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SpliceMutr Enables Pan-Cancer Analysis of Splicing-Derived Neoantigen Burden in Tumors.
Palmer T, Kessler MD, Shao XM, Balan A, Yarchoan M, Zaidi N, Lopez-Vidal TY, Saeed AM, Gore J, Azad NS, Jaffee EM, Favorov AV, Anagnostou V, Karchin R, Gaykalova DA, Fertig EJ, Danilova L. Palmer T, et al. Among authors: favorov av. Cancer Res Commun. 2024 Dec 1;4(12):3137-3150. doi: 10.1158/2767-9764.CRC-23-0309. Cancer Res Commun. 2024. PMID: 39470352 Free PMC article.
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC; FANTOM consortium; Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH. Grapotte M, et al. Nat Commun. 2021 Jun 2;12(1):3297. doi: 10.1038/s41467-021-23143-7. Nat Commun. 2021. PMID: 34078885 Free PMC article.
Inferring causal molecular networks: empirical assessment through a community-based effort.
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium; Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Hill SM, et al. Among authors: favorov av. Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22. Nat Methods. 2016. PMID: 26901648 Free PMC article.
CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network.
Fertig EJ, Ozawa H, Thakar M, Howard JD, Kagohara LT, Krigsfeld G, Ranaweera RS, Hughes RM, Perez J, Jones S, Favorov AV, Carey J, Stein-O'Brien G, Gaykalova DA, Ochs MF, Chung CH. Fertig EJ, et al. Among authors: favorov av. Oncotarget. 2016 Nov 8;7(45):73845-73864. doi: 10.18632/oncotarget.12075. Oncotarget. 2016. PMID: 27650546 Free PMC article.
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.
Stein-O'Brien GL, Carey JL, Lee WS, Considine M, Favorov AV, Flam E, Guo T, Li S, Marchionni L, Sherman T, Sivy S, Gaykalova DA, McKay RD, Ochs MF, Colantuoni C, Fertig EJ. Stein-O'Brien GL, et al. Among authors: favorov av. Bioinformatics. 2017 Jun 15;33(12):1892-1894. doi: 10.1093/bioinformatics/btx058. Bioinformatics. 2017. PMID: 28174896 Free PMC article.
104 results