GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data von Liu, Xiaochuan, Bienkowska, Jadwiga R, Zhong, Wenyan

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Expanding control of the tumor cell cycle with a CDK2/4/6 inhibitor von Freeman-Cook, Kevin, Hoffman, Robert L., Miller, Nichol, Almaden, Jonathan, Chionis, John, Zhang, Qin, Eisele, Koleen, Liu, Chaoting, Zhang, Cathy, Huser, Nanni, Nguyen, Lisa, Costa-Jones, Cinthia, Niessen, Sherry, Carelli, Jordan, Lapek, John, Weinrich, Scott L., Wei, Ping, McMillan, Elizabeth, Wilson, Elizabeth, Wang, Tim S., McTigue, Michele, Ferre, Rose Ann, He, You-Ai, Ninkovic, Sacha, Behenna, Douglas, Tran, Khanh T., Sutton, Scott, Nagata, Asako, Ornelas, Martha A., Kephart, Susan E., Zehnder, Luke R., Murray, Brion, Xu, Meirong, Solowiej, James E., Visswanathan, Ravi, Boras, Britton, Looper, David, Lee, Nathan, Bienkowska, Jadwiga R., Zhu, Zhou, Kan, Zhengyan, Ding, Ying, Mu, Xinmeng Jasmine, Oderup, Cecilia, Salek-Ardakani, Shahram, White, Michael A., VanArsdale, Todd, Dann, Stephen G.

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Comparison of the molecular and cellular phenotypes of common mouse syngeneic models with human tumors von Zhong, Wenyan, Myers, Jeremy S, Wang, Fang, Wang, Kai, Lucas, Justin, Rosfjord, Edward, Lucas, Judy, Hooper, Andrea T, Yang, Sharon, Lemon, Lu Anna, Guffroy, Magali, May, Chad, Bienkowska, Jadwiga R, Rejto, Paul A

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Chemotherapy induces dynamic immune responses in breast cancers that impact treatment outcome von Park, Yeon Hee, Lal, Samir, Lee, Jeong Eon, Choi, Yoon-La, Wen, Ji, Ram, Sripad, Ding, Ying, Lee, Soo-Hyeon, Powell, Eric, Lee, Se Kyung, Yu, Jong Han, Ching, Keith A., Nam, Jae-Yong, Kim, Seok Won, Nam, Seok Jin, Kim, Ji-Yeon, Cho, Soo Youn, Park, Seri, Kim, Jinho, Hwang, Soohyn, Kim, Yu Jin, Bonato, Vinicius, Fernandez, Diane, Deng, Shibing, Wang, Shuoguo, Shin, Hyuntae, Kang, Eun-Suk, Park, Woong-Yang, Rejto, Paul A., Bienkowska, Jadwiga, Kan, Zhengyan

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Model to improve specificity for identification of clinically-relevant expanded T cells in peripheral blood von Rytlewski, Julie, Deng, Shibing, Xie, Tao, Davis, Craig, Robins, Harlan, Yusko, Erik, Bienkowska, Jadwiga

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Abstract 4143: Characterizing the immunogenicity of gastric cancer by transcriptomic expression based immune phenotyping von Wang, Kai, Siu, Hoicheong, Deng, Shibing, Bienkowska, Jadwiga R., Leung, Suet Yi

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Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation von Ford, Kyle, Munson, Brenton P., Fong, Samson H., Panwala, Rebecca, Chu, Wai Keung, Rainaldi, Joseph, Plongthongkum, Nongluk, Arunachalam, Vinayagam, Kostrowicki, Jarek, Meluzzi, Dario, Kreisberg, Jason F., Jensen-Pergakes, Kristen, VanArsdale, Todd, Paul, Thomas, Tamayo, Pablo, Zhang, Kun, Bienkowska, Jadwiga, Mali, Prashant, Ideker, Trey

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Lymphotoxin-LIGHT pathway regulates the interferon signature in rheumatoid arthritis von Bienkowska, Jadwiga, Allaire, Norm, Thai, Alice, Goyal, Jaya, Plavina, Tatiana, Nirula, Ajay, Weaver, Megan, Newman, Charlotte, Petri, Michelle, Beckman, Evan, Browning, Jeffrey L

