Publications


We are strong advocates of the Open Access/Open Science paradigms. Most of our (recent) publications are thus available to everyone. For those that are not, please contact us to get a copy via e-mail.

Google Scholar Profiles

Books

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).
http://www.springer.com/medicine/oncology/book/978-81-322-0842-6

Hernández-Lemus, E., Gene Chips: Entre lo Bio, lo Nano y la Salud Humana, Materiales Avanzados 1 (New Era), 1, 39-46, (2014)
http://materialesavanzados.org/2014/05/06/gene-chips-entre-lo-bio-lo-nano-y-la-salud-humana/

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)
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0092639

Hernández-Lemus, E.¤, Data integration, systems approach and multilevel description of complex biosystems, Journal of Physics: Conference Series, 475, 012006 (2013).
http://iopscience.iop.org/1742-6596/475/1/012006

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
http://link.springer.com/book/10.1007/978-81-322-1184-6

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]
http://www.frontiersin.org/Systems_Biology/10.3389/fphys.2013.00256/full

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,
http://dx.doi.org/10.5772/55524

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)
http://www.sciencedirect.com/science/article/pii/S0162013413001050

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
http://www.casmodeling.com/content/1/1/8/abstract

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)
http://dx.plos.org/10.1371/journal.pone.0054664

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 http://www.scirp.org/journal/PaperInformation.aspx?PaperID=27538

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)
http://dx.plos.org/10.1371/journal.pone.0045454

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
http://dx.plos.org/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 http://www.hindawi.com/journals/jtd/2012/432143/abs/

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
http://article.sapub.org/10.5923.j.biophysics.20120202.02.html

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: http://www.frontiersin.org/Membrane_Physiology_and_Biophysics/10.3389/fphys.2012.00158/full
Free full text on PubMed (PMC): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361070/

Hernández-Lemus, E.¤, Retos y oportunidades en la Física Biológica Contemporánea, Revista Digital Universitaria 13, 4, (2012)
http://www.revista.unam.mx/vol.13/num4/art40/index.html [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).
http://rmf.smf.mx/pdf/rmf-s/58/1/58_1_63.pdf

Hernández-Lemus, E. ¤, Nicasio-Collazo, L. A., Castañeda-Priego, R.¤, Hysteresis in pressure-driven DNA denaturation, PLoS ONE 7, 4, e33789 (2012)
http://dx.plos.org/10.1371/journal.pone.0033789

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.
http://www.pnas.org/content/early/2012/02/16/1121343109

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)
http://camda.bioinfo.cipf.es/camda2012/_media/camda2011_baca-lopez.pdf

To appear in Systems Biomedicine, 1, 2, April-June, 2013
https://www.landesbioscience.com/journals/systemsbiomedicine/toc/volume/1/issue/2

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)
http://www.degruyter.com/view/j/thai.2011.23.issue-3-4/v10179-011-0012-x/v10179-011-0012-x.xml

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) http://dx.plos.org/10.1371/journal.pone.0026449

Hernández-Lemus, E.¤, Correa-Rodríguez, M.D., Non-equilibrium hyperbolic transport in transcriptional regulation, PLoS ONE 6, 7, e21558 (2011)
http://dx.plos.org/10.1371/journal.pone.0021558

Hernández-Lemus, E.¤, Biological Physics in Mexico: Review and New Challenges, Journal of Biological Physics 37, 2, 167-184, (2011)
http://dx.doi.org/10.1007/s10867-011-9218-8
Free full text on PubMed (PMC): http://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+++++22379227

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).
http://www.sciencedirect.com/science/article/pii/S0377025710000546

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).
http://rmf.smf.mx/pdf/rmf/55/6/55_6_456.pdf

Hernández-Lemus, E.¤, Non-Equilibrium Thermodynamics of Gene Expression and Transcriptional Regulation, Journal of Non-Equilibrium Thermodynamics, 34, 4, 371-394, (2009).
Journal page: http://www.degruyter.com/view/j/jnet.2009.34.issue-4/jnetdy.2009.019/jnetdy.2009.019.xml
ArXiv version: http://arxiv.org/abs/0904.0662

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.
http://www.sciencedirect.com/science/article/pii/S037843710900661X

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.
http://www.pnas.org/content/early/2009/05/11/0903045106

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)
http://proceedings.aip.org/resource/2/apcpcs/978/1/34_1

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) .
www.ejtp.com/articles/ejtpv5i17p159.pdf‎

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) .
http://www.sciencedirect.com/science/article/pii/S0378437107004323

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)
http://bioinformatics.oxfordjournals.org/content/23/13/i167.abstract

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: http://www.degruyter.com/view/j/jnet.2006.31.issue-4/jnetdy.2006.017/jnetdy.2006.017.xml
ArXiv version: http://arxiv.org/abs/0908.2161

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) .
http://rmf.smf.mx/pdf/rmf-e/51/2/51_2_118.pdf

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).
http://rmf.smf.mx/pdf/rmf-s/48/1/48_1_38.pdf