Linear Regression Links Transcriptomic Data and Cellular Raman Spectra
Tài liệu tham khảo
Amorim, 2010, Global coordination of transcriptional control and mRNA decay during cellular differentiation, Mol. Syst. Biol., 6, 380, 10.1038/msb.2010.38
Baba, 2006, Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Mol. Syst. Biol., 2, 10.1038/msb4100050
Biswas, 2017, Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes, Nat. Commun., 8, 15309, 10.1038/ncomms15309
Boer, 2003, The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur, J. Biol. Chem., 278, 3265, 10.1074/jbc.M209759200
Boulesteix, 2007, Partial least squares: a versatile tool for the analysis of high-dimensional genomic data, Brief. Bioinform., 8, 32, 10.1093/bib/bbl016
Brauer, 2008, Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast, Mol. Biol. Cell, 19, 352, 10.1091/mbc.e07-08-0779
Butler, 2016, Using Raman spectroscopy to characterize biological materials, Nat. Protoc., 11, 664, 10.1038/nprot.2016.036
Camara, 2018, Methods and challenges in the analysis of single-cell RNA-sequencing data, Curr. Opin. Syst. Biol., 7, 47, 10.1016/j.coisb.2017.12.007
Carter-O’Connell, 2012, Genome-wide characterization of the phosphate starvation response in Schizosaccharomyces pombe, BMC Genomics, 13, 697, 10.1186/1471-2164-13-697
Chen, 2003, Global transcriptional responses of fission yeast to environmental stress, Mol. Biol. Cell, 14, 214, 10.1091/mbc.e02-08-0499
Delgado, 2013, Intracellular water exchange for measuring the dry mass, water mass and changes in chemical composition of living cells, PLoS One, 8, e67590, 10.1371/journal.pone.0067590
Filipowicz, 2002, Biogenesis of small nucleolar ribonucleoproteins, Curr. Opin. Cell Biol., 14, 319, 10.1016/S0955-0674(02)00334-4
Fisher, 1937
Galipon, 2013, Stress-induced lncRNAs evade nuclear degradation and enter the translational machinery, Genes Cells, 18, 353, 10.1111/gtc.12042
Gasch, 2000, Genomic expression programs in the response of yeast cells to environmental changes, Mol. Biol. Cell, 11, 4241, 10.1091/mbc.11.12.4241
Geladi, 1986, Partial least-squares regression: a tutorial, Anal. Chim. Acta, 185, 1, 10.1016/0003-2670(86)80028-9
Goodacre, 1998, Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks, Microbiology, 144, 1157, 10.1099/00221287-144-5-1157
Gromski, 2015, A tutorial review: metabolomics and partial least squares-discriminant analysis - a marriage of convenience or a shotgun wedding, Anal. Chim. Acta, 879, 10, 10.1016/j.aca.2015.02.012
Hamada, 2015, Raman microscopy for dynamic molecular imaging of living cells, J. Biomed. Opt., 13, 044027, 10.1117/1.2952192
Heimberg, 2016, Low dimensionality in gene expression data enables the accurate extraction of transcriptional programs from shallow sequencing, Cell Syst., 2, 239, 10.1016/j.cels.2016.04.001
Himeno, 2014, tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell, Front. Genet., 5, 66, 10.3389/fgene.2014.00066
Hobro, 2017, An evaluation of fixation methods: spatial and compositional cellular changes observed by Raman imaging, Vib. Spectrosc., 91, 31, 10.1016/j.vibspec.2016.10.012
Huang, 2013, Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms, Nat. Methods, 10, 653, 10.1038/nmeth.2488
Huang, 2004, Raman microscopic analysis of single microbial cells, Anal. Chem., 76, 4452, 10.1021/ac049753k
Ichimura, 2014, Visualizing cell state transition using Raman spectroscopy, PLoS One, 9, e84478, 10.1371/journal.pone.0084478
Ichimura, 2015, Visualizing the appearance and disappearance of the attractor of differentiation using Raman spectral imaging, Scientific Rep., 5, 11358, 10.1038/srep11358
Jaumot, 2005, A graphical user-friendly interface for MCR-ALS: a new tool for multivariate curve resolution in MATLAB, Chemom. Intell. Lab. Syst., 76, 101, 10.1016/j.chemolab.2004.12.007
Keiler, 1996, Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA, Science, 271, 990, 10.1126/science.271.5251.990