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Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer von Park, Yeon Hee, Im, Seock-Ah, Park, Kyunghee, Wen, Ji, Lee, Kyung-Hun, Choi, Yoon-La, Lee, Won-Chul, Min, Ahrum, Bonato, Vinicius, Park, Seri, Ram, Sripad, Lee, Dae-Won, Kim, Ji-Yeon, Lee, Su Kyeong, Lee, Won-Woo, Lee, Jisook, Kim, Miso, Kim, Hyun Seon, Weinrich, Scott L, Ryu, Han Suk, Kim, Tae Yong, Dann, Stephen, Kim, Yu-Jin, Fernandez, Diane R, Koh, Jiwon, Wang, Shuoguo, Park, Song Yi, Deng, Shibing, Powell, Eric, Ravi, Rupesh Kanchi, Bienkowska, Jadwiga, Rejto, Paul A, Park, Woong-Yang, Kan, Zhengyan

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Convergent random forest predictor: Methodology for predicting drug response from genome-scale data applied to anti-TNF response von Bienkowska, Jadwiga R., Dalgin, Gul S., Batliwalla, Franak, Allaire, Normand, Roubenoff, Ronenn, Gregersen, Peter K., Carulli, John P.

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TNER: a novel background error suppression method for mutation detection in circulating tumor DNA von Deng, Shibing, Lira, Maruja, Huang, Donghui, Wang, Kai, Valdez, Crystal, Kinong, Jennifer, Rejto, Paul A, Bienkowska, Jadwiga, Hardwick, James, Xie, Tao

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Crystal structure of the anthrax lethal factor von Pannifer, Andrew D., Wong, Thiang Yian, Schwarzenbacher, Robert, Renatus, Martin, Petosa, Carlo, Bienkowska, Jadwiga, Lacy, D. Borden, Collier, R. John, Park, Sukjoon, Leppla, Stephen H., Hanna, Philip, Liddington, Robert C.

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Causal modeling using network ensemble simulations of genetic and gene expression data predicts genes involved in rheumatoid arthritis von Xing, Heming, McDonagh, Paul D, Bienkowska, Jadwiga, Cashorali, Tanya, Runge, Karl, Miller, Robert E, Decaprio, Dave, Church, Bruce, Roubenoff, Ronenn, Khalil, Iya G, Carulli, John

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computational framework for boosting confidence in high-throughput protein-protein interaction datasets von Hosur, Raghavendra, Peng, Jian, Vinayagam, Arunachalam, Stelzl, Ulrich, Xu, Jinbo, Perrimon, Norbert, Bienkowska, Jadwiga, Berger, Bonnie

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Crystal structure of the zeta isoform of the 14-3-3 protein von Liu, Dong, Bienkowska, Jadwiga, Petosa, Carlo, Collier, R. John, Fu, Halan, Liddington, Robert

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Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol... von Allaire, Normand E, Bushnell, Steven E, Bienkowska, Jadwiga, Brock, Graham, Carulli, John

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iWRAP: An Interface Threading Approach with Application to Prediction of Cancer-Related Protein–Protein Interactions von Hosur, Raghavendra, Xu, Jinbo, Bienkowska, Jadwiga, Berger, Bonnie

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The von Willebrand Factor A3 Domain Does Not Contain a Metal Ion-dependent Adhesion Site Motif von Bienkowska, Jadwiga, Cruz, Miguel, Atiemo, Andrew, Handin, Robert, Liddington, Robert

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PINCER: improved CRISPR/Cas9 screening by efficient cleavage at conserved residues von Veeneman, Brendan, Gao, Ying, Grant, Joy, Fruhling, David, Ahn, James, Bosbach, Benedikt, Bienkowska, Jadwiga, Follettie, Maximillian, Arndt, Kim, Myers, Jeremy, Zhong, Wenyan

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Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data von Simmons, Sean, Peng, Jian, Bienkowska, Jadwiga, Berger, Bonnie

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