@article{bib1,
	author = {Anders, S and Pyl, PT and Huber, W},
	journal = {Bioinformatics},
	year = {2015},
	pages = {166--169},
	title = {HTSeq--a {Python} framework to work with high-throughput sequencing data},
	volume = {31},
}

@article{bib2,
	author = {Andreolas, C and Kalogeropoulou, M and Voulgari, A and Pintzas, A},
	journal = {International Journal of Cancer},
	year = {2008},
	pages = {1745--1756},
	title = {Fra-1 regulates vimentin during {Ha}-{RAS}-induced epithelial mesenchymal transition in human {Colon} carcinoma cells},
	volume = {122},
}

@article{bib3,
	author = {Annibali, D and Whitfield, JR and Favuzzi, E and Jauset, T and Serrano, E and Cuartas, I and Redondo-Campos, S and Folch, G and Gonz{\` a}lez-Junc{\` a}, A and Sodir, NM and Mass{\' o}-Vall{\' e}s, D and Beaulieu, M-E and Swigart, LB and Mc Gee, MM and Somma, MP and Nasi, S and Seoane, J and Evan, GI and Soucek, L},
	journal = {Nature Communications},
	year = {2014},
	pages = {1--11},
	title = {Myc inhibition is effective against glioma and reveals a role for myc in proficient mitosis},
	volume = {5},
}

@article{bib4,
	author = {Bakiri, L and Macho-Maschler, S and Custic, I and Niemiec, J and Gu{\' i}o-Carri{\' o}n, A and Hasenfuss, SC and Eger, A and M{\" u}ller, M and Beug, H and Wagner, EF},
	journal = {Cell Death & Differentiation},
	year = {2015},
	pages = {336--350},
	title = {Fra-1/{AP}-1 induces {EMT} in mammary epithelial cells by modulating {Zeb1}/2 and tgf\beta{} expression},
	volume = {22},
}

@article{bib5,
	author = {Bao, S and Wu, Q and McLendon, RE and Hao, Y and Shi, Q and Hjelmeland, AB and Dewhirst, MW and Bigner, DD and Rich, JN},
	journal = {Nature},
	year = {2006},
	pages = {756--760},
	title = {Glioma stem cells promote radioresistance by preferential activation of the {DNA} damage response},
	volume = {444},
}

@article{bib6,
	author = {Basso, K and Margolin, AA and Stolovitzky, G and Klein, U and Dalla-Favera, R and Califano, A},
	journal = {Nature Genetics},
	year = {2005},
	pages = {382--390},
	title = {Reverse engineering of regulatory networks in human {B} cells},
	volume = {37},
}

@article{bib7,
	author = {Bazzoli, E and Pulvirenti, T and Oberstadt, MC and Perna, F and Wee, B and Schultz, N and Huse, JT and Fomchenko, EI and Voza, F and Tabar, V and Brennan, CW and DeAngelis, LM and Nimer, SD and Holland, EC and Squatrito, M},
	journal = {Cell Stem Cell},
	year = {2012},
	pages = {836--844},
	title = {MEF promotes stemness in the pathogenesis of gliomas},
	volume = {11},
}

@article{bib8,
	author = {Belteki, G},
	journal = {Nucleic Acids Research},
	year = {2005},
	title = {Conditional and inducible transgene expression in mice through the combinatorial use of {Cre}-mediated recombination and tetracycline induction},
	volume = {33},
}

@article{bib9,
	author = {Bhat, KP and Salazar, KL and Balasubramaniyan, V and Wani, K and Heathcock, L and Hollingsworth, F and James, JD and Gumin, J and Diefes, KL and Kim, SH and Turski, A and Azodi, Y and Yang, Y and Doucette, T and Colman, H and Sulman, EP and Lang, FF and Rao, G and Copray, S and Vaillant, BD and Aldape, KD},
	journal = {Genes & Development},
	year = {2011},
	pages = {2594--2609},
	title = {The transcriptional coactivator {TAZ} regulates mesenchymal differentiation in malignant glioma},
	volume = {25},
}

@article{bib10,
	author = {Bhat, KPL and Balasubramaniyan, V and Vaillant, B and Ezhilarasan, R and Hummelink, K and Hollingsworth, F and Wani, K and Heathcock, L and James, JD and Goodman, LD and Conroy, S and Long, L and Lelic, N and Wang, S and Gumin, J and Raj, D and Kodama, Y and Raghunathan, A and Olar, A and Joshi, K and Pelloski, CE and Heimberger, A and Kim, SH and Cahill, DP and Rao, G and Den Dunnen, WFA and Boddeke, H and Phillips, HS and Nakano, I and Lang, FF and Colman, H and Sulman, EP and Aldape, K},
	journal = {Cancer Cell},
	year = {2013},
	pages = {331--346},
	title = {Mesenchymal differentiation mediated by {NF}-\kappa{}{B} promotes radiation resistance in glioblastoma},
	volume = {24},
}

@article{bib11,
	author = {Bowman, RL and Wang, Q and Carro, A and Verhaak, RG and Squatrito, M},
	journal = {Neuro-Oncology},
	year = {2017},
	pages = {139--141},
	title = {GlioVis data portal for visualization and analysis of brain tumor expression datasets},
	volume = {19},
}

