Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures
Pfeil, Jacob, Sanders, Lauren M, Anastopoulos, Ioannis, Lyle, A Geoffrey, Weinstein, Alana S, Xue, Yuanqing, Blair, Andrew, Beale, Holly C, Lee, Alex, Leung, Stanley G, Dinh, Phuong T, Shah, Avanthi Tayi, Breese, Marcus R, Devine, W Patrick, Bjork, Isabel, Salama, Sofie R, Sweet-Cordero, E Alejandro, Haussler, David, Vaske, Olena Morozova
Published in PLoS computational biology (10.04.2020)
Published in PLoS computational biology (10.04.2020)
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317 Omics based analysis to identify novel markers of TMZ response in Glioblastoma Multiforme
Reed, Megan R., De Loose, Annick, Guzman, Grace, Lyle, A. Geoffrey, Learned, Katrina, Vaske, Olena M., Rodriguez, Analiz
Published in Journal of clinical and translational science (01.04.2023)
Published in Journal of clinical and translational science (01.04.2023)
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A Functional Precision Medicine Pipeline Combines Comparative Transcriptomics and Tumor Organoid Modeling to Identify Bespoke Treatment Strategies for Glioblastoma
Reed, Megan R, Lyle, A Geoffrey, De Loose, Annick, Maddukuri, Leena, Learned, Katrina, Beale, Holly C, Kephart, Ellen T, Cheney, Allison, van den Bout, Anouk, Lee, Madison P, Hundley, Kelsey N, Smith, Ashley M, DesRochers, Teresa M, Vibat, Cecile Rose T, Gokden, Murat, Salama, Sofie, Wardell, Christopher P, Eoff, Robert L, Vaske, Olena M, Rodriguez, Analiz
Published in Cells (Basel, Switzerland) (02.12.2021)
Published in Cells (Basel, Switzerland) (02.12.2021)
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Identification of a differentiation stall in epithelial mesenchymal transition in histone H3–mutant diffuse midline glioma
Sanders, Lauren M, Cheney, Allison, Seninge, Lucas, van den Bout, Anouk, Chen, Marissa, Beale, Holly C, Kephart, Ellen Towle, Pfeil, Jacob, Learned, Katrina, Lyle, A Geoffrey, Bjork, Isabel, Haussler, David, Salama, Sofie R, Vaske, Olena M
Published in Gigascience (15.12.2020)
Published in Gigascience (15.12.2020)
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Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors
Sanders, Lauren M., Chandra, Rahul, Zebarjadi, Navid, Beale, Holly C., Lyle, A. Geoffrey, Rodriguez, Analiz, Kephart, Ellen Towle, Pfeil, Jacob, Cheney, Allison, Learned, Katrina, Currie, Rob, Gitlin, Leonid, Vengerov, David, Haussler, David, Salama, Sofie R., Vaske, Olena M.
Published in Communications biology (13.12.2022)
Published in Communications biology (13.12.2022)
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323 Generation of a functional precision medicine pipeline which combines comparative transcriptomics and tumor organoid modeling to identify bespoke treatment strategies for glioblastoma
Reed, Megan R., Lyle, A. Geoffrey, De Loose, Annick, Learned, Katrina, Vibat, Cecile Rose T., Wardell, Christopher P., Eoff, Robert L., Vaske, Olena M., Rodriguez, Analiz
Published in Journal of clinical and translational science (01.04.2022)
Published in Journal of clinical and translational science (01.04.2022)
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Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor
Sanders, Lauren M, Rangaswami, Arun, Bjork, Isabel, Lam, Du Linh, Beale, Holly C, Kephart, Ellen Towle, Durbin, Ann, Learned, Katrina, Currie, Rob, Lyle, A Geoffrey, Pfeil, Jacob, Shah, Avanthi Tayi, Lee, Alex G, Leung, Stanley G, Behroozfard, Inge H, Breese, Marcus R, Peralez, Jennifer, Hazard, Florette K, Lacayo, Norman, Spunt, Sheri L, Haussler, David, Salama, Sofie R, Sweet-Cordero, E Alejandro, Vaske, Olena M
Published in Cold Spring Harbor molecular case studies (01.10.2019)
Published in Cold Spring Harbor molecular case studies (01.10.2019)
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The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets
Beale, Holly C, Roger, Jacquelyn M, Cattle, Matthew A, McKay, Liam T, Thompson, Drew K A, Learned, Katrina, Lyle, A Geoffrey, Kephart, Ellen T, Currie, Rob, Lam, Du Linh, Sanders, Lauren, Pfeil, Jacob, Vivian, John, Bjork, Isabel, Salama, Sofie R, Haussler, David, Vaske, Olena M
Published in Gigascience (13.03.2021)
Published in Gigascience (13.03.2021)
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70. Epigenetic reprogramming in thalamic H3K27-altered glioma neural progenitor cells
Cheney, Allison, Xue, Yuanqing (Bianca), Lyle, A. Geoffrey, Kephart, Ellen T., Stuart, Josh M., Vaske, Olena M.
Published in Cancer genetics (01.11.2023)
Published in Cancer genetics (01.11.2023)
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Abstract 6154: H3K27M gliomas are characterized by a stall in the epithelial-mesenchymal transition
CHENEY, ALLISON R., Sanders, Lauren M., Seninge, Lucas, Beale, Holly C., Kephart, Ellen Towle, Pfeil, Jacob, Learned, Katrina, Lyle, A. Geoffrey, Bjork, Isabel, Haussler, David, Salama, Sofie R., Vaske, Olena M.
Published in Cancer research (Chicago, Ill.) (15.08.2020)
Published in Cancer research (Chicago, Ill.) (15.08.2020)
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Abstract B06: Candidate differentiation stall in epithelial mesenchymal transition in H3K27M diffuse midline glioma
Cheney, Allison R., Sanders, Lauren M., Seninge, Lucas, Beale, Holly C., Kephart, Ellen Towle, Pfeil, Jacob, Learned, Katrina, Lyle, A. Geoffrey, Bjork, Isabel, Haussler, David, Salama, Sofie R., Vaske, Olena M.
Published in Cancer research (Chicago, Ill.) (15.07.2020)
Published in Cancer research (Chicago, Ill.) (15.07.2020)
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Abstract A44: Comparative gene expression analysis for identification and prioritization of therapeutic targets in a cohort of childhood cancers
Sanders, Lauren M., Lyle, A. Geoffrey, Beale, Holly C., Kephart, Ellen Towle, Learned, Katrina, Peralez, Jennifer, Lacayo, Norman, Rangaswami, Arun, Spunt, Sheri L., Bjork, Isabel, Haussler, David, Salama, Sofie R., Vaske, Olena M.
Published in Cancer research (Chicago, Ill.) (15.07.2020)
Published in Cancer research (Chicago, Ill.) (15.07.2020)
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Abstract LB059: Subtype classification of pediatric high-grade glioma tumors by comparative transcriptomics
Mawla, Gina D., Lyle, A. Geoffrey, Kephart, Ellen T., Learned, Katrina, Beale, Holly C., Goldford, Joshua E., Vaske, Olena M.
Published in Cancer research (Chicago, Ill.) (15.06.2022)
Published in Cancer research (Chicago, Ill.) (15.06.2022)
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