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Swarup S, Verheyen EM.  2012.  Wnt/Wingless signaling in Drosophila.. Cold Spring Harbor perspectives in biology. 4(6) Abstract
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Harris KE, Schnittke N, Beckendorf SK.  2007.  Two ligands signal through the Drosophila PDGF/VEGF receptor to ensure proper salivary gland positioning.. Mechanisms of development. 124(6):441-8. Abstract
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Kiger AA, Jones DL, Schulz C, Rogers MB, Fuller MT.  2001.  Stem cell self-renewal specified by JAK-STAT activation in response to a support cell cue.. Science (New York, N.Y.). 294(5551):2542-5. Abstract
Fullaondo A, García-Sánchez S, Sanz-Parra A, Recio E, Lee SY, Gubb D.  2011.  Spn1 regulates the GNBP3-dependent Toll signaling pathway in Drosophila melanogaster.. Molecular and cellular biology. 31(14):2960-72. Abstract
Perrimon N, Pitsouli C, Shilo B-Z.  2012.  Signaling mechanisms controlling cell fate and embryonic patterning.. Cold Spring Harbor perspectives in biology. 4(8):a005975. Abstract
Sánchez L, Chaouiya C, Thieffry D.  2008.  Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module.. The International journal of developmental biology. 52(8):1059-75. Abstract
Sánchez L, Thieffry D.  2003.  Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. Journal of Theoretical Biology. 224(4):517-537.
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Eldar A, Dorfman R, Weiss D, Ashe H, Shilo B-Z, Barkai N.  2002.  Robustness of the BMP morphogen gradient in Drosophila embryonic patterning.. Nature. 419(6904):304-8. Abstract
Sun H, Towb P, Chiem DN, Foster BA, Wasserman SA.  2004.  Regulated assembly of the Toll signaling complex drives Drosophila dorsoventral patterning.. The EMBO journal. 23(1):100-10. Abstract
Micchelli CA, The I, Selva E, Mogila V, Perrimon N.  2002.  Rasp, a putative transmembrane acyltransferase, is required for Hedgehog signaling.. Development (Cambridge, England). 129(4):843-51. Abstract
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Simão E, REMY E, Thieffry D, Chaouiya C.  2005.  Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.coli.. Bioinformatics (Oxford, England). 21 Suppl 2:ii190-6. Abstract
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Sánchez L, Chaouiya C.  2016.  Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells.. BMC systems biology. 10(1):37. Abstract
Letort G, Montagud A, Stoll G, Heiland R, Calzone EBAZL, Macklin P.  2018.  PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. Bioinformatics. 35(7):1188–1196.
Sims D, Duchek P, Baum B.  2009.  PDGF/VEGF signaling controls cell size in Drosophila.. Genome biology. 10(2):R20. Abstract
Denef N, Schüpbach T.  2003.  Patterning: JAK-STAT signalling in the Drosophila follicular epithelium.. Current biology : CB. 13(10):R388-90. Abstract
Montagud A, Béal J, Tobalina L, Traynard P, Subramanian V, Szalai B, Alföldi R, Puskás L, Valencia A, Barillot E et al..  Submitted.  Patient-specific Boolean models of signaling networks guide personalized treatments.
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Zhang R, Shah MV, Yang J, Nyland SB, Liu X, Yun JK, Albert R, Loughran TP.  2008.  Network model of survival signaling in large granular lymphocyte leukemia.. Proceedings of the National Academy of Sciences of the United States of America. 105(42):16308-13. Abstract
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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
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
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
Klamt S, Saez-Rodriguez J, Lindquist JA, Simeoni L, Gilles ED.  2006.  A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics. 7(1):56.
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Sánchez L, Chaouiya C.  2018.  Logical modelling uncovers developmental constraints in primary sex determination of chicken gonads. J. R. Soc. Interface. . 15
Collombet S, van Oevelen C, Sardina Ortega JL, Abou-Jaoudé W, Di Stefano B, Thomas-Chollier M, Graf T, Thieffry D.  2017.  Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.. Proceedings of the National Academy of Sciences of the United States of America. 114(23):5792-5799. 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.
Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, Arndt B, Haus U-U, Weismantel R, Gilles ED, Klamt S et al..  2007.  A logical model provides insights into T cell receptor signaling.. PLoS computational biology. 3(8):e163. Abstract


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