@article{bib12,
	author = {Brennan, CW and Verhaak, RG and McKenna, A and Campos, B and Noushmehr, H and Salama, SR and Zheng, S and Chakravarty, D and Sanborn, JZ and Berman, SH and Beroukhim, R and Bernard, B and Wu, CJ and Genovese, G and Shmulevich, I and Barnholtz-Sloan, J and Zou, L and Vegesna, R and Shukla, SA and Ciriello, G and Yung, WK and Zhang, W and Sougnez, C and Mikkelsen, T and Aldape, K and Bigner, DD and Van Meir, EG and Prados, M and Sloan, A and Black, KL and Eschbacher, J and Finocchiaro, G and Friedman, W and Andrews, DW and Guha, A and Iacocca, M and O'Neill, BP and Foltz, G and Myers, J and Weisenberger, DJ and Penny, R and Kucherlapati, R and Perou, CM and Hayes, DN and Gibbs, R and Marra, M and Mills, GB and Lander, E and Spellman, P and Wilson, R and Sander, C and Weinstein, J and Meyerson, M and Gabriel, S and Laird, PW and Haussler, D and Getz, G and Chin, L and {TCGA Research Network}},
	journal = {Cell},
	year = {2013},
	pages = {462--477},
	title = {The somatic genomic landscape of glioblastoma},
	volume = {155},
}

@article{bib13,
	author = {Buenrostro, JD and Giresi, PG and Zaba, LC and Chang, HY and Greenleaf, WJ},
	journal = {Nature Methods},
	year = {2013},
	pages = {1213--1218},
	title = {Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, {DNA}-binding proteins and nucleosome position},
	volume = {10},
}

@article{bib14,
	author = {{Cancer Genome Atlas Research Network}},
	journal = {Nature},
	year = {2008},
	pages = {1061--1068},
	title = {Comprehensive genomic characterization defines human glioblastoma genes and core pathways},
	volume = {455},
}

@article{bib15,
	author = {Carro, MS and Lim, WK and Alvarez, MJ and Bollo, RJ and Zhao, X and Snyder, EY and Sulman, EP and Anne, SL and Doetsch, F and Colman, H and Lasorella, A and Aldape, K and Califano, A and Iavarone, A},
	journal = {Nature},
	year = {2010},
	pages = {318--325},
	title = {The transcriptional network for mesenchymal transformation of brain tumours},
	volume = {463},
}

@article{bib16,
	author = {Casalino, L and De Cesare, D and Verde, P},
	journal = {Molecular and Cellular Biology},
	year = {2003},
	pages = {4401--4415},
	title = {Accumulation of {Fra}-1 in ras-transformed cells depends on both transcriptional autoregulation and {MEK}-dependent posttranslational stabilization},
	volume = {23},
}

@article{bib17,
	author = {Castro, MA and de Santiago, I and Campbell, TM and Vaughn, C and Hickey, TE and Ross, E and Tilley, WD and Markowetz, F and Ponder, BA and Meyer, KB},
	journal = {Nature Genetics},
	year = {2016},
	pages = {12--21},
	title = {Regulators of genetic risk of breast {Cancer} identified by integrative network analysis},
	volume = {48},
}

@article{bib18,
	author = {Ceccarelli, M and Barthel, FP and Malta, TM and Sabedot, TS and Salama, SR and Murray, BA and Morozova, O and Newton, Y and Radenbaugh, A and Pagnotta, SM and Anjum, S and Wang, J and Manyam, G and Zoppoli, P and Ling, S and Rao, AA and Grifford, M and Cherniack, AD and Zhang, H and Poisson, L and Carlotti, CG and Tirapelli, DP and Rao, A and Mikkelsen, T and Lau, CC and Yung, WK and Rabadan, R and Huse, J and Brat, DJ and Lehman, NL and Barnholtz-Sloan, JS and Zheng, S and Hess, K and Rao, G and Meyerson, M and Beroukhim, R and Cooper, L and Akbani, R and Wrensch, M and Haussler, D and Aldape, KD and Laird, PW and Gutmann, DH and Noushmehr, H and Iavarone, A and Verhaak, RG and {TCGA Research Network}},
	journal = {Cell},
	year = {2016},
	pages = {550--563},
	title = {Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma},
	volume = {164},
}

@article{bib19,
	author = {Chen, J and Li, Y and Yu, TS and McKay, RM and Burns, DK and Kernie, SG and Parada, LF},
	journal = {Nature},
	year = {2012},
	pages = {522--526},
	title = {A restricted cell population propagates glioblastoma growth after chemotherapy},
	volume = {488},
}

@article{bib20,
	author = {Chiappetta, G and Ferraro, A and Botti, G and Monaco, M and Pasquinelli, R and Vuttariello, E and Arnaldi, L and Di Bonito, M and D'Aiuto, G and Pierantoni, GM and Fusco, A},
	journal = {BMC Cancer},
	year = {2007},
	title = {FRA-1 protein overexpression is a feature of hyperplastic and neoplastic breast disorders},
	volume = {7},
}

@article{bib21,
	author = {Cooper, LA and Gutman, DA and Chisolm, C and Appin, C and Kong, J and Rong, Y and Kurc, T and Van Meir, EG and Saltz, JH and Moreno, CS and Brat, DJ},
	journal = {The American Journal of Pathology},
	year = {2012},
	pages = {2108--2119},
	title = {The tumor microenvironment strongly impacts master transcriptional regulators and gene expression class of glioblastoma},
	volume = {180},
}

@article{bib22,
	author = {Cusulin, C and Chesnelong, C and Bose, P and Bilenky, M and Kopciuk, K and Chan, JA and Cairncross, JG and Jones, SJ and Marra, MA and Luchman, HA and Weiss, S},
	journal = {Stem Cell Reports},
	year = {2015},
	pages = {1--9},
	title = {Precursor states of brain tumor initiating cell lines are predictive of survival in {Xenografts} and {Associated} with {Glioblastoma} {Subtypes}},
	volume = {5},
}

