Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line.
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Niranjan Nagarajan | Wei-Shou Hu | Meiyappan Lakshmanan | Dong-Yup Lee | Yuansheng Yang | Faraaz Noor Khan Yusufi | Hock Chuan Yeo | Ying Swan Ho | N. Nagarajan | Xiaoan Ruan | P. Ariyaratne | Dong-Yup Lee | K. Sung | M. Bardor | M. Yap | Meiyappan Lakshmanan | Y. Ho | S. Ng | Hsueh Lee Lim | Shuwen Chen | F. N. Yusufi | G. Teo | Xiaoan Ruan | Corrine Wan | S. Ng | Pramila Ariyaratne | Muriel Bardor | Yuansheng Yang | Ju Xin Chin | Miranda Gek Sim Yap | Say Kong Ng | Corrine Wan | Bernard Liat Wen Loo | Tessa Rui Min Tan | Sze Wai Ng | Ai Ping Hiu | Chung Ping Chow | Shuwen Chen | Gavin Teo | Gao Song | Ken Wing Kin Sung | B. Loo | Gao-jie Song | T. Tan | Wei-Shou Hu | M. Lakshmanan | Juxin Chin | F. Yusufi | Dong‐Yup Lee
[1] Jan Schellenberger,et al. Use of Randomized Sampling for Analysis of Metabolic Networks* , 2009, Journal of Biological Chemistry.
[2] R. Linhardt,et al. An 'omics approach towards CHO cell engineering , 2013, Biotechnology and bioengineering.
[3] Rafibekov Sk,et al. ETV6/CBFA2 fusions in childhood B-cell precursor acute lymphoblastic leukemia with myeloid markers. , 2000 .
[4] L. Nielsen,et al. High-antibody-producing Chinese hamster ovary cells up-regulate intracellular protein transport and glutathione synthesis. , 2015, Journal of proteome research.
[5] Christoph Clemens,et al. CHO gene expression profiling in biopharmaceutical process analysis and design. , 2010, Biotechnology and bioengineering.
[6] R. Goodacre,et al. Metabolite profiling of recombinant CHO cells: designing tailored feeding regimes that enhance recombinant antibody production. , 2011, Biotechnology and bioengineering.
[7] Dong-Yup Lee,et al. LC‐MS‐based metabolic characterization of high monoclonal antibody‐producing Chinese hamster ovary cells , 2012, Biotechnology and bioengineering.
[8] Dong-Yup Lee,et al. Software applications for flux balance analysis , 2014, Briefings Bioinform..
[9] Steffen Neumann,et al. Highly sensitive feature detection for high resolution LC/MS , 2008, BMC Bioinformatics.
[10] Nathan E Lewis,et al. The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology. , 2013, Current opinion in biotechnology.
[11] Y. Ruan,et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). , 2012, Methods in molecular biology.
[12] J. Campisi,et al. Oxygen accelerates the accumulation of mutations during the senescence and immortalization of murine cells in culture , 2003, Aging cell.
[13] Joshua D. Knowles,et al. Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry , 2011, Nature Protocols.
[14] Katie F Wlaschin,et al. Recombinant protein therapeutics from CHO cells : 20 years and counting , 2007 .
[15] Z. Gerdtzen,et al. Comparative Metabolic Analysis of CHO Cell Clones Obtained through Cell Engineering, for IgG Productivity, Growth and Cell Longevity , 2015, PloS one.
[16] C. Clemens,et al. Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing , 2010, Nucleic acids research.
[17] A. Ross,et al. α‐Galactosylceramide stimulates splenic lymphocyte proliferation in vitro and increases antibody production in vivo in late neonatal‐age mice , 2015, Clinical and experimental immunology.
[18] L. Segovia,et al. Effect of Temperature Downshift on the Transcriptomic Responses of Chinese Hamster Ovary Cells Using Recombinant Human Tissue Plasminogen Activator Production Culture , 2016, PloS one.
[19] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[20] Andreas Tauch,et al. Chinese hamster genome sequenced from sorted chromosomes , 2013, Nature Biotechnology.
[21] Kelvin H. Lee,et al. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line , 2011, Nature Biotechnology.
[22] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[23] Bernhard O. Palsson,et al. Context-Specific Metabolic Networks Are Consistent with Experiments , 2008, PLoS Comput. Biol..
[24] Dong-Yup Lee,et al. Metabolomics-based identification of apoptosis-inducing metabolites in recombinant fed-batch CHO culture media. , 2011, Journal of biotechnology.
[25] Edward J. O'Brien,et al. Using Genome-scale Models to Predict Biological Capabilities , 2015, Cell.
[26] Ronan M. T. Fleming,et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.
[27] Daniel C. Zielinski,et al. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. , 2016, Cell systems.
[28] A. Gomez-Muñoz. Ceramide 1-phosphate/ceramide, a switch between life and death. , 2006, Biochimica et biophysica acta.
[29] Wei-Shou Hu,et al. Transcriptome and proteome analysis of Chinese hamster ovary cells under low temperature and butyrate treatment. , 2010, Journal of biotechnology.
[30] Oliver Fiehn,et al. LipidBlast - in-silico tandem mass spectrometry database for lipid identification , 2013, Nature Methods.
