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Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes.
Zaitsev A, Chelushkin M, Dyikanov D, Cheremushkin I, Shpak B, Nomie K, Zyrin V, Nuzhdina E, Lozinsky Y, Zotova A, Degryse S, Kotlov N, Baisangurov A, Shatsky V, Afenteva D, Kuznetsov A, Paul SR, Davies DL, Reeves PM, Lanuti M, Goldberg MF, Tazearslan C, Chasse M, Wang I, Abdou M, Aslanian SM, Andrewes S, Hsieh JJ, Ramachandran A, Lyu Y, Galkin I, Svekolkin V, Cerchietti L, Poznansky MC, Ataullakhanov R, Fowler N, Bagaev A. Zaitsev A, et al. Among authors: baisangurov a. Cancer Cell. 2022 Aug 8;40(8):879-894.e16. doi: 10.1016/j.ccell.2022.07.006. Cancer Cell. 2022. PMID: 35944503 Free article.
Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data.
Kotlov N, Shaposhnikov K, Tazearslan C, Chasse M, Baisangurov A, Podsvirova S, Fernandez D, Abdou M, Kaneunyenye L, Morgan K, Cheremushkin I, Zemskiy P, Chelushkin M, Sorokina M, Belova E, Khorkova S, Lozinsky Y, Nuzhdina K, Vasileva E, Kravchenko D, Suryamohan K, Nomie K, Curran J, Fowler N, Bagaev A. Kotlov N, et al. Among authors: baisangurov a. Commun Biol. 2024 Mar 30;7(1):392. doi: 10.1038/s42003-024-06020-z. Commun Biol. 2024. PMID: 38555407 Free PMC article.