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Genomic signatures and gene networking: challenges and promises.
Zhang K, Pirooznia M, Arabnia HR, Yang JY, Wang L, Luo Z, Deng Y. Zhang K, et al. BMC Genomics. 2011 Dec 23;12 Suppl 5(Suppl 5):I1. doi: 10.1186/1471-2164-12-S5-I1. Epub 2011 Dec 23. BMC Genomics. 2011. PMID: 22369358 Free PMC article.
From genes to networks: in systematic points of view.
Zhang K, Liu Y, Yang JY, Arabnia HR, Niemierko A, Ghafoor A, Li W, Deng Y. Zhang K, et al. BMC Syst Biol. 2011;5 Suppl 3(Suppl 3):I1. doi: 10.1186/1752-0509-5-S3-I1. Epub 2011 Dec 23. BMC Syst Biol. 2011. PMID: 22784614 Free PMC article.
The current trend of genomics research for human diseases.
Zhang KK, Arabnia HR, Wang Y, Deng Y. Zhang KK, et al. BMC Med Genomics. 2013;6 Suppl 1(Suppl 1):S1. doi: 10.1186/1755-8794-6-S1-S1. Epub 2013 Jan 23. BMC Med Genomics. 2013. PMID: 23369188 Free PMC article.
Gene set analysis for longitudinal gene expression data.
Zhang K, Wang H, Bathke AC, Harrar SW, Piepho HP, Deng Y. Zhang K, et al. BMC Bioinformatics. 2011 Jul 3;12:273. doi: 10.1186/1471-2105-12-273. BMC Bioinformatics. 2011. PMID: 21722407 Free PMC article.
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.
Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D, Wang J, Furlanello C, Devanarayan V, Cheng J, Deng Y, Hero B, Hong H, Jia M, Li L, Lin SM, Nikolsky Y, Oberthuer A, Qing T, Su Z, Volland R, Wang C, Wang MD, Ai J, Albanese D, Asgharzadeh S, Avigad S, Bao W, Bessarabova M, Brilliant MH, Brors B, Chierici M, Chu TM, Zhang J, Grundy RG, He MM, Hebbring S, Kaufman HL, Lababidi S, Lancashire LJ, Li Y, Lu XX, Luo H, Ma X, Ning B, Noguera R, Peifer M, Phan JH, Roels F, Rosswog C, Shao S, Shen J, Theissen J, Tonini GP, Vandesompele J, Wu PY, Xiao W, Xu J, Xu W, Xuan J, Yang Y, Ye Z, Dong Z, Zhang KK, Yin Y, Zhao C, Zheng Y, Wolfinger RD, Shi T, Malkas LH, Berthold F, Wang J, Tong W, Shi L, Peng Z, Fischer M. Zhang W, et al. Among authors: zhang j, zhang kk. Genome Biol. 2015 Jun 25;16(1):133. doi: 10.1186/s13059-015-0694-1. Genome Biol. 2015. PMID: 26109056 Free PMC article.
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.
Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, Fang H, Hong H, Shen J, Su Z, Meehan J, Li X, Yang L, Li H, Łabaj PP, Kreil DP, Megherbi D, Gaj S, Caiment F, van Delft J, Kleinjans J, Scherer A, Devanarayan V, Wang J, Yang Y, Qian HR, Lancashire LJ, Bessarabova M, Nikolsky Y, Furlanello C, Chierici M, Albanese D, Jurman G, Riccadonna S, Filosi M, Visintainer R, Zhang KK, Li J, Hsieh JH, Svoboda DL, Fuscoe JC, Deng Y, Shi L, Paules RS, Auerbach SS, Tong W. Wang C, et al. Among authors: zhang kk. Nat Biotechnol. 2014 Sep;32(9):926-32. doi: 10.1038/nbt.3001. Epub 2014 Aug 24. Nat Biotechnol. 2014. PMID: 25150839 Free PMC article.
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