An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma von Sumazin, Pavel, Yang, Xuerui, Chiu, Hua-Sheng, Chung, Wei-Jen, Iyer, Archana, Llobet-Navas, David, Rajbhandari, Presha, Bansal, Mukesh, Guarnieri, Paolo, Silva, Jose, Califano, Andrea

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Pan‐cancer clinical and molecular analysis of racial disparities von Lara, Olivia D., Wang, Ying, Asare, Amma, Xu, Tao, Chiu, Hua‐Sheng, Liu, Yuexin, Hu, Wei, Sumazin, Pavel, Uppal, Shitanshu, Zhang, Lin, Rauh‐Hain, J. Alejandro, Sood, Anil K.

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Cell lines of the same anatomic site and histologic type show large variability in intrinsic radiosensitivity and relative biological effectiveness to protons and carbon ions von Flint, David B., Bright, Scott J., McFadden, Conor H., Konishi, Teruaki, Ohsawa, Daisuke, Turner, Broderick, Lin, Steven H., Grosshans, David R., Chiu, Hua‐Sheng, Sumazin, Pavel, Shaitelman, Simona F., Sawakuchi, Gabriel O.

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Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes von Cobos, Francisco Avila, Panah, Mohammad Javad Najaf, Epps, Jessica, Long, Xiaochen, Man, Tsz-Kwong, Chiu, Hua-Sheng, Chomsky, Elad, Kiner, Evgeny, Krueger, Michael J, di Bernardo, Diego, Voloch, Luis, Molenaar, Jan, van Hooff, Sander R, Westermann, Frank, Jansky, Selina, Redell, Michele L, Mestdagh, Pieter, Sumazin, Pavel

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High-throughput validation of ceRNA regulatory networks von Chiu, Hua-Sheng, Martínez, María Rodríguez, Bansal, Mukesh, Subramanian, Aravind, Golub, Todd R, Yang, Xuerui, Sumazin, Pavel, Califano, Andrea

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Deciphering Early-Stage Molecular Mechanisms of Negative Pressure Wound Therapy in a Murine Model von Shyu, Yu-Chiau, Huang, Ting-Shuo, Chiu, Hua-Sheng, Sumazin, Pavel, Lin, Xin-Yu, Liao, Po-Cheng, Liou, Cai-Cin, Hsu, Fang-Chia, Lin, Jyuan-Siou, Hsu, Chih-Chin, Hsu, Pang-Hung, Sun, Chi-Chin, Chen, Chien-Tzung

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Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes von Rombaut, Dries, Chiu, Hua-Sheng, Decaesteker, Bieke, Everaert, Celine, Yigit, Nurten, Peltier, Agathe, Janoueix-Lerosey, Isabelle, Bartenhagen, Christoph, Fischer, Matthias, Roberts, Stephen, D’Haene, Nicky, De Preter, Katleen, Speleman, Frank, Denecker, Geertrui, Sumazin, Pavel, Vandesompele, Jo, Lefever, Steve, Mestdagh, Pieter

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LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs von Ustianenko, Dmytro, Chiu, Hua-Sheng, Treiber, Thomas, Weyn-Vanhentenryck, Sebastien M., Treiber, Nora, Meister, Gunter, Sumazin, Pavel, Zhang, Chaolin

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Protein subcellular localization prediction based on compartment-specific features and structure conservation von Su, Emily Chia-Yu, Chiu, Hua-Sheng, Lo, Allan, Hwang, Jenn-Kang, Sung, Ting-Yi, Hsu, Wen-Lian

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The RNA Atlas expands the catalog of human non-coding RNAs von Lorenzi, Lucia, Chiu, Hua-Sheng, Avila Cobos, Francisco, Gross, Stephen, Volders, Pieter-Jan, Cannoodt, Robrecht, Nuytens, Justine, Vanderheyden, Katrien, Anckaert, Jasper, Lefever, Steve, Tay, Aidan P., de Bony, Eric J., Trypsteen, Wim, Gysens, Fien, Vromman, Marieke, Goovaerts, Tine, Hansen, Thomas Birkballe, Kuersten, Scott, Nijs, Nele, Taghon, Tom, Vermaelen, Karim, Bracke, Ken R., Saeys, Yvan, De Meyer, Tim, Deshpande, Nandan P., Anande, Govardhan, Chen, Ting-Wen, Wilkins, Marc R., Unnikrishnan, Ashwin, De Preter, Katleen, Kjems, Jørgen, Koster, Jan, Schroth, Gary P., Vandesompele, Jo, Sumazin, Pavel, Mestdagh, Pieter

