TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data von Colaprico, Antonio, Silva, Tiago C, Olsen, Catharina, Garofano, Luciano, Cava, Claudia, Garolini, Davide, Sabedot, Thais S, Malta, Tathiane M, Pagnotta, Stefano M, Castiglioni, Isabella, Ceccarelli, Michele, Bontempi, Gianluca, Noushmehr, Houtan

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New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx von Mounir, Mohamed, Lucchetta, Marta, Silva, Tiago C, Olsen, Catharina, Bontempi, Gianluca, Chen, Xi, Noushmehr, Houtan, Colaprico, Antonio, Papaleo, Elena

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TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations] von Silva, Tiago C, Colaprico, Antonio, Olsen, Catharina, D'Angelo, Fulvio, Bontempi, Gianluca, Ceccarelli, Michele, Noushmehr, Houtan

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Glioma CpG island methylator phenotype (G-CIMP): biological and clinical implications von Malta, Tathiane M, de Souza, Camila F, Sabedot, Thais S, Silva, Tiago C, Mosella, Maritza S, Kalkanis, Steven N, Snyder, James, Castro, Ana Valeria B, Noushmehr, Houtan

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ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles von Silva, Tiago C, Coetzee, Simon G, Gull, Nicole, Yao, Lijing, Hazelett, Dennis J, Noushmehr, Houtan, Lin, De-Chen, Berman, Benjamin P

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Genome-scale analysis of aberrant DNA methylation in colorectal cancer von Hinoue, Toshinori, Weisenberger, Daniel J, Lange, Christopher P E, Shen, Hui, Byun, Hyang-Min, Van Den Berg, David, Malik, Simeen, Pan, Fei, Noushmehr, Houtan, van Dijk, Cornelis M, Tollenaar, Rob A E M, Laird, Peter W

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Interpreting pathways to discover cancer driver genes with Moonlight von Colaprico, Antonio, Olsen, Catharina, Bailey, Matthew H., Odom, Gabriel J., Terkelsen, Thilde, Silva, Tiago C., Olsen, André V., Cantini, Laura, Zinovyev, Andrei, Barillot, Emmanuel, Noushmehr, Houtan, Bertoli, Gloria, Castiglioni, Isabella, Cava, Claudia, Bontempi, Gianluca, Chen, Xi Steven, Papaleo, Elena

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Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology von Golebiewska, Anna, Hau, Ann-Christin, Oudin, Anaïs, Stieber, Daniel, Yabo, Yahaya A., Baus, Virginie, Barthelemy, Vanessa, Klein, Eliane, Bougnaud, Sébastien, Keunen, Olivier, Wantz, May, Michelucci, Alessandro, Neirinckx, Virginie, Muller, Arnaud, Kaoma, Tony, Nazarov, Petr V., Azuaje, Francisco, De Falco, Alfonso, Flies, Ben, Richart, Lorraine, Poovathingal, Suresh, Arns, Thais, Grzyb, Kamil, Mock, Andreas, Herold-Mende, Christel, Steino, Anne, Brown, Dennis, May, Patrick, Miletic, Hrvoje, Malta, Tathiane M., Noushmehr, Houtan, Kwon, Yong-Jun, Jahn, Winnie, Klink, Barbara, Tanner, Georgette, Stead, Lucy F., Mittelbronn, Michel, Skupin, Alexander, Hertel, Frank, Bjerkvig, Rolf, Niclou, Simone P.

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A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants von Gusev, Alexander, Lawrenson, Kate, Lin, Xianzhi, Lyra, Paulo C., Kar, Siddhartha, Vavra, Kevin C., Segato, Felipe, Fonseca, Marcos A. S., Lee, Janet M., Pejovic, Tanya, Liu, Gang, Karlan, Beth Y., Freedman, Matthew L., Noushmehr, Houtan, Monteiro, Alvaro N., Pharoah, Paul D. P., Pasaniuc, Bogdan, Gayther, Simon A.

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A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence von de Souza, Camila Ferreira, Sabedot, Thais S., Malta, Tathiane M., Stetson, Lindsay, Morozova, Olena, Sokolov, Artem, Laird, Peter W., Wiznerowicz, Maciej, Iavarone, Antonio, Snyder, James, deCarvalho, Ana, Sanborn, Zachary, McDonald, Kerrie L., Friedman, William A., Tirapelli, Daniela, Poisson, Laila, Mikkelsen, Tom, Carlotti, Carlos G., Kalkanis, Steven, Zenklusen, Jean, Salama, Sofie R., Barnholtz-Sloan, Jill S., Noushmehr, Houtan

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Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens von Prendergast, Emily N, de Souza Fonseca, Marcos Abraão, Dezem, Felipe Segato, Lester, Jenny, Karlan, Beth Y, Noushmehr, Houtan, Lin, Xianzhi, Lawrenson, Kate

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Expression and regulatory roles of lncRNAs in G-CIMP-low vs G-CIMP-high Glioma: an in-silico analysis von Datta, Indrani, Noushmehr, Houtan, Brodie, Chaya, Poisson, Laila M.

