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This folder holds the following references to publications, sorted by year and author.

There are 15 references in this bibliography folder.

Francesconi, M, Di Stefano, B, Berenguer, C, de Andrés-Aguayo, L, Plana-Carmona, M, Mendez-Lago, M, Guillaumet-Adkins, A, Rodriguez-Esteban, G, Gut, M, Gut, IG, Heyn, H, Lehner, B, and Graf, T (2019).
Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming
eLife, 8:e41627.

Perez, MF, Francesconi, M, Hidalgo-Carcedo, C, and Lehner, B (2017).
Maternal age generates phenotypic variation in Caenorhabditis elegans.
Nature, 552(7683):106-109.

Di Stefano, B, Collombet, S, Jakobsen, JS, Wierer, M, Sardina, JL, Lackner, A, Stadhouders, R, Segura-Morales, C, Francesconi, M, Limone, F, Mann, M, Porse, B, Thieffry, D, and Graf, T (2016).
C/EBPalpha creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4.
Nat Cell Biol, 18(4):371-81.

Li, Y, Lauriola, M, Kim, D, Francesconi, M, D'Uva, G, Shibata, D, Malafa, MP, Yeatman, TJ, Coppola, D, Solmi, R, and Cheng, JQ (2016).
Adenomatous polyposis coli (APC) regulates miR17-92 cluster through beta-catenin pathway in colorectal cancer.
Oncogene, 35(35):4558-4568.

Baumstark, R, Hanzelmann, S, Tsuru, S, Schaerli, Y, Francesconi, M, Mancuso, FM, Castelo, R, and Isalan, M (2015).
The propagation of perturbations in rewired bacterial gene networks.
Nat Commun, 6:10105.

Francesconi, M and Lehner, B (2015).
Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells.
Mol Biosyst, 11(10):2690-8.

Latorre, I, Chesney, MA, Garrigues, JM, Stempor, P, Appert, A, Francesconi, M, Strome, S, and Ahringer, J (2015).
The DREAM complex promotes gene body H2A.Z for target repression.
Genes Dev, 29(5):495-500.

Francesconi, M and Lehner, B (2014).
The effects of genetic variation on gene expression dynamics during development.
Nature, 505(7482):208-11.

Francesconi, M, Jelier, R, and Lehner, B (2011).
Integrated genome-scale prediction of detrimental mutations in transcription networks.
PLoS Genet, 7(5):e1002077.

Jimenez, RH, Lee, J, Francesconi, M, Castellani, G, Neretti, N, Sanders, JA, Sedivy, J, and Gruppuso, PA (2010).
Regulation of gene expression in hepatic cells by the mammalian Target of Rapamycin (mTOR).
PLoS One, 5(2):e9084.

Remondini, D, Salvioli, S, Francesconi, M, Pierini, M, Mazzatti, DJ, Powell, JR, Zironi, I, Bersani, F, Castellani, G, and Franceschi, C (2010).
Complex patterns of gene expression in human T cells during in vivo aging.
Mol Biosyst, 6(10):1983-92.

Jimenez, RH, Boylan, JM, Lee, J, Francesconi, M, Castellani, G, Sanders, JA, and Gruppuso, PA (2009).
Rapamycin response in tumorigenic and non-tumorigenic hepatic cell lines.
PLoS One, 4(10):e7373.

Scotlandi, K, Remondini, D, Castellani, G, Manara, MC, Nardi, F, Cantiani, L, Francesconi, M, Mercuri, M, Caccuri, AM, Serra, M, Knuutila, S, and Picci, P (2009).
Overcoming resistance to conventional drugs in Ewing sarcoma and identification of molecular predictors of outcome.
J Clin Oncol, 27(13):2209-16.

Francesconi, M, Remondini, D, Neretti, N, Sedivy, JM, Cooper, LN, Verondini, E, Milanesi, L, and Castellani, G (2008).
Reconstructing networks of pathways via significance analysis of their intersections
BMC Bioinformatics, 9(4):S9.

Solmi, R, Lauriola, M, Francesconi, M, Martini, D, Voltattorni, M, Ceccarelli, C, Ugolini, G, Rosati, G, Zanotti, S, Montroni, I, Mattei, G, Taffurelli, M, Santini, D, Pezzetti, F, Ruggeri, A, Castellani, G, Guidotti, L, Coppola, D, and Strippoli, P (2008).
Displayed correlation between gene expression profiles and submicroscopic alterations in response to cetuximab, gefitinib and EGF in human colon cancer cell lines
BMC cancer, 8:227-227.

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