@article{bib23,
	author = {Debinski, W and Gibo, DM},
	journal = {Molecular Cancer Research},
	year = {2005},
	pages = {237--249},
	title = {Fos-related antigen 1 modulates malignant features of glioma cells},
	volume = {3},
}

@article{bib24,
	author = {Diesch, J and Sanij, E and Gilan, O and Love, C and Tran, H and Fleming, NI and Ellul, J and Amalia, M and Haviv, I and Pearson, RB and Tulchinsky, E and Mariadason, JM and Sieber, OM and Hannan, RD and Dhillon, AS},
	journal = {PLOS ONE},
	year = {2014},
	title = {Widespread {FRA1}-{Dependent} control of mesenchymal transdifferentiation programs in colorectal {Cancer} cells},
	volume = {9},
}

@article{bib25,
	author = {Dobin, A and Davis, CA and Schlesinger, F and Drenkow, J and Zaleski, C and Jha, S and Batut, P and Chaisson, M and Gingeras, TR},
	journal = {Bioinformatics},
	year = {2013},
	pages = {15--21},
	title = {STAR: ultrafast universal {RNA}-seq aligner},
	volume = {29},
}

@article{bib26,
	author = {Eferl, R and Wagner, EF},
	journal = {Nature Reviews Cancer},
	year = {2003},
	pages = {859--868},
	title = {AP-1: a double-edged sword in tumorigenesis},
	volume = {3},
}

@article{bib27,
	author = {Esnault, C and Gualdrini, F and Horswell, S and Kelly, G and Stewart, A and East, P and Matthews, N and Treisman, R},
	journal = {Molecular Cell},
	year = {2017},
	pages = {1081--1095},
	title = {ERK-{Induced} activation of {TCF} family of {SRF} cofactors initiates a chromatin modification cascade associated with transcription},
	volume = {65},
}

@article{bib28,
	author = {Fedele, V and Dai, F and Masilamani, AP and Heiland, DH and Kling, E and G{\" a}tjens-Sanchez, AM and Ferrarese, R and Platania, L and Soroush, D and Kim, H and Nelander, S and Weyerbrock, A and Prinz, M and Califano, A and Iavarone, A and Bredel, M and Carro, MS},
	journal = {Molecular Cancer Research},
	year = {2017},
	pages = {998--1011},
	title = {Epigenetic regulation of {ZBTB18} promotes glioblastoma progression},
	volume = {15},
}

@article{bib29,
	author = {Fedele, M and Cerchia, L and Pegoraro, S and Sgarra, R and Manfioletti, G},
	journal = {International Journal of Molecular Sciences},
	year = {2019},
	title = {Proneural-{Mesenchymal} transition: phenotypic plasticity to acquire multitherapy resistance in glioblastoma},
	volume = {20},
}

@article{bib30,
	author = {Fiscon, G and Conte, F and Paci, P},
	journal = {BMC Bioinformatics},
	year = {2018},
	title = {SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines},
	volume = {19},
}

@article{bib31,
	author = {Fletcher, MN and Castro, MA and Wang, X and de Santiago, I and O'Reilly, M and Chin, SF and Rueda, OM and Caldas, C and Ponder, BA and Markowetz, F and Meyer, KB},
	journal = {Nature Communications},
	year = {2013},
	title = {Master regulators of {FGFR2} signalling and breast {Cancer} risk},
	volume = {4},
}

@article{bib32,
	author = {Friedmann-Morvinski, D and Bushong, EA and Ke, E and Soda, Y and Marumoto, T and Singer, O and Ellisman, MH and Verma, IM},
	journal = {Science},
	year = {2012},
	pages = {1080--1084},
	title = {Dedifferentiation of neurons and astrocytes by oncogenes can induce gliomas in mice},
	volume = {338},
}

@article{bib33,
	author = {Gao, X-Q and Ge, Y-S and Shu, Q-H and Ma, H-X},
	journal = {Tumor Biology},
	year = {2017},
	title = {Expression of {Fra}-1 in human hepatocellular carcinoma and its prognostic significance},
	volume = {39},
}

@article{bib34,
	author = {Gargiulo, G and Cesaroni, M and Serresi, M and de Vries, N and Hulsman, D and Bruggeman, SW and Lancini, C and van Lohuizen, M},
	journal = {Cancer Cell},
	year = {2013},
	pages = {660--676},
	title = {In vivo {RNAi} screen for {BMI1} targets identifies {TGF}-\beta{}/{BMP}-{ER} stress pathways as key regulators of neural- and malignant glioma-stem cell homeostasis},
	volume = {23},
}

@article{bib35,
	author = {Gautier, L and Cope, L and Bolstad, BM and Irizarry, RA},
	journal = {Bioinformatics},
	year = {2004},
	pages = {307--315},
	title = {Affy--analysis of affymetrix {GeneChip} data at the probe level},
	volume = {20},
}

@article{bib36,
	author = {Gel, B and Serra, E},
	journal = {Bioinformatics},
	year = {2017},
	pages = {3088--3090},
	title = {karyoploteR: an {R}/{Bioconductor} package to plot customizable genomes displaying arbitrary data},
	volume = {33},
}

@article{bib37,
	author = {Gra{\~ n}a, O and Rubio-Camarillo, M and Fdez-Riverola, F and Pisano, DG and Glez-Pe{\~ n}a, D},
	journal = {Current Bioinformatics},
	year = {2018},
	pages = {583--591},
	title = {Nextpresso: next generation sequencing expression analysis pipeline},
	volume = {13},
}

@article{bib38,
	author = {G{\" u}nther, HS and Schmidt, NO and Phillips, HS and Kemming, D and Kharbanda, S and Soriano, R and Modrusan, Z and Meissner, H and Westphal, M and Lamszus, K},
	journal = {Oncogene},
	year = {2008},
	pages = {2897--2909},
	title = {Glioblastoma-derived stem cell-enriched cultures form distinct subgroups according to molecular and phenotypic criteria},
	volume = {27},
}

