Bioinformatics. 2015 Aug 30. RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets. Guo Z, Tzvetkova B, Bassik JM, Bodziak T, Wojnar BM, Qiao W, Obaida MA, Nelson SB, Hu BH, Yu P Abstract Gene targeting is a protocol for introducing a mutation to a specific gene in

[continue reading…]

Fangjun Li, Cheng Cheng, Fuhao Cui, Marcos VV de Oliveira, Xiao Yu, Xiangzong Meng, Aline C Intorne, Kevin Babilonia, Maoying Li, Bo Li, Sixue Chen, Xianfeng Ma, Shunyuan Xiao, Yi Zheng, Zhangjun Fei, Richard P Metz, Charles D Johnson, Hisashi Koiwa, Wenxian Sun, Zhaohu Li, Gonçalo A de Souza Filho, Libo Shan, Ping He, "Modulation of RNA Polymerase II Phosphorylation Downstream of Pathogen Perception Orchestrates Plant Immunity", Cell Host & Microbe doi:10.1016/j.chom.2014.10.018  (Journal Publication)  [More Details]  [Online]

Noushin Ghaffari, Alejandro Sanchez-Flores, Ryan Doan, Karina D. Garcia-Orozco, Patricia L. Chen, Adrian Ochoa-Leyva, Alonso A. Lopez-Zavala, J. Salvador Carrasco, Chris Hong, Luis G. Brieba, Enrique Rudiño-Piñera, Philip D. Blood, Jason E. Sawyer, Charles D. Johnson, Scott V. Dindot, Rogerio R. Sotelo-Mundo, Michael F. Criscitiello, "Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture", Nature Scientific Reports 4, Article number: 7081  (Journal Publication)  [More Details]  [Online]

IC Paschalidis, Y Shen, P Vakili, S Vajda, "SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking", Automatic Control, IEEE Transactions on 52 (4), 664-676   (Journal Publication)  [More Details]  [Online]

Comeau, S. R., Kozakov, D., Brenke, R., Shen, Y., Beglov, D. and Vajda, S, "ClusPro: Performance in CAPRI rounds 6–11 and the new server", Proteins, 69: 781–785. doi: 10.1002/prot.21795  (Journal Publication)  [More Details]  [Online]

Shen, Y., Brenke, R., Kozakov, D., Comeau, S. R., Beglov, D. and Vajda, S. , "Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI", Proteins, 69: 734–742. doi: 10.1002/prot.21754  (Journal Publication)  [More Details]  [Online]

Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, "Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes", PLoS Comput Biol 4(10): e1000191. doi: 10.1371/journal.pcbi.1000191 (2008)  (Journal Publication)  [More Details]  [Online]

Kozakov, D., Hall, D. R., Beglov, D., Brenke, R., Comeau, S. R., Shen, Y., Li, K., Zheng, J., Vakili, P., Paschalidis, I. Ch. and Vajda, S, "Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19", Proteins, 78: 3124–3130. doi: 10.1002/prot.22835 (2010)  (Journal Publication)  [More Details]  [Online]

Dmitri Beglov, Ryan Brenke, Gwo-Yu Chuang, David Hall, Melissa Landon, Chi Ho Ngan, Yang Shen, Spencer Thiel, Brandon Zerbe, Dima Kozakov, Sandor Vajda, "Identification of Druggable Hot Spots on Proteins and in Protein–Protein Interfaces", In D Beglov, R Brenke, GY Chuang, D Hall, M Landon eds., Computational Protein-Protein Interactions, 2010, CRC Press  (Book Chapter)  [More Details]

Yang Shen, Michael K. Gilson, and Bruce Tidor, "Charge Optimization Theory for Induced-Fit Ligands", Journal of Chemical Theory and Computation 2012 8 (11), 4580-4592  (Journal Publication)  [More Details]  [Online]