwalkar P, Pun M, Ghali A, Bayliss J, Pratt D, Shankar A, Ravikumar V, Rao A, Cieslik M, Wilder-Romans K, Scott AJ, Wahl DR, Jessa S, Kleinman CL, Jabado N, Mackay A, Jones C, Martinez D, Santi M, Judkins AR, Yadav VN, Qin T, Phoenix TN, Koschmann CJ, Baker SJ, Chinnaiyan AM, Venneti S. Epigenetically defined therapeutic targeting in H3.3G34R/V high-grade gliomas. Sci Transl Med. 13(615):eabf7860. 2021.
DeSisto J, Lucas JT Jr, Xu K, Donson A, Lin T, Sanford B, Wu G, Tran QT, Hedges D, Hsu CY, Armstrong GT, Arnold M, Bhatia S, Flannery P, Lemma R, Hardie L, Schüller U, Venkataraman S, Hoffman LM, Dorris K, Mulcahy Levy JM, Hankinson TC, Handler M, Liu AK, Foreman N, Vibhakar R, Jones K, Allen S, Zhang J, Baker SJ, Merchant TE, Orr BA, Green AL. Comprehensive molecular characterization of pediatric radiation-induced high-grade glioma. Nat Commun. 12(1):5531. 2021.
He C, Xu K, Zhu X, Dunphy PS, Gudenas B, Lin W, Twarog N, Hover LD, Kwon CH, Kasper LH, Zhang J, Li X, Dalton J, Jonchere B, Mercer KS, Currier DG, Caufield W, Wang Y, Xie J, Broniscer A, Wetmore C, Upadhyaya SA, Qaddoumi I, Klimo P, Boop F, Gajjar A, Zhang J, Orr BA, Robinson GW, Monje M, Freeman Iii BB, Roussel MF, Northcott PA, Chen T, Rankovic Z, Wu G, Chiang J, Tinkle CL, Shelat AA, Baker SJ. Patient-derived models recapitulate heterogeneity of molecular signatures and drug response in pediatric high-grade glioma. Nat Commun. 12(1):4089. 2021.
Husband HR, Campagne O, He C, Zhu X, Bianski BM, Baker SJ, Shelat AA, Tinkle CL, Stewart CF. Model-based evaluation of image-guided fractionated whole-brain radiation therapy in pediatric diffuse intrinsic pontine glioma xenografts. CPT Pharmacometrics Syst Pharmacol. 10(6):599-610. 2021.
Dahl NA, Donson AM, Sanford B, Wang D, Walker FM, Gilani A, Foreman NK, Tinkle CL, Baker SJ, Hoffman LM, Venkataraman S, Vibhakar R. NTRK Fusions Can Co-Occur With H3K27M Mutations and May Define Druggable Subclones Within Diffuse Midline Gliomas. J Neuropathol Exp Neurol. 80(4):345-353. 2021.
Zhou X, Wang J, Patel J, Valentine M, Shao Y, Newman S, Sioson E, Tian L, Liu Y, Brady SW, Flasch D, Ma X, Liu Y, Paul R, Edmonson MN, Rusch MC, Li C, Baker SJ, Easton J, Zhang J. Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint. Cancer Cell. 39(1):83-95.e4. 2021.
McLeod C, Gout AM, Zhou X, Thrasher A, Rahbarinia D, Brady SW, Macias M, Birch K, Finkelstein D, Sunny J, Mudunuri R, Orr BA, Treadway M, Davidson B, Ard TK, Chiao A, Swistak A, Wiggins S, Foy S, Wang J, Sioson E, Wang S, Michael JR, Liu Y, Ma X, Patel A, Edmonson MN, Wilkinson MR, Frantz AM, Chang TC, Tian L, Lei S, Islam SMA, Meyer C, Thangaraj N, Tater P, Kandali V, Ma S, Nguyen T, Serang O, McGuire I, Robison N, Gentry D, Tang X, Palmer LE, Wu G, Suh E, Tanner L, McMurry J, Lear M, Pappo AS, Wang Z, Wilson CL, Cheng Y, Meshinchi S, Alexandrov LB, Weiss MJ, Armstrong GT, Robison LL, Yasui Y, Nichols KE, Ellison DW, Bangur C, Mullighan CG, Baker SJ, Dyer MA, Miller G, Newman S, Rusch M, Daly R, Perry K, Downing JR, Zhang J. St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem. Cancer Discov. 11(5):1082-1099. 2021.