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Molecular landscape of IDH-mutant primary astrocytoma Grade IV/glioblastomas von Wong, Queenie Hoi-Wing, Li, Kay Ka-Wai, Wang, Wei-Wei, Malta, Tathiane M., Noushmehr, Houtan, Grabovska, Yura, Jones, Chris, Chan, Aden Ka-Yin, Kwan, Johnny Sheung-Him, Huang, Queenie Jun-Qi, Wong, Gabriel Chun-Hei, Li, Wen-Cai, Liu, Xian-Zhi, Chen, Hong, Chan, Danny Tat-Ming, Mao, Ying, Zhang, Zhen-Yu, Shi, Zhi-Feng, Ng, Ho-Keung

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A Study of High-Grade Serous Ovarian Cancer Origins Implicates the SOX18 Transcription Factor in Tumor Development von Lawrenson, Kate, Fonseca, Marcos A.S., Liu, Annie Y., Segato Dezem, Felipe, Lee, Janet M., Lin, Xianzhi, Corona, Rosario I., Abbasi, Forough, Vavra, Kevin C., Dinh, Huy Q., Gill, Navjot Kaur, Seo, Ji-Heui, Coetzee, Simon, Lin, Yvonne G., Pejovic, Tanja, Mhawech-Fauceglia, Paulette, Rowat, Amy C., Drapkin, Ronny, Karlan, Beth Y., Hazelett, Dennis J., Freedman, Matthew L., Gayther, Simon A., Noushmehr, Houtan

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Gene reactivation by 5-aza-2'-deoxycytidine-induced demethylation requires SRCAP-mediated H2A.Z insertion to establish nucleosome depleted regions von Yang, Xiaojing, Noushmehr, Houtan, Han, Han, Andreu-Vieyra, Claudia, Liang, Gangning, Jones, Peter A

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Correction to: Molecular landscape of IDH-mutant primary astrocytoma Grade IV/Glioblastomas von Wong, Queenie Hoi-Wing, Li, Kay Ka-Wai, Wang, Wei-Wei, Malta, Tathiane M., Noushmehr, Houtan, Grabovska, Yura, Jones, Chris, Chan, Aden Ka-Yin, Kwan, Johnny Sheung-Him, Huang, Queenie Jun-Qi, Wong, Gabriel Chun-Hei, Li, Wen-Cai, Liu, Xian-Zhi, Chen, Hong, Chan, Danny Tat-Ming, Mao, Ying, Zhang, Zhen-Yu, Shi, Zhi-Feng, Ng, Ho-Keung

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Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells von Rhie, Suhn Kyong, Hazelett, Dennis J, Coetzee, Simon G, Yan, Chunli, Noushmehr, Houtan, Coetzee, Gerhard A

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Machine Learning Applications in the Neuro ICU: A Solution to Big Data Mayhem? von Chaudhry, Farhan, Hunt, Rachel J., Hariharan, Prashant, Anand, Sharath Kumar, Sanjay, Surya, Kjoller, Ellen E., Bartlett, Connor M., Johnson, Kipp W., Levy, Phillip D., Noushmehr, Houtan, Lee, Ian Y.

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Comprehensive functional annotation of seventy-one breast cancer risk Loci von Rhie, Suhn Kyong, Coetzee, Simon G, Noushmehr, Houtan, Yan, Chunli, Kim, Jae Mun, Haiman, Christopher A, Coetzee, Gerhard A

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Super-Enhancer-Associated LncRNA UCA1 Interacts Directly with AMOT to Activate YAP Target Genes in Epithelial Ovarian Cancer von Lin, Xianzhi, Spindler, Tassja J., de Souza Fonseca, Marcos Abraão, Corona, Rosario I., Seo, Ji-Heui, Dezem, Felipe Segato, Li, Lewyn, Lee, Janet M., Long, Henry W., Sellers, Thomas A., Karlan, Beth Y., Noushmehr, Houtan, Freedman, Matthew L., Gayther, Simon A., Lawrenson, Kate

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