Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data von Sun, Duanchen, Guan, Xiangnan, Moran, Amy E., Wu, Ling-Yun, Qian, David Z., Schedin, Pepper, Dai, Mu-Shui, Danilov, Alexey V., Alumkal, Joshi J., Adey, Andrew C., Spellman, Paul T., Xia, Zheng

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Postpartum breast cancer has a distinct molecular profile that predicts poor outcomes von Jindal, Sonali, Pennock, Nathan D., Sun, Duanchen, Horton, Wesley, Ozaki, Michelle K., Narasimhan, Jayasri, Bartlett, Alexandra Q., Weinmann, Sheila, Goss, Paul E., Borges, Virginia F., Xia, Zheng, Schedin, Pepper

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Mesenchymal Lineage Heterogeneity Underlies Nonredundant Functions of Pancreatic Cancer-Associated Fibroblasts von Helms, Erin J, Berry, Mark W, Chaw, R Crystal, DuFort, Christopher C, Sun, Duanchen, Onate, M Kathrina, Oon, Chet, Bhattacharyya, Sohinee, Sanford-Crane, Hannah, Horton, Wesley, Finan, Jennifer M, Sattler, Ariana, Makar, Rosemary, Dawson, David W, Xia, Zheng, Hingorani, Sunil R, Sherman, Mara H

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Highly scalable generation of DNA methylation profiles in single cells von Mulqueen, Ryan M, Pokholok, Dmitry, Norberg, Steven J, Torkenczy, Kristof A, Fields, Andrew J, Sun, Duanchen, Sinnamon, John R, Shendure, Jay, Trapnell, Cole, O'Roak, Brian J, Xia, Zheng, Steemers, Frank J, Adey, Andrew C

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BET bromodomain inhibition blocks the function of a critical AR-independent master regulator network in lethal prostate cancer von Coleman, Daniel J., Gao, Lina, King, Carly J., Schwartzman, Jacob, Urrutia, Joshua, Sehrawat, Archana, Tayou, Junior, Balter, Ariel, Burchard, Julja, Chiotti, Kami E., Derrick, Daniel S., Sun, Duanchen, Xia, Zheng, Heiser, Laura M., Alumkal, Joshi J.

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Genomic Drivers of Poor Prognosis and Enzalutamide Resistance in Metastatic Castration-resistant Prostate Cancer von Chen, William S., Aggarwal, Rahul, Zhang, Li, Zhao, Shuang G., Thomas, George V., Beer, Tomasz M., Quigley, David A., Foye, Adam, Playdle, Denise, Huang, Jiaoti, Lloyd, Paul, Lu, Eric, Sun, Duanchen, Guan, Xiangnan, Rettig, Matthew, Gleave, Martin, Evans, Christopher P., Youngren, Jack, True, Lawrence, Lara, Primo, Kothari, Vishal, Xia, Zheng, Chi, Kim N., Reiter, Robert E., Maher, Christopher A., Feng, Felix Y., Small, Eric J., Alumkal, Joshi J.

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Identification of DNA motif pairs on paired sequences based on composite heterogeneous graph von Wu, Qiuqin, Li, Yang, Wang, Qi, Zhao, Xiaoyu, Sun, Duanchen, Liu, Bingqiang

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CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma von Thieme, Elana, Bruss, Nur, Sun, Duanchen, Dominguez, Edward C, Coleman, Daniel, Liu, Tingting, Roleder, Carly, Martinez, Melissa, Garcia-Mansfield, Krystine, Ball, Brian, Pirrotte, Patrick, Wang, Lili, Xia, Zheng, Danilov, Alexey V

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RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery von Pennock, Nathan D, Jindal, Sonali, Horton, Wesley, Sun, Duanchen, Narasimhan, Jayasri, Carbone, Lucia, Fei, Suzanne S, Searles, Robert, Harrington, Christina A, Burchard, Julja, Weinmann, Sheila, Schedin, Pepper, Xia, Zheng

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Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4 von Coleman, Daniel J., Sampson, David A., Sehrawat, Archana, Kumaraswamy, Anbarasu, Sun, Duanchen, Wang, Yuzhuo, Schwartzman, Jacob, Urrutia, Joshua, Lee, Ahn R., Coleman, Ilsa M., Nelson, Peter S., Dong, Xuesen, Morrissey, Colm, Corey, Eva, Xia, Zheng, Yates, Joel A., Alumkal, Joshi J.