Haydar D, Houke H, Chiang J, Yi Z, Odé Z, Caldwell K, Zhu X, Mercer KS, Stripay JL, Shaw TI, Vogel P, DeRenzo C, Baker SJ, Roussel MF, Gottschalk S, Krenciute G. Cell-surface antigen profiling of pediatric brain tumors: B7-H3 is consistently expressed and can be targeted via local or systemic CAR T-cell delivery. Neuro Oncol. 23(6):999-1011. 2021.
Sinha A, Saleh A, Endersby R, Yuan SH, Chokshi CR, Brown KR, Kuzio B, Kauppinen T, Singh SK, Baker SJ, McKinnon PJ, Katyal S. RAD51-Mediated DNA Homologous Recombination Is Independent of PTEN Mutational Status. Cancers (Basel). 12(11):3178. 2020.
Jiao F, Li Z, He C, Xu W, Yang G, Liu T, Shen H, Cai J, Anastas JN, Mao Y, Yu Y, Lan F, Shi YG, Jones C, Xu Y, Baker SJ, Shi Y, Guo R. RACK7 recognizes H3.3G34R mutation to suppress expression of MHC class II complex components and their delivery pathway in pediatric glioblastoma. Sci Adv. 6(29):eaba2113. 2020.
Smith KS, Xu K, Mercer KS, Boop F, Klimo P, DeCupyere M, Grenet J, Robinson S, Dunphy P, Baker SJ, Ellison DW, Merchant TE, Upadayaya SA, Gajjar A, Wu G, Orr BA, Robinson GW, Northcott PA, Roussel MF. Patient-derived orthotopic xenografts of pediatric brain tumors: a St. Jude resource. Acta Neuropathol. 140(2):209-225. 2020.
Tian L, Li Y, Edmonson MN, Zhou X, Newman S, McLeod C, Thrasher A, Liu Y, Tang B, Rusch MC, Easton J, Ma J, Davis E, Trull A, Michael JR, Szlachta K, Mullighan C, Baker SJ, Downing JR, Ellison DW, Zhang J. CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data. Genome Biol. 21(1):126. 2020.
Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med. 26(5):792-802. 2020.
Chiang J, Diaz AK, Makepeace L, Li X, Han Y, Li Y, Klimo P Jr, Boop FA, Baker SJ, Gajjar A, Merchant TE, Ellison DW, Broniscer A, Patay Z, Tinkle CL. Clinical, imaging, and molecular analysis of pediatric pontine tumors lacking characteristic imaging features of DIPG. Acta Neuropathol Commun. 8(1):57. 2020.