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PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis von Chang, Jia-Ming, Su, Emily Chia-Yu, Lo, Allan, Chiu, Hua-Sheng, Sung, Ting-Yi, Hsu, Wen-Lian

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The number of titrated microRNA species dictates ceRNA regulation von Chiu, Hua-Sheng, Martínez, María Rodríguez, . Komissarova, Elena V, Llobet-Navas, David, Bansal, Mukesh, Paull, Evan O, Silva, José, Yang, Xuerui, Sumazin, Pavel, Califano, Andrea

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MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis von Zheng, Jun-Jie, Wang, Po-Wen, Huang, Tzu-Wen, Yang, Yao-Jong, Chiu, Hua-Sheng, Sumazin, Pavel, Chen, Ting-Wen

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Enhanced Membrane Protein Topology Prediction Using a Hierarchical Classification Method and a New Scoring Function von Lo, Allan, Chiu, Hua-Sheng, Sung, Ting-Yi, Lyu, Ping-Chiang, Hsu, Wen-Lian

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Publisher Correction: The RNA Atlas expands the catalog of human non-coding RNAs von Lorenzi, Lucia, Chiu, Hua-Sheng, Avila Cobos, Francisco, Gross, Stephen, Volders, Pieter-Jan, Cannoodt, Robrecht, Nuytens, Justine, Vanderheyden, Katrien, Anckaert, Jasper, Lefever, Steve, Tay, Aidan P., de Bony, Eric J., Trypsteen, Wim, Gysens, Fien, Vromman, Marieke, Goovaerts, Tine, Hansen, Thomas Birkballe, Kuersten, Scott, Nijs, Nele, Taghon, Tom, Vermaelen, Karim, Bracke, Ken R., Saeys, Yvan, De Meyer, Tim, Deshpande, Nandan P., Anande, Govardhan, Chen, Ting-Wen, Wilkins, Marc R., Unnikrishnan, Ashwin, De Preter, Katleen, Kjems, Jørgen, Koster, Jan, Schroth, Gary P., Vandesompele, Jo, Sumazin, Pavel, Mestdagh, Pieter

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Author Correction: Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes von Rombaut, Dries, Chiu, Hua-Sheng, Decaesteker, Bieke, Everaert, Celine, Yigit, Nurten, Peltier, Agathe, Janoueix-Lerosey, Isabelle, Bartenhagen, Christoph, Fischer, Matthias, Roberts, Stephen, D’Haene, Nicky, De Preter, Katleen, Speleman, Frank, Denecker, Geertrui, Sumazin, Pavel, Vandesompele, Jo, Lefever, Steve, Mestdagh, Pieter

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Estimating individual risk of catheter-associated urinary tract infections using explainable artificial intelligence on clinical data von Sufriyana, Herdiantri, Chen, Chieh, Chiu, Hua-Sheng, Sumazin, Pavel, Yang, Po-Yu, Kang, Jiunn-Horng, Su, Emily Chia-Yu

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Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks von Chiu, Hua-Sheng, Llobet-Navas, David, Yang, Xuerui, Chung, Wei-Jen, Ambesi-Impiombato, Alberto, Iyer, Archana, Kim, Hyunjae Ryan, Seviour, Elena G, Luo, Zijun, Sehgal, Vasudha, Moss, Tyler, Lu, Yiling, Ram, Prahlad, Silva, José, Mills, Gordon B, Califano, Andrea, Sumazin, Pavel

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Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes von Cobos, Francisco Avila, Panah, Mohammad Javad Najaf, Epps, Jessica, Long, Xiaochen, Man, Tsz Kwong, Chiu, Hua Sheng, Chomsky, Elad, Kiner, Evgeny, Krueger, Michael J, di Bernardo, Diego, Voloch, Luis, Molenaar, Jan, van Hooff, Sander R, Westermann, Frank, Jansky, Selina, Redell, Michele L, Mestdagh, Pieter, Sumazin, Pavel

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Abstract IA14: Genomic alterations dysregulate cancer genes by modulating microRNA activity von Chiu, Hua-Sheng, Yang, Xuerui, Califano, Andrea, Sumazin, Pavel

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