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Journal Articles and Book Chapters

Hernández-Lemus, E., Systems Biology and Integrative Omics in Breast Cancer, in Omics of Breast Cancer, Barh, D. (ed.), Springer (2014) (In Press).

Hernández-Lemus, E., Gene Chips: Entre lo Bio, lo Nano y la Salud Humana, Materiales Avanzados 1 (New Era), 1, 39-46, (2014)

Siqueiros-García, J.M., Hernández-Lemus, E., García-Herrera, R., Robina- Galatas, A. Mapping the structure and dynamics of Genomics-related MeSH terms Complex Networks, PLoS ONE 9(4): e92639, (2014)

Hernández-Lemus, E.¤, Data integration, systems approach and multilevel description of complex biosystems, Journal of Physics: Conference Series, 475, 012006 (2013).

Hernández-Lemus, E., Computational Pharmacogenomics, en Omics for Personalized Medicine, Barh, D., Dhawan, D., Ganguly, N.K. (ed.), Springer (2013) Chapter 9, Pages: 163-186 ISBN: 978-8-132-21183-9

Hernández-Lemus, E.¤, Further steps towards functional systems biology of cancer, Frontiers in Physiology (Frontiers in Systems Biology), 4, 256, (2013) doi:10.3389/fphys.2013.00256
[Editorial comment]

Hernández-Lemus, E., Gutiérrez, A. G., Vázquez-Aguirre, A., Palma-Tirado, M.L., Ruíz-Azuara, L., Mejía, M.C.¤, Analysis of Apoptotic and Autophagic Pathways in Neuroblastoma by Treatment with Copper Compounds in Shimada, H. (ed.) Neuroblastoma, InTech Open Publishing (2013), ISBN: 978-953-51-1128-3,

Gutiérrez, A.G., Vázquez-Aguirre, A., García-Ramos, J.C., Flores-Alamo, M., Hernández-Lemus, E., Ruiz-Azuara, L., Mejía, C.¤, Copper (II) mixed chelate compounds induce apoptosis through reactive oxygen species in neuroblastoma cell line CHP-212, Journal of Inorganic Biochemistry (2013)

Hernández-Lemus, E.¤, Siqueiros-García, J.M., Information theoretical methods for complex network structure reconstruction, Complex Adaptive Systems Modeling 1, 8, (2013) doi:10.1186/2194-3206-1-8

Valencia-Cruz, A.I., Uribe-Figueroa, L., Galindo-Murillo, R., Baca-López, K., Gutiérrez, A.G., Vázquez-Aguirre, A., Ruíz-Azuara, L., Hernández-Lemus, E.¤, Mejía, C.¤ Whole Genome Gene Expression Analysis reveals Casiopeína-induced apoptosis pathways, PLoS ONE 8(1): e54664. doi:10.1371/journal.pone.0054664 (2013)

Martínez-García, M., Hernández-Lemus, E.¤, Health systems as complex systems, American Journal of Operations Research, 3, 113-126, (2013) doi:10.4236/ajor.2013.31A011

Hernández-Lemus, E., Mejía, C., Inference and analysis of apoptotic pathways in Papillary Thyroid Cancer, in Kreuger, E., Trommler, B. (eds.) Thyroid Cancer: Diagnosis, Treatment and Prognosis, Nova Publishing (2012) ISBN: 978-1-62257-884-9

De Miguel, F.F., Santamaría-Holek, I., Noguez, P., Bustos, C., Hernández-Lemus, E., Rubí, J.M., Biophysics of active vesicle transport, an intermediate step that couples excitation and exocytosis of serotonin in the neuronal soma, PLoS ONE 7, 10, e45454, (2012)

Baca-López, K., Hidalgo-Miranda, A., Mayorga, M., Gutiérrez-Nájera, N., Hernández-Lemus, E.¤, The role of master regulators in the metabolic / transcriptional coupling in breast carcinomas, PLoS ONE 7, 8, e42678, (2012). doi:10.1371/journal.pone.0042678

Hernández-Lemus, E.¤, Non-equilibrium thermodynamics of cell signaling, Journal of Thermodynamics e432143, 1-10, (2012) doi:10.1155/2012/432143

Hernández-Lemus, E.¤, Transcriptional network structure assessment via the Data Processing Inequality, International Journal of Biophysics 2, 2, 18- 25,(2012) doi:10.5923/j.biophysics.20120202.02

Hernández-Lemus, E.¤, Extrasynaptic release of serotonin affects the social dynamics of leeches, Frontiers in Physiology 3, 158 (2012)
doi:10.3389/fphys.2012.00158 [Editorial comment]
Open Access in Frontiers:
Free full text on PubMed (PMC):

Hernández-Lemus, E.¤, Retos y oportunidades en la Física Biológica Contemporánea, Revista Digital Universitaria 13, 4, (2012) [In Spanish]

Hernández-Lemus, E. ¤, Baca-López, K., Bursting and synchronization in gene regulatory dynamics, Revista Mexicana de Física S 58, 1, 63-68 (2012).