Clarke M, Mackay A, Ismer B, Pickles JC, Tatevossian RG, Newman S, Bale TA, Stoler I, Izquierdo E, Temelso S, Carvalho DM, Molinari V, Burford A, Howell L, Virasami A, Fairchild AR, Avery A, Chalker J, Kristiansen M, Haupfear K, Dalton JD, Orisme W, Wen J, Hubank M, Kurian KM, Rowe C, Maybury M, Crosier S, Knipstein J, Schüller U, Kordes U, Kram DE, Snuderl M, Bridges L, Martin AJ, Doey LJ, Al-Sarraj S, Chandler C, Zebian B, Cairns C, Natrajan R, Boult JKR, Robinson SP, Sill M, Dunkel IJ, Gilheeney SW, Rosenblum MK, Hughes D, Proszek PZ, Macdonald TJ, Preusser M, Haberler C, Slavc I, Packer R, Ng HK, Caspi S, Popović M, Faganel Kotnik B, Wood MD, Baird L, Davare MA, Solomon DA, Olsen TK, Brandal P, Farrell M, Cryan JB, Capra M, Karremann M, Schittenhelm J, Schuhmann MU, Ebinger M, Dinjens WNM, Kerl K, Hettmer S, Pietsch T, Andreiuolo F, Driever PH, Korshunov A, Hiddingh L, Worst BC, Sturm D, Zuckermann M, Witt O, Bloom T, Mitchell C, Miele E, Colafati GS, Diomedi-Camassei F, Bailey S, Moore AS, Hassall TEG, Lowis SP, Tsoli M, Cowley MJ, Ziegler DS, Karajannis MA, Aquilina K, Hargrave DR, Carceller F, Marshall LV, von Deimling A, Kramm CM, Pfister SM, Sahm F, Baker SJ, Mastronuzzi A, Carai A, Vinci M, Capper D, Popov S, Ellison DW, Jacques TS, Jones DTW, Jones C. Infant High-Grade Gliomas Comprise Multiple Subgroups Characterized by Novel Targetable Gene Fusions and Favorable Outcomes. Cancer Discov. 10(7):942-963. 2020.
Tinkle CL, Simone B, Chiang J, Li X, Campbell K, Han Y, Li Y, Hover LD, Molitoris JK, Becksfort J, Lucas JT Jr, Patay Z, Baker SJ, Broniscer A, Merchant TE. Defining Optimal Target Volumes of Conformal Radiation Therapy for Diffuse Intrinsic Pontine Glioma. Int J Radiat Oncol Biol Phys. 2020 Mar 15;106(4):838-847.
Jin H, Kasper LH, Larson JD, Wu G, Baker SJ, Zhang J, Fan Y. ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in. Bioinformatics. 36(4):1270-1272. 2020.
Kasper LH, Baker SJ. Invited Review: Emerging functions of histone H3 mutations in paediatric diffuse high-grade gliomas. Neuropathol Appl Neurobiol. 46(1):73-85. 2020.
Wang H, Diaz AK, Shaw TI, Li Y, Niu M, Cho JH, Paugh BS, Zhang Y, Sifford J, Bai B, Wu Z, Tan H, Zhou S, Hover LD, Tillman HS, Shirinifard A, Thiagarajan S, Sablauer A, Pagala V, High AA, Wang X, Li C, Baker SJ, Peng J. Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes. Nat Commun.10(1):3718. 2019.
Baker SJ, Vogelstein B. p53: a tumor suppressor hiding in plain sight. J Mol Cell Biol. 11(7):536-538. 2019.
Patel YT, Davis A, Baker SJ, Campagne O, Stewart CF. CNS penetration of the CDK4/6 inhibitor ribociclib in non-tumor bearing mice and mice bearing pediatric brain tumors. Cancer Chemother Pharmacol. 84(2):447-452. 2019.
Larson JD, Kasper LH, Paugh BS, Jin H, Wu G, Kwon CH, Fan Y, Shaw TI, Silveira AB, Qu C, Xu R, Zhu X, Zhang J, Russell HR, Peters JL, Finkelstein D, Xu B, Lin T, Tinkle CL, Patay Z, Onar-Thomas A, Pounds SB, McKinnon PJ, Ellison DW, Zhang J, Baker SJ. Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression. Cancer Cell 35:1-16, 2019.
Silveira AB, Kasper LH, Fan Y, Jin H, Wu G, Shaw TI, Zhu X, Larson JD, Easton J, Shao Y, Yergeau DA, Rosencrance C, Boggs K, Rusch MC, Ding L, Zhang J, Finkelstein D, Noyes RM, Russell BL, Xu B, Broniscer A, Wetmore C, Pounds SB, Ellison DW, Zhang J, Baker SJ. H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. Acta Neuropathol. 137(4):637-655. 2019.
