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Page 1
Enter the Matrix: Factorization Uncovers Knowledge from Omics.
Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Stein-O'Brien GL, et al. Among authors: fertig ej. Trends Genet. 2018 Oct;34(10):790-805. doi: 10.1016/j.tig.2018.07.003. Epub 2018 Aug 22. Trends Genet. 2018. PMID: 30143323 Free PMC article. Review.
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence.
Zhang S, Yuan L, Danilova L, Mo G, Zhu Q, Deshpande A, Bell ATF, Elisseeff J, Popel AS, Anders RA, Jaffee EM, Yarchoan M, Fertig EJ, Kagohara LT. Zhang S, et al. Among authors: fertig ej. bioRxiv [Preprint]. 2023 Jan 12:2023.01.10.523481. doi: 10.1101/2023.01.10.523481. bioRxiv. 2023. Update in: Genome Med. 2023 Sep 18;15(1):72. doi: 10.1186/s13073-023-01218-y PMID: 36712023 Free PMC article. Updated. Preprint.
Transfer learning in a biomaterial fibrosis model identifies in vivo senescence heterogeneity and contributions to vascularization and matrix production across species and diverse pathologies.
Cherry C, Andorko JI, Krishnan K, Mejías JC, Nguyen HH, Stivers KB, Gray-Gaillard EF, Ruta A, Han J, Hamada N, Hamada M, Sturmlechner I, Trewartha S, Michel JH, Davenport Huyer L, Wolf MT, Tam AJ, Peña AN, Keerthivasan S, Le Saux CJ, Fertig EJ, Baker DJ, Housseau F, van Deursen JM, Pardoll DM, Elisseeff JH. Cherry C, et al. Among authors: fertig ej. Geroscience. 2023 Aug;45(4):2559-2587. doi: 10.1007/s11357-023-00785-7. Epub 2023 Apr 20. Geroscience. 2023. PMID: 37079217 Free PMC article.
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence.
Zhang S, Yuan L, Danilova L, Mo G, Zhu Q, Deshpande A, Bell ATF, Elisseeff J, Popel AS, Anders RA, Jaffee EM, Yarchoan M, Fertig EJ, Kagohara LT. Zhang S, et al. Among authors: fertig ej. Genome Med. 2023 Sep 18;15(1):72. doi: 10.1186/s13073-023-01218-y. Genome Med. 2023. PMID: 37723590 Free PMC article.
Age-associated Senescent - T Cell Signaling Promotes Type 3 Immunity that Inhibits the Biomaterial Regenerative Response.
Han J, Cherry C, Mejías JC, Krishnan K, Ruta A, Maestas DR Jr, Peña AN, Nguyen HH, Nagaraj S, Yang B, Gray-Gaillard EF, Rutkowski N, Browne M, Tam AJ, Fertig EJ, Housseau F, Ganguly S, Moore EM, Pardoll DM, Elisseeff JH. Han J, et al. Among authors: fertig ej. Adv Mater. 2024 Oct;36(43):e2310476. doi: 10.1002/adma.202310476. Epub 2023 Dec 28. Adv Mater. 2024. PMID: 38087458
Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial-Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma.
Guinn S, Kinny-Köster B, Tandurella JA, Mitchell JT, Sidiropoulos DN, Loth M, Lyman MR, Pucsek AB, Zabransky DJ, Lee JW, Kartalia E, Ramani M, Seppälä TT, Cherry C, Suri R, Zlomke H, Patel J, He J, Wolfgang CL, Yu J, Zheng L, Ryan DP, Ting DT, Kimmelman A, Gupta A, Danilova L, Elisseeff JH, Wood LD, Stein-O'Brien G, Kagohara LT, Jaffee EM, Burkhart RA, Fertig EJ, Zimmerman JW. Guinn S, et al. Among authors: fertig ej. Cancer Res. 2024 May 2;84(9):1517-1533. doi: 10.1158/0008-5472.CAN-23-1660. Cancer Res. 2024. PMID: 38587552 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: fertig ej. 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.
Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.
Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. Ando M, et al. Among authors: fertig ej. Nat Commun. 2019 May 16;10(1):2188. doi: 10.1038/s41467-019-09937-w. Nat Commun. 2019. PMID: 31097695 Free PMC article.
Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development.
Lu Y, Shiau F, Yi W, Lu S, Wu Q, Pearson JD, Kallman A, Zhong S, Hoang T, Zuo Z, Zhao F, Zhang M, Tsai N, Zhuo Y, He S, Zhang J, Stein-O'Brien GL, Sherman TD, Duan X, Fertig EJ, Goff LA, Zack DJ, Handa JT, Xue T, Bremner R, Blackshaw S, Wang X, Clark BS. Lu Y, et al. Among authors: fertig ej. Dev Cell. 2020 May 18;53(4):473-491.e9. doi: 10.1016/j.devcel.2020.04.009. Epub 2020 May 7. Dev Cell. 2020. PMID: 32386599 Free PMC article.
175 results