Hernández-Lemus, E. ¤, Nicasio-Collazo, L. A., Castañeda-Priego, R.¤, Hysteresis in pressure-driven DNA denaturation, PLoS ONE 7, 4, e33789 (2012)

Lohr, J., Stojanov, P., Lawrence, M.S., Auclair, D., Chapuy, B., Carter, S., Sougnez, C., Cruz-Gordillo, P., Knoechel, ,Asmann, Y.W., Slager, S.L., Novak, A.J., Dogan, A., Ansell, S.M., Link, B.K., Zou, L., Gould, J., Saksena, G., Stransky, N., Rangel-Escareño, C., Fernández-López, J.C., Hidalgo-Miranda, A., Meléndez- Zajgla, J., Hernández-Lemus, E., Schwartz, A., Imaz, I., Ojesina, A., Jung, J., Pedamallu, C., Lander, E.S., Habermann, T.M., Cerhan, J.R., Shipp, M.A., Getz, G., Golub, T.R., Discovery and Prioritization of Somatic Mutations in DLBCL by Whole Exome Sequencing, Proceedings of the National Academy of Sciences 109, 10, 3879-3884, (2012) doi: 10.1073/pnas.112134310.

Hernández-Lemus, E. ¤, Acoplamientos no-lineales entre metabolismo y regulación transcripcional: Un enfoque de Termodinámica Irreversible, in Cincuenta años de Física estadística en México, Del Río-Correa, J.L., García-Colín, L.S. (eds.), El Colegio Nacional (2011) pp.313-332 ISBN 978-607-7630-94-4. [In Spanish]

Hernández-Lemus, E.¤, Rangel-Escareño, C., The role of information theory in gene regulatory network inference in Information Theory: New Research, Pierre Deloumeaux, Jose D. Gorzalka (Ed.), Mathematics Research Developments Series, Nova Publishing (2011) ISBN: 978-1-62100-395-3 .

Baca-López, K, Correa-Rodríguez, MD, Flores-Espinosa, R, Garcia-Herrera, R, Hernández-Armenta CI,Hidalgo-Miranda A, Huerta-Verde, AJ, Imaz-Rosshandler, I, Martínez-Rubio, AV, Medina-Escareno, A,Mendoza-Smith, R, Rodriguez-Dorantes, M, Salido-Guadarrama, I, Hernández-Lemus, E¤, Rangel-Escareño, C¤, A three state model for multidimensional genomic data integration, Proceedings of the ninth international conference for the Critical Assessment of Massive Data Analysis CAMDA,(2011)

To appear in Systems Biomedicine, 1, 2, April-June, 2013

Hernández-Lemus, E.¤, On the Application of Compressive Sampling Techniques to High Throughput Data in Computational Genomics, Theoretical and Applied Informatics 23, 3-4, 177-192, (2011)
DOI: 10.2478/v10179-011-0012-x (Open Access)

Rodríguez, E. E., Hernández-Lemus, E. ¤, Itzá-Ortíz, B. A., Jiménez, I., Rudomín, P.¤, Multichannel detrended fluctuations analysis reveals synchronized patterns of spontaneous spinal activity in anesthetized cats, PLoS ONE 6, 10, e26449, (2011)

Hernández-Lemus, E.¤, Correa-Rodríguez, M.D., Non-equilibrium hyperbolic transport in transcriptional regulation, PLoS ONE 6, 7, e21558 (2011)

Hernández-Lemus, E.¤, Biological Physics in Mexico: Review and New Challenges, Journal of Biological Physics 37, 2, 167-184, (2011)
Free full text on PubMed (PMC):

Jiménez-Sánchez, G, Hernández-Lemus, E.¤, Hidalgo-Miranda, A. La variabilidad Genómica y sus implicaciones en el cuidado de la salud in Introducción a la Física Biológica, García-Colín, L.S., Dagdug, L., (eds.), El Colegio Nacional, (2010) [In Spanish]

Hernández-Lemus, E.¤, Non-equilibrium thermodynamics of transcriptional bursts, in New Trends in Statistical Physics: Festschrift in honor of Leopoldo García-Colín’s 80 th Birthday, Macías, A., Dagdug, L. (eds.), World Scientific, (2010).