Xu K, Ding L, Chang TC, Shao Y, Chiang J, Mulder H, Wang S, Shaw TI, Wen J, Hover L, McLeod C, Wang YD, Easton J, Rusch M, Dalton J, Downing JR, Ellison DW, Zhang J, Baker SJ, Wu G. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta Neuropathol 137:123-137, 2019.
Larson JD, Baker SJ. Engineering Inducible Knock-In Mice to Model Oncogenic Brain Tumor Mutations from Endogenous Loci. Methods Mol Biol 1869:207-230, 2019.
Zhu G, Rankin SL, Larson JD, Zhu X, Chow LM, Qu C, Zhang J, Ellison DW, Baker SJ. PTEN Signaling in the Postnatal Perivascular Progenitor Niche Drives Medulloblastoma Formation. Cancer Res 1:123-133, 2017.
Mackay A, Burford A, Carvalho D, Izquierdo E, Fazal-Salom J, Taylor KR, Bjerke L, Clarke M, Vinci M, Nandhabalan M, Temelso S, Popov S, Molinari V, Raman P, Waanders AJ, Han HJ, Gupta S, Marshall L, Zacharoulis S, Vaidya S, Mandeville HC, Bridges LR, Martin AJ, Al-Sarraj S, Chandler C, Ng HK, Li X, Mu K, Trabelsi S, Brahim DH, Kisljakov AN, Konovalov DM, Moore AS, Carcaboso AM, Sunol M, de Torres C, Cruz O, Mora J, Shats LI, Stavale JN, Bidinotto LT, Reis RM, Entz-Werle N, Farrell M, Cryan J, Crimmins D, Caird J, Pears J, Monje M, Debily MA, Castel D, Grill J, Hawkins C, Nikbakht H, Jabado N, Baker SJ, Pfister SM, Jones DTW, Fouladi M, von Bueren AO, Baudis M, Resnick A, Jones C. Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma. Cancer Cell 32:520-537, 2017.
Tinkle, CL, Orr, BA, Lucas JT Jr, Klimo P, Patay Z, Baker SJ, Broniscer A, Qaddoumi I. Rapid and fulminant leptomeningeal spread following radiotherapy in diffuse intrinsic pontine glioma. Pediatr Blood Cancer 64(8). doi: 10.1002/pbc.26416. Epub 2017
Jones C, Karajannis MA, Jones DT, Kieran MW, Monje M, Baker SJ, Becher OJ, Cho YJ, Gupta N, Hawkins C, Hargrave D, Haas-Kogan DA, Jabado N, Li XN, Mueller S, Nicolaides T, Packer RJ, Persson AI, Phillips JJ, Simonds EF, Stafford JM, Tang Y, Pfister SM, Weiss WA. Pediatric high-grade glioma: biologically and clinically in need of new thinking. Neuro Oncol 19:153-161, 2017.
Baker SJ, Ellison DW, Gutmann DH. Pediatric gliomas as neurodevelopmental disorders. Glia 64:879-95, 2016.
Qaddoumi I, Orisme W, Wen J, Santiago T, Gupta K, Dalton JD, Tang B, Haupfear K, Punchihewa C, Easton J, Mulder H, Boggs K, Shao Y, Rusch M, Becksfort J, Gupta P, Wang S, Lee RP, Brat D, Peter Collins V, Dahiya S, George D, Konomos W, Kurian KM, McFadden K, Serafini LN, Nickols H, Perry A, Shurtleff S, Gajjar A, Boop FA, Klimo PD, Jr., Mardis ER, Wilson RK, Baker SJ, Zhang J, Wu G, Downing JR, Tatevossian RG, Ellison DW. Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology. Acta neuropathologica 2016.