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Reverse network diffusion to remove indirect noise for better inference of gene regulatory networks von Yu, Jiating, Leng, Jiacheng, Yuan, Fan, Sun, Duanchen, Wu, Ling-Yun

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ActivePPI: quantifying protein–protein interaction network activity with Markov random fields von Wang, Chuanyuan, Xu, Shiyu, Sun, Duanchen, Liu, Zhi-Ping

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Network Refinement: Denoising complex networks for better community detection von Yu, Jiating, Leng, Jiacheng, Sun, Duanchen, Wu, Ling-Yun

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Pharmacologic Targeting of Mcl-1 Induces Mitochondrial Dysfunction and Apoptosis in B-Cell Lymphoma Cells in a TP53- and BAX- Dependent Manner von Liu, Tingting, Lam, Vi, Thieme, Elana, Sun, Duanchen, Wang, Xiaoguang, Xu, Fei, Wang, Lili, Danilova, Olga V, Xia, Zheng, Tyner, Jeffrey W, Kurtz, Stephen E, Danilov, Alexey V

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Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis von Yu, Jiating, Leng, Jiacheng, Hou, Zhichao, Sun, Duanchen, Wu, Ling-Yun

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A Cancer Cell-Intrinsic GOT2-PPARδ Axis Suppresses Antitumor Immunity von Abrego, Jaime, Sanford-Crane, Hannah, Oon, Chet, Xiao, Xu, Betts, Courtney B, Sun, Duanchen, Nagarajan, Shanthi, Diaz, Luis, Sandborg, Holly, Bhattacharyya, Sohinee, Xia, Zheng, Coussens, Lisa M, Tontonoz, Peter, Sherman, Mara H

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Transcriptional Reprogramming of Super-Enhancer Associated Oncogenes Following Inhibition of Cyclin-Dependent Kinase-9 (CDK9) in Aggressive Non-Hodgkin Lymphoma (NHL) von Thieme, Elana, Sun, Duanchen, Sharma, Geeta G, Bruss, Nur, Liu, Tingting, Coleman, Daniel J, Xia, Zheng, Danilov, Alexey V.

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Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance von Alumkal, Joshi J., Sun, Duanchen, Lu, Eric, Beer, Tomasz M., Thomas, George V., Latour, Emile, Aggarwal, Rahul, Cetnar, Jeremy, Ryan, Charles J., Tabatabaei, Shaadi, Bailey, Shawna, Turina, Claire B., Quigley, David A., Guan, Xiangnan, Foye, Adam, Youngren, Jack F., Urrutia, Joshua, Huang, Jiaoti, Weinstein, Alana S., Friedl, Verena, Rettig, Matthew, Reiter, Robert E., Spratt, Daniel E., Gleave, Martin, Evans, Christopher P., Stuart, Joshua M., Chen, Yiyi, Feng, Felix Y., Small, Eric J., Witte, Owen N., Xia, Zheng

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Abstract PO-095: A cancer cell-intrinsic GOT2-PPARδ axis suppresses antitumor immunity von Abrego, Jaime, Sanford-Crane, Hannah, Oon, Chet, Xiao, Xu, Betts, Courtney, Sun, Duanchen, Nagarajan, Shanthi, Xia, Zheng, Coussens, Lisa, Tontonoz, Peter, Sherman, Mara

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BET Bromodomain Inhibition Blocks an AR-Repressed, E2F1-Activated Treatment-Emergent Neuroendocrine Prostate Cancer Lineage Plasticity Program von Kim, Dae-Hwan, Sun, Duanchen, Storck, William K, Welker Leng, Katherine, Jenkins, Chelsea, Coleman, Daniel J, Sampson, David, Guan, Xiangnan, Kumaraswamy, Anbarasu, Rodansky, Eva S, Urrutia, Joshua A, Schwartzman, Jacob A, Zhang, Chao, Beltran, Himisha, Labrecque, Mark P, Morrissey, Colm, Lucas, Jared M, Coleman, Ilsa M, Nelson, Peter S, Corey, Eva, Handelman, Samuel K, Sexton, Jonathan Z, Aggarwal, Rahul, Abida, Wassim, Feng, Felix Y, Small, Eric J, Spratt, Daniel E, Bankhead, 3rd, Armand, Rao, Arvind, Gesner, Emily M, Attwell, Sarah, Lakhotia, Sanjay, Campeau, Eric, Yates, Joel A, Xia, Zheng, Alumkal, Joshi J

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