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Book Chapter

Sánchez-Osorio I, Hernández-Martínez1 CA, Martínez-Antonio A. Submitted. Exploring Asymmetric Cell Division in Caulobacter Crescentus Using Logic Modeling.

Chaouiya C, Remy E, Mossé B, Thieffry D. 2003. Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework. Positive Systems. 294:830-832.

Journal Article

Weber ANR, Tauszig-Delamasure S, Hoffmann JA, Lelièvre E, Gascan H, Ray KP, Morse MA, Imler J-L, Gay NJ. 2003. Binding of the Drosophila cytokine Spätzle to Toll is direct and establishes signaling.. Nature immunology. 4(8):794-800. Abstract

Niarakis A, Bounab Y, Grieco L, Roncagalli R, Hesse A-M, Garin J, Malissen B, Daëron M, Thieffry D. 2014. Computational modeling of the main signaling pathways involved in mast cell activation. Current topics in microbiology and immunology. 382:69-93. Abstract

Floc’hlay S, Molina MD, Hernandez C, Haillot E, Thomas-Chollier M, Lepage T, Thieffry D. 2020. Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo. Development.

Gobert V, Gottar M, Matskevich AA, Rutschmann S, Royet J, Belvin M, Hoffmann JA, Ferrandon D. 2003. Dual activation of the Drosophila toll pathway by two pattern recognition receptors.. Science (New York, N.Y.). 302(5653):2126-30. Abstract

Wartlick O, Mumcu P, Kicheva A, Bittig T, Seum C, Jülicher F, González-Gaitán M. 2011. Dynamics of Dpp signaling and proliferation control.. Science (New York, N.Y.). 331(6021):1154-9. Abstract

Bischoff V, Vignal C, Boneca IG, Michel T, Hoffmann JA, Royet J. 2004. Function of the drosophila pattern-recognition receptor PGRP-SD in the detection of Gram-positive bacteria.. Nature immunology. 5(11):1175-80. Abstract

MENDOZA L, Thieffry D, Alvarez-Buylla ER. 1999. Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. Bioinformatics. 15(7):593-606.

Xi R, McGregor JR, Harrison DA. 2003. A gradient of JAK pathway activity patterns the anterior-posterior axis of the follicular epithelium.. Developmental cell. 4(2):167-77. Abstract

Ingham PW, McMahon AP. 2001. Hedgehog signaling in animal development: paradigms and principles.. Genes & development. 15(23):3059-87.

Selvaggio G, Canato S, Pawar A, Monteiro PT, Janody F, Chaouiya C. 2020. Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors. Cancer Research.

Pepinsky RB, Zeng C, Wen D, Rayhorn P, Baker DP, Williams KP, Bixler SA, Ambrose CM, Garber EA, Miatkowski K et al.. 1998. Identification of a palmitic acid-modified form of human Sonic hedgehog.. The Journal of biological chemistry. 273(22):14037-45. Abstract

Lum L, Yao S, Mozer B, Rovescalli A, Von Kessler D, Nirenberg M, Beachy PA. 2003. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells.. Science (New York, N.Y.). 299(5615):2039-45. Abstract

Desterke C, Martinaud C, Ruzehaji N, Le Bousse-Kerdilès M-C. 2015. Inflammation as a Keystone of Bone Marrow Stroma Alterations in Primary Myelofibrosis.. Mediators of inflammation. 2015:415024. Abstract

Johnson AN, Mokalled MH, Haden TN, Olson EN. 2011. JAK/Stat signaling regulates heart precursor diversification in Drosophila. Development. 138(21):4627-4638. Abstract

Nuñez-Reza KJ, Naldi A, Sánchez-Jiménez A, Leon-Apodaca AV, Santana A, Thomas-Chollier M, Thieffry D, Medina-Rivera A. 2021. Logical modeling of in vitro differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions.

Mbodj A, Junion G, Brun C, Furlong EEM, Thieffry D. 2013. Logical modelling of Drosophila signalling pathways.. Molecular bioSystems. 9(9):2248-58. Abstract

Cohen DPA, Martignetti L, Robine S, Barillot E, Zinovyev A, Calzone L. 2015. Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration.. PLoS computational biology. 11(11):e1004571. Abstract

Abou-Jaoudé W, Monteiro PT, Naldi A, Grandclaudon M, Soumelis V, Chaouiya C, Thieffry D. 2015. Model checking to assess T-helper cell plasticity. Frontiers in Bioengineering and Biotechnology. 2(86) Abstract

Sánchez-Osorio I, Hernández-Martínez CA, Martínez-Antonio A. 2017. Modeling Asymmetric Cell Division in Caulobacter crescentus Using a Boolean Logic Approach.. Results and problems in cell differentiation. 61:1-21. Abstract

Sahin O, Fröhlich H, Löbke C, Korf U, Burmester S, Majety M, Mattern J, Schupp I, Chaouiya C, Thieffry D et al.. 2009. Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC systems biology. 3:1. Abstract

Enciso J, Mayani H, Mendoza L, Pelayo R. 2016. Modeling the pro-inflammatory tumor microenvironment in acute lymphoblastic leukemia predicts a breakdown of hematopoietic-mesenchymal communication networks. Frontiers in Physiology. 7

Enciso J, Mayani H, Mendoza L, Pelayo R. Submitted. Modeling the pro-inflammatory tumor microenvironment in acute lymphoblastic leukemia predicts a breakdown of hematopoieticmesenchymal communication networks..

Mombach J, Bugs C, Chaouiya C. 2014. Modelling the onset of senescence at the G1/S cell cycle checkpoint. BMC Genomics. 15:S7.