@article{bib39,
	author = {Halliday, J and Helmy, K and Pattwell, SS and Pitter, KL and LaPlant, Q and Ozawa, T and Holland, EC},
	journal = {PNAS},
	year = {2014},
	pages = {5248--5253},
	title = {In vivo radiation response of proneural glioma characterized by protective p53 transcriptional program and proneural-mesenchymal shift},
	volume = {111},
}

@article{bib40,
	author = {Hambardzumyan, D and Amankulor, NM and Helmy, KY and Becher, OJ and Holland, EC},
	journal = {Translational Oncology},
	year = {2009},
	pages = {89--95},
	title = {Modeling adult gliomas using {RCAS}/t-va technology},
	volume = {2},
}

@article{bib41,
	author = {Hara, T and Chanoch-Myers, R and Mathewson, ND and Myskiw, C and Atta, L and Bussema, L and Eichhorn, SW and Greenwald, AC and Kinker, GS and Rodman, C and Gonzalez Castro, LN and Wakimoto, H and Rozenblatt-Rosen, O and Zhuang, X and Fan, J and Hunter, T and Verma, IM and Wucherpfennig, KW and Regev, A and Suv{\` a}, ML and Tirosh, I},
	journal = {Cancer Cell},
	year = {2021},
	pages = {779--792},
	title = {Interactions between {Cancer} cells and immune cells drive transitions to mesenchymal-like states in glioblastoma},
	volume = {39},
}

@article{bib42,
	author = {Hasenfuss, SC and Bakiri, L and Thomsen, MK and Hamacher, R and Wagner, EF},
	journal = {Hepatology},
	year = {2014},
	pages = {261--273},
	title = {Activator protein 1 transcription factor {Fos}-related antigen 1 ({Fra}-1) is dispensable for murine liver fibrosis, but modulates xenobiotic metabolism},
	volume = {59},
}

@article{bib43,
	author = {Hennig, BP and Velten, L and Racke, I and Tu, CS and Thoms, M and Rybin, V and Besir, H and Remans, K and Steinmetz, LM},
	journal = {G3: Genes, Genomes, Genetics},
	year = {2018},
	pages = {79--89},
	title = {Large-{Scale} {Low}-{Cost} {NGS} library preparation using a robust {Tn5} purification and tagmentation protocol},
	volume = {8},
}

@article{bib44,
	author = {Holland, EC and Celestino, J and Dai, C and Schaefer, L and Sawaya, RE and Fuller, GN},
	journal = {Nature Genetics},
	year = {2000},
	pages = {55--57},
	title = {Combined activation of ras and akt in neural progenitors induces glioblastoma formation in mice},
	volume = {25},
}

@article{bib45,
	author = {Koschmann, C and Calinescu, AA and Nunez, FJ and Mackay, A and Fazal-Salom, J and Thomas, D and Mendez, F and Kamran, N and Dzaman, M and Mulpuri, L and Krasinkiewicz, J and Doherty, R and Lemons, R and Brosnan-Cashman, JA and Li, Y and Roh, S and Zhao, L and Appelman, H and Ferguson, D and Gorbunova, V and Meeker, A and Jones, C and Lowenstein, PR and Castro, MG},
	journal = {Science Translational Medicine},
	year = {2016},
	title = {ATRX loss promotes tumor growth and impairs nonhomologous end joining {DNA} repair in glioma},
	volume = {8},
}

@article{bib46,
	author = {Lambert, SA and Jolma, A and Campitelli, LF and Das, PK and Yin, Y and Albu, M and Chen, X and Taipale, J and Hughes, TR and Weirauch, MT},
	journal = {Cell},
	year = {2018},
	pages = {650--665},
	title = {The human transcription factors},
	volume = {172},
}

@article{bib47,
	author = {Langmead, B and Salzberg, SL},
	journal = {Nature Methods},
	year = {2012},
	pages = {357--359},
	title = {Fast gapped-read alignment with bowtie 2},
	volume = {9},
}

@article{bib48,
	author = {Lau, EY and Lo, J and Cheng, BY and Ma, MK and Lee, JM and Ng, JK and Chai, S and Lin, CH and Tsang, SY and Ma, S and Ng, IO and Lee, TK},
	journal = {Cell Reports},
	year = {2016},
	pages = {1175--1189},
	title = {Cancer-{Associated} fibroblasts regulate {Tumor}-{Initiating} cell plasticity in hepatocellular carcinoma through c-{Met}/{FRA1}/{HEY1} signaling},
	volume = {15},
}

@article{bib49,
	author = {Li, T and Fu, J and Zeng, Z and Cohen, D and Li, J and Chen, Q and Li, B and Liu, XS},
	journal = {Nucleic Acids Research},
	year = {2020},
	title = {TIMER2.0 for analysis of tumor-infiltrating immune cells},
	volume = {48},
}

@article{bib50,
	author = {Liu, H and Ren, G and Wang, T and Chen, Y and Gong, C and Bai, Y and Wang, B and Qi, H and Shen, J and Zhu, L and Qian, C and Lai, M and Shao, J},
	journal = {Carcinogenesis},
	year = {2015},
	pages = {459--468},
	title = {Aberrantly expressed {Fra}-1 by {IL}-6/{STAT3} transactivation promotes colorectal {Cancer} aggressiveness through epithelial-mesenchymal transition},
	volume = {36},
}