Kim, 2013, Tophat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol., 14, R36, 10.1186/gb-2013-14-4-r36
Kiss, 2002, Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions, Cell, 109, 145, 10.1016/S0092-8674(02)00718-3
Kunapareddy, 2008, Raman spectroscopic characterization of necrotic cell death, J. Biomed. Opt., 13, 054002, 10.1117/1.2978061
Luchinat, 2017, In-cell NMR: a topical review, IUCrJ, 4, 108, 10.1107/S2052252516020625
Maaten, 2008, Visualizing data using t-SNE, J. Machine Learn. Res., 9, 2579
Marguerat, 2012, Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells, Cell, 151, 671, 10.1016/j.cell.2012.09.019
McDowall, 2014, Pombase 2015: updates to the fission yeast database, Nucleic Acids Res., 43, D656, 10.1093/nar/gku1040
Mehmood, 2012, A review of variable selection methods in partial least squares regression, Chemom. Intell. Lab. Syst., 118, 62, 10.1016/j.chemolab.2012.07.010
Milo, 2015
Mourant, 2005, Biochemical differences in tumorigenic and nontumorigenic cells measured by Raman and infrared spectroscopy, J. Biomed. Opt., 10, 031106, 10.1117/1.1928050
Nomura, 1999, Regulation of ribosome biosynthesis in Escherichia coli and Saccharomyces cerevisiae: diversity and common principles, J. Bacteriol., 181, 6857, 10.1128/JB.181.22.6857-6864.1999
Nygaard, 2015, Spectral snapshots of bacterial cell-wall composition and the influence of antibiotics by whole-cell NMR, Biophys. J., 108, 1380, 10.1016/j.bpj.2015.01.037
Ozsolak, 2011, RNA sequencing: advances, challenges and opportunities, Nat. Rev. Genet., 12, 87, 10.1038/nrg2934
Perlman, 1969, Pleiotropic deficiency of carbohydrate utilization in an adenyl cyclase deficient mutant of Escherichia coli, Biochem. Biophys. Res. Commun., 37, 151, 10.1016/0006-291X(69)90893-6
Phipson, 2010, Permutation p-values should never be zero: calculating exact p-values when permutations are randomly drawn, Stat. Appl. Genet. Mol. Biol., 9, 10.2202/1544-6115.1585
Pitman, 1937, Significance tests which may be applied to samples from any populations, Suppl. J. R. Stat. Soc., 4, 119, 10.2307/2984124
Riley, 2006, Escherichia coli k-12: a cooperatively developed annotation snapshot-2005, Nucleic Acids Res., 34, 1, 10.1093/nar/gkj405
Ruckebusch, 2016, volume 30
Savitzky, 1964, Smoothing and differentiation of data by simplified least squares procedures, Anal. Chem., 36, 1627, 10.1021/ac60214a047
Schie, 2013, Methods and applications of Raman microspectroscopy to single-cell analysis, Appl. Spectrosc., 67, 813, 10.1366/12-06971
Smith, 2016, Raman spectroscopy: an evolving technique for live cell studies, Analyst, 141, 3590, 10.1039/C6AN00152A
Tao, 1970, Some properties of Escherichia coli adenyl cyclase, Arch. Biochem. Biophys., 141, 236, 10.1016/0003-9861(70)90127-X
Teng, 2016, Label-free, rapid and quantitative phenotyping of stress response in E. coli via ramanome, Sci. Rep., 6, 34359, 10.1038/srep34359
Trapnell, 2013, Differential analysis of gene regulation at transcript resolution with RNA-seq, Nat. Biotechnol., 31, 46, 10.1038/nbt.2450
Trapnell, 2010, Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation, Nat. Biotechnol., 28, 511, 10.1038/nbt.1621
Wang, 2015, RNA-seq based transcriptomic analysis of single bacterial cells, Integr. Biol., 7, 1466, 10.1039/C5IB00191A
Wei, 2014, Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering, Nat. Methods, 11, 410, 10.1038/nmeth.2878
Wold, 2001, PLS-regression: a basic tool of chemometrics, Chemom. Intell. Lab. Syst., 58, 109, 10.1016/S0169-7439(01)00155-1
Wood, 2012, Pombase: a comprehensive online resource for fission yeast, Nucleic Acids Res., 40, D695, 10.1093/nar/gkr853
Yugi, 2016, Trans-omics: how to reconstruct biochemical networks across multiple ‘omic’ layers, Trends Biotechnol., 34, 276, 10.1016/j.tibtech.2015.12.013
Zenobi, 2013, Single-cell metabolomics: analytical and biological perspectives, Science, 342, 1243259, 10.1126/science.1243259