Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results von Rahman, Mumtahena, Jackson, Laurie K, Johnson, W Evan, Li, Dean Y, Bild, Andrea H, Piccolo, Stephen R

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Paradoxical cancer cell proliferation after FGFR inhibition through decreased p21 signaling in FGFR1-amplified breast cancer cells von Chi, Feng, Griffiths, Jason I, Nath, Aritro, Bild, Andrea H

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ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers von Nath, Aritro, Cohen, Adam L, Bild, Andrea H

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Phylogenetic inference from single-cell RNA-seq data von Liu, Xuan, Griffiths, Jason I., Bishara, Isaac, Liu, Jiayi, Bild, Andrea H., Chang, Jeffrey T.

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Leveraging Single-Cell Approaches in Cancer Precision Medicine von Nath, Aritro, Bild, Andrea H.

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Multiple ABCB1 transcriptional fusions in drug resistant high-grade serous ovarian and breast cancer von Christie, Elizabeth L., Pattnaik, Swetansu, Beach, Jessica, Copeland, Anthony, Rashoo, Nineveh, Fereday, Sian, Hendley, Joy, Alsop, Kathryn, Brady, Samuel L., Lamb, Greg, Pandey, Ahwan, deFazio, Anna, Thorne, Heather, Bild, Andrea, Bowtell, David D. L.

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Usefulness of Circulating Tumor DNA in Identifying Somatic Mutations and Tracking Tumor Evolution in Patients With Non-small Cell Lung Cancer von Roosan, Moom R., Mambetsariev, Isa, Pharaon, Rebecca, Fricke, Jeremy, Husain, Hatim, Reckamp, Karen L., Koczywas, Marianna, Massarelli, Erminia, Bild, Andrea H., Salgia, Ravi

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Cell facilitation promotes growth and survival under drug pressure in breast cancer von Emond, Rena, Griffiths, Jason I., Grolmusz, Vince Kornél, Nath, Aritro, Chen, Jinfeng, Medina, Eric F., Sousa, Rachel S., Synold, Timothy, Adler, Frederick R., Bild, Andrea H.

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RAGE ablation attenuates glioma progression and enhances tumor immune responses by suppressing galectin-3 expression von Zhang, Ian Y, Liu, Shunan, Zhang, Leying, Liang, Rongrui, Fang, Qingxiao, Zhao, Jie, Ren, Lyuzhi, Medina, Eric F, Filippov, Aleksandr, Bonjoc, Kimberley-Jane, Chaudhry, Ammar, Dayyani, Mojtaba, Bild, Andrea H, Badie, Behnam

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Oncogenic pathway signatures in human cancers as a guide to targeted therapies von Nevins, Joseph R, Bild, Andrea H, Yao, Guang, Chang, Jeffrey T, Wang, Quanli, Potti, Anil, Chasse, Dawn, Joshi, Mary-Beth, Harpole, David, Lancaster, Johnathan M, Berchuck, Andrew, Olson, John A, Marks, Jeffrey R, Dressman, Holly K, West, Mike

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A single-sample microarray normalization method to facilitate personalized-medicine workflows von Piccolo, Stephen R., Sun, Ying, Campbell, Joshua D., Lenburg, Marc E., Bild, Andrea H., Johnson, W. Evan

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Circulating immune cell phenotype dynamics reflect the strength of tumor–immune cell interactions in patients during immunotherapy von Griffiths, Jason I., Wallet, Pierre, Pflieger, Lance T., Stenehjem, David, Liu, Xuan, Cosgrove, Patrick A., Leggett, Neena A., McQuerry, Jasmine A., Shrestha, Gajendra, Rossetti, Maura, Sunga, Gemalene, Moos, Philip J., Adler, Frederick R., Chang, Jeffrey T., Sharma, Sunil, Bild, Andrea H.

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Multiplatform single-sample estimates of transcriptional activation von Piccolo, Stephen R., Withers, Michelle R., Francis, Owen E., Bild, Andrea H., Johnson, W. Evan

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Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer von Nath, Aritro, Cosgrove, Patrick A., Mirsafian, Hoda, Christie, Elizabeth L., Pflieger, Lance, Copeland, Benjamin, Majumdar, Sumana, Cristea, Mihaela C., Han, Ernest S., Lee, Stephen J., Wang, Edward W., Fereday, Sian, Traficante, Nadia, Salgia, Ravi, Werner, Theresa, Cohen, Adam L., Moos, Philip, Chang, Jeffrey T., Bowtell, David D. L., Bild, Andrea H.

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ONC201/TIC10 enhances durability of mTOR inhibitor everolimus in metastatic ER+ breast cancer von Farmaki, Elena, Nath, Aritro, Emond, Rena, Karimi, Kimya L, Grolmusz, Vince K, Cosgrove, Patrick A, Bild, Andrea H

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A Pan-ALDH1A Inhibitor Induces Necroptosis in Ovarian Cancer Stem-like Cells von Chefetz, Ilana, Grimley, Edward, Yang, Kun, Hong, Linda, Vinogradova, Ekaterina V., Suciu, Radu, Kovalenko, Ilya, Karnak, David, Morgan, Cynthia A., Chtcherbinine, Mikhail, Buchman, Cameron, Huddle, Brandt, Barraza, Scott, Morgan, Meredith, Bernstein, Kara A., Yoon, Euisik, Lombard, David B., Bild, Andrea, Mehta, Geeta, Romero, Iris, Chiang, Chun-Yi, Landen, Charles, Cravatt, Benjamin, Hurley, Thomas D., Larsen, Scott D., Buckanovich, Ronald J.

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A machine learning framework for scRNA-seq UMI threshold optimization and accurate classification of cell types von Bishara, Isaac, Chen, Jinfeng, Griffiths, Jason I, Bild, Andrea H, Nath, Aritro

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Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes von McQuerry, Jasmine A, Jenkins, David F, Yost, Susan E, Zhang, Yuqing, Schmolze, Daniel, Johnson, W Evan, Yuan, Yuan, Bild, Andrea H

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Combating subclonal evolution of resistant cancer phenotypes von Brady, Samuel W., McQuerry, Jasmine A., Qiao, Yi, Piccolo, Stephen R., Shrestha, Gajendra, Jenkins, David F., Layer, Ryan M., Pedersen, Brent S., Miller, Ryan H., Esch, Amanda, Selitsky, Sara R., Parker, Joel S., Anderson, Layla A., Dalley, Brian K., Factor, Rachel E., Reddy, Chakravarthy B., Boltax, Jonathan P., Li, Dean Y., Moos, Philip J., Gray, Joe W., Heiser, Laura M., Buys, Saundra S., Cohen, Adam L., Johnson, W. Evan, Quinlan, Aaron R., Marth, Gabor, Werner, Theresa L., Bild, Andrea H.

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Mechanisms and clinical implications of tumor heterogeneity and convergence on recurrent phenotypes von McQuerry, Jasmine A., Chang, Jeffrey T., Bowtell, David D. L., Cohen, Adam, Bild, Andrea H.

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