Roy A, Skibo J, Kalume F, Ni J, Rankin S, Lu Y, Dobyns WB, Mills GB, Zhao JJ, Baker SJ, Millen KJ. Mouse models of human PIK3CA-related brain overgrowth have acutely treatable epilepsy. eLife 2015; 4.
Zong H, Parada LF, Baker SJ. Cell of Origin for Malignant Gliomas and Its Implication in Therapeutic Development.Cold Spring Harbor Perspectives in Biology 7, 2015.
Joshi A, Miller C, Jr, Baker SJ, Ellenson LH. Activated mutant p110alpha causes endometrial carcinoma in the setting of biallelic Pten deletion. The American Journal of Pathology 185: 1104-13, 2015.
Chen X, Gupta P, Wang J, Nakitandwe J, Roberts K, Dalton JD, Parker M, Patel S, Holmfeldt L, Payne D, Easton J, Ma J, Rusch M, Wu G, Patel A, Baker SJ, Dyer MA, Shurtleff S, Espy S, Pounds S, Downing JR, Ellison DW, Mullighan CG, Zhang J. CONSERTING: integrating copy-number analysis with structural-variation detection. Nature Methods 12:527-530, 2015.
Jones C, Baker SJ. Unique genetic and epigenetic mechanisms driving paediatric diffuse high-grade glioma. Nature Reviews Cancer Oct;14(10), 2014.
Wu G, Diaz AK, Paugh BS, Rankin SL, Ju B, Li Y, Zhu X, Qu C, Chen X, Zhang J, Easton J, Edmonson M, Ma X, Lu C, Nagahawatte P, Hedlund E, Rusch M, Pounds S, Lin T, Onar-Thomas A, Heuther R, Kriwacki R, Parker M, Gupta P, Becksfort J, Wei L, Mulder HL, Boggs K, Vadodaria B, Yergeau D, Russell JC, Ochoa K, Fulton RS, Fulton LL, Jones C, Boop FA, Bronsicer A, Wetmore C, Gajjar A, Ding L, Mardis ER, Wilson RK, Taylor MR, Downing JR, Ellison DW, Zhang J, Baker SJ. The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nat Genet 46:444-50, 2014.
Diaz AK, Baker SJ. The genetic signatures of pediatric high-grade glioma: no longer a one-act play.Semin Radiat Oncol 24:240-247, 2014.
Huether R, Dong L, Chen X, Wu G, Parker M, Wei L, Ma J, Edmonson MN, Hedlund EK, Rusch MC, Shurtleff SA, Mulder HL, Boggs K, Vadordaria B, Cheng J, Yergeau D, Song G, Becksfort J, Lemmon G, Weber C, Cai Z, Dang J, Walsh M, Gedman AL, Faber Z, Easton J, Gruber T, Kriwacki RW, Partridge JF, Ding L, Wilson RK, Mardis ER, Mullighan CG, Gilbertson RJ, Baker SJ, Zambetti G, Ellison DW, Zhang J, Downing JR. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun 5:3630, 2014.
Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet 45:602-12, 2013.
Paugh BS, Zhu X, Qu C, Endersby R, Diaz AK, Zhang J, Bax DA, Carvalho D, Reis RM, Onar-Thomas A, Broniscer A, Wetmore C, Zhang J, Jones C, Ellison DW, Baker SJ. Novel Oncogenic PDGFRA Mutations in Pediatric High-Grade Gliomas. Cancer Res 73:6219-29, 2013.
Zhu G, Chow LM, Bayazitov IT, Tong Y, Gilbertson RJ, Zakharenko SS, Solecki DJ, Baker SJ. Pten deletion causes mTorc1-dependent ectopic neuroblast differentiation without causing uniform migration defects. Development 139:3422-31, 2012.
Paugh BS, Broniscer A, Qu C, Miller CP, Zhang J, Tatevossian RG, Olson JM, Geyer JR, Chi SN, da Silva NS, Onar-Thomas A, Baker JN, Gajjar A, Ellison DW, Baker SJ. Genome-wide analyses identify recurrent amplifications of receptor tyrosine kinases and cell-cycle regulatory genes in diffuse intrinsic pontine glioma. J Clin Oncol 29(30):3999-4006, 2011.
