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CellMix: a comprehensive toolbox for gene expression deconvolution.
Gaujoux R, Seoighe C. Gaujoux R, et al. Bioinformatics. 2013 Sep 1;29(17):2211-2. doi: 10.1093/bioinformatics/btt351. Epub 2013 Jul 3. Bioinformatics. 2013. PMID: 23825367
To facilitate and popularize the application of such methods, we developed CellMix, an R package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gen …
To facilitate and popularize the application of such methods, we developed CellMix, an R package that incorporates most state-of-the- …
A flexible R package for nonnegative matrix factorization.
Gaujoux R, Seoighe C. Gaujoux R, et al. BMC Bioinformatics. 2010 Jul 2;11:367. doi: 10.1186/1471-2105-11-367. BMC Bioinformatics. 2010. PMID: 20598126 Free PMC article.
For that purpose, we have developed a package for the R/BioConductor platform. The package ports public code to R, and is structured to enable users to easily modify and/or add algorithms. ...
For that purpose, we have developed a package for the R/BioConductor platform. The package ports public code to R, and is stru …
NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments.
Semegni JY, Wamalwa M, Gaujoux R, Harkins GW, Gray A, Martin DP. Semegni JY, et al. Bioinformatics. 2011 Sep 1;27(17):2443-5. doi: 10.1093/bioinformatics/btr417. Epub 2011 Jul 14. Bioinformatics. 2011. PMID: 21757466 Free PMC article.
Systems immunology reveals markers of susceptibility to West Nile virus infection.
Qian F, Goel G, Meng H, Wang X, You F, Devine L, Raddassi K, Garcia MN, Murray KO, Bolen CR, Gaujoux R, Shen-Orr SS, Hafler D, Fikrig E, Xavier R, Kleinstein SH, Montgomery RR. Qian F, et al. Among authors: gaujoux r. Clin Vaccine Immunol. 2015 Jan;22(1):6-16. doi: 10.1128/CVI.00508-14. Epub 2014 Oct 29. Clin Vaccine Immunol. 2015. PMID: 25355795 Free PMC article.
A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.
Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM, Melton DA, Yanai I. Baron M, et al. Among authors: gaujoux r. Cell Syst. 2016 Oct 26;3(4):346-360.e4. doi: 10.1016/j.cels.2016.08.011. Epub 2016 Sep 22. Cell Syst. 2016. PMID: 27667365 Free PMC article.
A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring.
Alpert A, Pickman Y, Leipold M, Rosenberg-Hasson Y, Ji X, Gaujoux R, Rabani H, Starosvetsky E, Kveler K, Schaffert S, Furman D, Caspi O, Rosenschein U, Khatri P, Dekker CL, Maecker HT, Davis MM, Shen-Orr SS. Alpert A, et al. Among authors: gaujoux r. Nat Med. 2019 Mar;25(3):487-495. doi: 10.1038/s41591-019-0381-y. Epub 2019 Mar 6. Nat Med. 2019. PMID: 30842675 Free PMC article.
Found In Translation: a machine learning model for mouse-to-human inference.
Normand R, Du W, Briller M, Gaujoux R, Starosvetsky E, Ziv-Kenet A, Shalev-Malul G, Tibshirani RJ, Shen-Orr SS. Normand R, et al. Among authors: gaujoux r. Nat Methods. 2018 Dec;15(12):1067-1073. doi: 10.1038/s41592-018-0214-9. Epub 2018 Nov 26. Nat Methods. 2018. PMID: 30478323
Cell-centred meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD.
Gaujoux R, Starosvetsky E, Maimon N, Vallania F, Bar-Yoseph H, Pressman S, Weisshof R, Goren I, Rabinowitz K, Waterman M, Yanai H, Dotan I, Sabo E, Chowers Y, Khatri P, Shen-Orr SS; Israeli IBD research Network (IIRN). Gaujoux R, et al. Gut. 2019 Apr;68(4):604-614. doi: 10.1136/gutjnl-2017-315494. Epub 2018 Apr 4. Gut. 2019. PMID: 29618496 Free PMC article.
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