@article{bib51,
	author = {Louis, DN and Perry, A and Reifenberger, G and von Deimling, A and Figarella-Branger, D and Cavenee, WK and Ohgaki, H and Wiestler, OD and Kleihues, P and Ellison, DW},
	journal = {Acta Neuropathologica},
	year = {2016},
	pages = {803--820},
	title = {The 2016 world health organization classification of tumors of the central nervous system: a summary},
	volume = {131},
}

@article{bib52,
	author = {Love, MI and Huber, W and Anders, S},
	journal = {Genome Biology},
	year = {2014},
	title = {Moderated estimation of fold change and dispersion for {RNA}-seq data with {DESeq2}},
	volume = {15},
}

@article{bib53,
	author = {Mack, SC and Singh, I and Wang, X and Hirsch, R and Wu, Q and Villagomez, R and Bernatchez, JA and Zhu, Z and Gimple, RC and Kim, LJY and Morton, A and Lai, S and Qiu, Z and Prager, BC and Bertrand, KC and Mah, C and Zhou, W and Lee, C and Barnett, GH and Vogelbaum, MA and Sloan, AE and Chavez, L and Bao, S and Scacheri, PC and Siqueira-Neto, JL and Lin, CY and Rich, JN},
	journal = {Journal of Experimental Medicine},
	year = {2019},
	pages = {1071--1090},
	title = {Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma},
	volume = {216},
}

@article{bib54,
	author = {Mani, SA and Guo, W and Liao, MJ and Eaton, EN and Ayyanan, A and Zhou, AY and Brooks, M and Reinhard, F and Zhang, CC and Shipitsin, M and Campbell, LL and Polyak, K and Brisken, C and Yang, J and Weinberg, RA},
	journal = {Cell},
	year = {2008},
	pages = {704--715},
	title = {The epithelial-mesenchymal transition generates cells with properties of stem cells},
	volume = {133},
}

@article{bib55,
	author = {Mansuy, IM and Bujard, H},
	journal = {Current Opinion in Neurobiology},
	year = {2000},
	pages = {593--596},
	title = {Tetracycline-regulated gene expression in the brain},
	volume = {10},
}

@article{bib56,
	author = {Mao, P and Joshi, K and Li, J and Kim, SH and Li, P and Santana-Santos, L and Luthra, S and Chandran, UR and Benos, PV and Smith, L and Wang, M and Hu, B and Cheng, SY and Sobol, RW and Nakano, I},
	journal = {PNAS},
	year = {2013},
	pages = {8644--8649},
	title = {Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1a3},
	volume = {110},
}

@article{bib57,
	author = {Matsuo, K and Owens, JM and Tonko, M and Elliott, C and Chambers, TJ and Wagner, EF},
	journal = {Nature Genetics},
	year = {2000},
	pages = {184--187},
	title = {Fosl1 is a transcriptional target of c-{Fos} during osteoclast differentiation},
	volume = {24},
}

@article{bib58,
	author = {McCormick, F},
	journal = {Molecular Carcinogenesis},
	year = {1990},
	pages = {185--187},
	title = {GAP as ras effector or negative regulator?},
	volume = {3},
}

@article{bib59,
	author = {Mu{\~ n}oz, DM and Tung, T and Agnihotri, S and Singh, S and Guha, A and Zadeh, G and Hawkins, C},
	journal = {Glia},
	year = {2013},
	pages = {1862--1872},
	title = {Loss of p53 cooperates with {K}-ras activation to induce glioma formation in a region-independent manner},
	volume = {61},
}

@article{bib60,
	author = {Neftel, C and Laffy, J and Filbin, MG and Hara, T and Shore, ME and Rahme, GJ and Richman, AR and Silverbush, D and Shaw, ML and Hebert, CM and Dewitt, J and Gritsch, S and Perez, EM and Gonzalez Castro, LN and Lan, X and Druck, N and Rodman, C and Dionne, D and Kaplan, A and Bertalan, MS and Small, J and Pelton, K and Becker, S and Bonal, D and Nguyen, Q-D and Servis, RL and Fung, JM and Mylvaganam, R and Mayr, L and Gojo, J and Haberler, C and Geyeregger, R and Czech, T and Slavc, I and Nahed, BV and Curry, WT and Carter, BS and Wakimoto, H and Brastianos, PK and Batchelor, TT and Stemmer-Rachamimov, A and Martinez-Lage, M and Frosch, MP and Stamenkovic, I and Riggi, N and Rheinbay, E and Monje, M and Rozenblatt-Rosen, O and Cahill, DP and Patel, AP and Hunter, T and Verma, IM and Ligon, KL and Louis, DN and Regev, A and Bernstein, BE and Tirosh, I and Suv{\` a}, ML},
	journal = {Cell},
	year = {2019},
	pages = {835--849},
	title = {An integrative model of cellular states, plasticity, and genetics for glioblastoma},
	volume = {178},
}

@article{bib61,
	author = {Oldrini, B and Curiel-Garc{\' i}a, {\' A} and Marques, C and Matia, V and Ulu{\c c}kan, {\" O} and Gra{\~ n}a-Castro, O and Torres-Ruiz, R and Rodriguez-Perales, S and Huse, JT and Squatrito, M},
	journal = {Nature Communications},
	year = {2018},
	title = {Somatic genome editing with the {RCAS}-{TVA}-{CRISPR}-{Cas9} system for precision tumor modeling},
	volume = {9},
}

@article{bib62,
	author = {Ozawa, T and Riester, M and Cheng, YK and Huse, JT and Squatrito, M and Helmy, K and Charles, N and Michor, F and Holland, EC},
	journal = {Cancer Cell},
	year = {2014},
	pages = {288--300},
	title = {Most human non-{GCIMP} glioblastoma subtypes evolve from a common proneural-like precursor glioma},
	volume = {26},
}

