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Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS.
Johnson JAI, Tsang AP, Mitchell JT, Zhou DL, Bowden J, Davis-Marcisak E, Sherman T, Liefeld T, Loth M, Goff LA, Zimmerman JW, Kinny-Köster B, Jaffee EM, Tamayo P, Mesirov JP, Reich M, Fertig EJ, Stein-O'Brien GL. Johnson JAI, et al. Among authors: liefeld t. Nat Protoc. 2023 Dec;18(12):3690-3731. doi: 10.1038/s41596-023-00892-x. Epub 2023 Nov 21. Nat Protoc. 2023. PMID: 37989764 Free PMC article. Review.
NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data.
Overbey EG, Saravia-Butler AM, Zhang Z, Rathi KS, Fogle H, da Silveira WA, Barker RJ, Bass JJ, Beheshti A, Berrios DC, Blaber EA, Cekanaviciute E, Costa HA, Davin LB, Fisch KM, Gebre SG, Geniza M, Gilbert R, Gilroy S, Hardiman G, Herranz R, Kidane YH, Kruse CPS, Lee MD, Liefeld T, Lewis NG, McDonald JT, Meller R, Mishra T, Perera IY, Ray S, Reinsch SS, Rosenthal SB, Strong M, Szewczyk NJ, Tahimic CGT, Taylor DM, Vandenbrink JP, Villacampa A, Weging S, Wolverton C, Wyatt SE, Zea L, Costes SV, Galazka JM. Overbey EG, et al. Among authors: liefeld t. iScience. 2021 Mar 26;24(4):102361. doi: 10.1016/j.isci.2021.102361. eCollection 2021 Apr 23. iScience. 2021. PMID: 33870146 Free PMC article.
Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes.
Gevaert O, Nabian M, Bakr S, Everaert C, Shinde J, Manukyan A, Liefeld T, Tabor T, Xu J, Lupberger J, Haas BJ, Baumert TF, Hernaez M, Reich M, Quintana FJ, Uhlmann EJ, Krichevsky AM, Mesirov JP, Carey V, Pochet N. Gevaert O, et al. Among authors: liefeld t. JCO Clin Cancer Inform. 2020 May;4:421-435. doi: 10.1200/CCI.19.00125. JCO Clin Cancer Inform. 2020. PMID: 32383980 Free PMC article.
Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P Jr, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. Barretina J, et al. Among authors: liefeld t. Nature. 2019 Jan;565(7738):E5-E6. doi: 10.1038/s41586-018-0722-x. Nature. 2019. PMID: 30559381 No abstract available.
GeNets: a unified web platform for network-based genomic analyses.
Li T, Kim A, Rosenbluh J, Horn H, Greenfeld L, An D, Zimmer A, Liberzon A, Bistline J, Natoli T, Li Y, Tsherniak A, Narayan R, Subramanian A, Liefeld T, Wong B, Thompson D, Calvo S, Carr S, Boehm J, Jaffe J, Mesirov J, Hacohen N, Regev A, Lage K. Li T, et al. Among authors: liefeld t. Nat Methods. 2018 Jul;15(7):543-546. doi: 10.1038/s41592-018-0039-6. Epub 2018 Jun 18. Nat Methods. 2018. PMID: 29915188 Free PMC article.
The GenePattern Notebook Environment.
Reich M, Tabor T, Liefeld T, Thorvaldsdóttir H, Hill B, Tamayo P, Mesirov JP. Reich M, et al. Among authors: liefeld t. Cell Syst. 2017 Aug 23;5(2):149-151.e1. doi: 10.1016/j.cels.2017.07.003. Epub 2017 Aug 16. Cell Syst. 2017. PMID: 28822753 Free PMC article.
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.
Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. Qu K, et al. Among authors: liefeld t. Nat Methods. 2016 Mar;13(3):245-247. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18. Nat Methods. 2016. PMID: 26780094 Free PMC article.
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