Endersby R, Zhu X, Hay N, Ellison DW, Baker SJ. Nonredundant functions for Akt isoforms in astrocyte growth and gliomagenesis in an orthotopic transplantation model. Cancer Res 71(12):4106-16, 2011.
Chow LM, Endersby R, Zhu X, Rankin S, Qu C, Zhang J, Broniscer A, Ellison DW, Baker SJ. Cooperativity within and among Pten, p53, and Rb pathways induces high-grade astrocytoma in adult brain. Cancer Cell 19(3):305-16, 2011.
Paugh BS, Qu C, Jones C, Liu Z, Adamowicz-Brice M, Zhang J, Bax DA, Coyle B, Barrow J, Hargrave D, Lowe J, Gajjar A, Zhao W, Broniscer A, Ellison DW, Grundy RG, Baker SJ. Integrated molecular genetic profiling of pediatric high-grade gliomas reveals key differences with the adult disease. J Clin Oncol 28(18):3061-3068, 2010.
Broniscer A, Baker JN, Baker SJ, Chi SN, Geyer JR, Morris EB, Gajjar A. Prospective collection of tissue samples at autopsy in children with diffuse intrinsic pontine glioma. Cancer 116(19):4632-4637, 2010.
Chalhoub N, Zuo G, Zuo , Baker SJ. Cell-type specificity of PI3K signaling in Pdk1- and Pten-deficient brain. Genes Dev 23(14):1619-1624, 2009.
Frappart P-O, Lee Y, Russell HR, Chalhoub N, Wang Y-D, Orii KE, Zhao J, Kondo N, Baker SJ,McKinnon PJ. Genetic Alterations in medulloblastoma from mice with defective DNA double strand break repair. Proc Natl Acad Sci USA 106:1880-1885, 2009.
Chalhoub N, Baker SJ. PTEN and the PI3K Signaling Pathway in Cancer. Annu Rev Pathol 4:127-150, 2009.
Endersby R, Baker SJ. PTEN Signaling in Brain: Neuropathology and Tumorigenesis. Oncogene 27:5416-5430, 2008.
Chow LML, Zhang J, Baker SJ. Inducible Cre recombinase activity in mouse mature astrocytes and adult neural precursor cells. Transgenic Research 17:919-928, 2008.
Fraser MM, Bayazitov IT, Zakharenko SS, Baker SJ. Pten deficiency in brain causes defects in synaptic structure, transmission and plasticity, and myelination abnormalities. Neuroscience 151:476-488, 2008.
Broniscer A, Baker SJ, West AN, Fraser MM, Proko E, Kocak M, Dalton J, Zambetti GP, Ellison DW, Kun LE, Gajjar A, Gilbertson RJ, Fuller CE. Clinical and molecular characteristics of malignant transformation of low-grade glioma in children. J Clin Oncol 25:682-689, 2007.
Baker SJ. PTEN Enters the Nuclear Age. Cell 128:125-8, 2007.
Chow LM, Tian Y, Weber T, Corbett M, Zuo J, Baker SJ. Inducible Cre recombinase activity in mouse cerebellar granule cell precursors and inner ear hair cells. Dev Dyn 11:2991-8, 2006.
Chalhoub N, Kozma SC, Baker SJ. S6k1 is not required for Pten-deficient neuronal hypertrophy.Brain Res 1100:32-41, 2006.
Kwon C-H, Luikart BW, Powell CM, Zhou J, Matheny SA, Zhang W, Li Y, Baker SJ, Parada LF. Pten regulates neuronal arborization and social interaction in mice. Neuron 50:377-388, 2006.
Chow LM, Baker SJ. PTEN function in normal and neoplastic growth. Cancer Lett 241:184-196, 2006.
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Last update: August 2025