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

There are 19 references in this bibliography folder.

Torcal Garcia, G, Kowenz-Leutz, E, Tian, TV, Klonizakis, A, Lerner, J, De Andres-Aguayo, L, Sapozhnikova, V, Berenguer, C, Carmona, MP, Casadesus, MV, Bulteau, R, Francesconi, M, Peiro, S, Mertins, P, Zaret, K, Leutz, A, and Graf, T (2023).
Carm1-arginine methylation of the transcription factor C/EBPα regulates transdifferentiation velocity
eLife, 12:e83951.

Bulteau, R and Francesconi, M (2022).
Real age prediction from the transcriptome with RAPToR
Nature Methods:1–7.

Plana-Carmona, M, Stik, G, Bulteau, R, Segura-Morales, C, Alcázar, N, Wyatt, CDR, Klonizakis, A, de Andrés-Aguayo, L, Gasnier, M, Tian, TV, Torcal Garcia, G, Vila-Casadesús, M, Plachta, N, Serrano, M, Francesconi, M, and Graf, T (2022).
The trophectoderm acts as a niche for the inner cell mass through C/EBPα-regulated IL-6 signaling
Stem Cell Reports.

Perez, MF, Shamalnasab, M, Mata-Cabana, A, Della Valle, S, Olmedo, M, Francesconi, M, and Lehner, B (2021).
Neuronal perception of the social environment generates an inherited memory that controls the development and generation time of C. elegans
Current Biology.

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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