Carlos Ramírez and Luis Mendoza (ms).
Phenotypic stability and plasticity in GMP-derived cells as determined by their undelying regulatory network.
Bioinformatics in press.

Nathan Weinstein, Luis Mendoza, Isidoro Gitler, and Jaime Klapp (2017).
A network model to explore the effect of the micro-environment on endothelial cell behavior during angiogenesis.
Frontiers in Physiology 8: 960.

Eugenio Azpeitia, Stalin Munoz, Daniel Gonzalez-Tokman, Mariana Esther Martinez-Sanchez, Nathan Weinstein, Aurelien Naldi, Elena ER Alvarez-Buylla, David A Rosenblueth, and Luis Mendoza (2017).
The combination of the functionalities of feedback circuits is determinant for the number and size of attractors of molecular networks.
Scientific Reports 7: 42023

Jennifer Enciso, Hector Mayani, Luis Mendoza, and Rosana Pelayo (2016).
Modeling the pro-inflammatory tumor microenvironment in acute lymphoblastic leukemia predicts a breakdown of hematopoietic-mesenchymal communication networks.
Frontiers in Physiology 7: 349.

Akram Méndez and Luis Mendoza (2016).
A Network Model to Describe the Terminal Differentiation of B Cells.
PLOS Computational Biology 12: e1004696.

Luis Mendoza and Akram Méndez (2015).
A dynamical model of the regulatory network controlling lymphopoiesis.
BioSystems 137: 26-33.

Osiris Ríos, Sara Frías, Alfredo Rodríguez, Susana Kofman, Horacio Merchant, Leda Torres, and Luis Mendoza (2015).
A Boolean network model of human gonadal sex determination.
Theoretical Biology and Medical Modelling 12: 26.

Alfredo Rodríguez, Leda Torres, Ulises Juárez, David Sosa, Eugenio Azpeitia, Benilde García-de Teresa, Edith Cortés, Rocío Ortíz, Ana M. Salazar, Patricia Ostrosky-Wegman, Luis Mendoza, and Sara Frías (2015).
Fanconi Anemia Cells with Unrepaired DNA Damage Activate Components of the Checkpoint Recovery Process.
Theoretical Biology and Medical Modelling 12: 19.

Jennifer Enciso, Luis Mendoza, and Rosana Pelayo (2015).
Normal vs Malignant Hematopoiesis: the Complexity of Acute Leukemia Through Systems Biology.
Frontiers in Genetics 6: 290.

Mariana Martínez-Sánchez, Luis Mendoza, Carlos Villarreal, and Elena R. Álvarez-Buylla (2015).
A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity.
PLOS Computational Biology 11(6): e1004324.

Mariana Díaz-Zaragoza, Ricardo Hernández-Ávila, Tzipe Govezensky, Luis Mendoza, Dulce María Meneses-Ruíz, and Pedro Ostoa-Saloma (2015).
Comparison patterns of 4 T1 antigens recognized by humoral immune response mediated by IgG and IgM antibodies in female and male mice with breast cancer using 2D-immnunoblots.
Immunobiology. 220: 1050-1058.

Nathan Weinstein, Elizabeth Ortiz-Gutierrez, Stalin Muñoz, David A. Rosenblueth, Elena R. Álvarez-Buylla, and Luis Mendoza (2015).
A model of the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva.
BMC Bioinformatics 16: 81.

Pablo Martínez-Sosa and Luis Mendoza (2013).
The regulatory network that controls the differentiation of T lymphocytes.
BioSystems 113: 96-103.

Luis Mendoza (2013).
A virtual culture of CD4+ T lymphocytes.
Bulletin of Mathematical Biology 75: 1012-1029.

Nathan Weinstein and Luis Mendoza (2013).
A network model for the specification of vulval precursor cells and cell fusion control in Caenorhabditis elegans.
Frontiers in Genetics 4: 112.