@article{bib63,
	author = {Patel, AP and Tirosh, I and Trombetta, JJ and Shalek, AK and Gillespie, SM and Wakimoto, H and Cahill, DP and Nahed, BV and Curry, WT and Martuza, RL and Louis, DN and Rozenblatt-Rosen, O and Suv{\` a}, ML and Regev, A and Bernstein, BE},
	journal = {Science},
	year = {2014},
	pages = {1396--1401},
	title = {Single-cell {RNA}-seq highlights intratumoral heterogeneity in primary glioblastoma},
	volume = {344},
}

@article{bib64,
	author = {Phillips, HS and Kharbanda, S and Chen, R and Forrest, WF and Soriano, RH and Wu, TD and Misra, A and Nigro, JM and Colman, H and Soroceanu, L and Williams, PM and Modrusan, Z and Feuerstein, BG and Aldape, K},
	journal = {Cancer Cell},
	year = {2006},
	pages = {157--173},
	title = {Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis},
	volume = {9},
}

@article{bib65,
	author = {Ram{\' i}rez, F and Ryan, DP and Gr{\" u}ning, B and Bhardwaj, V and Kilpert, F and Richter, AS and Heyne, S and D{\" u}ndar, F and Manke, T},
	journal = {Nucleic Acids Research},
	year = {2016},
	title = {deepTools2: a next generation web server for deep-sequencing data analysis},
	volume = {44},
}

@article{bib66,
	author = {Ricci-Vitiani, L and Pallini, R and Larocca, LM and Lombardi, DG and Signore, M and Pierconti, F and Petrucci, G and Montano, N and Maira, G and De Maria, R},
	journal = {Cell Death & Differentiation},
	year = {2008},
	pages = {1491--1498},
	title = {Mesenchymal differentiation of glioblastoma stem cells},
	volume = {15},
}

@article{bib67,
	author = {Richards, LM and Whitley, OKN and MacLeod, G and Cavalli, FMG and Coutinho, FJ and Jaramillo, JE and Svergun, N and Riverin, M and Croucher, DC and Kushida, M and Yu, K and Guilhamon, P and Rastegar, N and Ahmadi, M and Bhatti, JK and Bozek, DA and Li, N and Lee, L and Che, C and Luis, E and Park, NI and Xu, Z and Ketela, T and Moore, RA and Marra, MA and Spears, J and Cusimano, MD and Das, S and Bernstein, M and Haibe-Kains, B and Lupien, M and Luchman, HA and Weiss, S and Angers, S and Dirks, PB and Bader, GD and Pugh, TJ},
	journal = {Nature Cancer},
	year = {2021},
	pages = {157--173},
	title = {Gradient of developmental and injury response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity},
	volume = {2},
}

@article{bib68,
	author = {Ritchie, ME and Phipson, B and Wu, D and Hu, Y and Law, CW and Shi, W and Smyth, GK},
	journal = {Nucleic Acids Research},
	year = {2015},
	title = {Limma powers differential expression analyses for {RNA}-sequencing and microarray studies},
	volume = {43},
}

@article{bib69,
	author = {Sandberg, CJ and Altschuler, G and Jeong, J and Str\o{}mme, KK and Stangeland, B and Murrell, W and Grasmo-Wendler, UH and Myklebost, O and Helseth, E and Vik-Mo, EO and Hide, W and Langmoen, IA},
	journal = {Experimental Cell Research},
	year = {2013},
	pages = {2230--2243},
	title = {Comparison of glioma stem cells to neural stem cells from the adult human brain identifies dysregulated wnt- signaling and a fingerprint associated with clinical outcome},
	volume = {319},
}

@article{bib70,
	author = {Schep, AN and Wu, B and Buenrostro, JD and Greenleaf, WJ},
	journal = {Nature Methods},
	year = {2017},
	pages = {975--978},
	title = {chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data},
	volume = {14},
}

@article{bib71,
	author = {Schmitt, MJ and Company, C and Dramaretska, Y and Barozzi, I and G{\" o}hrig, A and Kertalli, S and Gro\ss{}mann, M and Naumann, H and Sanchez-Bailon, MP and Hulsman, D and Glass, R and Squatrito, M and Serresi, M and Gargiulo, G},
	journal = {Cancer Discovery},
	year = {2021},
	pages = {754--777},
	title = {Phenotypic mapping of pathologic {Cross}-{Talk} between glioblastoma and innate immune cells by synthetic genetic tracing},
	volume = {11},
}

@article{bib72,
	author = {Serresi, M and Kertalli, S and Li, L and Schmitt, MJ and Dramaretska, Y and Wierikx, J and Hulsman, D and Gargiulo, G},
	journal = {Science Advances},
	year = {2021},
	title = {Functional antagonism of chromatin modulators regulates epithelial-mesenchymal transition},
	volume = {7},
}

@article{bib73,
	author = {Sottoriva, A and Spiteri, I and Piccirillo, SG and Touloumis, A and Collins, VP and Marioni, JC and Curtis, C and Watts, C and Tavar{\' e}, S},
	journal = {PNAS},
	year = {2013},
	pages = {4009--4014},
	title = {Intratumor heterogeneity in human glioblastoma reflects {Cancer} evolutionary dynamics},
	volume = {110},
}

@article{bib74,
	author = {Squatrito, M},
	year = {2021},
	title = {marques2020},
	howpublished = {https://archive.softwareheritage.org/swh:1:dir:9a190c31dcd2e5c1208d3701aedd95ee40cd3a52;origin=https://github.com/squatrim/marques2020;visit=swh:1:snp:d5d44f19da835e0a371b432aa30cf3dedc117fa1;anchor=swh:1:rev:45e31e7d17f006d2d3a17e66a63449f758bf5998},
}