Hernández-Lemus, E.¤, Extended Irreversible Thermodynamics of Gene Regulation, Journal of Non-Newtonian Fluid Mechanics, 165, 1029-1032, (2010).

Baca-López, K. Hernández-Lemus, E. ¤, Mayorga, M., Information-theoretical analysis of gene expression data to infer transcriptional interactions, Revista Mexicana de Física 55, 6, 456-466, (2009).

Hernández-Lemus, E.¤, Non-Equilibrium Thermodynamics of Gene Expression and Transcriptional Regulation, Journal of Non-Equilibrium Thermodynamics, 34, 4, 371-394, (2009).
Journal page:
ArXiv version:

Hernández-Lemus, E. ¤, Velázquez-Fernández, D., Estrada-Gil, J.K., Silva-Zolezzi, I., Herrera-Hernández, M.F., Jiménez-Sánchez, G., Information Theoretical Methods to Deconvolute Genetic Regulatory Networks applied to Thyroid Neoplasms, Physica A 388 (2009) 5057-5069.

Silva-Zolezzi I, Hidalgo-Miranda A, Estrada-Gil J, Fernández-López JC, Uribe- Figueroa L, Contreras A, Balam-Ortiz E, del Bosque-Plata L, Velázquez- Fernández D, Lara C, Goya R, Hernández-Lemus E, Dávila C, Barrientos E, March S, Jimenez-Sanchez G., Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico, Proceedings of the National Academy of Sciences (2009) May 26;106 (21):8611-6.

Hernández-Lemus, E.¤ , Fenómenos multiescala, complejidad y flujos de información en sistemas Biológicos in La Física Biológica en México: Temas Selectos 2, García-Colín, L.S., Dagdug, L., Picquart, M. Vázquez, E., (eds.), El Colegio Nacional, (2008) . [In Spanish]

Hernández-Lemus, E.¤, Estrada-Gil, J.K., Silva-Zolezzi, I., Fernández-López, J.C., Hidalgo-Miranda, A., Jiménez-Sánchez, G., Nonlinear Analysis of Time Series in Genome-Wide Linkage Disequilibrium Data, American Institute of Physics Conf. Proc. Volume 978 (Biological Physics), 1, 34-56, (2008)

Hernández-Lemus, E.¤, Estrada-Gil, J.K., Stochastic measures and modular evolution in non-equilibrium thermodynamics, Electronic Journal of Theoretical Physics 5, 17, 163-184, (2008) .‎

Dagdug, L., Álvarez-Ramírez, J., López, C., Moreno, R., Hernández-Lemus, E., Correlations in a Mozart’s Music Score (K-73x) with Palindromic and Upside-Down Structure, Physica A 383, 2, 570-584, (2007) .

Estrada-Gil, J.K., Fernández-López, J.C., Hernández-Lemus, E., Silva-Zolezzi, I., Hidalgo-Miranda, A., Jiménez-Sánchez, G. Vallejo-Clemente, E.E., GPDTI: A Genetic Programming Decision Tree Induction method to find epistatic effects in common complex diseases, Bioinformatics 23(13):i167-74 (2007)

Cantú-Bolán, B., Hernández-Lemus, E. ¤, El carácter lingüístico y la coherencia textual presentes en el ADN no codificante, Estudios de Antropología Biológica 13, (2007) .

Hernández-Lemus, E.¤, García-Colín, L.S., Non-equilibrium critical behavior: An extended irreversible thermodynamics approach, Journal of Non-Equilibrium Thermodynamics, 31, 4, 397-417, (2006).
Journal page:
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Cantú-Bolán, B., Hernández-Lemus, E.¤, Statistical properties and linguistic coherence in noncoding DNA sequences, Revista Mexicana de Física E 51 (2) 118-125, (2005) .

Hernández-Lemus, E.¤, Orgaz, E., Hysteresis in nonequilibrium steady states: the role of dissipative couplings, Revista Mexicana de Física 48 Sup. 1 38-45 (2002).