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Page 1
Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains.
McCulloch LH, Sambasivam V, Hughes AL, Annaluru N, Ramalingam S, Fanfani V, Lobzaev E, Mitchell LA, Cai J; Build-A-Genome Class; Jiang H, LaCava J, Taylor MS, Bishai WR, Stracquadanio G, Steinmetz LM, Bader JS, Zhang W, Boeke JD, Chandrasegaran S. McCulloch LH, et al. Among authors: fanfani v. Cell Genom. 2023 Nov 9;3(11):100419. doi: 10.1016/j.xgen.2023.100419. eCollection 2023 Nov 8. Cell Genom. 2023. PMID: 38020974 Free PMC article.
Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics.
Blount BA, Lu X, Driessen MRM, Jovicevic D, Sanchez MI, Ciurkot K, Zhao Y, Lauer S, McKiernan RM, Gowers GF, Sweeney F, Fanfani V, Lobzaev E, Palacios-Flores K, Walker RSK, Hesketh A, Cai J, Oliver SG, Cai Y, Stracquadanio G, Mitchell LA, Bader JS, Boeke JD, Ellis T. Blount BA, et al. Among authors: fanfani v. Cell Genom. 2023 Nov 9;3(11):100418. doi: 10.1016/j.xgen.2023.100418. eCollection 2023 Nov 8. Cell Genom. 2023. PMID: 38020971 Free PMC article.
Context-dependent neocentromere activity in synthetic yeast chromosome VIII.
Lauer S, Luo J, Lazar-Stefanita L, Zhang W, McCulloch LH, Fanfani V, Lobzaev E, Haase MAB, Easo N, Zhao Y, Yu F, Cai J; Build-A-Genome Class; Bader JS, Stracquadanio G, Boeke JD. Lauer S, et al. Among authors: fanfani v. Cell Genom. 2023 Nov 9;3(11):100437. doi: 10.1016/j.xgen.2023.100437. eCollection 2023 Nov 8. Cell Genom. 2023. PMID: 38020969 Free PMC article.
Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO).
Saha E, Fanfani V, Mandros P, Ben-Guebila M, Fischer J, Hoff-Shutta K, Glass K, DeMeo DL, Lopes-Ramos C, Quackenbush J. Saha E, et al. Among authors: fanfani v. bioRxiv [Preprint]. 2023 Nov 17:2023.11.16.567119. doi: 10.1101/2023.11.16.567119. bioRxiv. 2023. PMID: 38014256 Free PMC article. Preprint.
Manipulating the 3D organization of the largest synthetic yeast chromosome.
Zhang W, Lazar-Stefanita L, Yamashita H, Shen MJ, Mitchell LA, Kurasawa H, Lobzaev E, Fanfani V, Haase MAB, Sun X, Jiang Q, Goldberg GW, Ichikawa DM, Lauer SL, McCulloch LH, Easo N, Lin SJ, Camellato BR, Zhu Y, Cai J, Xu Z, Zhao Y, Sacasa M; Build-A-Genome Class; Noyes MB, Bader JS, Deutsch S, Stracquadanio G, Aizawa Y, Dai J, Boeke JD. Zhang W, et al. Among authors: fanfani v. Mol Cell. 2023 Dec 7;83(23):4424-4437.e5. doi: 10.1016/j.molcel.2023.10.015. Epub 2023 Nov 8. Mol Cell. 2023. PMID: 37944526 Free article.
Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions.
Zhao Y, Coelho C, Hughes AL, Lazar-Stefanita L, Yang S, Brooks AN, Walker RSK, Zhang W, Lauer S, Hernandez C, Cai J, Mitchell LA, Agmon N, Shen Y, Sall J, Fanfani V, Jalan A, Rivera J, Liang FX, Bader JS, Stracquadanio G, Steinmetz LM, Cai Y, Boeke JD. Zhao Y, et al. Among authors: fanfani v. Cell. 2023 Nov 22;186(24):5220-5236.e16. doi: 10.1016/j.cell.2023.09.025. Epub 2023 Nov 8. Cell. 2023. PMID: 37944511 Free article.
Gene regulatory Networks Reveal Sex Difference in Lung Adenocarcinoma.
Saha E, Guebila MB, Fanfani V, Fischer J, Shutta KH, Mandros P, DeMeo DL, Quackenbush J, Lopes-Ramos CM. Saha E, et al. Among authors: fanfani v. bioRxiv [Preprint]. 2023 Sep 24:2023.09.22.559001. doi: 10.1101/2023.09.22.559001. bioRxiv. 2023. PMID: 37790409 Free PMC article. Preprint.
Biologically informed NeuralODEs for genome-wide regulatory dynamics.
Hossain I, Fanfani V, Fischer J, Quackenbush J, Burkholz R. Hossain I, et al. Among authors: fanfani v. bioRxiv [Preprint]. 2024 Jan 3:2023.02.24.529835. doi: 10.1101/2023.02.24.529835. bioRxiv. 2024. PMID: 36909563 Free PMC article. Preprint.
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.
Ben Guebila M, Wang T, Lopes-Ramos CM, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson JN, Altenbuchinger M, Shutta KH, Sonawane AR, Lim J, Calderer G, van IJzendoorn DGP, Morgan D, Marin A, Chen CY, Song Q, Saha E, DeMeo DL, Padi M, Platig J, Kuijjer ML, Glass K, Quackenbush J. Ben Guebila M, et al. Among authors: fanfani v. Genome Biol. 2023 Mar 9;24(1):45. doi: 10.1186/s13059-023-02877-1. Genome Biol. 2023. PMID: 36894939 Free PMC article.
15 results