@article{bib75,
	author = {Subramanian, A and Tamayo, P and Mootha, VK and Mukherjee, S and Ebert, BL and Gillette, MA and Paulovich, A and Pomeroy, SL and Golub, TR and Lander, ES and Mesirov, JP},
	journal = {PNAS},
	year = {2005},
	pages = {15545--15550},
	title = {Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles},
	volume = {102},
}

@article{bib76,
	author = {Suv{\` a}, ML and Rheinbay, E and Gillespie, SM and Patel, AP and Wakimoto, H and Rabkin, SD and Riggi, N and Chi, AS and Cahill, DP and Nahed, BV and Curry, WT and Martuza, RL and Rivera, MN and Rossetti, N and Kasif, S and Beik, S and Kadri, S and Tirosh, I and Wortman, I and Shalek, AK and Rozenblatt-Rosen, O and Regev, A and Louis, DN and Bernstein, BE},
	journal = {Cell},
	year = {2014},
	pages = {580--594},
	title = {Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells},
	volume = {157},
}

@article{bib77,
	author = {Tam, WL and Lu, H and Buikhuisen, J and Soh, BS and Lim, E and Reinhardt, F and Wu, ZJ and Krall, JA and Bierie, B and Guo, W and Chen, X and Liu, XS and Brown, M and Lim, B and Weinberg, RA},
	journal = {Cancer Cell},
	year = {2013},
	pages = {347--364},
	title = {Protein kinase {C} \alpha{} is a central signaling node and therapeutic target for breast {Cancer} stem cells},
	volume = {24},
}

@article{bib78,
	author = {Tam, WL and Weinberg, RA},
	journal = {Nature Medicine},
	year = {2013},
	pages = {1438--1449},
	title = {The epigenetics of epithelial-mesenchymal plasticity in {Cancer}},
	volume = {19},
}

@article{bib79,
	author = {Tso, CL and Shintaku, P and Chen, J and Liu, Q and Liu, J and Chen, Z and Yoshimoto, K and Mischel, PS and Cloughesy, TF and Liau, LM and Nelson, SF},
	journal = {Molecular Cancer Research},
	year = {2006},
	pages = {607--619},
	title = {Primary glioblastomas express mesenchymal stem-like properties},
	volume = {4},
}

@article{bib80,
	author = {Uhrbom, L and Dai, C and Celestino, JC and Rosenblum, MK and Fuller, GN and Holland, EC},
	journal = {Cancer Research},
	year = {2002},
	pages = {5551--5558},
	title = {Ink4a-{Arf} loss cooperates with {KRas} activation in astrocytes and neural progenitors to generate glioblastomas of various morphologies depending on activated akt},
	volume = {62},
}

@article{bib81,
	author = {Usui, A and Hoshino, I and Akutsu, Y and Sakata, H and Nishimori, T and Murakami, K and Kano, M and Shuto, K and Matsubara, H},
	journal = {Cancer},
	year = {2012},
	pages = {3387--3396},
	title = {The molecular role of {Fra}-1 and its prognostic significance in human esophageal squamous cell carcinoma},
	volume = {118},
}

@article{bib82,
	author = {Vallejo, A and Perurena, N and Guruceaga, E and Mazur, PK and Martinez-Canarias, S and Zandueta, C and Valencia, K and Arricibita, A and Gwinn, D and Sayles, LC and Chuang, CH and Guembe, L and Bailey, P and Chang, DK and Biankin, A and Ponz-Sarvise, M and Andersen, JB and Khatri, P and Bozec, A and Sweet-Cordero, EA and Sage, J and Lecanda, F and Vicent, S},
	journal = {Nature Communications},
	year = {2017},
	title = {An integrative approach unveils {FOSL1} as an oncogene vulnerability in {KRAS}-driven lung and pancreatic {Cancer}},
	volume = {8},
}

@article{bib83,
	author = {Varn, FS and Johnson, KC and Wade, TE and Malta, TM and Sabedot, TS and Barthel, FP and Kim, H and Ahmed, N and Datta, I and Barnholtz-Sloan, JS and Bakas, S and D\textquoteright{}Angelo, F and Gan, HK and Garofano, L and Huse, JT and Khasraw, M and Kocakavuk, E and Migliozzi, S and Ormond, DR and Paek, SH and Van, MEG and Walenkamp, AME and Watts, C and Weller, M and Weiss, T and Wesseling, P and Stead, LF and Poisson, LM and Noushmehr, H and Iavarone, A and Verhaak, RG and Consortium, TG},
	journal = {bioRxiv},
	year = {2021},
	title = {Longitudinal analysis of diffuse glioma reveals cell state dynamics at recurrence associated with changes in genetics and the microenvironment},
}

@article{bib84,
	author = {Verde, P and Casalino, L and Talotta, F and Yaniv, M and Weitzman, JB},
	journal = {Cell Cycle},
	year = {2007},
	pages = {2633--2639},
	title = {Deciphering {AP}-1 function in {Tumorigenesis}: fra-ternizing on target promoters},
	volume = {6},
}

@article{bib85,
	author = {Verhaak, RG and Hoadley, KA and Purdom, E and Wang, V and Qi, Y and Wilkerson, MD and Miller, CR and Ding, L and Golub, T and Mesirov, JP and Alexe, G and Lawrence, M and O'Kelly, M and Tamayo, P and Weir, BA and Gabriel, S and Winckler, W and Gupta, S and Jakkula, L and Feiler, HS and Hodgson, JG and James, CD and Sarkaria, JN and Brennan, C and Kahn, A and Spellman, PT and Wilson, RK and Speed, TP and Gray, JW and Meyerson, M and Getz, G and Perou, CM and Hayes, DN and {Cancer Genome Atlas Research Network}},
	journal = {Cancer Cell},
	year = {2010},
	pages = {98--110},
	title = {Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in {PDGFRA}, {IDH1}, {EGFR}, and {NF1}},
	volume = {17},
}