[31] Brad T. Sherman,et al. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists , 2007, Genome Biology.
[32] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[33] J. Nielsen,et al. Uncovering transcriptional regulation of metabolism by using metabolic network topology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[34] G. Lee,et al. Initial transcriptome and proteome analyses of low culture temperature-induced expression in CHO cells producing erythropoietin. , 2006, Biotechnology and bioengineering.
[35] N. Nagarajan,et al. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees , 2016, Genome Biology.
[36] Rui Oliveira,et al. Systems biotechnology of animal cells: the road to prediction. , 2012, Trends in biotechnology.
[37] Dong-Yup Lee,et al. Global insights into the Chinese hamster and CHO cell transcriptomes , 2015, Biotechnology and bioengineering.
[38] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[39] N. Federspiel,et al. Novel DNA rearrangements are associated with dihydrofolate reductase gene amplification. , 1984, The Journal of biological chemistry.
[40] Edward J. O'Brien,et al. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome , 2013, Nature Biotechnology.
[41] Chee Seng Chan,et al. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. , 2011, Genome research.
[42] Kai Ye,et al. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..
[43] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[44] Gary Walsh,et al. Biopharmaceutical benchmarks 2014 , 2014, Nature Biotechnology.
[45] Kurt Brorson,et al. N-Glycosylation Design and Control of Therapeutic Monoclonal Antibodies. , 2016, Trends in biotechnology.
[46] Huanming Yang,et al. De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.
[47] M. Bardor,et al. IRES-mediated Tricistronic vectors for enhancing generation of high monoclonal antibody expressing CHO cell lines. , 2012, Journal of biotechnology.
[48] Eoin Fahy,et al. A comprehensive classification system for lipids11 The evaluation of this manuscript was handled by the former Editor-in-Chief Trudy Forte. Published, JLR Papers in Press, February 16, 2005. DOI 10.1194/jlr.E400004-JLR200 , 2005, Journal of Lipid Research.
[49] Jos Kleinjans,et al. Transcriptomic and metabolomic data integration , 2016, Briefings Bioinform..
[50] Cleo Kontoravdi,et al. Towards the implementation of quality by design to the production of therapeutic monoclonal antibodies with desired glycosylation patterns , 2010, Biotechnology progress.
[51] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[52] Ian W Marison,et al. Application of multi-omics techniques for bioprocess design and optimization in chinese hamster ovary cells. , 2014, Journal of proteome research.
[53] Niranjan Nagarajan,et al. Whole-genome reconstruction and mutational signatures in gastric cancer , 2012, Genome Biology.
[54] Niki S. C. Wong,et al. Metabolomics profiling of extracellular metabolites in recombinant Chinese Hamster Ovary fed-batch culture. , 2009, Rapid communications in mass spectrometry : RCM.
[55] Meiyappan Lakshmanan,et al. A genetic algorithm-based approach for pre-processing metabolomics and lipidomics LC–MS data , 2015, Metabolomics.
[56] G. Karypis,et al. Mining transcriptome data for function–trait relationship of hyper productivity of recombinant antibody , 2009, Biotechnology and bioengineering.
[57] M. Pfaffl,et al. A new mathematical model for relative quantification in real-time RT-PCR. , 2001, Nucleic acids research.
[58] K. Lam,et al. Production of Functional Soluble Dectin-1 Glycoprotein Using an IRES-Linked Destabilized-Dihydrofolate Reductase Expression Vector , 2012, PloS one.
[59] Richard D Cummings,et al. Symbol nomenclature for glycan representation , 2009, Proteomics.
[60] R. Abagyan,et al. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. , 2006, Analytical chemistry.
[61] B. Löwenberg,et al. Somatic heterozygous mutations in ETV6 (TEL) and frequent absence of ETV6 protein in acute myeloid leukemia , 2005, Oncogene.
[62] Dong-Yup Lee,et al. Precursor mass prediction by clustering ionization products in LC-MS-based metabolomics , 2013, Metabolomics.
[63] John D. Storey. A direct approach to false discovery rates , 2002 .
[64] C. Clarke,et al. Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity. , 2011, Journal of biotechnology.
[65] Christian Schrøder Kaas,et al. Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy , 2015, BMC Genomics.
[66] Wei-Shou Hu,et al. Comparative transcriptome analysis to unveil genes affecting recombinant protein productivity in mammalian cells , 2009, Biotechnology and bioengineering.
[67] F. Wurm. Production of recombinant protein therapeutics in cultivated mammalian cells , 2004, Nature Biotechnology.
[68] Niki S. C. Wong,et al. Combined in silico modeling and metabolomics analysis to characterize fed‐batch CHO cell culture , 2012, Biotechnology and bioengineering.
[69] Yu-Teh Li,et al. Ceramide glycosylation catalyzed by glucosylceramide synthase and cancer drug resistance. , 2013, Advances in cancer research.
[70] Dina Fomina-Yadlin,et al. Transcriptome analysis of a CHO cell line expressing a recombinant therapeutic protein treated with inducers of protein expression. , 2015, Journal of biotechnology.
[71] H. Ohtake,et al. Identification and analysis of specific chromosomal region adjacent to exogenous Dhfr-amplified region in Chinese hamster ovary cell genome. , 2010, Journal of bioscience and bioengineering.