Eugenio Azpeitia, Nathan Weinstein, Mariana Benítez, Luis Mendoza and Elena R. Alvarez-Buylla (2013).
Finding missing interactions of the Arabidopsis thaliana root stem cell niche gene regulatory network.
Frontiers in Plant Science 4: 110.

Nathan Weinstein and Luis Mendoza (2012).
Building qualitative models of plant regulatory networks with SQUAD.
Frontiers in Plant Science 3: 72.

Alfredo Rodríguez, David Sosa, Leda Torres, Bertha Molina, Sara Frías and Luis Mendoza (2012).
A Boolean network model of the FA/BRCA pathway.
Bioinformatics 28: 858-866.

María Fernanda Higareda, Otto Geiger, Luis Mendoza and Rafael A. Méndez-Sánchez (2012).
Evidence of codon usage in the nearest neighbor spacing distribution of bases in bacterial genomes.
Physica A 391: 1255-1269.

Luis Mendoza and Fátima Pardo (2010).
A robust model to describe the differentiation of T-helper cells.
Theory in Biosciences 129: 283-293.

Yara-Elena Sánchez-Corrales, Elena R. Álvarez-Buylla and Luis Mendoza (2010).
The Arabidopsis thaliana flower organ specification gene regulatory network determines a robust differentiation process.
Journal of Theoretical Biology 264: 971-983.

Abhishek Garg, Alessandro Di Cara, Ioannis Xenarios, Luis Mendoza and Giovanni De Micheli (2008).
Synchronous vs. asynchronous modelling of gene regulatory networks.
Bioinformatics 24: 1917-1925.

Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios and Luis Mendoza (2007).
Dynamic simulation of regulatory networks using SQUAD.
BMC Bioinformatics 8: 462.

Abhishek Garg, Luis Mendoza, Ioannis Xenarios and Giovanni De Micheli (2007).
Modeling of Multiple Valued Gene Regulatory Networks.
Conf. Proc. IEEE Eng. Med. Biol. Soc. 2007 1: 1398-1404.

Abhishek Garg, Ioannis Xenarios, Luis Mendoza and Giovanni DeMicheli (2007).
An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experiments.
RECOMB 2007, Lecture Notes in Computer Science 4453: 62-76.

Luis Mendoza (2006).
A network model for the control of the differentiation process in Th cells.
BioSystems 84: 101-114

Luis Mendoza and Ioannis Xenarios (2006).
A method for the generation of standardized qualitative dynamical systems of regulatory networks.
Theoretical Biology and Medical Modelling 3:13

Elisabeth Remy, Paul Ruet, Luis Mendoza, Denis Thieffry and Claudine Chaouiya (2006).
From logical regulatory graphs to standard petri nets: Dynamical roles and functionality of feedback circuits.
Transactions on Computational Systems Biology VII, Lecture Notes in Computer Science 4230: 56-72

Boris Lenhard, Albin Sandelin, Luis Mendoza, Pär Engström, Niclas Jareborg and Wyeth W. Wasserman (2003).
Identification of conserved regulatory elements by comparative genome analysis.
Journal of Biology 2:13

Luis Mendoza and Elena R. Alvarez-Buylla (2000).
Genetic regulation of root hair development in Arabidopsis thaliana: a network model.
Journal of Theoretical Biology 204:311

Luis Mendoza, Denis Thieffry and Elena R. Alvarez-Buylla (1999).
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis.
Bioinformatics 15:593

Luis Mendoza and Elena R. Alvarez-Buylla (1998).
Dynamics of the genetic regulatory network for flowering in Arabidopsis thaliana.
Journal of Theoretical Biology 193: 307-319.

Luis Mendoza, Mariana Mondragón and Jaime Lagúnez-Otero (1998).
Interactions of the 530 ribosomal site with subregions of mRNA.
Biosystems 46:293

Luis Mendoza and Jaime Lagúnez-Otero (1996).
The ribosome as an exon detector.
Biosystems 38:45