@article{bib86,
	author = {Wang, J and Cazzato, E and Ladewig, E and Frattini, V and Rosenbloom, DIS and Zairis, S and Abate, F and Liu, Z and Elliott, O and Shin, Y-J and Lee, J-K and Lee, I-H and Park, W-Y and Eoli, M and Blumberg, AJ and Lasorella, A and Nam, D-H and Finocchiaro, G and Iavarone, A and Rabadan, R},
	journal = {Nat Genet},
	year = {2016},
	pages = {768--776},
	title = {Clonal evolution of glioblastoma under therapy},
	volume = {48},
}

@article{bib87,
	author = {Wang, Q and Hu, B and Hu, X and Kim, H and Squatrito, M and Scarpace, L and deCarvalho, AC and Lyu, S and Li, P and Li, Y and Barthel, F and Cho, HJ and Lin, YH and Satani, N and Martinez-Ledesma, E and Zheng, S and Chang, E and Sauv{\' e}, CG and Olar, A and Lan, ZD and Finocchiaro, G and Phillips, JJ and Berger, MS and Gabrusiewicz, KR and Wang, G and Eskilsson, E and Hu, J and Mikkelsen, T and DePinho, RA and Muller, F and Heimberger, AB and Sulman, EP and Nam, DH and Verhaak, RGW},
	journal = {Cancer Cell},
	year = {2017},
	pages = {42--56},
	title = {Tumor evolution of {Glioma}-{Intrinsic} gene expression subtypes associates with immunological changes in the microenvironment},
	volume = {32},
}

@article{bib88,
	author = {Wang, L and Babikir, H and M{\" u}ller, S and Yagnik, G and Shamardani, K and Catalan, F and Kohanbash, G and Alvarado, B and Di Lullo, E and Kriegstein, A and Shah, S and Wadhwa, H and Chang, SM and Phillips, JJ and Aghi, MK and Diaz, AA},
	journal = {Cancer Discovery},
	year = {2019},
	pages = {1708--1719},
	title = {The phenotypes of proliferating glioblastoma cells reside on a single {Axis} of variation},
	volume = {9},
}

@article{bib89,
	author = {Wu, J and Ji, A and Wang, X and Zhu, Y and Yu, Y and Lin, Y and Liu, Y and Li, S and Liang, Z and Xu, X and Zheng, X and Xie, L},
	journal = {Journal of Translational Medicine},
	year = {2015},
	title = {MicroRNA-195-5p, a new regulator of {Fra}-1, suppresses the migration and invasion of prostate {Cancer} cells},
	volume = {13},
}

@article{bib90,
	author = {Wu, Y and Fletcher, M and Gu, Z and Wang, Q and Costa, B and Bertoni, A and Man, KH and Schlotter, M and Felsberg, J and Mangei, J and Barbus, M and Gaupel, AC and Wang, W and Weiss, T and Eils, R and Weller, M and Liu, H and Reifenberger, G and Korshunov, A and Angel, P and Lichter, P and Herrmann, C and Radlwimmer, B},
	journal = {Nature Communications},
	year = {2020},
	title = {Glioblastoma epigenome profiling identifies {SOX10} as a master regulator of molecular tumour subtype},
	volume = {11},
}

@article{bib91,
	author = {Xu, H and Jin, X and Yuan, Y and Deng, P and Jiang, L and Zeng, X and Li, XS and Wang, ZY and Chen, QM},
	journal = {Scientific Reports},
	year = {2017},
	title = {Prognostic value from integrative analysis of transcription factors c-{Jun} and {Fra}-1 in oral squamous cell carcinoma: a multicenter cohort study},
	volume = {7},
}

@article{bib92,
	author = {Ye, X and Tam, WL and Shibue, T and Kaygusuz, Y and Reinhardt, F and Ng Eaton, E and Weinberg, RA},
	journal = {Nature},
	year = {2015},
	pages = {256--260},
	title = {Distinct {EMT} programs control normal mammary stem cells and tumour-initiating cells},
	volume = {525},
}

@article{bib93,
	author = {Younesy, H and Nielsen, CB and Lorincz, MC and Jones, SJ and Karimi, MM and M{\" o}ller, T},
	journal = {Bioinformatics},
	year = {2016},
	pages = {3324--3326},
	title = {ChAsE: chromatin analysis and exploration tool},
	volume = {32},
}

@article{bib94,
	author = {Yu, G and Wang, L-G and Han, Y and He, Q-Y},
	journal = {OMICS: A Journal of Integrative Biology},
	year = {2012},
	pages = {284--287},
	title = {clusterProfiler: an {R} package for comparing biological themes among gene clusters},
	volume = {16},
}

@article{bib95,
	author = {Zhang, Y and Liu, T and Meyer, CA and Eeckhoute, J and Johnson, DS and Bernstein, BE and Nusbaum, C and Myers, RM and Brown, M and Li, W and Liu, XS},
	journal = {Genome Biology},
	year = {2008},
	title = {Model-based analysis of {ChIP}-{Seq} ({MACS})},
	volume = {9},
}

@article{bib96,
	author = {Zhao, Z and Meng, F and Wang, W and Wang, Z and Zhang, C and Jiang, T},
	journal = {Scientific Data},
	year = {2017},
	pages = {1--7},
	title = {Comprehensive {RNA}-seq transcriptomic profiling in the malignant progression of gliomas},
	volume = {4},
}
